Script: Fix pep8.

Stricklers and friction.

.editorconfig

@@ -0,0 +1,12 @@
+# Pamhyr .editorconfig
+
+root = true
+
+[*.py]
+charset = utf-8
+indent_style = space
+indent_size = 4
+tab_width = 8
+end_of_line = lf
+trim_trailing_whitespace = true
+insert_final_newline = true

.gitignore

@@ -1,6 +1,7 @@
 ### CUSTOM ###
 
 *.exe
+*.msi
 *.tar.xz
 *.zip
 *.spec
@@ -9,15 +10,33 @@
 
 tmp
 
+*.tar
 *.tar.*
+*.tgz
 *.zip
 
+*.html
+*.pdf
+*.odt
+
+doc/dev/images/auto_*
+doc/dev/documentation.*
+!doc/dev/*.org
+
+doc/dev/images/auto_*
+doc/users/documentation.*
+!doc/users/*.org
+
+TAGS
+
 pamhyrBuild
 wine-pamhyr-build*
 
 _PAMHYR_
 __old__
 
+*-venv
+
 ### END CUSTOM ###
 
 # Created by https://www.toptal.com/developers/gitignore/api/python
@@ -309,3 +328,318 @@ compile_commands.json
 *_qmlcache.qrc
 
 # End of https://www.toptal.com/developers/gitignore/api/qt
+
+# Created by https://www.toptal.com/developers/gitignore/api/latex
+# Edit at https://www.toptal.com/developers/gitignore?templates=latex
+
+### LaTeX ###
+## Core latex/pdflatex auxiliary files:
+*.aux
+*.lof
+*.log
+*.lot
+*.fls
+*.out
+*.toc
+*.fmt
+*.fot
+*.cb
+*.cb2
+.*.lb
+
+## Intermediate documents:
+*.dvi
+*.xdv
+*-converted-to.*
+# these rules might exclude image files for figures etc.
+# *.ps
+# *.eps
+# *.pdf
+
+## Generated if empty string is given at "Please type another file name for output:"
+.pdf
+
+## Bibliography auxiliary files (bibtex/biblatex/biber):
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.run.xml
+
+## Build tool auxiliary files:
+*.fdb_latexmk
+*.synctex
+*.synctex(busy)
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+
+## Build tool directories for auxiliary files
+# latexrun
+latex.out/
+
+## Auxiliary and intermediate files from other packages:
+# algorithms
+*.alg
+*.loa
+
+# achemso
+acs-*.bib
+
+# amsthm
+*.thm
+
+# beamer
+*.nav
+*.pre
+*.snm
+*.vrb
+
+# changes
+*.soc
+
+# comment
+*.cut
+
+# cprotect
+*.cpt
+
+# elsarticle (documentclass of Elsevier journals)
+*.spl
+
+# endnotes
+*.ent
+
+# fixme
+*.lox
+
+# feynmf/feynmp
+*.mf
+*.mp
+*.t[1-9]
+*.t[1-9][0-9]
+*.tfm
+
+#(r)(e)ledmac/(r)(e)ledpar
+*.end
+*.?end
+*.[1-9]
+*.[1-9][0-9]
+*.[1-9][0-9][0-9]
+*.[1-9]R
+*.[1-9][0-9]R
+*.[1-9][0-9][0-9]R
+*.eledsec[1-9]
+*.eledsec[1-9]R
+*.eledsec[1-9][0-9]
+*.eledsec[1-9][0-9]R
+*.eledsec[1-9][0-9][0-9]
+*.eledsec[1-9][0-9][0-9]R
+
+# glossaries
+*.acn
+*.acr
+*.glg
+*.glo
+*.gls
+*.glsdefs
+*.lzo
+*.lzs
+*.slg
+*.slo
+*.sls
+
+# uncomment this for glossaries-extra (will ignore makeindex's style files!)
+# *.ist
+
+# gnuplot
+*.gnuplot
+*.table
+
+# gnuplottex
+*-gnuplottex-*
+
+# gregoriotex
+*.gaux
+*.glog
+*.gtex
+
+# htlatex
+*.4ct
+*.4tc
+*.idv
+*.lg
+*.trc
+*.xref
+
+# hyperref
+*.brf
+
+# knitr
+*-concordance.tex
+# TODO Uncomment the next line if you use knitr and want to ignore its generated tikz files
+# *.tikz
+*-tikzDictionary
+
+# listings
+*.lol
+
+# luatexja-ruby
+*.ltjruby
+
+# makeidx
+*.idx
+*.ilg
+*.ind
+
+# minitoc
+*.maf
+*.mlf
+*.mlt
+*.mtc[0-9]*
+*.slf[0-9]*
+*.slt[0-9]*
+*.stc[0-9]*
+
+# minted
+_minted*
+*.pyg
+
+# morewrites
+*.mw
+
+# newpax
+*.newpax
+
+# nomencl
+*.nlg
+*.nlo
+*.nls
+
+# pax
+*.pax
+
+# pdfpcnotes
+*.pdfpc
+
+# sagetex
+*.sagetex.sage
+*.sagetex.py
+*.sagetex.scmd
+
+# scrwfile
+*.wrt
+
+# svg
+svg-inkscape/
+
+# sympy
+*.sout
+*.sympy
+sympy-plots-for-*.tex/
+
+# pdfcomment
+*.upa
+*.upb
+
+# pythontex
+*.pytxcode
+pythontex-files-*/
+
+# tcolorbox
+*.listing
+
+# thmtools
+*.loe
+
+# TikZ & PGF
+*.dpth
+*.md5
+*.auxlock
+
+# titletoc
+*.ptc
+
+# todonotes
+*.tdo
+
+# vhistory
+*.hst
+*.ver
+
+# easy-todo
+*.lod
+
+# xcolor
+*.xcp
+
+# xmpincl
+*.xmpi
+
+# xindy
+*.xdy
+
+# xypic precompiled matrices and outlines
+*.xyc
+*.xyd
+
+# endfloat
+*.ttt
+*.fff
+
+# Latexian
+TSWLatexianTemp*
+
+## Editors:
+# WinEdt
+*.bak
+*.sav
+
+# Texpad
+.texpadtmp
+
+# LyX
+*.lyx~
+
+# Kile
+*.backup
+
+# gummi
+.*.swp
+
+# KBibTeX
+*~[0-9]*
+
+# TeXnicCenter
+*.tps
+
+# auto folder when using emacs and auctex
+./auto/*
+*.el
+
+# expex forward references with \gathertags
+*-tags.tex
+
+# standalone packages
+*.sta
+
+# Makeindex log files
+*.lpz
+
+# xwatermark package
+*.xwm
+
+# REVTeX puts footnotes in the bibliography by default, unless the nofootinbib
+# option is specified. Footnotes are the stored in a file with suffix Notes.bib.
+# Uncomment the next line to have this generated file ignored.
+#*Notes.bib
+
+### LaTeX Patch ###
+# LIPIcs / OASIcs
+*.vtc
+
+# glossaries
+*.glstex
+
+# End of https://www.toptal.com/developers/gitignore/api/latex

.gitlab-ci.yml

@@ -15,97 +15,57 @@
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 stages:
-  - build
+  - downloads
+  - configure
   - test
+  - build
   - package
   - release
 
-#########
-# BUILD #
-#########
+#############
+# DOWNLOADS #
+#############
 
-build-mage-linux:
-  stage: build
+dl-mage-linux:
+  stage: downloads
   tags:
     - linux
   rules:
-    - if: $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   script:
-    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/Test5/downloads/packages/mage_linux.tgz
-    - mkdir -p mage
-    - cd mage
+    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/Test6/downloads/packages/mage_linux.tgz
+    - mkdir -p mage-linux
+    - cd mage-linux
     - tar xvf ../mage.tgz
   artifacts:
     paths:
-      - mage/mage
-      - mage/mage_extraire
-      - mage/mailleurPF
+      - mage-linux/mage
+      - mage-linux/mage_extraire
+      - mage-linux/mailleurPF
 
-# build-mage-linux:
-#   stage: build
-#   tags:
-#     - linux
-#   rules:
-#     - if: $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
-#   variables:
-#     GIT_SUBMODULE_STRATEGY: recursive
-#     GIT_SUBMODULE_DEPTH: 20
-#   script:
-#     - cd mage/src/
-#     - mkdir -p build
-#     - cd build
-#     - cmake ..
-#     - make
-#   artifacts:
-#     paths:
-#       - mage/src/build/mage
-#       - mage/src/build/mage_extraire
-#       - mage/src/build/mailleurPF
-
-build-mage-windows:
-  stage: build
+dl-mage-windows:
+  stage: downloads
   tags:
     - linux
   rules:
-    - if: $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   script:
-    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/Test5/downloads/packages/mage_windows.tgz
-    - mkdir -p mage
-    - cd mage
+    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/Test6/downloads/packages/mage_windows.tgz
+    - mkdir -p mage-windows
+    - cd mage-windows
     - tar xvf ../mage.tgz
   artifacts:
     paths:
-      - mage/mage.exe
-      - mage/mage_extraire.exe
-      - mage/mailleurPF.exe
+      - mage-windows/mage.exe
+      - mage-windows/mage_extraire.exe
+      - mage-windows/mailleurPF.exe
 
-# build-mage-windows:
-#   stage: build
-#   tags:
-#     - wine
-#   rules:
-#     - if: $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
-#   variables:
-#     GIT_SUBMODULE_STRATEGY: recursive
-#     GIT_SUBMODULE_DEPTH: 20
-#   script:
-#     - cd mage/src/
-#     - sed s/add_compile_definitions(win)/add_compile_definitions(windows)/ CMakeLists.txt > __tmp__
-#     - echo set(CMAKE_Fortran_COMPILER "C:/Program\ Files/gcc/bin/gfortran.exe") > CMakeLists.txt
-#     - echo set(CMAKE_MAKE_PROGRAM "C:/Program Files\ \(x86\)/GnuWin32/bin/make.exe") >> CMakeLists.txt
-#     - type __tmp__ >> CMakeLists.txt
-#     - mkdir build
-#     - cd build
-#     - cmake -G "MinGW Makefiles" ..
-#     - make
-#   artifacts:
-#     paths:
-#       - mage/src/build/mage.exe
-#       - mage/src/build/mage_extraire.exe
-#       - mage/src/build/mailleurPF.exe
+#############
+# CONFIGURE #
+#############
 
-build:
-  stage: build
+set-version:
+  stage: configure
   tags:
     - linux
   script:
@@ -116,7 +76,7 @@ build:
       - VERSION
 
 build-lang:
-  stage: build
+  stage: configure
   tags:
     - linux
   script:
@@ -130,56 +90,261 @@ build-lang:
 # TESTS #
 #########
 
-test:
+unittest:
   stage: test
+  tags:
+    - linux
+  needs:
+    - job: set-version
+      artifacts: true
   script:
-    - echo "TODO PAMHYR tests"
+    - python3 -m venv venv
+    - . venv/bin/activate
+    - pip3 install -U pip
+    - pip3 install -r ./full-requirements.txt
+    - pip3 install -U -r ./full-requirements.txt
+    - cd src
+    - python3 -m unittest discover -t .
+
+test-pep8:
+  stage: test
+  tags:
+    - linux
+  needs:
+    - job: set-version
+      artifacts: true
+    - job: unittest
+  script:
+    # Setup virtual env
+    - python3 -m venv venv
+    - . venv/bin/activate
+    - pip3 install -U pip
+    - pip3 install -r ./requirements.txt
+    - pip3 install -U -r ./requirements.txt
+    - pip3 install pycodestyle
+    - pycodestyle ./src
+  allow_failure: true
+
+#########
+# BUILD #
+#########
+
+build-users-doc:
+  stage: build
+  tags:
+    - linux
+  needs:
+    - job: set-version
+      artifacts: true
+  script:
+    - cd ./doc/users/
+    - ./build.sh
+  artifacts:
+    paths:
+      - doc/users/documentation.pdf
+      - doc/users/documentation.html
+      - doc/users/images/
+  allow_failure: true
+
+build-developers-doc:
+  stage: build
+  tags:
+    - linux
+  needs:
+    - job: set-version
+      artifacts: true
+  script:
+    - cd ./doc/dev/
+    - ./build.sh
+    # Create html documentation
+    - cd ../../src
+    - python3 -m venv doc-venv
+    - . doc-venv/bin/activate
+    - pip3 install -U pip
+    - pip3 install -r ../full-requirements.txt
+    - pip3 install -U -r ../full-requirements.txt
+    - pip3 install pdoc3
+    - pdoc --html .
+    # Create archive
+    - tar cf html.tar ./html
+    - cd ../doc/dev
+    - mv ../../src/html.tar ./
+  artifacts:
+    paths:
+      - doc/dev/documentation.pdf
+      - doc/dev/documentation.html
+      - doc/dev/html.tar
+      - doc/dev/images/
+  allow_failure: true
+
+build-linux:
+  stage: build
+  tags:
+    - linux
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  needs:
+    - job: dl-mage-linux
+      artifacts: true
+    - job: set-version
+      artifacts: true
+    - job: build-lang
+      artifacts: true
+    - job: build-developers-doc
+      artifacts: true
+    - job: build-users-doc
+      artifacts: true
+  script:
+    - mkdir -p linux
+    - cd linux
+    # Setup virtual env
+    - python3 -m venv linux-venv
+    - . linux-venv/bin/activate
+    - pip3 install -U pip
+    - pip3 install -r ../requirements.txt
+    - pip3 install -U -r ../requirements.txt
+    # Run Pyinstaller
+    - pyinstaller -y --paths linux-venv/lib/python3.8/site-packages ../src/pamhyr.py
+    # Create directory
+    - mkdir -p pamhyr
+    - mkdir -p pamhyr/pamhyr
+    - mkdir -p pamhyr/pamhyr/_internal
+    # Copy Pamhyr info
+    - cp -v ../VERSION pamhyr/pamhyr/_internal/
+    - cp -v ../AUTHORS pamhyr/pamhyr/_internal/
+    - cp -v ../LICENSE pamhyr/pamhyr/_internal/
+    - cp -v ../src/motd.txt pamhyr/pamhyr/_internal/
+    # Copy mage
+    - mkdir -p pamhyr/mage
+    - cp -v ../mage-linux/* pamhyr/mage/
+    # Copy Pamhyr
+    - cp -r dist/pamhyr pamhyr/
+    # Copy Pamhyr resources
+    - mkdir -p pamhyr/pamhyr/_internal/View
+    - mkdir -p pamhyr/pamhyr/_internal/View/ui
+    - mkdir -p pamhyr/pamhyr/_internal/View/ui/Widgets
+    - cp -r ../src/View/ui/*.ui pamhyr/pamhyr/_internal/View/ui/
+    - cp -r ../src/View/ui/ressources/ pamhyr/pamhyr/_internal/View/ui
+    - cp -r ../src/View/ui/Widgets/*.ui pamhyr/pamhyr/_internal/View/ui/Widgets
+    # Copy lang
+    - mkdir -p pamhyr/pamhyr/_internal/lang
+    - cp -r ../src/lang/*.qm pamhyr/pamhyr/_internal/lang
+    # Copy tests cases
+    - mkdir -p pamhyr/tests_cases/
+    - mkdir -p pamhyr/tests_cases/Saar
+    - cp ../tests_cases/Saar/Saar.pamhyr pamhyr/tests_cases/Saar/
+    # Copy documentations
+    - mkdir -p pamhyr/doc/
+    - mkdir -p pamhyr/doc/images/
+    - mkdir -p pamhyr/doc/html/
+    - cp ../doc/users/documentation.pdf pamhyr/doc/Pamhyr2-users.pdf
+    - cp ../doc/users/documentation.html pamhyr/doc/Pamhyr2-users.html
+    - cp ../doc/dev/documentation.pdf pamhyr/doc/Pamhyr2-dev.pdf
+    - cp ../doc/dev/documentation.html pamhyr/doc/Pamhyr2-dev.html
+    #- cp ../doc/users/images/* pamhyr/doc/images
+    - cp ../doc/dev/images/* pamhyr/doc/images
+    - cp ../doc/images/* pamhyr/doc/images
+    # Create running script
+    - echo "#!/bin/sh" > pamhyr/Pamhyr2
+    - echo "./pamhyr/pamhyr $@" >> pamhyr/Pamhyr2
+    - chmod u+x pamhyr/Pamhyr2
+  artifacts:
+    paths:
+      - linux/pamhyr
+
+build-windows:
+  stage: build
+  tags:
+    - wine
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  needs:
+    - job: dl-mage-windows
+      artifacts: true
+    - job: set-version
+      artifacts: true
+    - job: build-lang
+      artifacts: true
+    - job: build-developers-doc
+      artifacts: true
+    - job: build-users-doc
+      artifacts: true
+  script:
+    - mkdir windows
+    - cd windows
+    # Setup env
+    - python -m pip install -r ..\requirements.txt
+    - python -m pip install -U -r ..\requirements.txt
+    # Run Pyinstaller
+    - pyinstaller -y ..\src\pamhyr.py
+    # Create directory
+    - mkdir pamhyr
+    - dir
+    - copy ..\packages\make-windows-dir.bat .\make-windows-dir.bat
+    - .\make-windows-dir.bat
+  artifacts:
+    paths:
+      - windows/pamhyr
 
 ############
 # PACKAGES #
 ############
 
-linux-package:
+linux-package-tar:
   stage: package
   tags:
     - release
     - linux
   needs:
-    - job: build-lang
-      artifacts: true
-    - job: build
-      artifacts: true
-    - job: build-mage-linux
+    # - job: test-linux
+    - job: build-linux
       artifacts: true
   rules:
-    - if: $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_TAG
   artifacts:
     paths:
-      - packages/pamhyr-gnulinux-amd64.tar.xz
+      - linux/pamhyr-gnulinux.tar.xz
   script:
-    - cd packages
-    - ./linux.sh
+    - cd linux
+    - tar --xz -cf pamhyr-gnulinux.tar.xz ./pamhyr --checkpoint=.100
 
-windows-package:
+windows-package-zip:
+  stage: package
+  tags:
+    - release
+    - linux
+  needs:
+    # - job: test-windows
+    - job: build-windows
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_TAG
+  artifacts:
+    paths:
+      - windows/pamhyr-windows.zip
+  script:
+    - cd windows
+    - zip -r pamhyr-windows.zip pamhyr
+
+windows-package-exe:
   stage: package
   tags:
     - release
     - wine
   needs:
-    - job: build-lang
-      artifacts: true
-    - job: build
-      artifacts: true
-    - job: build-mage-windows
+    # - job: test-windows
+    - job: build-windows
       artifacts: true
   rules:
-    - if: $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_TAG
   artifacts:
     paths:
-      - packages/pamhyr-win-amd64.exe
+      - windows/pamhyr-windows.exe
   script:
-    - cd packages
-    - ./windows.bat
+    - cd windows
+    - copy ..\packages\make-windows-exe.bat make-windows-exe.bat
+    - copy ..\packages\pamhyr.nsi pamhyr.nsi
+    - .\make-windows-exe.bat
 
 ###########
 # RELEASE #
@@ -191,16 +356,25 @@ tag-release:
     - release
     - linux
   needs:
-    - job: linux-package
+    - job: linux-package-tar
       artifacts: true
-    - job: windows-package
+    - job: windows-package-zip
+      artifacts: true
+    - job: windows-package-exe
+      artifacts: true
+    - job: build-users-doc
+      artifacts: true
+    - job: build-developers-doc
       artifacts: true
   rules:
     - if: $CI_COMMIT_TAG
   artifacts:
     paths:
-      - packages/pamhyr-gnulinux-amd64.tar.xz
-      - packages/pamhyr-win-amd64.exe
+      - linux/pamhyr-gnulinux.tar.xz
+      - windows/pamhyr-windows.zip
+      - windows/pamhyr-windows.exe
+      - doc/dev/documentation.pdf
+      - doc/users/documentation.pdf
   script:
     - cd packages
   release:
@@ -210,11 +384,23 @@ tag-release:
     ref: '$CI_COMMIT_SHA'
     assets:
       links:
-        - name: 'GNU/Linux amd64 (tar.xz)'
-          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/packages/pamhyr-gnulinux-amd64.tar.xz'
-          filepath: '/packages/pamhyr-gnulinux-amd64.tar.xz'
+        - name: 'GNU/Linux (tar.xz)'
+          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/linux/pamhyr-gnulinux.tar.xz'
+          filepath: '/linux/pamhyr-gnulinux.tar.xz'
           link_type: 'package'
-        - name: 'Windows amd64 (exe)'
-          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/packages/pamhyr-win-amd64.exe'
-          filepath: '/packages/pamhyr-win-amd64.exe'
+        - name: 'Windows (exe)'
+          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/windows/pamhyr-windows.exe'
+          filepath: '/windows/pamhyr-windows.exe'
           link_type: 'package'
+        - name: 'Windows (zip)'
+          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/windows/pamhyr-windows.zip'
+          filepath: '/windows/pamhyr-windows.zip'
+          link_type: 'package'
+        - name: 'User documentations (pdf)'
+          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/doc/users/documentation.pdf'
+          filepath: '/doc/users/documentation.pdf'
+          link_type: 'other'
+        - name: 'Dev documentations (pdf)'
+          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/doc/dev/documentation.pdf'
+          filepath: '/doc/dev/documentation.pdf'
+          link_type: 'other'

README.md

@@ -1 +1,50 @@
-# PamHyr (Programme d’Aide à la Modélisation en Hydraulique des Rivières)
+# Pamhyr2
+
+Pamhyr is a free and open source graphical user interface for 1D hydro-sedimentary
+modelling of rivers.
+
+## Features
+
++ Edit a complex river hydraulics network
++ Define the river geometry
++ Define boundary conditions
++ Define lateral contribution
++ Edit river friction
++ Generate initial conditions
++ Edit river sedimentary layers
++ Save the study in a unique file
++ Run Mage 8 on a study and visualize results
+
+## Install
+
+### GNU/Linux
+
+Downloads [last
+realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
+GNU/Linux binary archive.
+
+```shell
+tar xf pamhyr-gnulinux-amd64.tar.xz
+cd pamhyr
+./pamhyr
+```
+
+### Windows
+
+Downloads [last
+realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
+Windows installer.
+
+### From source code
+
+```shell
+# Get source code
+git clone https://gitlab.irstea.fr/theophile.terraz/pamhyr/
+cd pamhyr
+
+# Install dependencies
+pip3 install -r requirements.txt
+
+# Run pamhyr
+./src/pamhyr.py
+```

doc/dev/build.sh

@@ -0,0 +1,18 @@
+#! /bin/sh
+
+echo " PDF  documentation.org"
+emacs -nw --batch                                       \
+      --eval "(require 'org)"                           \
+      --eval "(require 'ox-latex)"                      \
+      --eval "(load-file \"../tools/setup.el\")"        \
+      --file ./documentation.org                        \
+      -f org-latex-export-to-pdf
+
+echo " HTML documentation.org"
+emacs -nw --batch                                       \
+      --eval "(require 'org)"                           \
+      --eval "(require 'ox-latex)"                      \
+      --eval "(require 'ox-html)"                       \
+      --eval "(load-file \"../tools/setup.el\")"        \
+      --file ./documentation.org                        \
+      -f org-html-export-to-html

doc/dev/documentation.bib

@@ -0,0 +1 @@
+../tools/ref.bib

doc/paper/2023/simhydro/ajustement-for-paper.patch

@@ -0,0 +1,692 @@
+diff --git a/packages/linux.sh b/packages/linux.sh
+index 215047e..a19bfb6 100755
+--- a/packages/linux.sh
++++ b/packages/linux.sh
+@@ -76,11 +76,11 @@ mv ../pamhyr-src.tar.gz ./
+ 
+ echo " *** MAKE BIN PACKAGE"
+ 
+-OLD_PWD=$PWD
+-cd dist/
+-tar --xz -cf pamhyr-gnulinux-amd64.tar.xz pamhyr --checkpoint=.100
+-cd $OLD_PWD
++# OLD_PWD=$PWD
++# cd dist/
++# tar --xz -cf pamhyr-gnulinux-amd64.tar.xz pamhyr --checkpoint=.100
++# cd $OLD_PWD
+ 
+-mv dist/pamhyr-gnulinux-amd64.tar.xz ./
++# mv dist/pamhyr-gnulinux-amd64.tar.xz ./
+ 
+ echo " *** DONE"
+diff --git a/src/Model/Friction/Friction.py b/src/Model/Friction/Friction.py
+index 18167a8..5bf2302 100644
+--- a/src/Model/Friction/Friction.py
++++ b/src/Model/Friction/Friction.py
+@@ -170,6 +170,7 @@ class Friction(SQLSubModel):
+     @begin_strickler.setter
+     def begin_strickler(self, strickler):
+         self._begin_strickler = strickler
++        self._end_strickler = strickler # HACK: Only one Strickler
+         self._status.modified()
+ 
+     @property
+diff --git a/src/Model/Stricklers/Stricklers.py b/src/Model/Stricklers/Stricklers.py
+index baa484f..a5670d2 100644
+--- a/src/Model/Stricklers/Stricklers.py
++++ b/src/Model/Stricklers/Stricklers.py
+@@ -38,7 +38,7 @@ class Stricklers(SQLSubModel):
+         else:
+             self.id = id
+ 
+-        Stricklers._id_cnt = max(Stricklers._id_cnt + 1, self.id)
++        Stricklers._id_cnt = max(Stricklers._id_cnt + 1, id + 1)
+ 
+         self._name = name
+         self._comment = comment
+diff --git a/src/View/BoundaryCondition/translate.py b/src/View/BoundaryCondition/translate.py
+index c4ff8f8..172999a 100644
+--- a/src/View/BoundaryCondition/translate.py
++++ b/src/View/BoundaryCondition/translate.py
+@@ -29,9 +29,9 @@ _translate = QCoreApplication.translate
+ long_types = {
+     "ND": _translate("BoundaryCondition", "Not defined"),
+     "PC": _translate("BoundaryCondition", "Ponctual contribution"),
+-    "TZ": _translate("BoundaryCondition", "Time over Z"),
+-    "TD": _translate("BoundaryCondition", "Time over Discharge"),
+-    "ZD": _translate("BoundaryCondition", "Z over Discharge"),
++    "TZ": _translate("BoundaryCondition", "TimeZ"),
++    "TD": _translate("BoundaryCondition", "TimeDischarge"),
++    "ZD": _translate("BoundaryCondition", "ZDischarge"),
+     "SL": _translate("BoundaryCondition", "Solid"),
+ }
+ 
+diff --git a/src/View/Frictions/PlotStricklers.py b/src/View/Frictions/PlotStricklers.py
+index 71ff6e6..b9060bc 100644
+--- a/src/View/Frictions/PlotStricklers.py
++++ b/src/View/Frictions/PlotStricklers.py
+@@ -106,6 +106,8 @@ class PlotStricklers(APlot):
+                 )
+                 self.draw_frictions(lst, color="b")
+ 
++        self.canvas.axes.invert_xaxis()
++
+         self.canvas.figure.tight_layout()
+         self.canvas.figure.canvas.draw_idle()
+         if self.toolbar is not None:
+diff --git a/src/View/Frictions/Window.py b/src/View/Frictions/Window.py
+index 4af3b66..f46fae3 100644
+--- a/src/View/Frictions/Window.py
++++ b/src/View/Frictions/Window.py
+@@ -112,10 +112,10 @@ class FrictionsWindow(ASubMainWindow, ListedSubWindow):
+         )
+ 
+         table.setItemDelegateForColumn(
+-            3, self._delegate_stricklers
++            2, self._delegate_stricklers
+         )
+         table.setItemDelegateForColumn(
+-            4, self._delegate_stricklers
++            3, self._delegate_stricklers
+         )
+ 
+         table.setSelectionBehavior(QAbstractItemView.SelectRows)
+diff --git a/src/View/Frictions/translate.py b/src/View/Frictions/translate.py
+index 21981ab..82071e9 100644
+--- a/src/View/Frictions/translate.py
++++ b/src/View/Frictions/translate.py
+@@ -21,10 +21,10 @@ from PyQt5.QtCore import QCoreApplication
+ _translate = QCoreApplication.translate
+ 
+ table_headers = {
+-    "name": _translate("Frictions", "Name"),
++    # "name": _translate("Frictions", "Name"),
+     # "edge": _translate("Frictions", "Reach"),
+     "begin_kp": _translate("Frictions", "Begin kp (m)"),
+     "end_kp": _translate("Frictions", "End kp (m)"),
+-    "begin_strickler": _translate("Frictions", "Begin strickler"),
+-    "end_strickler": _translate("Frictions", "End strickler"),
++    "begin_strickler": _translate("Frictions", "Strickler"),
++    # "end_strickler": _translate("Frictions", "End strickler"),
+ }
+diff --git a/src/View/Geometry/PlotAC.py b/src/View/Geometry/PlotAC.py
+index fe6d933..e43f39e 100644
+--- a/src/View/Geometry/PlotAC.py
++++ b/src/View/Geometry/PlotAC.py
+@@ -67,18 +67,18 @@ class PlotAC(APlot):
+         gl = self.data.profile(selected_profile).names()
+ 
+         self.canvas.axes.set_xlabel(
+-            _translate("MainWindow_reach", "Abscisse en travers (m)"),
++            _translate("MainWindow_reach", "Transverse abscissa (m)"),
+             color='green', fontsize=12
+         )
+         self.canvas.axes.set_ylabel(
+-            _translate("MainWindow_reach", "Cote (m)"),
++            _translate("MainWindow_reach", "Height (m)"),
+             color='green', fontsize=12
+         )
+         self.canvas.figure.tight_layout()
+ 
+-        label_before_plot_selected = _translate("MainWindow_reach", "Profil précédent")
+-        label_plot_selected = _translate("MainWindow_reach", "Profil sélectionné")
+-        label_after_plot_selected = _translate("MainWindow_reach", "Profil suivant")
++        label_before_plot_selected = _translate("MainWindow_reach", "Previous cross-section")
++        label_plot_selected = _translate("MainWindow_reach", "Cross-section")
++        label_after_plot_selected = _translate("MainWindow_reach", "Next cross-section")
+         color_before_plot_selected = "k"  # 'grey'
+         color_plot_selected = 'b'
+         color_after_plot_selected = 'm'
+diff --git a/src/View/Geometry/PlotKPZ.py b/src/View/Geometry/PlotKPZ.py
+index eb7d5e2..64057aa 100644
+--- a/src/View/Geometry/PlotKPZ.py
++++ b/src/View/Geometry/PlotKPZ.py
+@@ -158,6 +158,8 @@ class PlotKPZ(APlot):
+             color='lightgrey'
+         )
+ 
++        self.canvas.axes.invert_xaxis()
++
+         self.canvas.figure.tight_layout()
+         self.canvas.figure.canvas.draw_idle()
+         if self.toolbar is not None:
+diff --git a/src/View/Geometry/Window.py b/src/View/Geometry/Window.py
+index 7776d73..1c8cb5d 100644
+--- a/src/View/Geometry/Window.py
++++ b/src/View/Geometry/Window.py
+@@ -111,7 +111,7 @@ class GeometryWindow(ASubMainWindow, ListedSubWindow):
+         self.ui.btn_sort_desc.triggered.connect(self.sort_descending)
+         self.ui.btn_move_up.triggered.connect(self.move_row_up)
+         self.ui.btn_move_down.triggered.connect(self.move_row_down)
+-        self.ui.btn_end_editing.triggered.connect(self.handleSave)
++        # self.ui.btn_end_editing.triggered.connect(self.handleSave)
+         self.ui.btn_add.triggered.connect(self.insert_row)
+         self.ui.btn_delete.triggered.connect(self.delete_rows)
+         self.ui.btn_edit.triggered.connect(self.edit_profile)
+diff --git a/src/View/Geometry/mainwindow_ui_reach.py b/src/View/Geometry/mainwindow_ui_reach.py
+index 897b698..60bcfa6 100644
+--- a/src/View/Geometry/mainwindow_ui_reach.py
++++ b/src/View/Geometry/mainwindow_ui_reach.py
+@@ -95,29 +95,29 @@ class Ui_MainWindow(object):
+         self.btn_edit.setIcon(icon_btn_edit)
+         self.toolBar.addAction(self.btn_edit)
+ 
+-        self.btn_copy_selected_profile = QtWidgets.QAction(self.widget)
+-        self.btn_copy_selected_profile.setObjectName("btn_copy_selected_profile")
+-        icon_btn_copy_selected_profile = QtGui.QIcon()
+-        icon_btn_copy_selected_profile.addPixmap(
+-            QtGui.QPixmap(f"{icon_path}gtk-copy.png"))
+-        self.btn_copy_selected_profile.setIcon(icon_btn_copy_selected_profile)
+-        self.toolBar.addAction(self.btn_copy_selected_profile)
+-
+-        self.btn_paste_selected_profile = QtWidgets.QAction(self.widget)
+-        self.btn_paste_selected_profile.setObjectName("btn_paste_selected_profile")
+-        icon_btn_paste_selected_profile = QtGui.QIcon()
+-        icon_btn_paste_selected_profile.addPixmap(
+-            QtGui.QPixmap(f"{icon_path}gtk-paste.png"))
+-        self.btn_paste_selected_profile.setIcon(icon_btn_paste_selected_profile)
+-        self.toolBar.addAction(self.btn_paste_selected_profile)
+-
+-        self.btn_duplicate_selected_profile = QtWidgets.QAction(self.widget)
+-        self.btn_duplicate_selected_profile.setObjectName("btn_duplicate_selected_profile")
+-        icon_btn_duplicate_selected_profile = QtGui.QIcon()
+-        icon_btn_duplicate_selected_profile.addPixmap(
+-            QtGui.QPixmap(f"{icon_path}gtk-dnd-multiple.png"))
+-        self.btn_duplicate_selected_profile.setIcon(icon_btn_duplicate_selected_profile)
+-        self.toolBar.addAction(self.btn_duplicate_selected_profile)
++        # self.btn_copy_selected_profile = QtWidgets.QAction(self.widget)
++        # self.btn_copy_selected_profile.setObjectName("btn_copy_selected_profile")
++        # icon_btn_copy_selected_profile = QtGui.QIcon()
++        # icon_btn_copy_selected_profile.addPixmap(
++        #     QtGui.QPixmap(f"{icon_path}gtk-copy.png"))
++        # self.btn_copy_selected_profile.setIcon(icon_btn_copy_selected_profile)
++        # self.toolBar.addAction(self.btn_copy_selected_profile)
++
++        # self.btn_paste_selected_profile = QtWidgets.QAction(self.widget)
++        # self.btn_paste_selected_profile.setObjectName("btn_paste_selected_profile")
++        # icon_btn_paste_selected_profile = QtGui.QIcon()
++        # icon_btn_paste_selected_profile.addPixmap(
++        #     QtGui.QPixmap(f"{icon_path}gtk-paste.png"))
++        # self.btn_paste_selected_profile.setIcon(icon_btn_paste_selected_profile)
++        # self.toolBar.addAction(self.btn_paste_selected_profile)
++
++        # self.btn_duplicate_selected_profile = QtWidgets.QAction(self.widget)
++        # self.btn_duplicate_selected_profile.setObjectName("btn_duplicate_selected_profile")
++        # icon_btn_duplicate_selected_profile = QtGui.QIcon()
++        # icon_btn_duplicate_selected_profile.addPixmap(
++        #     QtGui.QPixmap(f"{icon_path}gtk-dnd-multiple.png"))
++        # self.btn_duplicate_selected_profile.setIcon(icon_btn_duplicate_selected_profile)
++        # self.toolBar.addAction(self.btn_duplicate_selected_profile)
+ 
+         self.btn_sort_asc = QtWidgets.QAction(self.widget)
+         self.btn_sort_asc.setObjectName("btn_sort_asc")
+@@ -151,13 +151,13 @@ class Ui_MainWindow(object):
+         self.btn_move_down.setIcon(icon_btn_move_down)
+         self.toolBar.addAction(self.btn_move_down)
+ 
+-        self.btn_end_editing = QtWidgets.QAction(self.widget)
+-        self.btn_end_editing.setObjectName("btn_end_editing")
+-        icon_btn_save = QtGui.QIcon()
+-        icon_btn_save.addPixmap(
+-            QtGui.QPixmap(f"{icon_path}gtk-apply.png"))
+-        self.btn_end_editing.setIcon(icon_btn_save)
+-        self.toolBar.addAction(self.btn_end_editing)
++        # self.btn_end_editing = QtWidgets.QAction(self.widget)
++        # self.btn_end_editing.setObjectName("btn_end_editing")
++        # icon_btn_save = QtGui.QIcon()
++        # icon_btn_save.addPixmap(
++        #     QtGui.QPixmap(f"{icon_path}gtk-apply.png"))
++        # self.btn_end_editing.setIcon(icon_btn_save)
++        # self.toolBar.addAction(self.btn_end_editing)
+ 
+         self.verticalLayout.addLayout(self.horizontalLayout)
+         self.tableView = QtWidgets.QTableView(self.widget)
+@@ -314,30 +314,23 @@ class Ui_MainWindow(object):
+     def retranslateUi(self, MainWindow_reach):
+         _translate = QtCore.QCoreApplication.translate
+         self.name_reach = ""
+-        self.mainwindow_title = _translate("MainWindow_reach", "Jeu de sections du Bief")
++        self.mainwindow_title = _translate("MainWindow_reach", "Geometry reach edit")
+         MainWindow_reach.setWindowTitle(self.mainwindow_title + f"{self.name_reach}")
+-        self.text_section_order = _translate("MainWindow_reach", "\nOrdre des sections : "
+-                                                                 "Amont --> Aval")
+         # self.label_section_order.setText(f"{self.text_section_order}")
+         self.vertical_slider_value = ""
+-        self.vertical_slider_label.setText(_translate("MainWindow_reach", "Pk = ") + f"{self.vertical_slider_value}")
+-        self.btn_open.setToolTip(_translate("MainWindow_reach", " Importer une géométrie"))
+-        self.btn_add.setToolTip(_translate("MainWindow_reach", " Nouveau profil"))
+-        self.btn_delete.setToolTip(_translate("MainWindow_reach", " Supprimer le profil sélectionné"))
+-        self.btn_edit.setToolTip(_translate("MainWindow_reach", " Éditer le profil sélectionné"))
+-        self.btn_copy_selected_profile.setToolTip(_translate("MainWindow_reach", " Copier le profil sélectionné"))
+-        self.btn_paste_selected_profile.setToolTip(_translate("MainWindow_reach", "Coller le profil en fin de liste ("
+-                                                                                  "penser à modifier le Pk avant de "
+-                                                                                  "trier)"))
+-        self.btn_duplicate_selected_profile.setToolTip(
+-            _translate("MainWindow_reach", " Dupliquer la section sélectionnée"))
++        self.vertical_slider_label.setText(_translate("MainWindow_reach", "Kp = ") + f"{self.vertical_slider_value}")
++        self.btn_open.setToolTip(_translate("MainWindow_reach", " Import geometry"))
++        self.btn_add.setToolTip(_translate("MainWindow_reach", " New profile"))
++        self.btn_delete.setToolTip(_translate("MainWindow_reach", " Delete selected profile"))
++        self.btn_edit.setToolTip(_translate("MainWindow_reach", " Editer selected profile"))
++
+         self.btn_sort_asc.setToolTip(_translate("MainWindow_reach", " Trier les profils par ordre croissant des Pk"))
+         self.btn_sort_desc.setToolTip(_translate("MainWindow_reach", " Trier les profils par ordre décroissant des Pk"))
+         self.btn_move_up.setToolTip(_translate("MainWindow_reach", " Changer l'ordre des profils (en décalant le "
+                                                                    "profil sélectionné vers le haut)"))
+         self.btn_move_down.setToolTip(_translate("MainWindow_reach", " Changer l'ordre des profils (en décalant le "
+                                                                      "profil sélectionné vers le bas)"))
+-        self.btn_end_editing.setToolTip(_translate("MainWindow_reach", " Terminer l'édition"))
++        # self.btn_end_editing.setToolTip(_translate("MainWindow_reach", " Terminer l'édition"))
+         self.tableView_header = [_translate("MainWindow_reach", "Name"),
+                                  _translate("MainWindow_reach", "Kp (m)"),
+                                  _translate("MainWindow_reach", "Type")]
+diff --git a/src/View/InitialConditions/PlotDKP.py b/src/View/InitialConditions/PlotDKP.py
+index 58a8321..445cc08 100644
+--- a/src/View/InitialConditions/PlotDKP.py
++++ b/src/View/InitialConditions/PlotDKP.py
+@@ -71,6 +71,8 @@ class PlotDKP(APlot):
+                 color='b', marker='+', lw=1.
+             )
+ 
++        self.canvas.axes.invert_xaxis()
++
+         self.canvas.figure.tight_layout()
+         self.canvas.figure.canvas.draw_idle()
+         if self.toolbar is not None:
+diff --git a/src/View/InitialConditions/PlotDischarge.py b/src/View/InitialConditions/PlotDischarge.py
+index 1fe05de..0703c59 100644
+--- a/src/View/InitialConditions/PlotDischarge.py
++++ b/src/View/InitialConditions/PlotDischarge.py
+@@ -65,6 +65,8 @@ class PlotDischarge(APlot):
+                 color='r', lw=1.
+             )
+ 
++        self.canvas.axes.invert_xaxis()
++
+         self.canvas.figure.tight_layout()
+         self.canvas.figure.canvas.draw_idle()
+         if self.toolbar is not None:
+diff --git a/src/View/InitialConditions/translate.py b/src/View/InitialConditions/translate.py
+index 370d4a2..3fe45f7 100644
+--- a/src/View/InitialConditions/translate.py
++++ b/src/View/InitialConditions/translate.py
+@@ -21,11 +21,11 @@ from PyQt5.QtCore import QCoreApplication
+ _translate = QCoreApplication.translate
+ 
+ table_headers = {
+-    "name": _translate("LateralContribution", "Name"),
++    # "name": _translate("LateralContribution", "Name"),
+     "kp": _translate("LateralContribution", "KP (m)"),
+     # "speed": _translate("LateralContribution", "Speed (m/s)"),
+     "discharge": _translate("LateralContribution", "Discharge (m³/s)"),
+     "elevation": _translate("LateralContribution", "Elevation (m)"),
+     "height": _translate("LateralContribution", "Height (m)"),
+-    "comment": _translate("LateralContribution", "Comment"),
++    # "comment": _translate("LateralContribution", "Comment"),
+ }
+diff --git a/src/View/SedimentLayers/Edit/translate.py b/src/View/SedimentLayers/Edit/translate.py
+index fe9e44a..f9f02cb 100644
+--- a/src/View/SedimentLayers/Edit/translate.py
++++ b/src/View/SedimentLayers/Edit/translate.py
+@@ -6,7 +6,7 @@ _translate = QCoreApplication.translate
+ 
+ table_headers = {
+     "name": _translate("SedimentLayers", "Name"),
+-    "type": _translate("SedimentLayers", "Type"),
++    # "type": _translate("SedimentLayers", "Type"),
+     "height": _translate("Sedimentlayers", "Height"),
+     "d50": _translate("Sedimentlayers", "D50"),
+     "sigma": _translate("Sedimentlayers", "Sigma"),
+diff --git a/src/View/SedimentLayers/Reach/Plot.py b/src/View/SedimentLayers/Reach/Plot.py
+index a312a8c..5764abf 100644
+--- a/src/View/SedimentLayers/Reach/Plot.py
++++ b/src/View/SedimentLayers/Reach/Plot.py
+@@ -78,6 +78,8 @@ class Plot(APlot):
+                 color='grey' if i == len(z_sl) - 1 else None
+             )
+ 
++        self.canvas.axes.invert_xaxis()
++
+         self.canvas.figure.tight_layout()
+         self.canvas.figure.canvas.draw_idle()
+         if self.toolbar is not None:
+diff --git a/src/lang/fr.ts b/src/lang/fr.ts
+index 8034809..031f349 100644
+--- a/src/lang/fr.ts
++++ b/src/lang/fr.ts
+@@ -60,21 +60,6 @@
+         <source>Ponctual contribution</source>
+         <translation>Contributions ponctuelles</translation>
+     </message>
+-    <message>
+-        <location filename="../View/BoundaryCondition/translate.py" line="32"/>
+-        <source>Time over Z</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message>
+-        <location filename="../View/BoundaryCondition/translate.py" line="33"/>
+-        <source>Time over Discharge</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message>
+-        <location filename="../View/BoundaryCondition/translate.py" line="34"/>
+-        <source>Z over Discharge</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+     <message>
+         <location filename="../View/BoundaryCondition/translate.py" line="39"/>
+         <source>Name</source>
+@@ -110,6 +95,21 @@
+         <source>Solid</source>
+         <translation type="unfinished">Solide</translation>
+     </message>
++    <message>
++        <location filename="../View/BoundaryCondition/translate.py" line="32"/>
++        <source>TimeZ</source>
++        <translation type="unfinished"></translation>
++    </message>
++    <message>
++        <location filename="../View/BoundaryCondition/translate.py" line="33"/>
++        <source>TimeDischarge</source>
++        <translation type="unfinished"></translation>
++    </message>
++    <message>
++        <location filename="../View/BoundaryCondition/translate.py" line="34"/>
++        <source>ZDischarge</source>
++        <translation type="unfinished"></translation>
++    </message>
+ </context>
+ <context>
+     <name>Checker</name>
+@@ -533,7 +533,7 @@
+     <message>
+         <location filename="../View/Frictions/translate.py" line="24"/>
+         <source>Name</source>
+-        <translation>Nom</translation>
++        <translation type="obsolete">Nom</translation>
+     </message>
+     <message>
+         <location filename="../View/Frictions/translate.py" line="26"/>
+@@ -548,12 +548,17 @@
+     <message>
+         <location filename="../View/Frictions/translate.py" line="28"/>
+         <source>Begin strickler</source>
+-        <translation>strickler de départ</translation>
++        <translation type="obsolete">strickler de départ</translation>
+     </message>
+     <message>
+         <location filename="../View/Frictions/translate.py" line="29"/>
+         <source>End strickler</source>
+-        <translation>Strickler de fin</translation>
++        <translation type="obsolete">Strickler de fin</translation>
++    </message>
++    <message>
++        <location filename="../View/Frictions/translate.py" line="28"/>
++        <source>Strickler</source>
++        <translation type="unfinished"></translation>
+     </message>
+ </context>
+ <context>
+@@ -587,7 +592,7 @@
+ <context>
+     <name>LateralContribution</name>
+     <message>
+-        <location filename="../View/InitialConditions/translate.py" line="24"/>
++        <location filename="../View/LateralContribution/translate.py" line="35"/>
+         <source>Name</source>
+         <translation>Nom</translation>
+     </message>
+@@ -602,7 +607,7 @@
+         <translation>Lit moyen</translation>
+     </message>
+     <message>
+-        <location filename="../View/InitialConditions/translate.py" line="30"/>
++        <location filename="../View/Stricklers/translate.py" line="31"/>
+         <source>Comment</source>
+         <translation>Commentaire</translation>
+     </message>
+@@ -1715,7 +1720,7 @@ sur le plan défini par les deux points nommés extrêmes </source>
+         <translation type="unfinished"></translation>
+     </message>
+ </context>
+-<context>
++<context encoding="UTF-8">
+     <name>MainWindow_reach</name>
+     <message>
+         <location filename="../View/Frictions/PlotStricklers.py" line="76"/>
+@@ -1723,7 +1728,7 @@ sur le plan défini par les deux points nommés extrêmes </source>
+         <translation></translation>
+     </message>
+     <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="342"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="335"/>
+         <source>Kp (m)</source>
+         <translation>Pk (m)</translation>
+     </message>
+@@ -1778,68 +1783,47 @@ sur le plan défini par les deux points nommés extrêmes </source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="317"/>
+-        <source>Jeu de sections du Bief</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="319"/>
+-        <source>
+-Ordre des sections : Amont --&gt; Aval</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="323"/>
+-        <source>Pk = </source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="325"/>
+-        <source> Nouveau profil</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="334"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="327"/>
+         <source> Trier les profils par ordre croissant des Pk</source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="341"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="334"/>
+         <source>Name</source>
+         <translation>Nom</translation>
+     </message>
+     <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="343"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="336"/>
+         <source>Type</source>
+         <translation>Type</translation>
+     </message>
+     <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="345"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="338"/>
+         <source>Alt+Z</source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="348"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="341"/>
+         <source>Alt+E</source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="351"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="344"/>
+         <source>Alt+R</source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="355"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="348"/>
+         <source>Vue globale automatique (Alt+S)</source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="359"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="352"/>
+         <source>Vue globale automatique (Alt+D)</source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message>
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="363"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="356"/>
+         <source>Vue globale automatique (Alt+F)</source>
+         <translation type="unfinished"></translation>
+     </message>
+@@ -1889,68 +1873,33 @@ Seuls les 5 premiers seront édités.</source>
+         <source>Profil sélectionné</source>
+         <translation type="unfinished"></translation>
+     </message>
+-    <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="324"/>
+-        <source> Importer une géométrie</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="326"/>
+-        <source> Supprimer le profil sélectionné</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="327"/>
+-        <source> Éditer le profil sélectionné</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+     <message encoding="UTF-8">
+         <location filename="../View/Geometry/mainwindow_ui_reach.py" line="328"/>
+-        <source> Copier le profil sélectionné</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="329"/>
+-        <source>Coller le profil en fin de liste (penser à modifier le Pk avant de trier)</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="332"/>
+-        <source> Dupliquer la section sélectionnée</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="335"/>
+         <source> Trier les profils par ordre décroissant des Pk</source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="336"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="329"/>
+         <source> Changer l&apos;ordre des profils (en décalant le profil sélectionné vers le haut)</source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="338"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="331"/>
+         <source> Changer l&apos;ordre des profils (en décalant le profil sélectionné vers le bas)</source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="340"/>
+-        <source> Terminer l&apos;édition</source>
+-        <translation type="unfinished"></translation>
+-    </message>
+-    <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="346"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="339"/>
+         <source>Vue isométrique (Alt+Z)</source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="349"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="342"/>
+         <source>Vue isométrique (Alt+E)</source>
+         <translation type="unfinished"></translation>
+     </message>
+     <message encoding="UTF-8">
+-        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="352"/>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="345"/>
+         <source>Vue isométrique (Alt+R)</source>
+         <translation type="unfinished"></translation>
+     </message>
+@@ -1960,7 +1909,7 @@ Seuls les 5 premiers seront édités.</source>
+         <translation type="unfinished">Altitude (m)</translation>
+     </message>
+     <message>
+-        <location filename="../View/Geometry/PlotKPZ.py" line="66"/>
++        <location filename="../View/Geometry/PlotAC.py" line="73"/>
+         <source>Height (m)</source>
+         <translation type="unfinished">Hauteur (m)</translation>
+     </message>
+@@ -1969,6 +1918,56 @@ Seuls les 5 premiers seront édités.</source>
+         <source>Select destination file</source>
+         <translation type="unfinished"></translation>
+     </message>
++    <message>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="317"/>
++        <source>Geometry reach edit</source>
++        <translation type="unfinished"></translation>
++    </message>
++    <message>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="321"/>
++        <source>Kp = </source>
++        <translation type="unfinished"></translation>
++    </message>
++    <message>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="322"/>
++        <source> Import geometry</source>
++        <translation type="unfinished"></translation>
++    </message>
++    <message>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="323"/>
++        <source> New profile</source>
++        <translation type="unfinished"></translation>
++    </message>
++    <message>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="324"/>
++        <source> Delete selected profile</source>
++        <translation type="unfinished"></translation>
++    </message>
++    <message>
++        <location filename="../View/Geometry/mainwindow_ui_reach.py" line="325"/>
++        <source> Editer selected profile</source>
++        <translation type="unfinished"></translation>
++    </message>
++    <message>
++        <location filename="../View/Geometry/PlotAC.py" line="69"/>
++        <source>Transverse abscissa (m)</source>
++        <translation type="unfinished"></translation>
++    </message>
++    <message>
++        <location filename="../View/Geometry/PlotAC.py" line="79"/>
++        <source>Previous cross-section</source>
++        <translation type="unfinished"></translation>
++    </message>
++    <message>
++        <location filename="../View/Geometry/PlotAC.py" line="80"/>
++        <source>Cross-section</source>
++        <translation type="unfinished"></translation>
++    </message>
++    <message>
++        <location filename="../View/Geometry/PlotAC.py" line="81"/>
++        <source>Next cross-section</source>
++        <translation type="unfinished"></translation>
++    </message>
+ </context>
+ <context>
+     <name>Network</name>
+@@ -2071,7 +2070,7 @@ Seuls les 5 premiers seront édités.</source>
+     <message>
+         <location filename="../View/SedimentLayers/Edit/translate.py" line="9"/>
+         <source>Type</source>
+-        <translation type="unfinished">Type</translation>
++        <translation type="obsolete">Type</translation>
+     </message>
+     <message>
+         <location filename="../View/SedimentLayers/Reach/Profile/Window.py" line="68"/>

doc/paper/2023/simhydro/paper.txt

@@ -0,0 +1,131 @@
+Pamhyr2: a graphical user interface for 1D hydro-sedimentary modelling of rivers 
+Pierre-Antoine Rouby1, Benoît Camenen, Lionel Pénard, Léa Kieffer, Théophile Terraz1
+INRAE, UR RiverLy, centre de Lyon-Grenoble, 5 rue de la Doua, CS20244, 69625, Villeurbanne, France.
+pierre-antoine.rouby@inrae.fr, benoit.camenen@inrae.fr, lionel.penard@inrae.fr, 
+lea.kieffer@inrae.fr, theophile.terraz@inrae.fr
+KEY WORDS
+1D modelling, sedimentary modelling, user interface
+Abstract
+In numerical river simulation, one-dimensional models are commonly used to study water level and discharge for large domains or long time series. These models are less time-consuming than two- and three-dimensional numerical models, and require fewer input parameters and allow ensemble runs. To build a one-dimensional hydraulic model, a pre- and post-processing tool is needed for creating reach geometry, specifying initial and boundary conditions, friction coefficients and other numerical parameters. Such a tool needs to ensure the consistency of the model and provide a user-friendly graphical user interface. In this article, we present Pamhyr2, the fully rebuilt version of the PAMHYR modelling platform. It is developed using Python, PyQt and Matplotlib. Pamhyr2 is free and open-source, multilingual, cross-platform (Linux, Windows) and is generic enough to accept various one-dimensional solvers. Pamhyr2 includes and enhances all the features from the previous version: multiple-reach modelling, geometry definition from cross-section data, initial and boundary conditions, friction coefficients, hydraulic structures, lateral inflow, punctual intake and the results visualization window. In addition, this version includes new features such as pollutants modelling, bed-load and bed evolution. We describe several windows: the creation of sedimentary layers in the river bed, the sediment characteristics for each layer, the sediment, and pollutant boundary conditions and the lateral inputs. These functionalities are illustrated with simple examples. We finally show the visualization windows for bed evolution. 
+1.	introduction
+Numerous tools are available to simulate river flow. Among them, one-dimensional (1D) numerical hydraulic models have the advantage of being accurate while being inexpensive in terms of computation time, making it possible to simulate long rivers over very long timescales. A lot of 1D numerical solvers for river hydraulics are available, including HEC-RAS2, Mike 113 and Mascaret4 for example. However, in order to investigate specific research issues it is essential to have the ability to edit the source code of numeric solvers and to have an ergonomic Graphical User Interace (GUI). Most of the widespread 1D modeling tools are either written with a proprietary source code (such as HEC-RAS and Mike 11) or are research tools with irregularly maintained GUI. On its side, INRAE has been developing two 1D solvers for over 40 years: Mage5 [5]  and RubarBE6. In parallel, a GUI named PAMHyR has been developed to enable modelers to build river models, parameterize calculations, launch Mage and RubarBE solvers and post-process the results [3].
+
+	PAMHyR, developed in Java since the end of 90s (originally named X-NT), it is written with the following constraints in mind: 
+    • Multi-platform Windows, Unix-like,
+    • no dependence on an external graphics library with a paid license for user, 
+    • generate as much code as possible from a UML diagram.
+Now, PAMHyR suffers from complexity due to highly specific interface, as well as a significant technological debt [4]: old external library no longer maintained, over dated project architecture, and numerous modifications by multiple developers (and internship) over short periods of time, with no vision of long-term maintainability. What's more, the software is only in French and the code is closed (the sources are not available), which is a hindrance to the notoriety of the software as well as to the vitality of development. In addition, no significant changes have been made in the application since 2016, even if PAMHyR is still often used for river modeling [2].
+INRAE needs a new tool to keep up with today’s technologies and with the development of its numerical solvers. In this paper we introduce the current work on the new graphical user interface Pamhyr2.
+2.	Objective
+2.1	History and need 
+PAMHyR is available for two solvers, with two different types of studies: Mage and RubarBE. These two different kinds of studies have mostly similar interfaces, but have their own specific features. They can both be used to: define reach geometry, boundary conditions, lateral inflows, overflows, friction, and structures. In addition, you can run the solver on the study you are editing, and view the solver's results. Firstly, although both Mage and RubarBE are multiple-reach compatible, only the Mage interface enables multiple-reach study editing. Secondly, many small details change from one interface to the next. In addition, the latest Mage features, for example, are not available for modeling in the interface.
+
+	A total overhaul of the Java code would be too much work, given the technological debt accumulated since the beginning of its development. Given the workload involved in modernizing PAMHyR, the decision is made to develop a new version of the software from scratch. This version should be equivalent to the Java version in terms of functionality, and add new features, notably the new Mage functionalities. The aim is also to have an interface that is more modern, more user-friendly, more flexible, available on multiple platforms and in different languages. The interface must also have a certain degree of generality and be able to adapt to different solvers without major changes to the interface. It is also important that the code is open to contributions, to keep the project as lively as possible.
+2.2	Technical choices
+From a technical point of view, choices were made on the basis of the above-mentioned objectives (modernity, maintainability, multiplatform, multilingual, user-friendliness, flexibility), as well as: the ease of learning the technology to facilitate contribution to the software, the popularity of the technology in the scientific community and the interoperability of this technology.
+
+	We chose Python7 as our programming language. It is a popular language in the scientific world, but also in many other fields, with lot of very active software libraries. Moreover, it is a simple and interpreted language, often recommended for beginners, and practiced by beginners and experienced developers. In addition, there is the PyQT8 software library that lets you use the Qt9 GUI library, which is ideal for this project. It is very popular and active, and available on many platforms (GNU/Linux, Windows, MacOS, Unix, BSD, Android, iOS). Qt also includes a number of tools for translating interfaces into different languages. Here we use the community version of Qt, with no paid features. For graphics and visualization, the choice fell on Matplotlib10, which is very popular in the scientific community and can be used to draw a wide variety of graphics. For saving studies, the choice was made to use SQLite11, unlike the previous version which used a text file formatted in XML. The advantages of a SQLite database, in addition to being supplied with Python, include ease of use, interoperability, fast, formal structuring by table and consistency checking between tables. We have chosen to version the database to allow it to evolve with the software, and to make it possible to add columns to tables or make other minor modifications to the database without breaking the compatibility of studies from previous versions. However, PAMHyR and Pamhyr2 study files will not be compatible anymore, and previous studies have to be recreated for this version.
+
+	This new version Pamhyr2 remains closely linked to the Mage solver with which it is supplied. But the ambition of flexibility and generalization gives us the opportunity to develop an interface that can be adapted to other solvers. There can be two solutions for using a solver with Pamhyr2: either the solver adapts to Pamhyr2, or Pamhyr2 adapts to the solver. So Pamhyr2 must integrate a generic output containing the study data that can be used by other solvers, which will be launched via an external executable, and then a generic result input that must be supplied by the solver. In addition, Pamhyr2 must be able to handle the execution and reading of results for specific solvers, and the addition of a solver to Pamhyr2 must be reasonably easy for the solver developer. We have opted for the free and open source software (FOSS) [6] license GPLv312, which guarantees freedom to access, study, modify, redistribute and share. In addition, it guarantees that Pamhyr2's code will remain free and is not allowed to be added any closed-source modifications. However, it will still be possible to use closed-source solvers, because solver is not a part of Pamhyr2.
+3.	DEVELOPMENTS
+3.1	New version of PAMHYR 
+Pamhyr2 currently features the following interfaces: Editing of river network, geometry, boundary conditions, lateral contribution, friction, initial conditions, solver numerical parameters, as well as the interface for launching a solver and displaying hydraulic and sediment results.
+3.1.1	River network
+The river network corresponds to the topology of the hydraulic network of the river. River network editing (Figure 1) is performed via a window featuring a graphical network area and two tables, one with a list of nodes (zone 3) and the other with a list of reaches (zone 2). The graphic area (zone 1) lets you add, delete and move nodes. It can also be used to link nodes in the network by arrows that represent reaches. The color of the node in the graphic area depends on whether it is a downstream, upstream or internal network node. If there is more than one reach, you can use this interface to select a reach, which will then be selected for editing in the following reach-dependent windows. It is also possible to deactivate reaches, in which case they will not be used for the solver run. Tables can be used to edit additional information on nodes and reaches, such as giving them names.
+
+
+
+Figure 1: River network window for a dummy river with 8 reaches, 2 upstream node (yellow), 1 downstream node (green) and 5 internal node (blue).
+
+3.1.2	Geometry
+Geometry editing (Figure 2) is linked to a reach; the reach used will be the last reach selected in the river network window. This window contains a table with the list of the reach’s cross-sections (zone 1) and three graphics. A top view based on the XY positions of the cross-sections’ points and guidelines (zone 2). A longitudinal view of all cross-sections with the height of the guidelines’ points for each profile (zone 3). Finally, a cross-sectional view is displayed (zone 4)  showing the selected cross-section with the previous and the following one in dotted line. Each cross-section is defined by a Kilometer Point (KP) and an optional name. The KP represents the longitudinal coordinate of the cross-section in the numerical solver. It is possible to add cross-sections and then select them to access an editing window, or to import cross-sections from file. Cross-section editing window takes the form of a table showing the raw data of the points that make up the cross-section, and a graph showing the current cross-section.
+
+
+
+Figure 2: Geometry window for Saar river on the unique reach of the Saar river study.
+
+3.1.3	Boundary conditions
+Boundary conditions (BC) are associated with a network node. There are three different types: hydrograph, water level chart or rating curve, in three different categories: Liquid, solid and suspension. Boundary conditions can be added, deleted and edited. Editing a BC (Figure 3) takes the form of a two-column table (the type of column varies according to the type of BC) and a graph representing the data. Data can be copied and pasted from a spreadsheet, or edited by hand.
+
+
+
+Figure 3: Edition window of the boundary conditions hydrograph for the Saar river upstream node.
+
+
+3.1.3	Lateral contribution
+The user interface for lateral contributions is similar to that for boundary conditions, except that it applies to a part of a reach between two KP, and not to a node.
+3.1.4	Friction
+Friction editing is linked to a reach, a friction coefficient is defined and then applied to a portion of the reach between two KP (Figure 4). Friction is defined by two Strickler coefficients, one for the river's main channel and one for the flood plain. The list of available Strickler coefficients is defined at the study level.
+
+
+
+Figure 4: The reach portions for friction coefficient edition window for the Saar study.
+
+3.1.5	Initial conditions
+The initial conditions (Figure 5) are also linked to the reach, corresponding to the water level and flow rate at the initial time of the simulation. These two values can be defined separately for each cross-section of the reach. It is also possible to use predefined functions to generate a water line and flow rate.
+
+
+
+Figure 5:  Initial conditions edition window for the Saar study and the Saar reach. Initial conditions initialized with minimal height of 3 meter and a constant flow rate of 100 m3/s.
+
+3.1.6	Running a solver
+Solver numerical parameters are defined using a key/value table specific to each type of solver known to Pamhyr2. You can select and run the desired solver from the list of configured solvers. Then a window appears with a text area where you can follow the progress of file export and solver output in Figure 6 (zone 3). You can also pause, stop or restart the solver using buttons (zone 1). Once the simulation has finished, you can open a solver trace file, and if the simulation has finished correctly, you can open the results using the “results” button (zone 2).
+
+
+
+Figure 6:  Solver log window for “Elargissement” tests case with a mage solver named “src”.
+
+3.1.7	Results processing and visualization
+The post processing window is made up of tables allowing you to select the reaches, profiles, and timestamps for visualizing the results. The results are presented in different tabs according to the type of data displayed. The Figure 7 shows hydraulic data with water level at a given reach, profile, and time. The graphs shown here are the same as those in the geometry window, with the addition of water level results at a given time.
+
+
+
+Figure 7: Hydraulics results window for “Elargissement” tests case with a Mage solver at timestamps 2113200.0 sec for reach R1 and cross-section at KP 427.7778.
+
+3.2	New features
+Some new features are already implemented in Pamhyr2. First of all, the software is multilingual with English and French currently available. An other very useful enhancement, is the possibility to use the “Ctrl+Z” or “Ctrl+Shift+Z” shortcuts to undo or redo the user actions.
+
+	Another novelty lies in the initial conditions window. Previously the water line could be generated by constant height or altitude. It is now possible to give a minimum height with an increasing function from downstream to upstream, thus avoiding physically unrealistic water holes and getting a little closer to a real and physically coherent water line (Figure 5).
+
+	An important new feature in this version is the presence of sediment layers. They can be defined as shown in Figure 8. Sediment layers can be applied separately for each cross-section (Figure 9). As with friction, they must first be defined and then applied to a profile. They can also be applied separately to each point of a cross-section. Layers are defined by a thickness, a median diameter (D50), a grain size sorting coefficient (Sigma) and a critical shear stress as described in Pierre Balayn PhD thesis [1]. The visualization of sedimentary results is currently done using a plot of the river profile, which shows the evolution of the bed bottom and the thickness of layers as a function of time (Figure 10).
+
+
+
+Figure 8: Sediment layers definition window for Saar study. This sediment layers has three layers (L1, L2 and F).
+
+
+
+
+Figure 9: Sediment layers defined in Figure 8 applied to the reach Saar.
+
+
+
+
+Figure 10: Sedimentary results window for “Elargissement” tests case at timestamps 2113200.0 sec for reach R1 and cross-section at KP 427.7778. This example has only two sediment layers.
+
+4.	Future work
+Old PAMHyR functionalities and additional functionalities, allowed the definition of structures, traps, suspended solids or dissolved pollutants in water, have yet to be developed. Additional options for visualizing results also need to be added. One possibility would be a graph generation tool that would allow the user to select x-axis and y-axis values, as well as the time range, to create a customized graph. We also planned an advanced feature with code-editing window to enable the user to define his own Matplotlib drawing function, which would be saved in the study. Presentation work is also planned to harmonize the application's icons and visuals (images, graphics, etc.). The aim is to make the application clearer and more user-friendly.
+
+	Supporting new solvers and generic solvers will also be an important part of the remaining work. To use any solver, we need to define a generic output format for Pamhyr2 that is simple enough to be given as solver input without major code modification, or that can be processed by a simple Python script (for example). The same applies to the results file that Pamhyr2 will have to read. The main candidates for these generic formats are :
+    • SQLite, because it is easy to use and the library is compatible with most programming languages,
+    • HDF513, a hierarchical file format widely used in scientific circles and compatible with many programming languages.
+
+	As the project progresses, it becomes more and more complicated to test all the functionalities by hand. A suite of tests and unit tests is needed to prevent regression bugs and ensure that the code remains maintainable. For the moment, no such test has been defined. Unit tests will have to be developed on the model and each sub-module will have to include tests, but higher-level functionalities will also have to be tested, such as the recording and playback of a complete study. It will be difficult to test the graphical part automatically, so tests will continue to be carried out manually.
+
+	Full documentation must also be provided to give users an overview of the features offered by Pamhyr2. This documentation must include descriptions of the configuration options, as well as explanations and examples of how to use each feature. In addition, this documentation must include a section for contributors and developers, with a technical presentation of the application, as well as a presentation of the translation, development and debugging tools available.
+
+	For translations into other languages than English and French, we hope that external contributors will take on this work. But no languages other are currently planned by the development team. The application packages are currently available for GNU/Linux and Windows. Under GNU/Linux, a “.tar.xz” archive is available for download. For Windows, this is an installer for application and a compatible version of Mage. An installer for GNU/Linux systems is a work in progress. There are many choices for creating an installer, but their scope depends on the distribution for which they are intended. “.deb”, for example, is intended for Debian distributions and their derivatives (Ubuntu, Linux Mint, and so on). We do not exclude other, more generic options.
+5.	Conclusion
+After a great deal of preparatory work, experimentation, technical selection, proof-of-concept and several months of development, Pamhyr2 is currently in version “v0.0.0”14 and contains almost 20,000 lines of Python code. It allows to create a minimal 1D hydro-sedimentary study, run a Mage simulation and visualize some of the results obtained, all with a more user-friendly interface. But the software is still unstable and under development, and many modifications and improvements are still to be made before it can really be used by everyone. Furthermore, even though many of the features of the original version of PAMHyR are already available (see 3.1 page 3), there are still many to be added to make Pamhyr2 a complete, useful and fully functional piece of software.
+ACKNOWLEDGEMENTS
+The results presented here partially come from the Pamhyr PITI project funded by the Carnot Eau & Environnement institute and the French National Research Agency. Carnot Eau & Environnement was accredited in March 2020 by the French Ministry of Research and Higher Education on the proposal of the Agence Nationale de la Recherche. The signatory members are INRAE, CNRS, Aix Marseille University, IFTS, INSA Lyon, IRD, Université de Montpellier and Université de Savoie Mont-Blanc.
+
+The authors thank Sylvain Coulibaly for his preparatory work and his technical choices.
+REFERENCES and Citations
+[1]	Balayn, P. (2001). Contribution à la modélisation numérique de l'évolution morphologique des cours d'eau aménagés lors de crues. Université Claude Bernard - Lyon 1
+[2]	Camenen, B., Faure, J. Décanis, S. Diéval, L. (2021) A 1D numerical tool for real time modelling of a complex river network, SimHydro 2021
+[3]	Faure, J. (2013). An Integrated Simulation platform - PAMHyR. In John Wiley & Sons, Inc. eBooks (pp. 245–252). https://doi.org/10.1002/9781118557891.ch21
+[4]	Faure, J. (2017). Développement d’Adis-TS. OSR4 | Action V.1. https://hal.science/hal-03749339
+[5]	Faure, J-B., (2019). Mage, Résolution des équations de Barré de St Venant 1D en réseaux complexes, Documentation théorique et mode d’emploi. Techreport (in French)
+[6]	Walt, S. 2007. Free/open source software development. In Proceedings of the the 6th joint meeting of the European software engineering conference and the ACM SIGSOFT symposium on The foundations of software engineering (ESEC-FSE '07). Association for Computing Machinery, New York, NY, USA, 459–468. https://doi.org/10.1145/1287624.1287689
+

doc/tools/PamhyrDoc.cls

@@ -0,0 +1,163 @@
+\ProvidesClass{Pamhyr}[Pamhyr class]
+\NeedsTeXFormat{LaTeX2e}
+\ProcessOptions\relax
+\LoadClass[11pt,a4paper]{article}
+
+\usepackage[hmargin=2cm, vmargin=3cm]{geometry}
+\usepackage[british,UKenglish,USenglish,english,american]{babel}
+\usepackage[T1]{fontenc}
+\usepackage{times}
+\usepackage[usenames,dvipsnames]{xcolor}
+\usepackage[absolute]{textpos}
+\usepackage{titlesec}
+\usepackage{amssymb}
+\usepackage{tcolorbox}
+
+\usepackage{enumitem}
+\setlist[enumerate]{itemsep=-0.5em}
+\setlist[itemize]{itemsep=-0.5em}
+
+%%
+%% Bibtex
+%%
+
+\bibliographystyle{plain}
+
+%%
+%% Colors
+%%
+
+\definecolor{primary}{HTML}{212121}
+\definecolor{lightheadings}{HTML}{5c5c5c}
+\definecolor{headings}{HTML}{212121}
+\definecolor{links}{HTML}{e12121}
+
+%%
+%% Title
+%%
+
+\setlength{\columnsep}{20pt}
+\setlength{\parskip}{0pt}      %% inter paragraph space
+
+\renewcommand{\maketitle}{
+    {
+      \centering
+      {
+        \fontsize{35}{40}
+        \selectfont
+        \scshape
+        Pamhyr2 \\
+        \medskip
+      }
+      {
+        %\centering
+        \scshape
+        \fontsize{20pt}{24pt}
+        \selectfont
+        A graphical user interface for 1D hydro-sedimentary modelling
+        of rivers \\
+        \medskip
+      }
+      \rule{3cm}{0.4pt}\\
+      \vspace{0.3cm}
+      {
+        %\centering
+        \scshape
+        \fontsize{26pt}{24pt}
+        \selectfont
+        \@title \\
+        Document licence: GPLv3 \\
+        \medskip
+        \includegraphics[width=3cm]{../images/GPLv3_Logo.png} \\
+        \medskip
+        \fontsize{14pt}{16pt}
+        \selectfont
+        © \@author \\
+        \medskip
+      }
+      {
+        %\centering
+        %\scshape
+        \fontsize{12pt}{14pt}
+        \selectfont
+        \@date
+        %\medskip
+      }\\
+      \vspace{0.3cm}
+      \rule{3cm}{0.4pt}\\
+      \vspace{0.3cm}
+      {
+        \begin{minipage}[h]{0.24\textwidth}
+          \includegraphics[width=4cm]{../../src/View/ui/ressources/Logo-INRAE.png}
+        \end{minipage}
+        \begin{minipage}[h]{0.24\textwidth}
+          \includegraphics[width=4cm]{../images/riverly.png}
+        \end{minipage}
+      }\\
+      \vspace{0.3cm}
+      %%\rule{\textwidth}{0.4pt}
+      %%\newpage
+    }
+}
+
+
+%%
+%% Texttt
+%%
+
+\usepackage[htt]{hyphenat}      % Make texttt split at end of line
+
+%%
+%% Verbatim
+%%
+
+\AtBeginEnvironment{verbatim}{\footnotesize}
+
+%% Add box arrond of verbatim
+\BeforeBeginEnvironment{verbatim}{\begin{tcolorbox}[boxsep=0pt, left=0.1cm, right=0.1cm, arc=0pt, boxrule=0.5pt, colback=white]}%
+\AfterEndEnvironment{verbatim}{\end{tcolorbox}}%
+
+\makeatletter
+\AtBeginEnvironment{verbatim}{\dontdofcolorbox}
+
+\def\dontdofcolorbox{\renewcommand\fcolorbox[4][]{##4}}
+\makeatother
+
+%%
+%% Source code blocks
+%%
+
+%% Use minted
+\usepackage{minted}
+\usemintedstyle{tango}
+\setminted[c]{fontsize=\footnotesize,encoding=utf8,linenos}
+\setminted[c++]{breaklines,fontsize=\footnotesize,encoding=utf8,linenos}
+\setminted[python]{breaklines,fontsize=\footnotesize,encoding=utf8,linenos}
+\setminted[shell]{breaklines,fontsize=\footnotesize,encoding=utf8}
+\setminted[scheme]{breaklines,fontsize=\footnotesize,encoding=utf8}
+\setminted[commun-lisp]{breaklines,fontsize=\footnotesize,encoding=utf8}
+\setminted[text]{breaklines,fontsize=\footnotesize,encoding=utf8}
+\setminted[llvm]{breaklines,fontsize=\footnotesize,encoding=utf8}
+
+%% Add box arrond of minted
+\BeforeBeginEnvironment{minted}{\begin{tcolorbox}[boxsep=0pt, left=0.1cm, right=0.1cm, arc=0pt, boxrule=0.5pt, colback=white]}%
+\AfterEndEnvironment{minted}{\end{tcolorbox}}%
+
+\makeatletter
+\AtBeginEnvironment{minted}{\dontdofcolorbox}
+
+\def\dontdofcolorbox{\renewcommand\fcolorbox[4][]{##4}}
+\makeatother
+
+
+%%
+%% Water mark
+%%
+
+%% FIXME: Delete me for the first realease
+\usepackage{draftwatermark}
+\SetWatermarkLightness{0.8}
+\SetWatermarkAngle{25}
+\SetWatermarkScale{3}
+\SetWatermarkFontSize{1cm}
+\SetWatermarkText{Work in progress}

doc/tools/latex.org

@@ -0,0 +1,19 @@
+# latex.org -- Pamhyr documentation latex config
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+#+LaTeX_CLASS: PamhyrDoc

doc/tools/macro.org

@@ -0,0 +1,51 @@
+# macro.org -- Pamhyr documentation macro
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+# Constant name
+#+MACRO: oldPamhyr     PAMHyR
+#+MACRO: Pamhyr        Pamhyr2
+#+MACRO: Mage          Mage
+#+MACRO: Rubarbe       RubarBE
+#+MACRO: Inrae         INRAE
+#+MACRO: latex         \LaTeX
+
+# Information
+#+MACRO: version       (eval (pamhyr-version))
+#+MACRO: current-file  (eval (pamhyr-current-file))
+
+# Special format
+#+MACRO: file          =$1=
+
+# Biblio
+#+MACRO: cite          [cite:$1]
+#+MACRO: biblio        \bibliography{documentation}
+
+# Wrapper
+#+NAME: attr_wrap
+#+HEADER: :var width="\\textwidth"
+#+HEADER: :var caption=""
+#+HEADER: :var smallcaption=""
+#+HEADER: :var name=""
+#+HEADER: :var data=""
+#+HEADER: :var float="nil"
+#+BEGIN_SRC sh :results output :exports none
+  echo "#+CAPTION[$smallcaption]: $caption"
+  echo "#+NAME: $name"
+  echo "#+ATTR_LATEX: :width $width :float $float"
+  echo "$data"
+#+END_SRC

doc/tools/setup.el

@@ -0,0 +1,66 @@
+(require 'org)
+(require 'subr-x)
+
+;; LaTeX config
+
+(add-to-list
+ 'org-latex-classes
+ '("PamhyrDoc"
+   "\\documentclass{../tools/PamhyrDoc}"
+   ("\\section{%s}" . "\\section*{%s}")
+   ("\\subsection{%s}" . "\\subsection*{%s}")
+   ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+   ("\\paragraph{%s}" . "\\paragraph*{%s}")
+   ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+
+(setq org-confirm-babel-evaluate nil)
+(setq org-latex-caption-above nil)
+
+(org-babel-do-load-languages
+   'org-babel-load-languages
+   (add-to-list 'org-babel-load-languages '(shell . t)))
+
+(org-babel-do-load-languages
+ 'org-babel-load-languages
+ (add-to-list 'org-babel-load-languages '(dot . t)))
+
+(org-babel-do-load-languages
+ 'org-babel-load-languages
+ (add-to-list 'org-babel-load-languages '(python . t)))
+
+(add-to-list 'org-latex-packages-alist '("" "minted"))
+(setq org-latex-listings 'minted)
+(setq org-src-fontify-natively t)
+
+(setq org-latex-pdf-process
+      '("pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
+        "bibtex documentation"
+        "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
+        "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"))
+
+;; Citations
+
+(org-add-link-type
+ "cite" 'ebib
+ (lambda (path desc format)
+   (cond
+    ((eq format 'html)
+     (format "(<cite>%s</cite>)" path))
+    ((eq format 'latex)
+     (if (or (not desc) (equal 0 (search "cite:" desc)))
+         (format "\\cite{%s}" path)
+       (format "\\cite[%s][%s]{%s}"
+               (cadr (split-string desc ";"))
+               (car (split-string desc ";"))  path))))))
+
+;; Functools
+
+(defun pamhyr-version ()
+  "Return the contents of the pamhyr version file."
+  (with-temp-buffer
+    (insert-file-contents "../../VERSION")
+    (buffer-string)))
+
+(defun pamhyr-current-file ()
+  (let ((lst (split-string (buffer-file-name) "/")))
+    (string-join (nthcdr (- (length lst) 3) lst) "/")))

doc/users/build.sh

@@ -0,0 +1,18 @@
+#! /bin/sh
+
+echo " PDF  documentation.org"
+emacs -nw --batch                                       \
+      --eval "(require 'org)"                           \
+      --eval "(require 'ox-latex)"                      \
+      --eval "(load-file \"../tools/setup.el\")"        \
+      --file ./documentation.org                        \
+      -f org-latex-export-to-pdf
+
+echo " HTML documentation.org"
+emacs -nw --batch                                       \
+      --eval "(require 'org)"                           \
+      --eval "(require 'ox-latex)"                      \
+      --eval "(require 'ox-html)"                       \
+      --eval "(load-file \"../tools/setup.el\")"        \
+      --file ./documentation.org                        \
+      -f org-html-export-to-html

doc/users/documentation.bib

@@ -0,0 +1 @@
+../tools/ref.bib

doc/users/documentation.org

@@ -0,0 +1,20 @@
+#+STARTUP: indent
+
+#+INCLUDE: ../tools/macro.org
+#+INCLUDE: ../tools/latex.org
+
+#+TITLE: User documentation
+#+SUBTITLE: Version: {{{version}}}
+#+AUTHOR: {{{INRAE}}}
+
+#+OPTIONS: toc:t
+#+LANGUAGE: UKenglish
+
+* TODO Over view
+* TODO Get started
+** Installation
+*** Linux
+*** Windows
+* TODO Usage
+
+{{{biblio}}}

full-requirements.txt

@@ -0,0 +1,11 @@
+PyQt5==5.15.4
+PyQt5-Qt5==5.15.2
+PyQt5-sip==12.12.2
+PyQtWebEngine==5.15.6
+QScintilla>=2.14.1
+pyqtgraph>=0.12.1
+matplotlib>=3.4.1
+numpy>=1.24.2
+colorama>=0.4.3
+pyinstaller>=5.11.0
+shapely>=2.0.1

packages/linux.sh

@@ -25,6 +25,7 @@ echo " *** SETUP ENV"
 
 python3 -m venv linux-pamhyr-venv
 . linux-pamhyr-venv/bin/activate
+pip3 install -U pip
 pip3 install -r ../requirements.txt
 
 echo " *** PYINSTALL"
@@ -43,17 +44,22 @@ cd $OLD_PWD
 
 echo " *** COPY DATA"
 
-mkdir -p dist/pamhyr/View/ui
-cp -r ../src/View/ui/ressources/ dist/pamhyr/View/ui/
-cp -r ../src/View/ui/Widgets/*.ui dist/pamhyr/View/ui/
-cp -r ../src/View/ui/*.ui dist/pamhyr/View/ui/
+mkdir -p dist/pamhyr/_internal/View/ui
+mkdir -p dist/pamhyr/_internal/View/ui/Widgets
+cp -r ../src/View/ui/ressources/ dist/pamhyr/_internal/View/ui/
+cp -r ../src/View/ui/Widgets/*.ui dist/pamhyr/_internal/View/ui/Widgets/
+cp -r ../src/View/ui/*.ui dist/pamhyr/_internal/View/ui/
 
 mkdir -p dist/pamhyr/lang
 cp -r ../src/lang/*.qm dist/pamhyr/lang/
 
-cp ../VERSION dist/pamhyr/
-cp ../AUTHORS dist/pamhyr/
-cp ../LICENSE dist/pamhyr/
+mkdir dist/pamhyr/_internal/
+#cp ../VERSION dist/pamhyr/_internal/
+VERSION=$(cat ../VERSION)
+echo "local-build-$VERSION" > dist/pamhyr/_internal/VERSION
+cp ../AUTHORS dist/pamhyr/_internal/
+cp ../LICENSE dist/pamhyr/_internal/
+cp ../src/motd.txt dist/pamhyr/_internal/
 
 mkdir -p dist/pamhyr/mage/
 cp ../mage/mage dist/pamhyr/mage/
@@ -64,6 +70,18 @@ mkdir -p dist/pamhyr/tests_cases/
 mkdir -p dist/pamhyr/tests_cases/Saar
 cp ../tests_cases/Saar/Saar.pamhyr dist/pamhyr/tests_cases/Saar/
 
+mkdir -p dist/pamhyr/doc/
+cp ../doc/dev/documentation.pdf dist/pamhyr/doc/Pamhyr2-dev.pdf
+cp ../doc/dev/documentation.html dist/pamhyr/doc/Pamhyr2-dev.html
+
+cp ../doc/users/documentation.pdf dist/pamhyr/doc/Pamhyr2-users.pdf
+cp ../doc/users/documentation.html dist/pamhyr/doc/Pamhyr2-users.html
+
+mkdir -p dist/pamhyr/doc/images
+cp ../doc/users/images/* dist/pamhyr/doc/images/
+cp ../doc/dev/images/* dist/pamhyr/doc/images/
+cp ../doc/images/* dist/pamhyr/doc/images/
+
 echo " *** MAKE SRC PACKAGE"
 
 OLD_PWD=$PWD
@@ -75,11 +93,11 @@ mv ../pamhyr-src.tar.gz ./
 
 echo " *** MAKE BIN PACKAGE"
 
-OLD_PWD=$PWD
-cd dist/
-tar --xz -cf pamhyr-gnulinux-amd64.tar.xz pamhyr --checkpoint=.100
-cd $OLD_PWD
+# OLD_PWD=$PWD
+# cd dist/
+# tar --xz -cf pamhyr-gnulinux-amd64.tar.xz pamhyr --checkpoint=.100
+# cd $OLD_PWD
 
-mv dist/pamhyr-gnulinux-amd64.tar.xz ./
+# mv dist/pamhyr-gnulinux-amd64.tar.xz ./
 
 echo " *** DONE"

packages/make-windows-dir.bat

@@ -0,0 +1,61 @@
+rem windows.bat -- Pamhyr Windows batch for windows version building
+rem Copyright (C) 2023  INRAE
+rem
+rem This program is free software: you can redistribute it and/or modify
+rem it under the terms of the GNU General Public License as published by
+rem the Free Software Foundation, either version 3 of the License, or
+rem (at your option) any later version.
+rem
+rem This program is distributed in the hope that it will be useful,
+rem but WITHOUT ANY WARRANTY; without even the implied warranty of
+rem MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+rem GNU General Public License for more details.
+rem
+rem You should have received a copy of the GNU General Public License
+rem along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+@ECHO ON
+
+mkdir pamhyr\pamhyr\_internal
+xcopy /s /e /y dist\pamhyr pamhyr\pamhyr
+
+rem Copy data
+mkdir pamhyr\pamhyr\_internal\lang
+mkdir pamhyr\pamhyr\_internal\View\ui\ressources
+mkdir pamhyr\pamhyr\_internal\View\ui\Widgets
+
+rem UI
+copy /y ..\src\View\ui\ressources\ pamhyr\pamhyr\_internal\View\ui\ressources
+copy /y ..\src\View\ui\Widgets\*.ui pamhyr\pamhyr\_internal\View\ui\Widgets
+copy /y ..\src\View\ui\*.ui pamhyr\pamhyr\_internal\View\ui\
+
+rem Lang
+copy /y ..\src\lang\*.qm pamhyr\pamhyr\_internal\lang\
+
+rem Information
+copy /y ..\VERSION pamhyr\pamhyr\_internal
+copy /y ..\AUTHORS pamhyr\pamhyr\_internal
+copy /y ..\LICENSE pamhyr\pamhyr\_internal
+copy /y ..\src\motd.txt pamhyr\pamhyr\_internal
+
+rem MAGE
+mkdir pamhyr\mage
+copy /y ..\mage-windows\mage.exe pamhyr\mage\
+copy /y ..\mage-windows\mage_extraire.exe pamhyr\mage\
+copy /y ..\mage-windows\mailleurPF.exe pamhyr\mage\
+
+rem Copy tests_cases
+mkdir pamhyr\tests_cases
+mkdir pamhyr\tests_cases\Saar
+copy /y ..\tests_cases\Saar\Saar.pamhyr pamhyr\tests_cases\Saar\
+
+rem Documentations
+mkdir pamhyr\doc
+mkdir pamhyr\doc\images
+copy /y ..\doc\users\documentation.pdf pamhyr\doc\Pamhyr2-users.pdf
+copy /y ..\doc\dev\documentation.pdf pamhyr\doc\Pamhyr2-dev.pdf
+copy /y ..\doc\users\documentation.html pamhyr\doc\Pamhyr2-users.html
+copy /y ..\doc\dev\documentation.html pamhyr\doc\Pamhyr2-dev.html
+copy /y ..\doc\users\images\* pamhyr\doc\images
+copy /y ..\doc\dev\images\* pamhyr\doc\images
+copy /y ..\doc\images\* pamhyr\doc\images

packages/make-windows-exe.bat

@@ -0,0 +1,20 @@
+rem windows.bat -- Pamhyr Windows batch for windows version building
+rem Copyright (C) 2023  INRAE
+rem
+rem This program is free software: you can redistribute it and/or modify
+rem it under the terms of the GNU General Public License as published by
+rem the Free Software Foundation, either version 3 of the License, or
+rem (at your option) any later version.
+rem
+rem This program is distributed in the hope that it will be useful,
+rem but WITHOUT ANY WARRANTY; without even the implied warranty of
+rem MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+rem GNU General Public License for more details.
+rem
+rem You should have received a copy of the GNU General Public License
+rem along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+@ECHO ON
+
+rem Make installer
+"C:\Program Files (x86)\NSIS\makensis.exe" pamhyr.nsi

packages/pamhyr.nsi

@@ -3,17 +3,17 @@
 !define LIC_NAME "LICENSE"
 !define APP_NAME "PAMHYR"
 
-Name "PAMHYR"
-OutFile "pamhyr-win-amd64.exe"
-LicenseData "..\LICENSE"
+Name "Pamhyr2"
+OutFile "pamhyr-windows.exe"
+LicenseData "pamhyr\pamhyr\_internal\LICENSE"
 LicenseText "I Agree"
 
 RequestExecutionLevel admin
 
 Unicode True
-InstallDir $PROGRAMFILES\PAMHYR
+InstallDir $PROGRAMFILES\Pamhyr2
 
-InstallDirRegKey HKLM "Software\PAMHYR" "Install_Dir"
+InstallDirRegKey HKLM "Software\Pamhyr2" "Install_Dir"
 
 Page license
 Page components
@@ -23,35 +23,39 @@ Page instfiles
 UninstPage uninstConfirm
 UninstPage instfiles
 
-Section "PAMHYR"
+Section "Pamhyr2"
   SectionIn RO
 
   SetOutPath $INSTDIR
 
-  File /r "dist\pamhyr\*"
+  File /r "pamhyr\*"
 
-  WriteRegStr HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\PAMHYR" "DisplayName" "NSIS PAMHYR"
-  WriteRegStr HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\PAMHYR" "UninstallString" "$INSTDIR\uninstall.exe"
-  WriteRegDWORD HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\PAMHYR" "NoModify" 1
-  WriteRegDWORD HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\PAMHYR" "NoRepair" 1
+  WriteRegStr HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\Pamhyr2" "DisplayName" "NSIS Pamhyr2"
+  WriteRegStr HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\Pamhyr2" "UninstallString" "$INSTDIR\uninstall.exe"
+  WriteRegDWORD HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\Pamhyr2" "NoModify" 1
+  WriteRegDWORD HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\Pamhyr2" "NoRepair" 1
   WriteUninstaller "$INSTDIR\uninstall.exe"
 
 SectionEnd
 
 Section "Start Menu Shortcuts"
+  CreateDirectory "$SMPROGRAMS\Pamhyr2"
+  CreateShortcut "$SMPROGRAMS\Pamhyr2\Uninstall.lnk" "$INSTDIR\uninstall.exe"
+  CreateShortcut "$SMPROGRAMS\Pamhyr2\Pamhyr2.lnk" "$INSTDIR\pamhyr\pamhyr.exe"
+SectionEnd
 
-  CreateDirectory "$SMPROGRAMS\PAMHYR"
-  CreateShortcut "$SMPROGRAMS\PAMHYR\Uninstall.lnk" "$INSTDIR\uninstall.exe"
-  CreateShortcut "$SMPROGRAMS\PAMHYR\PAMHYR.lnk" "$INSTDIR\pamhyr.exe"
-
+Section "Desktop Shortcuts"
+  SetShellVarContext all
+  CreateShortcut "$desktop\Pamhyr2.lnk" "$instdir\pamhyr\pamhyr.exe"
 SectionEnd
 
 Section "Uninstall"
-  DeleteRegKey HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\PAMHYR"
-  DeleteRegKey HKLM SOFTWARE\NSIS_PAMHYR
+  DeleteRegKey HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\Pamhyr2"
+  DeleteRegKey HKLM SOFTWARE\NSIS_Pamhyr2
 
-  Delete "$SMPROGRAMS\PAMHYR\*.lnk"
+  Delete "$SMPROGRAMS\Pamhyr2\*.lnk"
+  Delete "$desktop\Pamhyr2.lnk"
 
-  RMDir "$SMPROGRAMS\PAMHYR"
+  RMDir "$SMPROGRAMS\Pamhyr2"
   RMDir /R "$INSTDIR"
 SectionEnd

packages/wine.sh

@@ -81,13 +81,42 @@ wine pyinstaller ../src/pamhyr.py -y
 
 echo " *** COPY DATA"
 
-mkdir -p dist/pamhyr/View/ui
-cp -r ../src/View/ui/ressources/ dist/pamhyr/View/ui/
-cp -r ../src/View/ui/Widgets/*.ui dist/pamhyr/View/ui/
-cp -r ../src/View/ui/*.ui dist/pamhyr/View/ui/
+mkdir -p pamhyr
+mkdir -p pamhyr/pamhyr
 
-cp ../VERSION dist/pamhyr/
-cp ../AUTHORS dist/pamhyr/
+# Copy Pamhyr info
+cp -v ../VERSION pamhyr/pamhyr/
+cp -v ../AUTHORS pamhyr/pamhyr/
+cp -v ../LICENSE pamhyr/pamhyr/
+
+# Copy mage
+mkdir -p pamhyr/mage
+cp -v ../mage/* pamhyr/mage/
+
+# Copy Pamhyr
+cp -r dist/pamhyr pamhyr/
+
+# Copy Pamhyr resources
+mkdir -p pamhyr/pamhyr/View
+mkdir -p pamhyr/pamhyr/View/ui
+mkdir -p pamhyr/pamhyr/View/ui/Widgets
+cp -r ../src/View/ui/*.ui pamhyr/pamhyr/View/ui/
+cp -r ../src/View/ui/ressources/ pamhyr/pamhyr/View/ui
+cp -r ../src/View/ui/Widgets/*.ui pamhyr/pamhyr/View/ui/Widgets
+
+# Copy lang
+mkdir -p pamhyr/pamhyr/lang
+cp -r ../src/lang/*.qm pamhyr/pamhyr/lang
+
+# Copy tests cases
+mkdir -p pamhyr/tests_cases/
+mkdir -p pamhyr/tests_cases/Saar
+cp ../tests_cases/Saar/Saar.pamhyr pamhyr/tests_cases/Saar/
+
+# Copy documentations
+mkdir -p pamhyr/doc/
+cp ../doc/users/documentation.pdf pamhyr/doc/Pamhyr2-users.pdf
+cp ../doc/dev/documentation.pdf pamhyr/doc/Pamhyr2-dev.pdf
 
 # Update TS and build QM files
 OLD_PWD=$PWD
@@ -102,19 +131,19 @@ echo " *** MAKE PACKAGES"
 
 echo " TAR pamhyr-win-amd64.tar.xz"
 
-OLD_PWD=$PWD
-cd dist/
-tar --xz -cf pamhyr-win-amd64.tar.xz pamhyr --checkpoint=.100
-cd $OLD_PWD
-mv dist/pamhyr-win-amd64.tar.xz ./
+# OLD_PWD=$PWD
+# cd dist/
+# tar --xz -cf pamhyr-win-amd64.tar.xz pamhyr --checkpoint=.100
+# cd $OLD_PWD
+# mv dist/pamhyr-win-amd64.tar.xz ./
 
 echo " ZIP pamhyr-win-amd64.zip"
 
-OLD_PWD=$PWD
-cd dist/
-zip -r pamhyr-win-amd64.zip pamhyr/
-cd $OLD_PWD
-mv dist/pamhyr-win-amd64.zip ./
+# OLD_PWD=$PWD
+# cd dist/
+# zip -r pamhyr-win-amd64.zip pamhyr/
+# cd $OLD_PWD
+# mv dist/pamhyr-win-amd64.zip ./
 
 echo " *** MAKE INSTALLER"
 

requirements.txt

@@ -1,6 +1,8 @@
 PyQt5==5.15.4
 PyQt5-Qt5==5.15.2
-PyQt5-sip==12.8.1
+PyQt5-sip==12.12.2
+#PyQtWebEngine==5.15.6
+QScintilla>=2.14.1
 pyqtgraph>=0.12.1
 matplotlib>=3.4.1
 numpy>=1.24.2

src/Checker/Checker.py

@@ -20,12 +20,14 @@ from enum import Enum
 
 from Model.Except import NotImplementedMethodeError
 
+
 class STATUS(Enum):
     UNKNOWN = -1
     OK = 0
     WARNING = 1
     ERROR = 2
 
+
 class AbstractModelChecker(object):
     def __init__(self):
         self._name = ""
@@ -62,6 +64,12 @@ class AbstractModelChecker(object):
 
     # Abstract function
 
+    def _run(self, study):
+        from Model.Study import Study
+
+        thread_study = Study.open(study._filename)
+        self.run(thread_study)
+
     def run(self, study):
         """Run checker function
 

src/Checker/Mage.py

@@ -27,8 +27,9 @@ from Checker.Checker import AbstractModelChecker, STATUS
 
 _translate = QCoreApplication.translate
 
+
 class MageNetworkGraphChecker(AbstractModelChecker):
-    def __init__(self, connectivity = True):
+    def __init__(self, connectivity=True):
         super(MageNetworkGraphChecker, self).__init__()
 
         self._mode_conn = connectivity
@@ -38,8 +39,10 @@ class MageNetworkGraphChecker(AbstractModelChecker):
         else:
             mode = "cycle"
 
-        self._name = _translate("Checker", f"Mage network graph {mode} checker")
-        self._description = _translate("Checker", "Check if the network graph is valid")
+        self._name = _translate(
+            "Checker", f"Mage network graph {mode} checker")
+        self._description = _translate(
+            "Checker", "Check if the network graph is valid")
 
     @timer
     def _connectivity(self, summary, status, graph):

src/Checker/Study.py

@@ -30,7 +30,8 @@ class StudyNetworkReachChecker(AbstractModelChecker):
         super(StudyNetworkReachChecker, self).__init__()
 
         self._name = _translate("Checker", "Study network reach checker")
-        self._description = _translate("Checker", "Check if exists at least one reach for study")
+        self._description = _translate(
+            "Checker", "Check if exists at least one reach for study")
 
     def run(self, study):
         if study is None:
@@ -54,12 +55,14 @@ class StudyNetworkReachChecker(AbstractModelChecker):
         self._status = STATUS.OK
         return True
 
+
 class StudyGeometryChecker(AbstractModelChecker):
     def __init__(self):
         super(StudyGeometryChecker, self).__init__()
 
         self._name = _translate("Checker", "Study geometry checker")
-        self._description = _translate("Checker", "Check if exists geometry for each reach of study")
+        self._description = _translate(
+            "Checker", "Check if exists geometry for each reach of study")
         self._reachs = []
 
     def run(self, study):
@@ -128,6 +131,7 @@ class DummyWARNING(AbstractModelChecker):
 
         return True
 
+
 class DummyERROR(AbstractModelChecker):
     def __init__(self):
         super(DummyERROR, self).__init__()

src/Model/AModelComponent.py

@@ -1,10 +0,0 @@
-# -*- coding: utf-8 -*-
-
-class AbstractModelComponent(object):
-    def __init__(self):
-        super(AbstractModelComponent, self).__init__()
-
-    def new(self, filename):
-
-
-    def export(self, filename):

src/Model/BoundaryCondition/BoundaryCondition.py

@@ -20,17 +20,18 @@ import logging
 
 from tools import trace, timer, old_pamhyr_date_to_timestamp
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrDB import SQLSubModel
 from Model.Except import NotImplementedMethodeError
 
 logger = logging.getLogger()
 
+
 class BoundaryCondition(SQLSubModel):
     _sub_classes = []
     _id_cnt = 0
 
-    def __init__(self, id:int = -1, name:str = "",
-                 status = None):
+    def __init__(self, id: int = -1, name: str = "",
+                 status=None):
         super(BoundaryCondition, self).__init__()
 
         self._status = status
@@ -83,7 +84,8 @@ class BoundaryCondition(SQLSubModel):
     def _get_ctor_from_type(cls, t):
         from Model.BoundaryCondition.BoundaryConditionTypes import (
             NotDefined, PonctualContribution,
-            TimeOverZ, TimeOverDischarge, ZOverDischarge
+            TimeOverZ, TimeOverDischarge, ZOverDischarge,
+            Solid,
         )
 
         res = NotDefined
@@ -95,10 +97,12 @@ class BoundaryCondition(SQLSubModel):
             res = TimeOverDischarge
         elif t == "ZD":
             res = ZOverDischarge
+        elif t == "SL":
+            res = Solid
         return res
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         new = []
         tab = data["tab"]
 
@@ -112,9 +116,9 @@ class BoundaryCondition(SQLSubModel):
             t = row[2]
             ctor = cls._get_ctor_from_type(t)
             bc = ctor(
-                id = row[0],
-                name = row[1],
-                status = data['status']
+                id=row[0],
+                name=row[1],
+                status=data['status']
             )
 
             bc.node = None
@@ -140,7 +144,7 @@ class BoundaryCondition(SQLSubModel):
 
         return new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         tab = data["tab"]
 
         execute(f"DELETE FROM boundary_condition WHERE id = {self.id}")
@@ -152,7 +156,7 @@ class BoundaryCondition(SQLSubModel):
 
         sql = (
             "INSERT INTO " +
-            "boundary_condition(id, name, type, tab, node) "+
+            "boundary_condition(id, name, type, tab, node) " +
             "VALUES (" +
             f"{self.id}, '{self._sql_format(self._name)}', " +
             f"'{self._sql_format(self._type)}', '{tab}', {node}" +
@@ -167,7 +171,7 @@ class BoundaryCondition(SQLSubModel):
 
             sql = (
                 "INSERT INTO " +
-                "boundary_condition_data(ind, data0, data1, bc) "+
+                "boundary_condition_data(ind, data0, data1, bc) " +
                 f"VALUES ({ind}, '{data0}', {data1}, {self.id})"
             )
             execute(sql)
@@ -184,7 +188,7 @@ class BoundaryCondition(SQLSubModel):
 
     @classmethod
     def time_convert(cls, data):
-        if type(data) == str and data.count(":") == 3:
+        if data is str and data.count(":") == 3:
             return old_pamhyr_date_to_timestamp(data)
 
         return int(data)
@@ -243,7 +247,7 @@ class BoundaryCondition(SQLSubModel):
         new_1 = self._default_1
 
         if len(header) != 0:
-            for i in [0,1]:
+            for i in [0, 1]:
                 for j in range(len(header)):
                     if self._header[i] == header[j]:
                         if i == 0:
@@ -256,13 +260,13 @@ class BoundaryCondition(SQLSubModel):
 
         return (new_0, new_1)
 
-    def add(self, index:int):
+    def add(self, index: int):
         value = (self._default_0, self._default_1)
         self._data.insert(index, value)
         self._status.modified()
         return value
 
-    def insert(self, index:int, value):
+    def insert(self, index: int, value):
         self._data.insert(index, value)
         self._status.modified()
 
@@ -298,11 +302,10 @@ class BoundaryCondition(SQLSubModel):
         return self.data[index]
 
     def get_range(self, _range):
-        l = []
+        lst = []
         for r in _range:
-            l.append(r)
-        return l
-
+            lst.append(r)
+        return lst
 
     def _set_i_c_v(self, index, column, value):
         v = list(self._data[index])
@@ -310,22 +313,22 @@ class BoundaryCondition(SQLSubModel):
         self._data[index] = tuple(v)
         self._status.modified()
 
-    def set_i_0(self, index:int, value):
+    def set_i_0(self, index: int, value):
         self._set_i_c_v(index, 0, value)
 
-    def set_i_1(self, index:int, value):
+    def set_i_1(self, index: int, value):
         self._set_i_c_v(index, 1, value)
 
     @timer
     def convert(self, cls):
-        new = cls(name = self.name, status = self._status)
+        new = cls(name=self.name, status=self._status)
         new.node = self.node
 
         for i, _ in enumerate(self.data):
             new.add(i)
 
-        for i in [0,1]:
-            for j in [0,1]:
+        for i in [0, 1]:
+            for j in [0, 1]:
                 if self._header[i] == new.header[j]:
                     for ind, v in self.data:
                         try:

src/Model/BoundaryCondition/BoundaryConditionList.py

@@ -19,43 +19,27 @@
 from copy import copy
 from tools import trace, timer
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrList import PamhyrModelListWithTab
 from Model.Except import NotImplementedMethodeError
 
 from Model.BoundaryCondition.BoundaryCondition import BoundaryCondition
 from Model.BoundaryCondition.BoundaryConditionTypes import (
     NotDefined,
     PonctualContribution,
-    TimeOverZ, TimeOverDischarge, ZOverDischarge
+    TimeOverZ, TimeOverDischarge, ZOverDischarge,
+    Solid,
 )
 
-class BoundaryConditionList(SQLSubModel):
+
+class BoundaryConditionList(PamhyrModelListWithTab):
+    _tabs_list = ["liquid", "solid", "suspenssion"]
     _sub_classes = [
         BoundaryCondition,
     ]
 
-    def __init__(self, status = None):
-        super(BoundaryConditionList, self).__init__()
-
-        self._status = status
-
-        self._tabs = {
-            "liquid" : [],
-            "solid" : [],
-            "suspenssion" : []
-        }
-
     @classmethod
-    def _sql_create(cls, execute):
-        return cls._create_submodel(execute)
-
-    @classmethod
-    def _sql_update(cls, execute, version):
-        return True
-
-    @classmethod
-    def _sql_load(cls, execute, data = None):
-        new = cls(status = data['status'])
+    def _sql_load(cls, execute, data=None):
+        new = cls(status=data['status'])
 
         if data is None:
             data = {}
@@ -68,7 +52,7 @@ class BoundaryConditionList(SQLSubModel):
 
         return new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         execute("DELETE FROM boundary_condition")
 
         if data is None:
@@ -77,83 +61,29 @@ class BoundaryConditionList(SQLSubModel):
         for tab in self._tabs:
             data["tab"] = tab
             for bc in self._tabs[tab]:
-                bc._sql_save(execute, data = data)
+                bc._sql_save(execute, data=data)
 
         return True
 
-    def len(self, lst):
-        return len(self._tabs[lst])
-
-    def get_tab(self, lst):
-        return self._tabs[lst].copy()
-
-    def get(self, lst, row):
-        return self._tabs[lst][row]
-
-    def set(self, lst, row, new):
-        self._tabs[lst][row] = new
-        self._status.modified()
-
     def new(self, lst, index):
         n = NotDefined(status=self._status)
         self._tabs[lst].insert(index, n)
         self._status.modified()
         return n
 
-    def insert(self, lst, index, new):
-        self._tabs[lst].insert(index, new)
-        self._status.modified()
-
-    def delete(self, lst, bcs):
-        for bc in bcs:
-            self._tabs[lst].remove(bc)
-        self._status.modified()
-
-    def delete_i(self, lst, indexes):
-        bcs = list(
-            map(
-                lambda x: x[1],
-                filter(
-                    lambda x: x[0] in indexes,
-                    enumerate(self._tabs[lst])
-                )
-            )
-        )
-        self.delete(lst, bcs)
-
-    def sort(self, lst, reverse=False, key=None):
-        self._tabs[lst].sort(reverse=reverse, key=key)
-        self._status.modified()
-
-    def move_up(self, lst, index):
-        if index < len(self._tabs[lst]):
-            next = index - 1
-
-            l = self._tabs[lst]
-            l[index], l[next] = l[next], l[index]
-            self._status.modified()
-
-    def move_down(self, lst, index):
-        if index >= 0:
-            prev = index + 1
-
-            l = self._tabs[lst]
-            l[index], l[prev] = l[prev], l[index]
-            self._status.modified()
-
     def __copy__(self):
         new = BoundaryConditionList()
 
-        for l in self._tabs:
-            new.tabs[l] = self._tabs[l].copy()
+        for lst in self._tabs:
+            new.tabs[lst] = self._tabs[lst].copy()
 
         return new
 
     def __deepcopy__(self):
         new = BoundaryConditionList()
 
-        for l in self._tabs:
-            new.tabs[l] = self._tabs[l].deepcopy()
+        for lst in self._tabs:
+            new.tabs[lst] = self._tabs[lst].deepcopy()
 
         return new
 

src/Model/BoundaryCondition/BoundaryConditionTypes.py

@@ -22,7 +22,7 @@ from Model.BoundaryCondition.BoundaryCondition import BoundaryCondition
 
 
 class NotDefined(BoundaryCondition):
-    def __init__(self, id:int = -1, name:str = "", status = None):
+    def __init__(self, id: int = -1, name: str = "", status=None):
         super(NotDefined, self).__init__(id=id, name=name, status=status)
 
         self._type = "ND"
@@ -32,9 +32,11 @@ class NotDefined(BoundaryCondition):
     def _default_0(self):
         return 0.0
 
+
 class PonctualContribution(BoundaryCondition):
-    def __init__(self, id:int = -1, name:str = "", status = None):
-        super(PonctualContribution, self).__init__(id=id, name=name, status=status)
+    def __init__(self, id: int = -1, name: str = "", status=None):
+        super(PonctualContribution, self).__init__(
+            id=id, name=name, status=status)
 
         self._type = "PC"
         self._header = ["time", "discharge"]
@@ -44,8 +46,9 @@ class PonctualContribution(BoundaryCondition):
     def compatibility(cls):
         return ["liquid"]
 
+
 class TimeOverZ(BoundaryCondition):
-    def __init__(self, id:int = -1, name:str = "", status = None):
+    def __init__(self, id: int = -1, name: str = "", status=None):
         super(TimeOverZ, self).__init__(id=id, name=name, status=status)
 
         self._type = "TZ"
@@ -56,9 +59,11 @@ class TimeOverZ(BoundaryCondition):
     def compatibility(cls):
         return ["liquid"]
 
+
 class TimeOverDischarge(BoundaryCondition):
-    def __init__(self, id:int = -1, name:str = "", status = None):
-        super(TimeOverDischarge, self).__init__(id=id, name=name, status=status)
+    def __init__(self, id: int = -1, name: str = "", status=None):
+        super(TimeOverDischarge, self).__init__(
+            id=id, name=name, status=status)
 
         self._type = "TD"
         self._header = ["time", "discharge"]
@@ -68,8 +73,9 @@ class TimeOverDischarge(BoundaryCondition):
     def compatibility(cls):
         return ["liquid"]
 
+
 class ZOverDischarge(BoundaryCondition):
-    def __init__(self, id:int = -1, name:str = "", status = None):
+    def __init__(self, id: int = -1, name: str = "", status=None):
         super(ZOverDischarge, self).__init__(id=id, name=name, status=status)
 
         self._type = "ZD"
@@ -83,3 +89,19 @@ class ZOverDischarge(BoundaryCondition):
     @property
     def _default_0(self):
         return 0.0
+
+
+class Solid(BoundaryCondition):
+    def __init__(self, id: int = -1, name: str = "", status=None):
+        super(Solid, self).__init__(id=id, name=name, status=status)
+
+        self.d50 = 0.002
+        self.sigma = 1
+
+        self._type = "SL"
+        self._header = ["time", "solid"]
+        self._types = [TimeOverDischarge.time_convert, float]
+
+    @classmethod
+    def compatibility(cls):
+        return ["solid"]

src/Model/Except.py

@@ -45,8 +45,9 @@ def exception_message_box(exception):
 # Custom error #
 ################
 
+
 class ExeceptionWithMessageBox(Exception):
-    def __init__(self, title = "Exeception"):
+    def __init__(self, title="Exeception"):
         self.title = title
 
     def header(self):
@@ -72,7 +73,7 @@ class ExeceptionWithMessageBox(Exception):
 class NotImplementedMethodeError(ExeceptionWithMessageBox):
     def __init__(self, obj, func):
         super(NotImplementedMethodeError, self).__init__(
-            title = _translate("Exception", "Method not implemented")
+            title=_translate("Exception", "Method not implemented")
         )
 
         self.obj = obj
@@ -81,12 +82,16 @@ class NotImplementedMethodeError(ExeceptionWithMessageBox):
         self.alert()
 
     def __str__(self):
+        class_type = self.obj
+        if self.obj.__class__ != type:
+            class_type = self.obj.__class__
+
         return (
             _translate("Exception", "Method") +
             f" '{self.func.__name__}' " +
             _translate("Exception", "not implemented") +
             _translate("Exception", "for class") +
-            f" '{self.obj.__class__ if self.obj.__class__ != type else self.obj}'"
+            f" '{class_type}'"
         )
 
     def header(self):
@@ -104,10 +109,11 @@ class NotImplementedMethodeError(ExeceptionWithMessageBox):
             f" '{self.obj.__class__}'"
         )
 
+
 class FileFormatError(ExeceptionWithMessageBox):
     def __init__(self, filename, reason):
         super(FileFormatError, self).__init__(
-            title = _translate("Exception", "FileFormatError")
+            title=_translate("Exception", "FileFormatError")
         )
 
         self.reason = reason
@@ -137,7 +143,7 @@ class FileFormatError(ExeceptionWithMessageBox):
 class ClipboardFormatError(ExeceptionWithMessageBox):
     def __init__(self, mime=None, header=None, data=None):
         super(ClipboardFormatError, self).__init__(
-            title = _translate("Exception", "Clipboard format error")
+            title=_translate("Exception", "Clipboard format error")
         )
 
         self._mime = mime

src/Model/Friction/Friction.py

@@ -18,10 +18,11 @@
 
 from tools import trace, timer
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrDB import SQLSubModel
+
 
 class Friction(SQLSubModel):
-    def __init__(self, name:str = "", status = None):
+    def __init__(self, name: str = "", status=None):
         super(Friction, self).__init__()
 
         self._status = status
@@ -57,7 +58,7 @@ class Friction(SQLSubModel):
         return True
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         new = []
         reach = data["parent"]  # Reach object
         status = data["status"]
@@ -78,22 +79,21 @@ class Friction(SQLSubModel):
             es = next(filter(lambda s: s.id == row[4], stricklers))
 
             # Create friction
-            sec = cls(status = status)
+            sec = cls(status=status)
             sec.edge = reach
             sec.begin_kp = row[1]
             sec.end_kp = row[2]
             sec.begin_strickler = bs
             sec.end_strickler = es
 
-            new[ind] = sec
+            yield ind, sec
 
-        return new
-
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         ind = data["ind"]
         execute(
             "INSERT INTO " +
-            "friction(ind, begin_kp, end_kp, reach, begin_strickler, end_strickler) " +
+            "friction(ind, begin_kp, end_kp, " +
+            "reach, begin_strickler, end_strickler) " +
             "VALUES (" +
             f"{ind}, {self._begin_kp}, {self._end_kp}, " +
             f"{self._edge.id}, " +
@@ -121,7 +121,7 @@ class Friction(SQLSubModel):
         self._edge = edge
         if (edge is not None and
             self._begin_kp == 0.0 and
-            self._end_kp == 0.0):
+                self._end_kp == 0.0):
             self._begin_kp = self._edge.reach.get_kp_min()
             self._end_kp = self._edge.reach.get_kp_max()
         self._status.modified()

src/Model/Friction/FrictionList.py

@@ -21,26 +21,19 @@ import logging
 from copy import copy
 from tools import trace, timer
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrDB import SQLSubModel
+from Model.Tools.PamhyrList import PamhyrModelList
+
 from Model.Friction.Friction import Friction
 
 logger = logging.getLogger()
 
-class FrictionList(SQLSubModel):
+
+class FrictionList(PamhyrModelList):
     _sub_classes = [
         Friction
     ]
 
-    def __init__(self, status = None):
-        super(FrictionList, self).__init__()
-
-        self._status = status
-        self._frictions = []
-
-    @classmethod
-    def _sql_create(cls, execute):
-        return cls._create_submodel(execute)
-
     @classmethod
     def _sql_update_0_0_1(cls, execute, version):
         execute("ALTER TABLE `section` RENAME TO `friction`")
@@ -54,85 +47,54 @@ class FrictionList(SQLSubModel):
         return True
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
-        new = cls(status = data['status'])
+    def _sql_load(cls, execute, data=None):
+        new = cls(status=data['status'])
 
-        new._frictions = Friction._sql_load(
+        new._lst = Friction._sql_load(
             execute, data
         )
 
         return new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         reach = data["reach"]
         execute(f"DELETE FROM friction WHERE reach = {reach.id}")
 
         ok = True
         ind = 0
-        for friction in self._frictions:
+        for friction in self._lst:
             data["ind"] = ind
-            ok &= friction._sql_save(execute, data = data)
+            ok &= friction._sql_save(execute, data=data)
             ind += 1
 
         return ok
 
-    def __len__(self):
-        return len(self._frictions)
-
-    @property
-    def frictions(self):
-        return self._frictions.copy()
-
-    def get(self, row):
-        return self._frictions[row]
-
-    def set(self, row, new):
-        self._frictions[row] = new
-        self._status.modified()
-
-    def new(self, index):
-        n = Friction(status = self._status)
-        self._frictions.insert(index, n)
-        self._status.modified()
-        return n
-
-    def insert(self, index, new):
-        self._frictions.insert(index, new)
-        self._status.modified()
-
-    def delete(self, frictions):
-        for friction in frictions:
-            self._frictions.remove(friction)
-        self._status.modified()
-
-    def delete_i(self, indexes):
-        frictions = list(
+    def _get_frictions_list(self):
+        # Frictions list generator is type (int, Point) with the first
+        # element the index of the Point in list
+        return list(
             map(
-                lambda x: x[1],
-                filter(
-                    lambda x: x[0] in indexes,
-                    enumerate(self._frictions)
+                lambda p: p[1],
+                sorted(
+                    self._lst,
+                    key=lambda p: p[0]
                 )
             )
         )
-        self.delete(frictions)
 
-    def sort(self, reverse=False, key=None):
-        self._frictions.sort(reverse=reverse, key=key)
+    @property
+    def lst(self):
+        if not isinstance(self._lst, list):
+            self._lst = self._get_frictions_list()
+
+        return self._lst
+
+    @property
+    def frictions(self):
+        return self.lst
+
+    def new(self, index):
+        n = Friction(status=self._status)
+        self._lst.insert(index, n)
         self._status.modified()
-
-    def move_up(self, index):
-        if index < len(self._frictions):
-            next = index - 1
-
-            l = self._frictions
-            l[index], l[next] = l[next], l[index]
-            self._status.modified()
-
-    def move_down(self, index):
-        if index >= 0:
-            prev = index + 1
-
-            l = self._frictions
-            l[index], l[prev] = l[prev], l[index]
-            self._status.modified()
+        return n

src/Model/Geometry/Point.py

@@ -18,13 +18,30 @@
 
 from Model.Except import NotImplementedMethodeError
 
+
 class Point(object):
-    def __init__(self, name:str = "", status = None):
+    def __init__(self, name: str = "", profile=None, status=None):
         super(Point, self).__init__()
 
         self._status = status
 
         self._name = name
+        self._profile = profile
+        self._sl = None
+
+    @property
+    def sl(self):
+        if self._sl is None:
+            return self._profile.sl
+
+        return self._sl
+
+    @sl.setter
+    def sl(self, sl):
+        if sl == self._profile.sl:
+            self._sl = None
+        else:
+            self._sl = sl
 
     @property
     def name(self):

src/Model/Geometry/PointXY.py

@@ -20,10 +20,11 @@ from math import dist
 
 from Model.Geometry.Point import Point
 
+
 class PointAC(Point):
-    def __init__(self, a:float = 0.0, c:float = 0.0,
-                 name: str = "", status = None):
-        super(PointXY, self).__init__(name = name, status = status)
+    def __init__(self, a: float = 0.0, c: float = 0.0,
+                 name: str = "", status=None):
+        super(PointXY, self).__init__(name=name, status=status)
 
         self._a = float(a)
         self._c = float(c)

src/Model/Geometry/PointXYZ.py

@@ -19,15 +19,17 @@
 from math import dist
 import numpy as np
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrDB import SQLSubModel
 from Model.Geometry.Point import Point
 
+
 class PointXYZ(Point, SQLSubModel):
     _sub_classes = []
 
-    def __init__(self, x:float = 0.0, y:float = 0.0, z:float = 0.0,
-                 name:str = "", status = None):
-        super(PointXYZ, self).__init__(name=name, status=status)
+    def __init__(self, x: float = 0.0, y: float = 0.0, z: float = 0.0,
+                 name: str = "", profile=None, status=None):
+        super(PointXYZ, self).__init__(
+            name=name, profile=profile, status=status)
 
         self._x = float(x)
         self._y = float(y)
@@ -44,7 +46,9 @@ class PointXYZ(Point, SQLSubModel):
             y INTEGER NOT NULL,
             z INTEGER NOT NULL,
             profile INTEGER NOT NULL,
-            FOREIGN KEY(profile) REFERENCES profileXYZ(id)
+            sl INTEGER,
+            FOREIGN KEY(profile) REFERENCES profileXYZ(id),
+            FOREIGN KEY(sl) REFERENCES sedimentary_layer(id)
           )
         """)
 
@@ -53,25 +57,30 @@ class PointXYZ(Point, SQLSubModel):
     @classmethod
     def _sql_update(cls, execute, version):
         cls._update_submodel(execute, version)
+
+        major, minor, release = version.strip().split(".")
+        if major == minor == "0":
+            if int(release) < 2:
+                execute(
+                    """
+                    ALTER TABLE geometry_pointXYZ
+                    ADD COLUMN sl INTEGER
+                    REFERENCES sedimentary_layer(id)
+                    """
+                )
         return True
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
-        points = []
-
+    def _sql_load(cls, execute, data=None):
         status = data["status"]
         profile = data["profile"]
 
         table = execute(
-            "SELECT ind, name, x, y, z " +
+            "SELECT ind, name, x, y, z, sl " +
             "FROM geometry_pointXYZ " +
-            f"WHERE profile = {profile}"
+            f"WHERE profile = {profile.id}"
         )
 
-        # Create points list
-        for _ in table:
-            points.append(None)
-
         # Fill points list with new point
         for row in table:
             ind = row[0]
@@ -79,35 +88,46 @@ class PointXYZ(Point, SQLSubModel):
             x = row[2]
             y = row[3]
             z = row[4]
+            sl = row[5]
 
             new = cls(
-                name = name,
-                x = x, y = y, z = z,
-                status = status
+                name=name,
+                x=x, y=y, z=z,
+                profile=profile,
+                status=status
             )
 
-            points[ind] = new
+            if sl == -1 or sl is None:
+                new._sl = None
+            else:
+                new._sl = next(
+                    filter(
+                        lambda s: s.id == sl,
+                        data["sediment_layers_list"].sediment_layers
+                    )
+                )
 
-        return points
+            yield ind, new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         profile = data["profile"]
         ind = data["ind"]
 
+        sl = self._sl.id if self._sl is not None else -1
+
         sql = (
             "INSERT OR REPLACE INTO " +
-            "geometry_pointXYZ(ind, name, x, y, z, profile) "+
+            "geometry_pointXYZ(ind, name, x, y, z, profile, sl) " +
             "VALUES (" +
             f"{ind}, '{self._sql_format(self._name)}', " +
             f"{self.x}, {self.y}, {self.z}, " +
-            f"{profile}" +
+            f"{profile.id}, {sl}" +
             ")"
         )
         execute(sql)
 
         return True
 
-
     @classmethod
     def from_data(cls, header, data):
         point = None
@@ -117,7 +137,7 @@ class PointXYZ(Point, SQLSubModel):
                     *data
                 )
             else:
-                valid_header = {'name', 'x', 'y', 'z'}
+                valid_header = {'name', 'x', 'y', 'z', 'profile'}
                 d = {}
                 for i, v in enumerate(data):
                     h = header[i].strip().lower().split(' ')[0]
@@ -130,7 +150,6 @@ class PointXYZ(Point, SQLSubModel):
 
         return point
 
-
     def __repr__(self):
         return f"({self._x}, {self._y}, {self._z}, {self._name})"
 

src/Model/Geometry/Profile.py

@@ -25,14 +25,15 @@ from Model.Except import NotImplementedMethodeError
 
 logger = logging.getLogger()
 
+
 class Profile(object):
     _id_cnt = 0
 
-    def __init__(self, id:int = -1, num:int = 0,
-                 kp:float = 0.0, name:str = "",
-                 code1:int = 0, code2:int = 0,
-                 _type:str = "", reach = None,
-                 status = None):
+    def __init__(self, id: int = -1, num: int = 0,
+                 kp: float = 0.0, name: str = "",
+                 code1: int = 0, code2: int = 0,
+                 _type: str = "", reach=None,
+                 status=None):
         super(Profile, self).__init__()
 
         self._status = status
@@ -50,18 +51,41 @@ class Profile(object):
         self._kp = float(kp)
         self._name = str(name)
         self._reach = reach
+        self._sl = None
 
         self._points: List[Point] = []
 
         self._profile_type = _type
 
+    def __len__(self):
+        return len(self.points)
+
     @property
     def number_points(self):
-        return len(self._points)
+        return len(self.points)
+
+    def _get_points_list(self):
+        # Points list generator is type (int, Point) with the first
+        # element the index of the Point in list
+        return list(
+            map(
+                lambda p: p[1],
+                sorted(
+                    self._points,
+                    key=lambda p: p[0]
+                )
+            )
+        )
 
     @property
     def points(self):
-        return self._points.copy()
+        if not isinstance(self._points, list):
+            self._points = self._get_points_list()
+
+        return self._points
+
+    def point(self, index):
+        return self.points[index]
 
     @property
     def reach(self):
@@ -108,7 +132,7 @@ class Profile(object):
 
     @property
     def nb_points(self):
-        return len(self._points)
+        return len(self.points)
 
     @property
     def kp(self):
@@ -136,6 +160,19 @@ class Profile(object):
         self._name = value.strip()
         self._status.modified()
 
+    @property
+    def sl(self):
+        """
+        Returns:
+            Profile sediment layers.
+        """
+        return self._sl
+
+    @sl.setter
+    def sl(self, value):
+        self._sl = value
+        self._status.modified()
+
     @property
     def profile_type(self):
         """
@@ -149,9 +186,9 @@ class Profile(object):
         self._profile_type = value
         self._status.modified()
 
-    def point(self, i:int):
-        if i < len(self._points):
-            return self._points[i]
+    def point(self, i: int):
+        if i < len(self.points):
+            return self.points[i]
 
         return None
 
@@ -161,11 +198,10 @@ class Profile(object):
         Returns:
             The list of named point
         """
-        return [point for point in self._points
+        return [point for point in self.points
                 if point.point_is_named()]
 
-
-    def insert_point(self, index: int, point:Point):
+    def insert_point(self, index: int, point: Point):
         """Insert point at index.
 
         Args:
@@ -175,10 +211,9 @@ class Profile(object):
         Returns:
             Nothing.
         """
-        self._points.insert(index, point)
+        self.points.insert(index, point)
         self._status.modified()
 
-
     def delete(self, indexes: int):
         """Delete points at index
 
@@ -198,7 +233,7 @@ class Profile(object):
             )
         )
 
-        self._points = list(
+        self.points = list(
             filter(
                 lambda p: p not in points,
                 self.points
@@ -215,7 +250,7 @@ class Profile(object):
         Returns:
             Nothing.
         """
-        self._points = list(
+        self.points = list(
             filter(
                 lambda p: p not in points,
                 self.points
@@ -226,10 +261,10 @@ class Profile(object):
     # Move
 
     def move_up_point(self, index: int):
-        if index < len(self._points):
+        if index < len(self.points):
             next = index - 1
 
-            p = self._points
+            p = self.points
             p[index], p[next] = p[next], p[index]
             self._status.modified()
 
@@ -237,7 +272,7 @@ class Profile(object):
         if index >= 0:
             prev = index + 1
 
-            p = self._points
+            p = self.points
             p[index], p[prev] = p[prev], p[index]
             self._status.modified()
 
@@ -245,14 +280,14 @@ class Profile(object):
 
     @timer
     def sort(self, column, is_reversed: bool = False):
-        predicate = lambda p: p.x
+        def predicate(p): return p.x
         if column == 'y':
-            predicate = lambda p: p.y
+            def predicate(p): return p.y
         elif column == 'z':
-            predicate = lambda p: p.z
+            def predicate(p): return p.z
 
-        self._points = sorted(
-            self._points,
+        self.points = sorted(
+            self.points,
             key=predicate,
             reverse=is_reversed
         )
@@ -260,10 +295,10 @@ class Profile(object):
 
     @timer
     def sort_with_indexes(self, indexes: list):
-        if len(self._points) != len(indexes):
+        if len(self.points) != len(indexes):
             logger.critical("Indexes list do not correspond to point list")
 
-        self._points = list(
+        self.points = list(
             map(
                 lambda x: x[1],
                 sorted(
@@ -274,6 +309,39 @@ class Profile(object):
         )
         self._status.modified()
 
+    # Sediment Layers
+
+    def get_sl(self):
+        """Get sediment layer height of points
+
+        Get sediment layer of points (without spesific point sl)
+
+        Returns:
+            List of sediment layers height
+        """
+        res = []
+        psl = [point.sl for point in self.points]
+
+        # Compute max number of layers
+        sl_max = 0
+        for sl in psl:
+            n = 0 if sl is None else len(sl)
+            sl_max = max(n, sl_max)
+
+        # Create list of height for each sl and each layer
+        for i in range(0, sl_max):
+            cur = []
+            # Compute new layer line for each sl
+            for sl in psl:
+                if sl is not None and i < len(sl):
+                    cur.append(sl.get(i).height)
+                else:
+                    cur.append(0)
+            # Add layer line to result
+            res.append(cur)
+
+        return res
+
     # Abstract method, must be implemented for in non abstract class
     def get_station(self):
         raise NotImplementedMethodeError(self, self.get_station)

src/Model/Geometry/ProfileXYZ.py

@@ -16,17 +16,21 @@
 
 # -*- coding: utf-8 -*-
 
+import logging
 import numpy as np
 from typing import List
 
 from tools import timer
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrDB import SQLSubModel
 from Model.Except import ClipboardFormatError
 from Model.Geometry.Profile import Profile
 from Model.Geometry.PointXYZ import PointXYZ
 from Model.Geometry.Vector_1d import Vector1d
 
+logger = logging.getLogger()
+
+
 class ProfileXYZ(Profile, SQLSubModel):
     _sub_classes = [
         PointXYZ,
@@ -36,11 +40,11 @@ class ProfileXYZ(Profile, SQLSubModel):
                  id: int = -1,
                  name: str = "",
                  kp: float = 0.,
-                 reach = None,
-                 num = 0,
+                 reach=None,
+                 num=0,
                  nb_point: int = 0,
                  code1: int = 0, code2: int = 0,
-                 status = None):
+                 status=None):
         """ProfileXYZ constructor
 
         Args:
@@ -54,14 +58,14 @@ class ProfileXYZ(Profile, SQLSubModel):
             Nothing.
         """
         super(ProfileXYZ, self).__init__(
-            id = id,
-            num = num,
-            name = name,
-            kp = kp,
-            code1 = code1, code2 = code2,
-            _type = "XYZ",
-            reach = reach,
-            status = status,
+            id=id,
+            num=num,
+            name=name,
+            kp=kp,
+            code1=code1, code2=code2,
+            _type="XYZ",
+            reach=reach,
+            status=status,
         )
 
     @classmethod
@@ -76,7 +80,9 @@ class ProfileXYZ(Profile, SQLSubModel):
             num INTEGER NOT NULL,
             code1 INTEGER NOT NULL,
             code2 INTEGER NOT NULL,
-            FOREIGN KEY(reach) REFERENCES river_reach(id)
+            sl INTEGER,
+            FOREIGN KEY(reach) REFERENCES river_reach(id),
+            FOREIGN KEY(sl) REFERENCES sedimentary_layer(id)
           )
         """)
 
@@ -84,18 +90,29 @@ class ProfileXYZ(Profile, SQLSubModel):
 
     @classmethod
     def _sql_update(cls, execute, version):
+        major, minor, release = version.strip().split(".")
+        if major == minor == "0":
+            if int(release) < 2:
+                execute(
+                    """
+                    ALTER TABLE geometry_profileXYZ
+                    ADD COLUMN sl INTEGER
+                    REFERENCES sedimentary_layer(id)
+                    """
+                )
+
         return cls._update_submodel(execute, version)
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         profiles = []
         status = data["status"]
         reach = data["reach"]
 
         table = execute(
-            "SELECT id, ind, name, kp, num, code1, code2 " +
+            "SELECT id, ind, name, kp, num, code1, code2, sl " +
             "FROM geometry_profileXYZ " +
-            f"WHERE reach = {reach}"
+            f"WHERE reach = {reach.id}"
         )
 
         for _ in table:
@@ -109,42 +126,58 @@ class ProfileXYZ(Profile, SQLSubModel):
             num = row[5]
             code1 = row[5]
             code2 = row[6]
+            sl = row[7]
 
             new = cls(
-                id=id, num = num,
-                name = name, kp = kp,
-                code1 = code1, code2 = code2,
-                reach = data["parent"],
-                status = status
+                id=id, num=num,
+                name=name, kp=kp,
+                code1=code1, code2=code2,
+                reach=data["parent"],
+                status=status
             )
 
-            data["profile"] = id
-            new._points = PointXYZ._sql_load(execute, data)
+            if sl == -1 or sl is None:
+                new._sl = None
+            else:
+                new._sl = next(
+                    filter(
+                        lambda s: s.id == sl,
+                        data["sediment_layers_list"].sediment_layers
+                    )
+                )
 
-            profiles[ind] = new
+            data["profile"] = new
+            new._points = PointXYZ._sql_load(execute, data.copy())
 
-        return profiles
+            yield ind, new
 
-    def _sql_save(self, execute, data = None):
+        #     profiles[ind] = new
+
+        # return profiles
+
+    def _sql_save(self, execute, data=None):
         ok = True
         ind = data["ind"]
 
+        sl = self._sl.id if self._sl is not None else -1
+
         sql = (
             "INSERT OR REPLACE INTO " +
-            "geometry_profileXYZ(id, ind, name, reach, kp, num, code1, code2) "+
+            "geometry_profileXYZ(id, ind, name, reach, " +
+            "kp, num, code1, code2, sl) " +
             "VALUES (" +
             f"{self.id}, {ind}, '{self._sql_format(self._name)}', " +
             f"{self.reach.id}, {self.kp}, {self.num}, " +
-            f"{self.code1}, {self.code1}" +
+            f"{self.code1}, {self.code1}, {sl}" +
             ")"
         )
         execute(sql)
 
-        data["profile"] = self.id
+        data["profile"] = self
         execute(f"DELETE FROM geometry_pointXYZ WHERE profile = {self.id}")
 
         ind = 0
-        for point in self._points:
+        for point in self.points:
             data["ind"] = ind
             ok &= point._sql_save(execute, data)
             ind += 1
@@ -178,11 +211,11 @@ class ProfileXYZ(Profile, SQLSubModel):
         try:
             if len(header) == 0:
                 point = PointXYZ(
-                    *data, status=self._status
+                    *data, profile=self, status=self._status
                 )
             else:
                 valid_header = {'name', 'x', 'y', 'z'}
-                d = {"status": self._status}
+                d = {"status": self._status, "profile": self}
                 for i, v in enumerate(data):
                     h = header[i].strip().lower().split(' ')[0]
                     if h in valid_header:
@@ -194,18 +227,17 @@ class ProfileXYZ(Profile, SQLSubModel):
 
         return point
 
-
     def x(self):
-        return [point.x for point in self._points]
+        return [point.x for point in self.points]
 
     def y(self):
-        return [point.y for point in self._points]
+        return [point.y for point in self.points]
 
     def z(self):
-        return [point.z for point in self._points]
+        return [point.z for point in self.points]
 
     def names(self):
-        return [point.name for point in self._points]
+        return [point.name for point in self.points]
 
     def x_max(self):
         return max(self.filter_isnan(self.x()))
@@ -235,8 +267,8 @@ class ProfileXYZ(Profile, SQLSubModel):
             Nothing.
         """
         for point in list_points:
-            pt = PointXYZ(*point, status=self._status)
-            self._points.append(pt)
+            pt = PointXYZ(*point, profile=self, status=self._status)
+            self.points.append(pt)
         self._status.modified()
 
     def get_point_i(self, index: int) -> PointXYZ:
@@ -249,7 +281,7 @@ class ProfileXYZ(Profile, SQLSubModel):
             The point.
         """
         try:
-            return self._points[index]
+            return self.points[index]
         except IndexError:
             raise IndexError(f"Invalid point index: {index}")
 
@@ -259,8 +291,8 @@ class ProfileXYZ(Profile, SQLSubModel):
         Returns:
             Nothing.
         """
-        point_xyz = PointXYZ(0., 0., 0., status=self._status)
-        self._points.append(point_xyz)
+        point_xyz = PointXYZ(0., 0., 0., profile=self, status=self._status)
+        self.points.append(point_xyz)
         self._status.modified()
 
     def insert(self, index: int):
@@ -272,8 +304,8 @@ class ProfileXYZ(Profile, SQLSubModel):
         Returns:
             The new point.
         """
-        point = PointXYZ(0., 0., 0., status=self._status)
-        self._points.insert(index, point)
+        point = PointXYZ(0., 0., 0., profile=self, status=self._status)
+        self.points.insert(index, point)
         self._status.modified()
         return point
 
@@ -289,9 +321,9 @@ class ProfileXYZ(Profile, SQLSubModel):
         return [x for x in lst if not np.isnan(x)]
 
     def _first_point_not_nan(self):
-        first_point = self._points[0]
+        first_point = self.points[0]
 
-        for point in self._points:
+        for point in self.points:
             if not point.is_nan():
                 first_point = point
                 break
@@ -299,9 +331,9 @@ class ProfileXYZ(Profile, SQLSubModel):
         return first_point
 
     def _last_point_not_nan(self):
-        last_point = self._points[-1]
+        last_point = self.points[-1]
 
-        for point in self._points[::-1]:
+        for point in self.points[::-1]:
             if not point.is_nan():
                 last_point = point
                 break
@@ -328,13 +360,13 @@ class ProfileXYZ(Profile, SQLSubModel):
             first_point_not_nan = self._first_point_not_nan()
             last_point_not_nan = self._last_point_not_nan()
 
-            for index, point in enumerate(self._points):
+            for index, point in enumerate(self.points):
                 if point.point_is_named():
                     index_first_named_point = index
                     first_named_point = point
                     break
 
-            for point in reversed(self._points):
+            for point in reversed(self.points):
                 if point.point_is_named():
                     last_named_point = point
                     break
@@ -343,32 +375,32 @@ class ProfileXYZ(Profile, SQLSubModel):
             constant = 0.0
 
             if (first_named_point is not None and
-                last_named_point is not None):
+                    last_named_point is not None):
                 if (first_named_point != last_named_point and
-                    first_named_point.x != last_named_point.x):
+                        first_named_point.x != last_named_point.x):
                     vector = Vector1d(first_named_point, last_named_point)
-                    normalized_direction_vec = vector.normalized_direction_vector()
+                    norm_dir_vec = vector.normalized_direction_vector()
                 else:
                     vector = Vector1d(first_point_not_nan, last_point_not_nan)
-                    normalized_direction_vec = vector.normalized_direction_vector()
+                    norm_dir_vec = vector.normalized_direction_vector()
 
-                for point in self._points:
+                for point in self.points:
                     xi = point.x - first_named_point.x
                     yi = point.y - first_named_point.y
-                    station_i = (normalized_direction_vec[0] * xi +
-                                 normalized_direction_vec[1] * yi)
+                    station_i = (norm_dir_vec[0] * xi +
+                                 norm_dir_vec[1] * yi)
                     station.append(station_i)
 
                 constant = station[index_first_named_point]
             elif first_named_point is None:
                 vector = Vector1d(first_point_not_nan, last_point_not_nan)
-                normalized_direction_vec = vector.normalized_direction_vector()
+                norm_dir_vec = vector.normalized_direction_vector()
 
-                for point in self._points:
+                for point in self.points:
                     xi = point.x - first_point_not_nan.x
                     yi = point.y - first_point_not_nan.y
-                    station_i = (normalized_direction_vec[0] * xi +
-                                 normalized_direction_vec[1] * yi)
+                    station_i = (norm_dir_vec[0] * xi +
+                                 norm_dir_vec[1] * yi)
                     station.append(station_i)
 
                 z_min = self.z_min()

src/Model/Geometry/Reach.py

@@ -27,7 +27,7 @@ from functools import reduce
 
 from tools import flatten, timer, trace
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrDB import SQLSubModel
 
 from Model.Geometry.Profile import Profile
 from Model.Geometry.ProfileXYZ import ProfileXYZ
@@ -36,13 +36,14 @@ from Model.Except import FileFormatError, exception_message_box
 
 logger = logging.getLogger()
 
+
 class Reach(SQLSubModel):
     _sub_classes = [
         ProfileXYZ,
     ]
 
     def __init__(self, status=None, parent=None):
-        self.id = parent.id
+        self.id = parent.id if parent is not None else 0
         self._status = status
         self._parent = parent
         self._profiles: List[Profile] = []
@@ -59,17 +60,17 @@ class Reach(SQLSubModel):
         return cls._update_submodel(execute, version)
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
-        new = cls(status = data["status"], parent = data["parent"])
+    def _sql_load(cls, execute, data=None):
+        new = cls(status=data["status"], parent=data["parent"])
 
         new._profiles = ProfileXYZ._sql_load(
             execute,
-            data = data
+            data=data
         )
 
         return new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         # Delete old data
         execute(f"DELETE FROM geometry_profileXYZ WHERE reach = {self.id}")
         # execute(f"DELETE FROM geometry_pointXYZ")
@@ -78,7 +79,7 @@ class Reach(SQLSubModel):
             data = {}
 
         ind = 0
-        for profile in self._profiles:
+        for profile in self.profiles:
             data["ind"] = ind
             profile._sql_save(execute, data)
             ind += 1
@@ -94,26 +95,49 @@ class Reach(SQLSubModel):
         Returns:
             The profile at index i
         """
-        if i < len(self._profiles):
-            return self._profiles[i]
+        if i < len(self.profiles):
+            return self.profiles[i]
 
         return None
 
     @property
     def name(self):
-        if self._parent == None:
+        if self._parent is None:
             return ""
 
         return self._parent.name
 
+    def _get_profiles_list(self):
+        # Profiles list generator is type (int, Point) with the first
+        # element the index of the Point in list
+        logger.info(f"Load profiles from reach {self.name}")
+        return list(
+            map(
+                lambda p: p[1],
+                sorted(
+                    self._profiles,
+                    key=lambda p: p[0]
+                )
+            )
+        )
+
+    def __len__(self):
+        if not isinstance(self._profiles, list):
+            self._profiles = self._get_profiles_list()
+
+        return len(self._profiles)
+
     @property
     def profiles(self):
-        return self._profiles.copy()
+        if not isinstance(self._profiles, list):
+            self._profiles = self._get_profiles_list()
+
+        return self._profiles
 
     def get_profiles_from_kp(self, kp):
         return list(
             filter(
-                lambda p: p.kp == kp, self._profiles
+                lambda p: p.kp == kp, self.profiles
             )
         )
 
@@ -123,14 +147,14 @@ class Reach(SQLSubModel):
         Returns:
             Number of profiles
         """
-        return len(self._profiles)
+        return len(self.profiles)
 
     def get_geometry(self) -> List[Profile]:
         """
         Returns:
             The profiles list.
         """
-        return self._profiles
+        return self.profiles
 
     def _update_profile_numbers(self):
         """Update profiles index
@@ -152,7 +176,7 @@ class Reach(SQLSubModel):
         """
         profile = ProfileXYZ(reach=self, status=self._status)
 
-        self._profiles.insert(index, profile)
+        self.profiles.insert(index, profile)
         self._update_profile_numbers()
 
         self._status.modified()
@@ -168,11 +192,10 @@ class Reach(SQLSubModel):
         Returns:
             Nothing.
         """
-        self._profiles.insert(index, profile)
+        self.profiles.insert(index, profile)
         self._update_profile_numbers()
         self._status.modified()
 
-
     def delete(self, indexes):
         """Delete some elements in profile list
 
@@ -192,7 +215,7 @@ class Reach(SQLSubModel):
             )
         )
 
-        self._profiles = list(
+        self.profiles = list(
             filter(
                 lambda p: p not in profiles,
                 self.profiles
@@ -210,7 +233,7 @@ class Reach(SQLSubModel):
         Returns:
             Nothing.
         """
-        self._profiles = list(
+        self.profiles = list(
             filter(
                 lambda p: p not in profiles,
                 self.profiles
@@ -219,12 +242,11 @@ class Reach(SQLSubModel):
         self._update_profile_numbers()
         self._status.modified()
 
-
     def move_up_profile(self, index: int):
         if index < len(self.profiles):
             next = index - 1
 
-            p = self._profiles
+            p = self.profiles
             p[index], p[next] = p[next], p[index]
             self._status.modified()
 
@@ -232,7 +254,7 @@ class Reach(SQLSubModel):
         if index >= 0:
             prev = index + 1
 
-            p = self._profiles
+            p = self.profiles
             p[index], p[prev] = p[prev], p[index]
             self._status.modified()
 
@@ -275,6 +297,38 @@ class Reach(SQLSubModel):
     def get_kp_max(self):
         return max(self.get_kp())
 
+    # Sediment Layers
+
+    def get_sl(self):
+        """Get sediment layer height of profile
+
+        Get sediment layer of profile (without spesific point sl)
+
+        Returns:
+            List of sediment layers height
+        """
+        res = []
+        psl = [profile.sl for profile in self.profiles]
+
+        # Compute max number of layers
+        sl_max = 0
+        for sl in psl:
+            n = 0 if sl is None else len(sl)
+            sl_max = max(n, sl_max)
+
+        # Create list of height for each sl and each layer
+        for i in range(0, sl_max):
+            cur = []
+            # Compute new layer line for each sl
+            for sl in psl:
+                if sl is not None and i < len(sl):
+                    cur.append(sl.get(i).height)
+                else:
+                    cur.append(0)
+            # Add layer line to result
+            res.append(cur)
+
+        return res
 
     # Guidelines
 
@@ -291,12 +345,12 @@ class Reach(SQLSubModel):
         for guide in guide_set:
             self._guidelines[guide] = flatten(
                 map(
-                    lambda l: list(
+                    lambda lst: list(
                         # Filter point with name (we assume we have
                         # only one point by profile)
                         filter(
                             lambda p: p.name == guide,
-                            l
+                            lst
                         )
                     ),
                     named_points
@@ -311,7 +365,7 @@ class Reach(SQLSubModel):
             Tuple of complete and incomplete guidelines name.
         """
         # Get all point contains into a guideline
-        named_points = [profile.named_points() for profile in self._profiles]
+        named_points = [profile.named_points() for profile in self.profiles]
         points_name = list(
             map(
                 lambda lst: list(map(lambda p: p.name, lst)),
@@ -331,7 +385,9 @@ class Reach(SQLSubModel):
             reduce(
                 lambda acc, h: acc + h,
                 map(
-                    lambda l: list(set(l).symmetric_difference(guide_set)),
+                    lambda lst: list(
+                        set(lst).symmetric_difference(guide_set)
+                    ),
                     points_name
                 ),
                 []
@@ -381,13 +437,12 @@ class Reach(SQLSubModel):
     def get_guidelines_z(self):
         return self._map_guidelines_points(lambda p: p.z)
 
-
     # Sort
 
     @timer
     def sort(self, is_reversed: bool = False):
-        self._profiles = sorted(
-            self._profiles,
+        self.profiles = sorted(
+            self.profiles,
             key=lambda profile: profile.kp,
             reverse=is_reversed
         )
@@ -395,10 +450,10 @@ class Reach(SQLSubModel):
 
     @timer
     def sort_with_indexes(self, indexes: list):
-        if len(self._profiles) != len(indexes):
+        if len(self.profiles) != len(indexes):
             logger.critical("Indexes list do not correspond to profile list")
 
-        self._profiles = list(
+        self.profiles = list(
             map(
                 lambda x: x[1],
                 sorted(
@@ -416,7 +471,8 @@ class Reach(SQLSubModel):
         """Import a geometry from file (.ST or .st)
 
         Args:
-            file_path_name: The absolute path of geometry file (.ST or .st) to import.
+            file_path_name: The absolute path of geometry file (.ST or .st)
+                            to import.
 
         Returns:
             Nothing.
@@ -426,7 +482,8 @@ class Reach(SQLSubModel):
 
         try:
             list_profile, list_header = self.read_file_st(str(file_path_name))
-            profile_header = ["num", "code1", "code2", "nb_point", "kp", "name"]
+            profile_header = ["num", "code1",
+                              "code2", "nb_point", "kp", "name"]
 
             if list_profile and list_header:
                 for ind, profile in enumerate(list_profile):
@@ -438,7 +495,7 @@ class Reach(SQLSubModel):
                         **d, reach=self, status=self._status
                     )
                     prof.import_points(profile)
-                    self._profiles.append(prof)
+                    self.profiles.append(prof)
                     self._update_profile_numbers()
 
                 self._status.modified()
@@ -502,8 +559,8 @@ class Reach(SQLSubModel):
     # TODO: Move this function to model reach
     def export_reach(self, filename):
         with open(f"{filename}", "w") as file_st:
-            for index in range(len(self._profiles)):
-                profile = self._profiles[index]
+            for index in range(len(self.profiles)):
+                profile = self.profiles[index]
 
                 for v in profile.header:
                     file_st.write(f"{v:>6}")

src/Model/Geometry/Vector_1d.py

@@ -19,6 +19,7 @@
 import numpy as np
 from Model.Geometry.PointXYZ import PointXYZ
 
+
 class Vector1d:
     def __init__(self, a: PointXYZ, b: PointXYZ):
         self.A = a

src/Model/InitialConditions/InitialConditions.py

@@ -20,14 +20,15 @@ from copy import copy, deepcopy
 from tools import trace, timer
 from functools import reduce
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrDB import SQLSubModel
+
 
 class Data(SQLSubModel):
-    def __init__(self, name:str = "",
-                 comment:str = "", reach = None,
-                 kp:float = 0.0, discharge:float = 0.0,
-                 height:float = 0.0,
-                 status = None):
+    def __init__(self, name: str = "",
+                 comment: str = "", reach=None,
+                 kp: float = 0.0, discharge: float = 0.0,
+                 height: float = 0.0,
+                 status=None):
         super(Data, self).__init__()
 
         self._status = status
@@ -73,7 +74,7 @@ class Data(SQLSubModel):
         return cls._update_submodel(execute, version)
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         id = data["reach"].id
         table = execute(
             "SELECT ind, name, comment, kp, discharge, height " +
@@ -95,25 +96,26 @@ class Data(SQLSubModel):
             height = row[5]
 
             d = cls(
-                reach = data["reach"],
-                status = data["status"],
-                name = name,
-                comment = comment,
-                kp = kp,
-                discharge = discharge,
-                height = height,
+                reach=data["reach"],
+                status=data["status"],
+                name=name,
+                comment=comment,
+                kp=kp,
+                discharge=discharge,
+                height=height,
             )
 
             new[ind] = d
 
         return new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         ind = data["ind"]
 
         execute(
             "INSERT INTO " +
-            "initial_conditions(ind, name, comment, kp, discharge, height, reach) " +
+            "initial_conditions(ind, name, comment, kp, " +
+            "discharge, height, reach) " +
             "VALUES (" +
             f"{ind}, '{self._sql_format(self.name)}', " +
             f"'{self._sql_format(self._comment)}', " +
@@ -124,16 +126,15 @@ class Data(SQLSubModel):
 
         return True
 
-
     def copy(self):
         new = Data(
-            name = self.name,
-            comment = self._comment,
-            kp = self._kp,
-            discharge = self._discharge,
-            height = self._height,
-            reach = self._reach,
-            status = self._status,
+            name=self.name,
+            comment=self._comment,
+            kp=self._kp,
+            discharge=self._discharge,
+            height=self._height,
+            reach=self._reach,
+            status=self._status,
         )
 
         return new
@@ -173,7 +174,7 @@ class Data(SQLSubModel):
 
     def _update_from_kp(self):
         min = self._update_get_min()
-        self._elevation = min - self._height
+        self._elevation = min + self._height
 
     def _update_from_elevation(self):
         min = self._update_get_min()
@@ -216,7 +217,7 @@ class InitialConditions(SQLSubModel):
         Data
     ]
 
-    def __init__(self, reach = None, status = None):
+    def __init__(self, reach=None, status=None):
         super(InitialConditions, self).__init__()
 
         self._status = status
@@ -233,23 +234,21 @@ class InitialConditions(SQLSubModel):
         return cls._update_submodel(execute, version)
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         new = cls(
-            reach = data["reach"],
-            status = data["status"]
+            reach=data["reach"],
+            status=data["status"]
         )
 
         new._data = Data._sql_load(
             execute,
-            data = data
+            data=data
         )
 
-        if new._data is None:
-            return None
+        if new._data is not None:
+            yield new
 
-        return new
-
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         ok = True
 
         ind = 0
@@ -288,7 +287,7 @@ class InitialConditions(SQLSubModel):
         self._status.modified()
 
     def new(self, index):
-        n = Data(reach = self._reach, status = self._status)
+        n = Data(reach=self._reach, status=self._status)
         self._data.insert(index, n)
         self._status.modified()
 
@@ -321,7 +320,6 @@ class InitialConditions(SQLSubModel):
         self._data.sort(reverse=reverse, key=key)
         self._status.modified()
 
-
     def _data_get(self, key):
         return list(
             map(
@@ -341,8 +339,8 @@ class InitialConditions(SQLSubModel):
 
     def _sort_by_z_and_kp(self, profiles):
         profiles.sort(
-            reverse = False,
-            key = lambda p: p.kp
+            reverse=False,
+            key=lambda p: p.kp
         )
 
         first_z = profiles[0].z()
@@ -350,11 +348,11 @@ class InitialConditions(SQLSubModel):
 
         if first_z > last_z:
             profiles.sort(
-                reverse = True,
-                key = lambda p: p.kp
+                reverse=True,
+                key=lambda p: p.kp
             )
 
-    def generate_growing_constante_height(self, height:float):
+    def generate_growing_constante_height(self, height: float):
         self._data = []
 
         profiles = self._reach.reach.profiles
@@ -362,7 +360,7 @@ class InitialConditions(SQLSubModel):
 
         prev = None
         for profile in profiles:
-            new = Data(reach = self._reach, status = self._status)
+            new = Data(reach=self._reach, status=self._status)
             new["kp"] = profile.kp
 
             if prev is None:
@@ -381,11 +379,11 @@ class InitialConditions(SQLSubModel):
             is_reverse = True
 
         self._data.sort(
-            reverse = not is_reverse,
-            key = lambda d: d['kp']
+            reverse=not is_reverse,
+            key=lambda d: d['kp']
         )
 
-    def generate_discharge(self, discharge:float):
+    def generate_discharge(self, discharge: float):
         self._new = []
 
         for d in self._data:

src/Model/InitialConditions/InitialConditionsDict.py

@@ -16,81 +16,62 @@
 
 # -*- coding: utf-8 -*-
 
+import types
 from copy import copy
 from tools import trace, timer
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrDict import PamhyrModelDict
 from Model.InitialConditions.InitialConditions import InitialConditions
 
-class InitialConditionsDict(SQLSubModel):
+
+class InitialConditionsDict(PamhyrModelDict):
     _sub_classes = [
         InitialConditions,
     ]
 
-    def __init__(self, status = None):
-        super(InitialConditionsDict, self).__init__()
-
-        self._status = status
-
-        self._reach = {}
-
     @classmethod
-    def _sql_create(cls, execute):
-        return cls._create_submodel(execute)
-
-    @classmethod
-    def _sql_update(cls, execute, version):
-        return cls._update_submodel(execute, version)
-
-    @classmethod
-    def _sql_load(cls, execute, data = None):
-        new = cls(status = data["status"])
+    def _sql_load(cls, execute, data=None):
+        new = cls(status=data["status"])
 
         for reach in data["edges"]:
             data["reach"] = reach
 
             ic = InitialConditions._sql_load(
                 execute,
-                data = data
+                data=data
             )
 
             if ic is not None:
-                new._reach[reach] = ic
+                new._dict[reach] = ic
 
         return new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         ok = True
         if data is None:
             data = {}
 
         execute("DELETE FROM initial_conditions")
 
-        for reach in self._reach:
+        for reach in self._dict:
             data["reach"] = reach
-            ok &= self._reach[reach]._sql_save(execute, data)
+            ok &= self._dict[reach]._sql_save(execute, data)
 
         return ok
 
-    def __len__(self):
-        return len(self._reach)
+    def get(self, key):
+        if key in self._dict:
+            v = self._dict[key]
+            if isinstance(v, types.GeneratorType):
+                self._dict[key] = list(v)[0]
 
-    def is_defined(self, reach):
-        return reach in self._reach
+            return self._dict[key]
 
-    def get(self, reach):
-        if reach in self._reach:
-            return self._reach[reach]
-
-        new = self.new(reach)
-        self.set(reach, new)
+        new = self.new(key)
+        self.set(key, new)
         return new
 
-    def set(self, reach, new):
-        self._reach[reach] = new
-        self._status.modified()
-
     def new(self, reach):
-        new = InitialConditions(reach = reach, status = self._status)
+        new = InitialConditions(reach=reach, status=self._status)
         self.set(reach, new)
         return new

src/Model/LateralContribution/LateralContribution.py

@@ -20,16 +20,17 @@ import logging
 
 from tools import trace, timer, old_pamhyr_date_to_timestamp
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrDB import SQLSubModel
 from Model.Except import NotImplementedMethodeError
 
 logger = logging.getLogger()
 
+
 class LateralContribution(SQLSubModel):
     _sub_classes = []
     _id_cnt = 0
 
-    def __init__(self, id:int = -1, name:str = "", status = None):
+    def __init__(self, id: int = -1, name: str = "", status=None):
         super(LateralContribution, self).__init__()
 
         self._status = status
@@ -39,7 +40,6 @@ class LateralContribution(SQLSubModel):
         else:
             self.id = id
 
-
         self._name = name
         self._type = ""
         self._edge = None
@@ -49,7 +49,8 @@ class LateralContribution(SQLSubModel):
         self._header = []
         self._types = [float, float]
 
-        LateralContribution._id_cnt = max(LateralContribution._id_cnt + 1, self.id)
+        LateralContribution._id_cnt = max(
+            LateralContribution._id_cnt + 1, self.id)
 
     @classmethod
     def _sql_create(cls, execute):
@@ -99,7 +100,7 @@ class LateralContribution(SQLSubModel):
         return res
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         new = []
         tab = data["tab"]
 
@@ -112,9 +113,9 @@ class LateralContribution(SQLSubModel):
             t = row[2]
             ctor = cls._get_ctor_from_type(t)
             lc = ctor(
-                id = row[0],
-                name = row[1],
-                status = data['status']
+                id=row[0],
+                name=row[1],
+                status=data['status']
             )
             lc.edge = None
             if row[3] != -1:
@@ -141,7 +142,7 @@ class LateralContribution(SQLSubModel):
 
         return new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         tab = data["tab"]
 
         execute(f"DELETE FROM lateral_contribution WHERE id = {self.id}")
@@ -153,7 +154,8 @@ class LateralContribution(SQLSubModel):
 
         sql = (
             "INSERT INTO " +
-            "lateral_contribution(id, name, type, tab, edge, begin_kp, end_kp) "+
+            "lateral_contribution(id, name, type, tab, " +
+            "edge, begin_kp, end_kp) " +
             "VALUES (" +
             f"{self.id}, '{self._sql_format(self._name)}', " +
             f"'{self._sql_format(self._type)}', '{tab}', {edge}, " +
@@ -169,7 +171,7 @@ class LateralContribution(SQLSubModel):
 
             sql = (
                 "INSERT INTO " +
-                "lateral_contribution_data(ind, data0, data1, lc) "+
+                "lateral_contribution_data(ind, data0, data1, lc) " +
                 f"VALUES ({ind}, '{data0}', {data1}, {self.id})"
             )
             execute(sql)
@@ -186,7 +188,7 @@ class LateralContribution(SQLSubModel):
 
     @classmethod
     def time_convert(cls, data):
-        if type(data) == str and data.count(":") == 3:
+        if data is str and data.count(":") == 3:
             return old_pamhyr_date_to_timestamp(data)
 
         return int(data)
@@ -282,7 +284,7 @@ class LateralContribution(SQLSubModel):
         new_1 = self._default_1
 
         if len(header) != 0:
-            for i in [0,1]:
+            for i in [0, 1]:
                 for j in range(len(header)):
                     if self._header[i] == header[j]:
                         if i == 0:
@@ -295,13 +297,13 @@ class LateralContribution(SQLSubModel):
 
         return (new_0, new_1)
 
-    def add(self, index:int):
+    def add(self, index: int):
         value = (self._default_0, self._default_1)
         self._data.insert(index, value)
         self._status.modified()
         return value
 
-    def insert(self, index:int, value):
+    def insert(self, index: int, value):
         self._data.insert(index, value)
         self._status.modified()
 
@@ -337,11 +339,10 @@ class LateralContribution(SQLSubModel):
         return self.data[index]
 
     def get_range(self, _range):
-        l = []
+        lst = []
         for r in _range:
-            l.append(r)
-        return l
-
+            lst.append(r)
+        return lst
 
     def _set_i_c_v(self, index, column, value):
         v = list(self._data[index])
@@ -349,15 +350,15 @@ class LateralContribution(SQLSubModel):
         self._data[index] = tuple(v)
         self._status.modified()
 
-    def set_i_0(self, index:int, value):
+    def set_i_0(self, index: int, value):
         self._set_i_c_v(index, 0, value)
 
-    def set_i_1(self, index:int, value):
+    def set_i_1(self, index: int, value):
         self._set_i_c_v(index, 1, value)
 
     @timer
     def convert(self, cls):
-        new = cls(name = self.name, status = self._status)
+        new = cls(name=self.name, status=self._status)
         new.edge = self.edge
         new.begin_kp = self.begin_kp
         new.end_kp = self.end_kp
@@ -365,8 +366,8 @@ class LateralContribution(SQLSubModel):
         for i, _ in enumerate(self.data):
             new.add(i)
 
-        for i in [0,1]:
-            for j in [0,1]:
+        for i in [0, 1]:
+            for j in [0, 1]:
                 if self._header[i] == new.header[j]:
                     for ind, v in self.data:
                         try:

src/Model/LateralContribution/LateralContributionList.py

@@ -19,7 +19,7 @@
 from copy import copy
 from tools import trace, timer
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrList import PamhyrModelListWithTab
 from Model.Except import NotImplementedMethodeError
 
 from Model.LateralContribution.LateralContribution import LateralContribution
@@ -27,33 +27,16 @@ from Model.LateralContribution.LateralContributionTypes import (
     NotDefined, LateralContrib, Rain, Evaporation,
 )
 
-class LateralContributionList(SQLSubModel):
+
+class LateralContributionList(PamhyrModelListWithTab):
+    _tabs_list = ["liquid", "solid", "suspenssion"]
     _sub_classes = [
         LateralContribution,
     ]
 
-    def __init__(self, status = None):
-        super(LateralContributionList, self).__init__()
-
-        self._status = status
-
-        self._tabs = {
-            "liquid" : [],
-            "solid" : [],
-            "suspenssion" : []
-        }
-
     @classmethod
-    def _sql_create(cls, execute):
-        return cls._create_submodel(execute)
-
-    @classmethod
-    def _sql_update(cls, execute, version):
-        return True
-
-    @classmethod
-    def _sql_load(cls, execute, data = None):
-        new = cls(status = data['status'])
+    def _sql_load(cls, execute, data=None):
+        new = cls(status=data['status'])
 
         if data is None:
             data = {}
@@ -66,7 +49,7 @@ class LateralContributionList(SQLSubModel):
 
         return new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         execute("DELETE FROM lateral_contribution")
 
         if data is None:
@@ -75,83 +58,29 @@ class LateralContributionList(SQLSubModel):
         for tab in self._tabs:
             data["tab"] = tab
             for lc in self._tabs[tab]:
-                lc._sql_save(execute, data = data)
+                lc._sql_save(execute, data=data)
 
         return True
 
-    def len(self, lst):
-        return len(self._tabs[lst])
-
-    def get_tab(self, lst):
-        return self._tabs[lst].copy()
-
-    def get(self, lst, row):
-        return self._tabs[lst][row]
-
-    def set(self, lst, row, new):
-        self._tabs[lst][row] = new
-        self._status.modified()
-
     def new(self, lst, index):
         n = NotDefined(status=self._status)
         self._tabs[lst].insert(index, n)
         self._status.modified()
         return n
 
-    def insert(self, lst, index, new):
-        self._tabs[lst].insert(index, new)
-        self._status.modified()
-
-    def delete(self, lst, bcs):
-        for bc in bcs:
-            self._tabs[lst].remove(bc)
-        self._status.modified()
-
-    def delete_i(self, lst, indexes):
-        bcs = list(
-            map(
-                lambda x: x[1],
-                filter(
-                    lambda x: x[0] in indexes,
-                    enumerate(self._tabs[lst])
-                )
-            )
-        )
-        self.delete(lst, bcs)
-
-    def sort(self, lst, reverse=False, key=None):
-        self._tabs[lst].sort(reverse=reverse, key=key)
-        self._status.modified()
-
-    def move_up(self, lst, index):
-        if index < len(self._tabs[lst]):
-            next = index - 1
-
-            l = self._tabs[lst]
-            l[index], l[next] = l[next], l[index]
-            self._status.modified()
-
-    def move_down(self, lst, index):
-        if index >= 0:
-            prev = index + 1
-
-            l = self._tabs[lst]
-            l[index], l[prev] = l[prev], l[index]
-            self._status.modified()
-
     def __copy__(self):
         new = LateralContributionList()
 
-        for l in self._tabs:
-            new.tabs[l] = self._tabs[l].copy()
+        for lst in self._tabs:
+            new.tabs[lst] = self._tabs[lst].copy()
 
         return new
 
     def __deepcopy__(self):
         new = LateralContributionList()
 
-        for l in self._tabs:
-            new.tabs[l] = self._tabs[l].deepcopy()
+        for lst in self._tabs:
+            new.tabs[lst] = self._tabs[lst].deepcopy()
 
         return new
 

src/Model/LateralContribution/LateralContributionTypes.py

@@ -22,7 +22,7 @@ from Model.LateralContribution.LateralContribution import LateralContribution
 
 
 class NotDefined(LateralContribution):
-    def __init__(self, id:int = -1, name:str = "", status=None):
+    def __init__(self, id: int = -1, name: str = "", status=None):
         super(NotDefined, self).__init__(id=id, name=name, status=status)
 
         self._type = "ND"
@@ -32,8 +32,9 @@ class NotDefined(LateralContribution):
     def _default_0(self):
         return 0.0
 
+
 class LateralContrib(LateralContribution):
-    def __init__(self, id:int = -1, name:str = "", status=None):
+    def __init__(self, id: int = -1, name: str = "", status=None):
         super(LateralContrib, self).__init__(id=id, name=name, status=status)
 
         self._type = "LC"
@@ -44,8 +45,9 @@ class LateralContrib(LateralContribution):
     def compatibility(cls):
         return ["liquid"]
 
+
 class Rain(LateralContribution):
-    def __init__(self, id:int = -1, name:str = "", status=None):
+    def __init__(self, id: int = -1, name: str = "", status=None):
         super(Rain, self).__init__(id=id, name=name, status=status)
 
         self._type = "RA"
@@ -56,8 +58,9 @@ class Rain(LateralContribution):
     def compatibility(cls):
         return ["liquid"]
 
+
 class Evaporation(LateralContribution):
-    def __init__(self, id:int = -1, name:str = "", status=None):
+    def __init__(self, id: int = -1, name: str = "", status=None):
         super(Evaporation, self).__init__(id=id, name=name, status=status)
 
         self._type = "EV"

src/Model/Network/Edge.py

@@ -18,13 +18,14 @@
 
 from Model.Network.Node import Node
 
+
 class Edge(object):
     _id_cnt = 0
 
-    def __init__(self, id:int, name:str,
-                 node1:Node = None,
-                 node2:Node = None,
-                 status = None):
+    def __init__(self, id: int, name: str,
+                 node1: Node = None,
+                 node2: Node = None,
+                 status=None):
         super(Edge, self).__init__()
 
         self._status = status
@@ -74,7 +75,10 @@ class Edge(object):
 
     @property
     def name(self):
-        return self._name if self._name != "" else f"{self.node1.name} -> {self.node2.name}"
+        name = self._name
+        if self._name == "":
+            name = f"{self.node1.name} -> {self.node2.name}"
+        return name
 
     def is_enable(self):
         return self._enable

src/Model/Network/Graph.py

@@ -21,8 +21,9 @@ from functools import reduce
 from Model.Network.Node import Node
 from Model.Network.Edge import Edge
 
+
 class Graph(object):
-    def __init__(self, status = None):
+    def __init__(self, status=None):
         super(Graph, self).__init__()
 
         self._status = status
@@ -83,7 +84,7 @@ class Graph(object):
             False
         )
 
-    def node(self, node_name:str):
+    def node(self, node_name: str):
         node = list(
             filter(
                 lambda n: n.name == node_name,
@@ -96,7 +97,7 @@ class Graph(object):
 
         return node[0]
 
-    def edge(self, edge_name:str):
+    def edge(self, edge_name: str):
         edge = list(
             filter(
                 lambda e: e.name == edge_name,
@@ -109,12 +110,12 @@ class Graph(object):
 
         return edge[0]
 
-    def _create_node(self, x:float, y:float):
+    def _create_node(self, x: float, y: float):
         node = self._node_ctor(
             -1,
             "",
-            x = x, y = y,
-            status = self._status
+            x=x, y=y,
+            status=self._status
         )
         return node
 
@@ -123,14 +124,14 @@ class Graph(object):
         self._status.modified()
         return node
 
-    def add_node(self, x:float = 0.0, y:float = 0.0):
+    def add_node(self, x: float = 0.0, y: float = 0.0):
         node = self._create_node(x, y)
         return self._add_node(node)
 
     def insert_node(self, node):
         return self._add_node(node)
 
-    def remove_node(self, node_name:str):
+    def remove_node(self, node_name: str):
         self._nodes = list(
             filter(
                 lambda n: n.name != node_name,
@@ -139,19 +140,18 @@ class Graph(object):
         )
         self._status.modified()
 
-    def create_node(self, x:float = 0.0, y:float = 0.0):
+    def create_node(self, x: float = 0.0, y: float = 0.0):
         node = self._create_node(x, y)
         return node
 
-    def _create_edge(self, n1:Node, n2:Node):
+    def _create_edge(self, n1: Node, n2: Node):
         edge = self._edge_ctor(
             -1,
             "", n1, n2,
-            status = self._status
+            status=self._status
         )
         return edge
 
-
     def _add_edge(self, edge):
         # This edge already exists ?
         if any(filter(lambda e: (e.node1 == edge.node1 and
@@ -164,17 +164,17 @@ class Graph(object):
         self._status.modified()
         return edge
 
-    def add_edge(self, n1:Node, n2:Node):
+    def add_edge(self, n1: Node, n2: Node):
         edge = self._create_edge(n1, n2)
         return self._add_edge(edge)
 
     def insert_edge(self, edge):
         return self._add_edge(edge)
 
-    def create_edge(self, n1:Node, n2:Node):
+    def create_edge(self, n1: Node, n2: Node):
         return self._create_edge(n1, n2)
 
-    def remove_edge(self, edge_name:str):
+    def remove_edge(self, edge_name: str):
         self._edges = list(
             filter(
                 lambda e: e.name != edge_name,

src/Model/Network/Node.py

@@ -18,12 +18,13 @@
 
 from Model.Network.Point import Point
 
+
 class Node(object):
     _id_cnt = 0
 
-    def __init__(self, id:int, name:str,
-                 x:float = 0.0, y:float = 0.0,
-                 status = None):
+    def __init__(self, id: int, name: str,
+                 x: float = 0.0, y: float = 0.0,
+                 status=None):
         super(Node, self).__init__()
 
         self._status = status
@@ -73,7 +74,6 @@ class Node(object):
     def y(self):
         return self.pos.y
 
-
     def setPos(self, x, y):
         self.pos.x = x
         self.pos.y = y

src/Model/Network/Point.py

@@ -17,7 +17,7 @@
 # -*- coding: utf-8 -*-
 
 class Point(object):
-    def __init__(self, x:float, y:float):
+    def __init__(self, x: float, y: float):
         super(Point, self).__init__()
 
         self.x = x

src/Model/Results/Results.py

@@ -0,0 +1,67 @@
+# Results.py -- Pamhyr
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+import logging
+import numpy as np
+
+from copy import deepcopy
+from datetime import datetime
+
+from Model.Results.River.River import River
+
+logger = logging.getLogger()
+
+
+class Results(object):
+    def __init__(self, study=None, solver=None,
+                 repertory="", name="0"):
+        self._study = study
+        self._solver = solver
+        self._repertory = repertory
+        self._name = name
+
+        self._river = River(self._study)
+
+        self._meta_data = {
+            # Keep results creation date
+            "creation_date": datetime.now(),
+        }
+
+    @property
+    def date(self):
+        date = self._meta_data["creation_date"]
+        return f"{date.isoformat(sep=' ')}"
+
+    @property
+    def river(self):
+        return self._river
+
+    @property
+    def study(self):
+        return self._study
+
+    def set(self, key, value):
+        self._meta_data[key] = value
+
+    def get(self, key):
+        return self._meta_data[key]
+
+    def reload(self):
+        return self._solver.results(
+            self._study,
+            self._repertory,
+            qlog=None,
+        )

src/Model/Results/River/River.py

@@ -0,0 +1,122 @@
+# River.py -- Pamhyr
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+import logging
+
+from datetime import datetime
+
+logger = logging.getLogger()
+
+
+class Profile(object):
+    def __init__(self, profile, study):
+        self._study = study
+        self._profile = profile  # Source profile in the study
+        self._data = {}  # Dict of dict {<ts>: {<key>: <value>, ...}, ...}
+
+    def __len__(self):
+        return len(self._data)
+
+    @property
+    def name(self):
+        return self._profile.name
+
+    @property
+    def kp(self):
+        return self._profile.kp
+
+    @property
+    def geometry(self):
+        return self._profile
+
+    def set(self, timestamp, key, data):
+        if timestamp not in self._data:
+            self._data[timestamp] = {}
+
+        self._data[timestamp][key] = data
+
+    def get_ts(self, timestamp):
+        return self._data[timestamp]
+
+    def get_key(self, key):
+        return list(
+            map(lambda ts: self._data[ts][key], self._data)
+        )
+
+    def get_ts_key(self, timestamp, key):
+        return self._data[timestamp][key]
+
+
+class Reach(object):
+    def __init__(self, reach, study):
+        self._study = study
+        self._reach = reach  # Source reach in the study
+        self._profiles = list(
+            map(
+                lambda p: Profile(p, self._study),
+                reach.profiles
+            )
+        )
+
+    def __len__(self):
+        return len(self._profiles)
+
+    @property
+    def name(self):
+        return self._reach.name
+
+    @property
+    def geometry(self):
+        return self._reach
+
+    @property
+    def profiles(self):
+        return self._profiles.copy()
+
+    def profile(self, id):
+        return self._profiles[id]
+
+    def set(self, profile_id, timestamp, key, data):
+        self._profiles[profile_id].set(timestamp, key, data)
+
+
+class River(object):
+    def __init__(self, study):
+        self._study = study
+
+        # Dict with timestamps as key
+        self._reachs = []
+
+    def __len__(self):
+        return len(self._reachs)
+
+    @property
+    def reachs(self):
+        return self._reachs.copy()
+
+    def reach(self, id):
+        return self._reachs[id]
+
+    def has_reach(self, id):
+        return 0 <= id < len(self._reachs)
+
+    def add(self, reach_id):
+        reachs = self._study.river.enable_edges()
+
+        new = Reach(reachs[reach_id].reach, self._study)
+
+        self._reachs.append(new)
+        return new

src/Model/River.py

@@ -16,7 +16,9 @@
 
 # -*- coding: utf-8 -*-
 
-from Model.DB import SQLSubModel
+from tools import flatten
+
+from Model.Tools.PamhyrDB import SQLSubModel
 
 from Model.Network.Node import Node
 from Model.Network.Edge import Edge
@@ -26,24 +28,28 @@ from Model.Geometry.Profile import Profile
 from Model.Geometry.Reach import Reach
 
 from Model.BoundaryCondition.BoundaryConditionList import BoundaryConditionList
-from Model.LateralContribution.LateralContributionList import LateralContributionList
+from Model.LateralContribution.LateralContributionList import (
+    LateralContributionList
+)
 from Model.InitialConditions.InitialConditionsDict import InitialConditionsDict
 from Model.Stricklers.StricklersList import StricklersList
 from Model.Friction.FrictionList import FrictionList
 from Model.SolverParameters.SolverParametersList import SolverParametersList
+from Model.SedimentLayer.SedimentLayerList import SedimentLayerList
 
 from Solver.Solvers import solver_type_list
 
+
 class RiverNode(Node, SQLSubModel):
     _sub_classes = []
 
-    def __init__(self, id:str, name:str,
-                 x:float, y:float,
-                 status = None):
+    def __init__(self, id: str, name: str,
+                 x: float, y: float,
+                 status=None):
         super(RiverNode, self).__init__(
             id, name,
             x, y,
-            status = status
+            status=status
         )
 
         self._locker = None
@@ -67,7 +73,7 @@ class RiverNode(Node, SQLSubModel):
         return True
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         nodes = []
 
         table = execute("SELECT id, name, x, y FROM river_node")
@@ -79,11 +85,11 @@ class RiverNode(Node, SQLSubModel):
 
         return nodes
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         sql = (
             "INSERT OR REPLACE INTO river_node(id, name, x, y) VALUES (" +
             f"{self.id}, '{self._sql_format(self.name)}', " +
-            f"{self.x}, {self.y}"+
+            f"{self.x}, {self.y}" +
             ")"
         )
         execute(sql)
@@ -105,18 +111,18 @@ class RiverReach(Edge, SQLSubModel):
         FrictionList,
     ]
 
-    def __init__(self, id:str, name:str,
-                 node1:RiverNode = None,
-                 node2:RiverNode = None,
-                 status = None):
+    def __init__(self, id: str, name: str,
+                 node1: RiverNode = None,
+                 node2: RiverNode = None,
+                 status=None):
         super(RiverReach, self).__init__(
             id, name,
             node1, node2,
-            status = status
+            status=status
         )
 
         self._reach = Reach(status=self._status, parent=self)
-        self._frictions = FrictionList(status = self._status)
+        self._frictions = FrictionList(status=self._status)
 
     @classmethod
     def _sql_create(cls, execute):
@@ -140,13 +146,14 @@ class RiverReach(Edge, SQLSubModel):
         return cls._update_submodel(execute, version)
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         reachs = []
 
         if data is None:
             data = {}
 
-        table = execute("SELECT id, name, enable, node1, node2 FROM river_reach")
+        table = execute(
+            "SELECT id, name, enable, node1, node2 FROM river_reach")
         for row in table:
             # Update id counter
             cls._id_cnt = max(cls._id_cnt, row[0])
@@ -158,8 +165,8 @@ class RiverReach(Edge, SQLSubModel):
             node1 = next(filter(lambda n: n.id == row[3], data["nodes"]))
             node2 = next(filter(lambda n: n.id == row[4], data["nodes"]))
 
-            new = cls(id, name, node1, node2, status = data["status"])
-            new.enable(enable = enable)
+            new = cls(id, name, node1, node2, status=data["status"])
+            new.enable(enable=enable)
 
             data["reach"] = id
             data["parent"] = new
@@ -171,14 +178,14 @@ class RiverReach(Edge, SQLSubModel):
 
         return reachs
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         sql = (
             "INSERT OR REPLACE INTO " +
-            "river_reach(id, name, enable, node1, node2) "+
+            "river_reach(id, name, enable, node1, node2) " +
             "VALUES (" +
             f"{self.id}, '{self._sql_format(self._name)}', " +
             f"{self._sql_format(self.is_enable())},"
-            f"{self.node1.id}, {self.node2.id}"+
+            f"{self.node1.id}, {self.node2.id}" +
             ")"
         )
         execute(sql)
@@ -199,6 +206,7 @@ class RiverReach(Edge, SQLSubModel):
     def frictions(self):
         return self._frictions
 
+
 class River(Graph, SQLSubModel):
     _sub_classes = [
         RiverNode,
@@ -208,6 +216,7 @@ class River(Graph, SQLSubModel):
         InitialConditionsDict,
         StricklersList,
         SolverParametersList,
+        SedimentLayerList,
     ]
 
     def __init__(self, status=None):
@@ -219,10 +228,12 @@ class River(Graph, SQLSubModel):
 
         self._current_reach = None
         self._boundary_condition = BoundaryConditionList(status=self._status)
-        self._lateral_contribution = LateralContributionList(status=self._status)
+        self._lateral_contribution = LateralContributionList(
+            status=self._status)
         self._initial_conditions = InitialConditionsDict(status=self._status)
         self._stricklers = StricklersList(status=self._status)
         self._parameters = {}
+        self._sediment_layers = SedimentLayerList(status=self._status)
 
     @classmethod
     def _sql_create(cls, execute):
@@ -235,7 +246,7 @@ class River(Graph, SQLSubModel):
         return True
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         new = cls(data["status"])
 
         # Stricklers (Stricklers is load in first because it's needed
@@ -246,6 +257,13 @@ class River(Graph, SQLSubModel):
         )
         data["stricklers"] = new._stricklers
 
+        # Initial conditions
+        new._sediment_layers = SedimentLayerList._sql_load(
+            execute,
+            data
+        )
+        data["sediment_layers_list"] = new._sediment_layers
+
         # Network
         new._nodes = RiverNode._sql_load(
             execute,
@@ -284,11 +302,12 @@ class River(Graph, SQLSubModel):
 
         return new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         objs = (self._nodes + self._edges)
         objs.append(self._boundary_condition)
         objs.append(self._initial_conditions)
         objs.append(self._lateral_contribution)
+        objs.append(self._sediment_layers)
         objs.append(self._stricklers)
 
         for solver in self._parameters:
@@ -297,14 +316,6 @@ class River(Graph, SQLSubModel):
         self._save_submodel(execute, objs, data)
         return True
 
-    @property
-    def reach(self):
-        return self._reach
-
-    @property
-    def frictions(self):
-        return self._frictions
-
     @property
     def boundary_condition(self):
         return self._boundary_condition
@@ -317,6 +328,10 @@ class River(Graph, SQLSubModel):
     def initial_conditions(self):
         return self._initial_conditions
 
+    @property
+    def sediment_layers(self):
+        return self._sediment_layers
+
     @property
     def stricklers(self):
         return self._stricklers
@@ -334,7 +349,6 @@ class River(Graph, SQLSubModel):
 
         return ret[0]
 
-
     @property
     def parameters(self):
         return self._parameters
@@ -344,8 +358,8 @@ class River(Graph, SQLSubModel):
             return self._parameters[solver]
 
         new = SolverParametersList(
-            solver_type = solver_type_list[solver],
-            status = self._status
+            solver_type=solver_type_list[solver],
+            status=self._status
         )
         self._parameters[solver] = new
         self._status.modified()
@@ -366,3 +380,16 @@ class River(Graph, SQLSubModel):
 
     def set_current_reach(self, reach):
         self._current_reach = reach
+
+    def has_sediment(self):
+        has = len(self._sediment_layers) != 0
+        has &= any(
+            filter(
+                lambda p: p.sl is not None,
+                flatten(
+                    map(lambda e: e.reach.profiles, self.edges())
+                )
+            )
+        )
+
+        return has

src/Model/Saved.py

@@ -20,6 +20,7 @@ import logging
 
 logger = logging.getLogger()
 
+
 class SavedStatus(object):
     def __init__(self):
         super(SavedStatus, self).__init__()
@@ -33,5 +34,5 @@ class SavedStatus(object):
         self._saved = True
 
     def modified(self):
-        logger.debug("model status set as modified")
+        # logger.debug("model status set as modified")
         self._saved = False

src/Model/SedimentLayer/SedimentLayer.py

@@ -0,0 +1,342 @@
+# -*- coding: utf-8 -*-
+
+from tools import trace, timer
+
+from Model.Tools.PamhyrDB import SQLSubModel
+from Model.Except import NotImplementedMethodeError
+
+
+class Layer(SQLSubModel):
+    _sub_classes = []
+    _id_cnt = 0
+
+    def __init__(self,
+                 id: int = -1, name: str = "",
+                 type="",
+                 height=0.0, d50=0.0, sigma=0.0,
+                 critical_constraint=0.0,
+                 sl=None, status=None):
+        super(Layer, self).__init__()
+
+        self._status = status
+
+        self._name = name
+        self._type = type
+
+        self._height = height
+        self._d50 = d50
+        self._sigma = sigma
+        self._critical_constraint = critical_constraint
+
+        if id == -1:
+            self.id = Layer._id_cnt
+        else:
+            self.id = id
+
+        Layer._id_cnt = max(id, Layer._id_cnt+1)
+
+    @property
+    def name(self):
+        return self._name
+
+    @name.setter
+    def name(self, name):
+        self._name = name
+
+    @property
+    def type(self):
+        return self._type
+
+    @type.setter
+    def type(self, type):
+        self._type = type
+
+    @property
+    def height(self):
+        return self._height
+
+    @height.setter
+    def height(self, height):
+        self._height = float(height)
+
+    @property
+    def d50(self):
+        return self._d50
+
+    @d50.setter
+    def d50(self, d50):
+        self._d50 = float(d50)
+
+    @property
+    def sigma(self):
+        return self._sigma
+
+    @sigma.setter
+    def sigma(self, sigma):
+        self._sigma = float(sigma)
+
+    @property
+    def critical_constraint(self):
+        return self._critical_constraint
+
+    @critical_constraint.setter
+    def critical_constraint(self, critical_constraint):
+        self._critical_constraint = float(critical_constraint)
+
+    @classmethod
+    def _sql_create(cls, execute):
+        execute("""
+          CREATE TABLE sedimentary_layer_layer(
+            id INTEGER NOT NULL PRIMARY KEY,
+            ind INTEGER NOT NULL,
+            name TEXT NOT NULL,
+            type TEXT NOT NULL,
+            height REAL NOT NULL,
+            d50 REAL NOT NULL,
+            sigma REAL NOT NULL,
+            critical_constraint REAL NOT NULL,
+            sl INTEGER,
+            FOREIGN KEY(sl) REFERENCES sedimentary_layer(id)
+          )
+        """)
+
+        return cls._create_submodel(execute)
+
+    @classmethod
+    def _sql_update(cls, execute, version):
+        major, minor, release = version.strip().split(".")
+        if major == minor == "0":
+            if int(release) < 2:
+                cls._sql_create(execute)
+
+        return True
+
+    @classmethod
+    def _sql_load(cls, execute, data=None):
+        new = []
+        sl = data["sl"]
+
+        table = execute(
+            "SELECT id, ind, name, type, height, " +
+            "d50, sigma, critical_constraint " +
+            "FROM sedimentary_layer_layer " +
+            f"WHERE sl = {sl}"
+        )
+
+        for _ in table:
+            new.append(None)
+
+        for row in table:
+            ind = row[1]
+
+            layer = cls(
+                id=row[0], name=row[2],
+                type=row[3], height=row[4],
+                d50=row[5], sigma=row[6],
+                critical_constraint=row[7],
+                sl=sl, status=data['status']
+            )
+
+            new[ind] = layer
+
+        return new
+
+    def _sql_save(self, execute, data=None):
+        ind = data["ind"]
+        sl = data["sl"]
+
+        sql = (
+            "INSERT INTO " +
+            "sedimentary_layer_layer(id, ind, name, type, height, " +
+            "d50, sigma, critical_constraint, sl) " +
+            "VALUES (" +
+            f"{self.id}, {ind}, '{self._sql_format(self._name)}', " +
+            f"'{self._sql_format(self._type)}', {self._height}, " +
+            f"{self._d50}, {self._sigma}, {self._critical_constraint}, " +
+            f"{sl.id}" +
+            ")"
+        )
+        execute(sql)
+
+        return True
+
+
+class SedimentLayer(SQLSubModel):
+    _sub_classes = [Layer]
+    _id_cnt = 0
+
+    def __init__(self, id: int = -1,
+                 name: str = "", comment: str = "",
+                 status=None):
+        super(SedimentLayer, self).__init__()
+
+        self._status = status
+        self._name = name
+        self._comment = comment
+        self._layers = []
+
+        if id == -1:
+            self.id = SedimentLayer._id_cnt
+        else:
+            self.id = id
+
+        SedimentLayer._id_cnt = max(id, SedimentLayer._id_cnt+1)
+
+    def __str__(self):
+        s = f"{self.name} ({len(self)})"
+
+        if self.comment != "":
+            s += f" - {self.comment}"
+
+        return s
+
+    def __len__(self):
+        return len(self._layers)
+
+    @property
+    def layers(self):
+        return self._layers.copy()
+
+    def height(self):
+        return list(
+            map(lambda layer: layer.height, self._layers)
+        )
+
+    @property
+    def name(self):
+        return self._name
+
+    @name.setter
+    def name(self, name):
+        self._name = name
+
+    def names(self):
+        return list(
+            map(lambda layer: layer.name, self._layers)
+        )
+
+    @property
+    def comment(self):
+        return self._comment
+
+    @comment.setter
+    def comment(self, comment):
+        self._comment = comment
+
+    @classmethod
+    def _sql_create(cls, execute):
+        execute("""
+          CREATE TABLE sedimentary_layer(
+            id INTEGER NOT NULL PRIMARY KEY,
+            name TEXT NOT NULL,
+            comment TEXT NOT NULL
+          )
+        """)
+
+        return cls._create_submodel(execute)
+
+    @classmethod
+    def _sql_update(cls, execute, version):
+        major, minor, release = version.strip().split(".")
+        if major == minor == "0":
+            if int(release) < 2:
+                cls._sql_create(execute)
+
+        return True
+
+    @classmethod
+    def _sql_load(cls, execute, data=None):
+        new = []
+
+        table = execute(
+            "SELECT id, name, comment " +
+            "FROM sedimentary_layer "
+        )
+
+        for row in table:
+            sl = cls(
+                id=row[0],
+                name=row[1],
+                comment=row[2],
+                status=data['status']
+            )
+
+            data["sl"] = sl.id
+            sl._layers = Layer._sql_load(execute, data)
+
+            new.append(sl)
+
+        return new
+
+    def _sql_save(self, execute, data=None):
+        if data is None:
+            data = {}
+
+        sql = (
+            "INSERT INTO sedimentary_layer (id, name, comment) " +
+            f"VALUES ({self.id}, '{self._sql_format(self._name)}', " +
+            f"'{self._sql_format(self._comment)}')"
+        )
+        execute(sql)
+
+        data["sl"] = self
+
+        ind = 0
+        for layer in self._layers:
+            data["ind"] = ind
+            layer._sql_save(execute, data)
+            ind += 1
+
+        return True
+
+    def get(self, index):
+        return self._layers[index]
+
+    def set(self, index, new):
+        self._layers[index] = new
+        self._status.modified()
+
+    def insert(self, index, new):
+        self._layers.insert(index, new)
+        self._status.modified()
+
+    def new(self, index):
+        n = Layer(sl=self, status=self._status)
+        self.insert(index, n)
+        self._status.modified()
+        return n
+
+    def delete(self, els):
+        for el in els:
+            self._layers.remove(el)
+        self._status.modified()
+
+    def delete_i(self, indexes):
+        els = list(
+            map(
+                lambda x: x[1],
+                filter(
+                    lambda x: x[0] in indexes,
+                    enumerate(self._layers)
+                )
+            )
+        )
+        self.delete(els)
+
+    def move_up(self, index):
+        if index >= 0:
+            next = index - 1
+
+            lst = self._layers
+            lst[index], lst[next] = lst[next], lst[index]
+
+            self._status.modified()
+
+    def move_down(self, index):
+        if index + 1 < len(self._layers):
+            prev = index + 1
+
+            lst = self._layers
+            lst[index], lst[prev] = lst[prev], lst[index]
+
+            self._status.modified()

src/Model/SedimentLayer/SedimentLayerList.py

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+
+from tools import trace, timer
+
+from Model.Except import NotImplementedMethodeError
+from Model.Tools.PamhyrList import PamhyrModelList
+from Model.SedimentLayer.SedimentLayer import SedimentLayer
+
+
+class SedimentLayerList(PamhyrModelList):
+    _sub_classes = [SedimentLayer]
+
+    @classmethod
+    def _sql_load(cls, execute, data=None):
+        new = cls(status=data["status"])
+
+        new._lst = SedimentLayer._sql_load(execute, data)
+
+        return new
+
+    def _sql_save(self, execute, data=None):
+        ok = True
+
+        # Delete previous data
+        execute("DELETE FROM sedimentary_layer")
+        execute("DELETE FROM sedimentary_layer_layer")
+
+        for sl in self._lst:
+            ok &= sl._sql_save(execute, data)
+
+        return ok
+
+    @property
+    def sediment_layers(self):
+        return self.lst
+
+    def new(self, index):
+        n = SedimentLayer(status=self._status)
+        self.insert(index, n)
+        self._status.modified()
+        return n

src/Model/Serializable.py

@@ -18,6 +18,7 @@
 
 import pickle
 
+
 class Serializable():
     def __init__(self):
         return

src/Model/SolverParameters/SolverParametersList.py

@@ -20,12 +20,13 @@ from copy import copy
 from tools import trace, timer
 from Solver.Solvers import solver_type_list
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrList import PamhyrModelList
+
 
 class Parameter():
     def __init__(self,
-                 name = "", value = "",
-                 status = None):
+                 name="", value="",
+                 status=None):
         self._status = status
 
         self._name = name
@@ -57,26 +58,26 @@ class Parameter():
 
     @classmethod
     def from_tuple(cls, data, status):
-        new = cls(status = status)
+        new = cls(status=status)
         new["name"] = data[0]
         new["value"] = data[1]
 
         return new
 
-class SolverParametersList(SQLSubModel):
-    def __init__(self, solver_type = None, status = None):
+
+class SolverParametersList(PamhyrModelList):
+    def __init__(self, solver_type=None, status=None):
         super(SolverParametersList, self).__init__()
 
         self._status = status
         self._solver = solver_type
-        self._parameters = list(
+        self._lst = list(
             map(
                 lambda t: Parameter.from_tuple(t, self._status),
                 solver_type.default_parameters()
             )
         )
 
-
     @classmethod
     def _sql_create(cls, execute):
         execute("""
@@ -93,10 +94,77 @@ class SolverParametersList(SQLSubModel):
 
     @classmethod
     def _sql_update(cls, execute, version):
+        major, minor, release = version.strip().split(".")
+
+        if major == minor == "0":
+            if int(release) < 3:
+                execute(
+                    "UPDATE solver_parameter SET name='mage_implicitation' " +
+                    "WHERE name='mage_implication'"
+                )
+                execute(
+                    "UPDATE solver_parameter SET name='mage_iteration_type' " +
+                    "WHERE name='mage_iter_type'"
+                )
+
+            if int(release) < 4:
+                solvers = execute(
+                    "SELECT DISTINCT solver FROM solver_parameter")
+
+                for solver in solvers:
+                    if solver != "mage8":
+                        continue
+
+                    data = execute("SELECT ind, name, value " +
+                                   "FROM solver_parameter " +
+                                   f"WHERE solver = '{solver}' " +
+                                   "ORDER BY ind ACS")
+
+                    execute(
+                        "DELETE FROM solver_parameter " +
+                        f"WHERE solver = '{solver}'"
+                    )
+
+                    def insert(name, value, ind): return execute(
+                        "INSERT INTO " +
+                        "solver_parameter(ind, name, value, solver) " +
+                        "VALUES (" +
+                        f"{ind}, " +
+                        f"'{cls._sql_format(name)}', " +
+                        f"'{cls._sql_format(value)}', " +
+                        f"'{cls._sql_format(solver)}'" +
+                        ")"
+                    )
+
+                    ind = 0
+                    lst = []
+                    for v in data:
+                        insert(v[0], v[1], ind)
+                        ind += 1
+
+                    new = [
+                        ("mage_sediment_masse_volumique", "2650.0"),
+                        ("mage_sediment_angle_repos", "40.0"),
+                        ("mage_sediment_porosity", "0.40"),
+                        ("mage_distance_han", "0.0"),
+                        ("mage_distance_chargement_d50", "100.0"),
+                        ("mage_distance_chargement_sigma", "100.0"),
+                        ("mage_methode_modification_geometrie", "1"),
+                        ("mage_shields_critique", "1"),
+                        ("mage_shields_correction", "1"),
+                        ("mage_capacite_solide", "1"),
+                        ("mage_pas_de_temps_charriage", "1"),
+                        ("mage_facteur_multiplicateur", "1.0"),
+                    ]
+
+                    for v in new:
+                        insert(v[0], v[1], ind)
+                        ind += 1
+
         return cls._update_submodel(execute, version)
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         status = data["status"]
         solvers = execute("SELECT DISTINCT solver FROM solver_parameter")
         new = {}
@@ -107,7 +175,7 @@ class SolverParametersList(SQLSubModel):
                 continue
 
             st = solver_type_list[solver]
-            n = cls(solver_type = st, status = status)
+            n = cls(solver_type=st, status=status)
 
             table = execute(
                 "SELECT ind, name, value " +
@@ -126,7 +194,7 @@ class SolverParametersList(SQLSubModel):
 
         return new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         t = self._solver._type
         execute(
             "DELETE FROM solver_parameter " +
@@ -134,10 +202,10 @@ class SolverParametersList(SQLSubModel):
         )
 
         ind = 0
-        for param in self._parameters:
+        for param in self._lst:
             sql = (
                 "INSERT INTO " +
-                "solver_parameter(ind, name, value, solver) "+
+                "solver_parameter(ind, name, value, solver) " +
                 "VALUES (" +
                 f"{ind}, " +
                 f"'{self._sql_format(param.name)}', " +
@@ -150,79 +218,46 @@ class SolverParametersList(SQLSubModel):
 
         return True
 
-    def __len__(self):
-        return len(self._parameters)
-
     @property
     def parameters(self):
-        return self._parameters.copy()
+        return self.lst
 
     def get(self, index):
-        return self._parameters[index]
+        return self._lst[index]
+
+    def get_by_key(self, key):
+        try:
+            return next(
+                filter(
+                    lambda p: p["name"] == key,
+                    self._lst
+                )
+            )["value"]
+        except Exception:
+            return None
 
     def set(self, index, new):
-        self._parameters[index] = new
+        self._lst[index] = new
         self._status.modified()
 
     def set_value(self, key, value):
-        for p in self._parameters:
+        for p in self._lst:
             if p["name"] == key:
                 p["value"] = value
                 self._status.modified()
                 return
 
-        self._parameters.append(
+        self._lst.append(
             Parameter(
-                name = key,
-                value = value,
-                status = self._status
+                name=key,
+                value=value,
+                status=self._status
             )
         )
         self._status.modified()
 
     def new(self, index):
-        n = Parameter(status = self._status)
-        self._parameters.insert(index, n)
+        n = Parameter(status=self._status)
+        self._lst.insert(index, n)
         self._status.modified()
         return n
-
-    def insert(self, index, new):
-        self._parameters.insert(index, new)
-        self._status.modified()
-
-    def delete(self, parameters):
-        for parameter in parameters:
-            self._parameters.remove(parameter)
-        self._status.modified()
-
-    def delete_i(self, indexes):
-        parameters = list(
-            map(
-                lambda x: x[1],
-                filter(
-                    lambda x: x[0] in indexes,
-                    enumerate(self._parameters)
-                )
-            )
-        )
-        self.delete(parameters)
-
-    def sort(self, reverse=False, key=None):
-        self._parameters.sort(reverse=reverse, key=key)
-        self._status.modified()
-
-    def move_up(self, index):
-        if index < len(self._parameters):
-            next = index - 1
-
-            l = self._parameters
-            l[index], l[next] = l[next], l[index]
-            self._status.modified()
-
-    def move_down(self, index):
-        if index >= 0:
-            prev = index + 1
-
-            l = self._parameters
-            l[index], l[prev] = l[prev], l[index]
-            self._status.modified()

src/Model/Stricklers/Stricklers.py

@@ -18,18 +18,19 @@
 
 from tools import trace, timer
 
-from Model.DB import SQLSubModel
+from Model.Tools.PamhyrDB import SQLSubModel
+
 
 class Stricklers(SQLSubModel):
     _id_cnt = 0
     _sub_classes = []
 
-    def __init__(self, id:int = -1,
-                 name:str = "",
-                 comment:str = "",
-                 minor:float = 35.0,
-                 medium:float = 15.0,
-                 status = None):
+    def __init__(self, id: int = -1,
+                 name: str = "",
+                 comment: str = "",
+                 minor: float = 35.0,
+                 medium: float = 15.0,
+                 status=None):
         super(Stricklers, self).__init__()
         self._status = status
 
@@ -38,7 +39,7 @@ class Stricklers(SQLSubModel):
         else:
             self.id = id
 
-        Stricklers._id_cnt = max(Stricklers._id_cnt + 1, self.id)
+        Stricklers._id_cnt = max(Stricklers._id_cnt + 1, id + 1)
 
         self._name = name
         self._comment = comment
@@ -46,7 +47,6 @@ class Stricklers(SQLSubModel):
         self._minor = minor
         self._medium = medium
 
-
     @classmethod
     def _sql_create(cls, execute):
         execute("""
@@ -66,7 +66,7 @@ class Stricklers(SQLSubModel):
         return cls._update_submodel(execute, version)
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         stricklers = []
         status = data["status"]
 
@@ -86,21 +86,21 @@ class Stricklers(SQLSubModel):
             medium = row[4]
 
             new = cls(
-                id = id,
-                name = name,
-                comment = comment,
-                minor = minor, medium = medium,
-                status = status
+                id=id,
+                name=name,
+                comment=comment,
+                minor=minor, medium=medium,
+                status=status
             )
 
             stricklers.append(new)
 
         return stricklers
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         sql = (
             "INSERT INTO " +
-            "stricklers(id, name, comment, minor, medium) "+
+            "stricklers(id, name, comment, minor, medium) " +
             "VALUES (" +
             f"{self.id}, " +
             f"'{self._sql_format(self.name)}', " +

src/Model/Stricklers/StricklersList.py

@@ -18,22 +18,16 @@
 
 from tools import trace, timer
 
-from Model.DB import SQLSubModel
 from Model.Saved import SavedStatus
+from Model.Tools.PamhyrList import PamhyrModelList
 from Model.Stricklers.Stricklers import Stricklers
 
-class StricklersList(SQLSubModel):
+
+class StricklersList(PamhyrModelList):
     _sub_classes = [
         Stricklers,
     ]
 
-    def __init__(self, status = None):
-        if status is None:
-            status = SavedStatus()
-        self._status = status
-
-        self._stricks = []
-
     @classmethod
     def _sql_create(cls, execute):
         return cls._create_submodel(execute)
@@ -43,74 +37,42 @@ class StricklersList(SQLSubModel):
         return cls._update_submodel(execute, version)
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
-        new = cls(status = data["status"])
+    def _sql_load(cls, execute, data=None):
+        new = cls(status=data["status"])
 
-        new._stricks = Stricklers._sql_load(
+        new._lst = Stricklers._sql_load(
             execute,
-            data = data
+            data=data
         )
 
         return new
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         execute("DELETE FROM stricklers")
 
-        objs = self._stricks
+        objs = self._lst
         return self._save_submodel(execute, objs, data)
 
-    def __len__(self):
-        return len(self._stricks)
-
     @property
     def stricklers(self):
-        return self._stricks.copy()
+        return self.lst
 
-    def get(self, index):
-        if 0 <= index < len(self._stricks):
-            return self._stricks[index]
-
-        return None
-
-    def insert(self, index, strick):
-        self._stricks.insert(index, strick)
-        self._status.modified()
-
-    def add(self, index):
-        s = Stricklers(status = self._status)
+    def new(self, index):
+        s = Stricklers(status=self._status)
         self.insert(index, s)
         return s
 
-    def delete(self, stricks):
-        self._stricks = list(
-            filter(
-                lambda s: s not in stricks,
-                self._stricks
-            )
-        )
-        self._status.modified()
-
-    def delete_i(self, indexes):
-        stricks = set(
-            map(
-                lambda e: e[1],
-                filter(
-                    lambda e: e[0] in indexes,
-                    enumerate(self._stricks)
-                )
-            )
-        )
-        self.delete(stricks)
-
     @timer
-    def sort(self, reverse:bool = False, key=None):
-        f = lambda st: st.name
+    def sort(self, reverse: bool = False, key=None):
+        def f(st): return st.name
         if key is not None:
             f = key
 
-        self._stricks = sorted(
-            self._stricks,
-            key = f,
-            reverse = reverse,
+        self._lst = sorted(
+            self._lst,
+            key=f,
+            reverse=reverse,
         )
-        self._status.modified()
+
+        if self._status is not None:
+            self._status.modified()

src/Model/Study.py

@@ -23,7 +23,7 @@ from datetime import datetime
 
 from tools import timer, timestamp
 
-from Model.DB import SQLModel
+from Model.Tools.PamhyrDB import SQLModel
 from Model.Saved import SavedStatus
 from Model.Serializable import Serializable
 from Model.Except import NotImplementedMethodeError
@@ -33,20 +33,21 @@ from Checker.Study import *
 
 logger = logging.getLogger()
 
+
 class Study(SQLModel):
     _sub_classes = [
         River,
     ]
 
-    def __init__(self, filename = None, init_new = True):
+    def __init__(self, filename=None, init_new=True):
         # Metadata
-        self._version = "0.0.1"
+        self._version = "0.0.4"
         self.creation_date = datetime.now()
         self.last_modification_date = datetime.now()
         self.last_save_date = datetime.now()
 
         self._filename = filename
-        super(Study, self).__init__(filename = filename)
+        super(Study, self).__init__(filename=filename)
 
         self.status = SavedStatus()
 
@@ -59,9 +60,9 @@ class Study(SQLModel):
 
         if init_new:
             # Study data
-            self._river = River(status = self.status)
+            self._river = River(status=self.status)
         else:
-            self._init_db_file(filename, is_new = False)
+            self._init_db_file(filename, is_new=False)
 
         self._old_save_id = 0
 
@@ -128,7 +129,7 @@ class Study(SQLModel):
     @filename.setter
     def filename(self, filename):
         self._filename = str(filename)
-        self._init_db_file(filename, is_new = True)
+        self._init_db_file(filename, is_new=True)
         self.status.modified()
 
     @property
@@ -139,7 +140,7 @@ class Study(SQLModel):
         self._time_system = "time"
         self.status.modified()
 
-    def use_date(self, date:datetime):
+    def use_date(self, date: datetime):
         self._time_system = "date"
         self._date = date
         self.status.modified()
@@ -158,7 +159,7 @@ class Study(SQLModel):
     #     return cls()
 
     @classmethod
-    def new(cls, name, description, date = None):
+    def new(cls, name, description, date=None):
         me = cls()
         me.name = name
         me.description = description
@@ -178,14 +179,17 @@ class Study(SQLModel):
 
     def _create(self):
         # Info (metadata)
-        self.execute("CREATE TABLE info(key TEXT NOT NULL UNIQUE, value TEXT NOT NULL)")
         self.execute(
-            f"INSERT INTO info VALUES ('version', '{self._sql_format(self._version)}')",
-            commit = True
+            "CREATE TABLE info(key TEXT NOT NULL UNIQUE, value TEXT NOT NULL)")
+        self.execute(
+            "INSERT INTO info VALUES ('version', " +
+            f"'{self._sql_format(self._version)}')",
+            commit=True
         )
         self.execute("INSERT INTO info VALUES ('name', '')")
         self.execute("INSERT INTO info VALUES ('description', '')")
-        self.execute(f"INSERT INTO info VALUES ('time_system', '{self._time_system}')")
+        self.execute(
+            f"INSERT INTO info VALUES ('time_system', '{self._time_system}')")
         self.execute(
             f"INSERT INTO info VALUES ('date', " +
             "'{self._date.timestamp()}')"
@@ -213,7 +217,8 @@ class Study(SQLModel):
         logger.info("Update database")
 
         if self._update_submodel(version[0]):
-            self.execute(f"UPDATE info SET value='{self._version}' WHERE key='version'")
+            self.execute(
+                f"UPDATE info SET value='{self._version}' WHERE key='version'")
             return True
 
         logger.info("TODO: update failed")
@@ -221,42 +226,75 @@ class Study(SQLModel):
 
     @classmethod
     def _load(cls, filename):
-        new = cls(init_new = False, filename = filename)
+        new = cls(init_new=False, filename=filename)
 
         # TODO: Load metadata
         new.name = new.execute("SELECT value FROM info WHERE key='name'")[0]
-        new.description = new.execute("SELECT value FROM info WHERE key='description'")[0]
-        new._time_system = new.execute("SELECT value FROM info WHERE key='time_system'")[0]
+        new.description = new.execute(
+            "SELECT value FROM info WHERE key='description'")[0]
+        new._time_system = new.execute(
+            "SELECT value FROM info WHERE key='time_system'")[0]
         new._date = datetime.fromtimestamp(
             float(new.execute("SELECT value FROM info WHERE key='date'")[0])
         )
 
         new.creation_date = datetime.fromtimestamp(
-            float(new.execute("SELECT value FROM info WHERE key='creation_date'")[0])
+            float(new.execute(
+                "SELECT value FROM info WHERE key='creation_date'")[0])
         )
         new.last_save_date = datetime.fromtimestamp(
-            float(new.execute("SELECT value FROM info WHERE key='last_save_date'")[0])
+            float(new.execute(
+                "SELECT value FROM info WHERE key='last_save_date'")[0])
         )
 
         # Load river data
         new._river = River._sql_load(
             lambda sql: new.execute(
                 sql,
-                fetch_one = False,
-                commit = True
+                fetch_one=False,
+                commit=True
             ),
-            data = {"status": new.status}
+            data={"status": new.status}
         )
 
         return new
 
     def _save(self):
-        self.execute(f"UPDATE info SET value='{self._sql_format(self.name)}' WHERE key='name'")
-        self.execute(f"UPDATE info SET value='{self._sql_format(self.description)}' WHERE key='description'")
-        self.execute(f"UPDATE info SET value='{self._time_system}' WHERE key='time_system'")
-        self.execute(f"UPDATE info SET value='{timestamp(self._date)}' WHERE key='date'")
-        self.execute(f"UPDATE info SET value='{timestamp(self.creation_date)}' WHERE key='creation_date'")
-        self.execute(f"UPDATE info SET value='{timestamp(self.last_save_date)}' WHERE key='last_save_date'")
+        self.execute(
+            f"UPDATE info SET " +
+            f"value='{self._sql_format(self.name)}' WHERE key='name'"
+        )
+        self.execute(
+            f"UPDATE info SET " +
+            f"value='{self._sql_format(self.description)}' " +
+            "WHERE key='description'"
+        )
+        self.execute(
+            f"UPDATE info SET " +
+            f"value='{self._time_system}' WHERE key='time_system'"
+        )
+        self.execute(
+            f"UPDATE info SET " +
+            f"value='{timestamp(self._date)}' WHERE key='date'"
+        )
+        self.execute(
+            f"UPDATE info SET " +
+            f"value='{timestamp(self.creation_date)}' " +
+            "WHERE key='creation_date'"
+        )
+        self.execute(
+            f"UPDATE info SET " +
+            f"value='{timestamp(self.last_save_date)}' " +
+            "WHERE key='last_save_date'"
+        )
 
         self._save_submodel([self._river])
         self.commit()
+
+    def close(self):
+        """Close db connection
+
+        Returns:
+            Nothing.
+        """
+        self._close()

src/Model/Tools/PamhyrDB.py

@@ -1,4 +1,4 @@
-# DB.py -- Pamhyr abstract model database classes
+# PamhyrDB.py -- Pamhyr abstract model database classes
 # Copyright (C) 2023  INRAE
 #
 # This program is free software: you can redistribute it and/or modify
@@ -28,10 +28,12 @@ from Model.Except import NotImplementedMethodeError
 logger = logging.getLogger()
 
 # Top level model class
+
+
 class SQLModel(SQL):
     _sub_classes = []
 
-    def _init_db_file(self, db, is_new = True):
+    def _init_db_file(self, db, is_new=True):
         exists = Path(db).exists()
 
         if exists and is_new:
@@ -48,15 +50,14 @@ class SQLModel(SQL):
             self._update()      # Update db scheme if necessary
             # self._load()        # Load data
 
-
-    def __init__(self, filename = None):
+    def __init__(self, filename=None):
         self._db = None
 
     def _create_submodel(self):
-        fn = lambda sql: self.execute(
+        def fn(sql): return self.execute(
             sql,
-            fetch_one = False,
-            commit = False
+            fetch_one=False,
+            commit=False
         )
 
         for cls in self._sub_classes:
@@ -69,10 +70,10 @@ class SQLModel(SQL):
         raise NotImplementedMethodeError(self, self._create)
 
     def _update_submodel(self, version):
-        fn = lambda sql: self.execute(
+        def fn(sql): return self.execute(
             sql,
-            fetch_one = False,
-            commit = False
+            fetch_one=False,
+            commit=False
         )
 
         ok = True
@@ -85,11 +86,11 @@ class SQLModel(SQL):
     def _update(self):
         raise NotImplementedMethodeError(self, self._update)
 
-    def _save_submodel(self, objs, data = None):
-        fn = lambda sql: self.execute(
+    def _save_submodel(self, objs, data=None):
+        def fn(sql): return self.execute(
             sql,
-            fetch_one = False,
-            commit = False
+            fetch_one=False,
+            commit=False
         )
 
         ok = True
@@ -103,18 +104,20 @@ class SQLModel(SQL):
         raise NotImplementedMethodeError(self, self._save)
 
     @classmethod
-    def _load(cls, filename = None):
+    def _load(cls, filename=None):
         raise NotImplementedMethodeError(cls, cls._load)
 
 # Sub model class
+
+
 class SQLSubModel(object):
     _sub_classes = []
 
     def _sql_format(self, value):
         # Replace ''' by ''' to preserve SQL injection
-        if type(value) == str:
+        if value is str:
             value = value.replace("'", "'")
-        elif type(value) == bool:
+        elif value is bool:
             value = 'TRUE' if value else 'FALSE'
         return value
 
@@ -154,7 +157,7 @@ class SQLSubModel(object):
         raise NotImplementedMethodeError(cls, cls._sql_update)
 
     @classmethod
-    def _sql_load(cls, execute, data = None):
+    def _sql_load(cls, execute, data=None):
         """Load instance of this class from SQL data base
 
         Args:
@@ -166,11 +169,11 @@ class SQLSubModel(object):
         """
         raise NotImplementedMethodeError(cls, cls._sql_load)
 
-    def _save_submodel(self, execute, objs, data = None):
+    def _save_submodel(self, execute, objs, data=None):
         for o in objs:
-            o._sql_save(execute, data = data)
+            o._sql_save(execute, data=data)
 
-    def _sql_save(self, execute, data = None):
+    def _sql_save(self, execute, data=None):
         """Save class data to data base
 
         Args:

src/Model/Tools/PamhyrDict.py

@@ -0,0 +1,74 @@
+# PamhyrDict.py -- Pamhyr abstract dict for model classes
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+import logging
+
+from copy import copy
+from tools import trace, timer
+
+from Model.Tools.PamhyrDB import SQLSubModel
+from Model.Except import NotImplementedMethodeError
+
+logger = logging.getLogger()
+
+
+class PamhyrModelDict(SQLSubModel):
+    _sub_classes = []
+
+    def __init__(self, status=None):
+        super(PamhyrModelDict, self).__init__()
+
+        self._status = status
+
+        self._dict = {}
+
+    @classmethod
+    def _sql_create(cls, execute):
+        return cls._create_submodel(execute)
+
+    @classmethod
+    def _sql_update(cls, execute, version):
+        return cls._update_submodel(execute, version)
+
+    @classmethod
+    def _sql_load(cls, execute, data=None):
+        raise NotImplementedMethodeError(cls, cls._sql_load)
+
+    def _sql_save(self, execute, data=None):
+        raise NotImplementedMethodeError(self, self._sql_save)
+
+    def __len__(self):
+        return len(self._dict)
+
+    def is_defined(self, key):
+        return key in self._dict
+
+    def set(self, key, new):
+        self._dict[key] = new
+        self._status.modified()
+
+    def get(self, key):
+        if key in self._dict:
+            return self._dict[key]
+
+        new = self.new(key)
+        self.set(key, new)
+        return new
+
+    def new(self, key):
+        raise NotImplementedMethodeError(self, self.new)

src/Model/Tools/PamhyrList.py

@@ -0,0 +1,241 @@
+# PamhyrList.py -- Pamhyr Abstract List object for the Model
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+import logging
+
+from copy import copy
+from tools import trace, timer
+
+from Model.Tools.PamhyrDB import SQLSubModel
+from Model.Except import NotImplementedMethodeError
+
+logger = logging.getLogger()
+
+
+class PamhyrModelList(SQLSubModel):
+    _sub_classes = [
+    ]
+
+    def __init__(self, status=None):
+        super(PamhyrModelList, self).__init__()
+
+        self._status = status
+        self._lst = []
+
+    #######
+    # SQL #
+    #######
+
+    @classmethod
+    def _sql_create(cls, execute):
+        return cls._create_submodel(execute)
+
+    @classmethod
+    def _sql_update(cls, execute, version):
+        return cls._update_submodel(execute, version)
+
+    @classmethod
+    def _sql_load(cls, execute, data=None):
+        raise NotImplementedMethodeError(cls, cls._sql_load)
+
+    def _sql_save(self, execute, data=None):
+        raise NotImplementedMethodeError(self, self._sql_save)
+
+    ################
+    # MODEL METHOD #
+    ################
+
+    @property
+    def lst(self):
+        return self._lst
+
+    def __len__(self):
+        return len(self.lst)
+
+    def get(self, row):
+        return self._lst[row]
+
+    def set(self, row, new):
+        self._lst[row] = new
+        if self._status is not None:
+            self._status.modified()
+
+    def new(self, index):
+        """Create new elements and add it to list
+
+        Args:
+            index: The index of new elements
+
+        Returns:
+            The new elements
+        """
+        raise NotImplementedMethodeError(self, self.new)
+
+    def insert(self, index, new):
+        self._lst.insert(index, new)
+
+        if self._status is not None:
+            self._status.modified()
+
+    def delete(self, lst):
+        for el in lst:
+            self._lst.remove(el)
+
+        if self._status is not None:
+            self._status.modified()
+
+    def delete_i(self, indexes):
+        lst = list(
+            map(
+                lambda x: x[1],
+                filter(
+                    lambda x: x[0] in indexes,
+                    enumerate(self._lst)
+                )
+            )
+        )
+        self.delete(lst)
+
+    def sort(self, reverse=False, key=None):
+        self._lst.sort(reverse=reverse, key=key)
+
+        if self._status is not None:
+            self._status.modified()
+
+    def move_up(self, index):
+        if index < len(self._lst):
+            next = index - 1
+
+            lst = self._lst
+            lst[index], lst[next] = lst[next], lst[index]
+
+            if self._status is not None:
+                self._status.modified()
+
+    def move_down(self, index):
+        if index >= 0:
+            prev = index + 1
+
+            lst = self._lst
+            lst[index], lst[prev] = lst[prev], lst[index]
+
+            if self._status is not None:
+                self._status.modified()
+
+
+class PamhyrModelListWithTab(SQLSubModel):
+    _tabs_list = []
+    _sub_classes = [
+    ]
+
+    def __init__(self, status=None):
+        super(PamhyrModelListWithTab, self).__init__()
+
+        self._status = status
+        self._tabs = {}
+        for tab in self._tabs_list:
+            self._tabs[tab] = []
+
+    #######
+    # SQL #
+    #######
+
+    @classmethod
+    def _sql_create(cls, execute):
+        return cls._create_submodel(execute)
+
+    @classmethod
+    def _sql_update(cls, execute, version):
+        return cls._update_submodel(execute, version)
+
+    @classmethod
+    def _sql_load(cls, execute, data=None):
+        raise NotImplementedMethodeError(cls, cls._sql_load)
+
+    def _sql_save(self, execute, data=None):
+        raise NotImplementedMethodeError(self, self._sql_save)
+
+    ################
+    # MODEL METHOD #
+    ################
+
+    def len(self, lst):
+        return len(self._tabs[lst])
+
+    def get_tab(self, lst):
+        return self._tabs[lst].copy()
+
+    def get(self, lst, row):
+        return self._tabs[lst][row]
+
+    def set(self, lst, row, new):
+        self._tabs[lst][row] = new
+        self._status.modified()
+
+    def new(self, lst, index):
+        """Create new elements and add it to list
+
+        Args:
+            lst: The tab name
+            index: The index of new elements
+
+        Returns:
+            The new elements
+        """
+        raise NotImplementedMethodeError(self, self.new)
+
+    def insert(self, lst, index, new):
+        self._tabs[lst].insert(index, new)
+        self._status.modified()
+
+    def delete(self, lst, els):
+        for el in els:
+            self._tabs[lst].remove(el)
+        self._status.modified()
+
+    def delete_i(self, lst, indexes):
+        els = list(
+            map(
+                lambda x: x[1],
+                filter(
+                    lambda x: x[0] in indexes,
+                    enumerate(self._tabs[lst])
+                )
+            )
+        )
+        self.delete(lst, els)
+
+    def sort(self, lst, reverse=False, key=None):
+        self._tabs[lst].sort(reverse=reverse, key=key)
+        self._status.modified()
+
+    def move_up(self, lst, index):
+        if index < len(self._tabs[lst]):
+            next = index - 1
+
+            lst = self._tabs[lst]
+            lst[index], lst[next] = lst[next], lst[index]
+            self._status.modified()
+
+    def move_down(self, lst, index):
+        if index >= 0:
+            prev = index + 1
+
+            lst = self._tabs[lst]
+            lst[index], lst[prev] = lst[prev], lst[index]
+            self._status.modified()

src/Model/__init__.py

@@ -0,0 +1,17 @@
+# __init__.py -- Pamhyr
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-

src/Model/test_Model.py

@@ -0,0 +1,110 @@
+# test_Model.py -- Pamhyr
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+import os
+import unittest
+import tempfile
+
+from Model.Saved import SavedStatus
+from Model.Study import Study
+from Model.River import River
+
+
+class StudyTestCase(unittest.TestCase):
+    def test_create_study(self):
+        study = Study.new("foo", "bar")
+        self.assertEqual(study.name, "foo")
+        self.assertEqual(study.description, "bar")
+
+    def test_open_study(self):
+        study = Study.open("../tests_cases/Enlargement/Enlargement.pamhyr")
+        self.assertNotEqual(study, None)
+        self.assertEqual(study.name, "Enlargement")
+
+    def test_save_open_study(self):
+        study = Study.new("foo", "bar")
+        dir = tempfile.mkdtemp()
+        f = os.path.join(dir, "foo.pamhyr")
+
+        # Save study
+        study.filename = f
+        study.save()
+        study.close()
+
+        # Reopen study
+        study = Study.open(f)
+
+        # Check
+        self.assertNotEqual(study, None)
+        self.assertEqual(study.name, "foo")
+        self.assertEqual(study.description, "bar")
+
+    def test_create_study_river(self):
+        study = Study.new("foo", "bar")
+        self.assertNotEqual(study.river, None)
+
+
+class RiverTestCase(unittest.TestCase):
+    def test_create_river(self):
+        status = SavedStatus()
+        river = River(status=status)
+
+        self.assertNotEqual(river, None)
+
+    def test_create_river_nodes(self):
+        status = SavedStatus()
+        river = River(status=status)
+
+        self.assertNotEqual(river, None)
+
+        # Add nodes
+        n0 = river.add_node()
+        n1 = river.add_node(x=1.0, y=0.0)
+        n2 = river.add_node(x=0.0, y=1.0)
+
+        # Checks
+        self.assertEqual(river.nodes_counts(), 3)
+
+        nodes = river.nodes()
+        self.assertEqual(nodes[0], n0)
+        self.assertEqual(nodes[1], n1)
+        self.assertEqual(nodes[2], n2)
+
+    def test_create_river_edges(self):
+        status = SavedStatus()
+        river = River(status=status)
+
+        self.assertNotEqual(river, None)
+
+        # Add nodes
+        n0 = river.add_node()
+        n1 = river.add_node(x=1.0, y=0.0)
+        n2 = river.add_node(x=0.0, y=1.0)
+
+        self.assertEqual(river.nodes_counts(), 3)
+
+        # Add edges
+        e0 = river.add_edge(n0, n1)
+        e1 = river.add_edge(n1, n2)
+
+        # Checks
+        self.assertEqual(river.edges_counts(), 2)
+
+        edges = river.edges()
+        self.assertEqual(edges[0], e0)
+        self.assertEqual(edges[1], e1)

src/Scripts/AScript.py

@@ -0,0 +1,37 @@
+# AScript.py -- Pamhyr abstract script class
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+from Model.Except import NotImplementedMethodeError
+
+
+class AScript(object):
+    name = ""
+    description = ""
+
+    def __init__(self, app, conf, args):
+        super(AScript, self).__init__()
+
+        self._app = app
+        self._conf = conf
+        self._args = args.copy()
+
+    def usage(self):
+        raise NotImplementedMethodeError(self, self.usage)
+
+    def run(self):
+        raise NotImplementedMethodeError(self, self.run)

src/Scripts/Hello.py

@@ -0,0 +1,34 @@
+# Hello.py -- Pamhyr
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+import logging
+from Scripts.AScript import AScript
+
+logger = logging.getLogger()
+
+
+class ScriptHello(AScript):
+    name = "Hello"
+    description = "Display hello"
+
+    def usage(self):
+        logger.info(f"Usage : {self._args[0]} hello")
+
+    def run(self):
+        logger.info("Hello from Pamhyr2 script !")
+        return 0

src/Scripts/ListSolver.py

@@ -0,0 +1,38 @@
+# ListSolver.py -- Pamhyr
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+import os
+import logging
+
+from Scripts.AScript import AScript
+
+logger = logging.getLogger()
+
+
+class ScriptListSolver(AScript):
+    name = "ListSolver"
+    description = "List configured solver(s) for Pamhyr2"
+
+    def usage(self):
+        logger.info(f"Usage : {self._args[0]} {self._args[1]}")
+
+    def run(self):
+        for solver in self._conf.solvers:
+            print(f"{solver.name:<16} ({solver.type}): {solver.description}")
+
+        return 0

src/Scripts/P3DST.py

@@ -0,0 +1,116 @@
+# P3DST.py -- Pamhyr
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+import sys
+import logging
+
+from matplotlib import pyplot as plt
+from numpy import mean
+
+from Scripts.AScript import AScript
+
+from Model.Saved import SavedStatus
+from Model.Geometry.Reach import Reach
+
+logger = logging.getLogger()
+
+
+class Script3DST(AScript):
+    name = "3DST"
+    description = "Display a 3D plot of a river reach from ST file"
+
+    def usage(self):
+        logger.info(f"Usage : {self._args[0]} 3DST <INPUT_ST_FILE>")
+
+    def set_axes_equal(self, ax):
+        """Make axes of 3D plot have equal scale
+
+        Make axes of 3D plot have equal scale so that spheres appear
+        as spheres, cubes as cubes, etc.. This is one possible
+        solution to Matplotlib's ax.set_aspect('equal') and
+        ax.axis('equal') not working for 3D.
+
+        Args:
+            ax: a matplotlib axis, e.g., as output from plt.gca()
+
+        Returns:
+            The input axis
+        """
+        x_limits = ax.get_xlim3d()
+        y_limits = ax.get_ylim3d()
+        z_limits = ax.get_zlim3d()
+
+        x_range = abs(x_limits[1] - x_limits[0])
+        x_middle = mean(x_limits)
+        y_range = abs(y_limits[1] - y_limits[0])
+        y_middle = mean(y_limits)
+        z_range = abs(z_limits[1] - z_limits[0])
+        z_middle = mean(z_limits)
+
+        # The plot bounding box is a sphere in the sense of the infinity
+        # norm, hence I call half the max range the plot radius.
+        plot_radius = 0.5*max([x_range, y_range, z_range])
+
+        ax.set_xlim3d([x_middle - plot_radius, x_middle + plot_radius])
+        ax.set_ylim3d([y_middle - plot_radius, y_middle + plot_radius])
+        ax.set_zlim3d([z_middle - plot_radius, z_middle + plot_radius])
+
+        return ax
+
+    def run(self):
+        try:
+            st_file = self._args[2]
+            logger.info(f"Use ST file: {st_file}")
+        except Exception as e:
+            logger.error(f"Arguments parcing: {str(e)}")
+            return 1
+
+        try:
+            status = SavedStatus()
+
+            my_reach = Reach(status=status)
+            my_reach.import_geometry(st_file)
+            my_reach.compute_guidelines()
+
+            ax = plt.figure().add_subplot(projection="3d")
+            logger.info(my_reach.get_x())
+            for x, y, z in zip(
+                    my_reach.get_x(),
+                    my_reach.get_y(),
+                    my_reach.get_z()
+            ):
+                ax.plot(x, y, z, color='r', lw=1.)
+
+            for x, y, z in zip(
+                    my_reach.get_guidelines_x(),
+                    my_reach.get_guidelines_y(),
+                    my_reach.get_guidelines_z()
+            ):
+                ax.plot(x, y, z, color='b', lw=1.)
+
+            ax.set_xlabel('X')
+            ax.set_ylabel('Y')
+            ax.set_zlabel('Z')
+            plt.tight_layout()
+            self.set_axes_equal(ax)
+            plt.show()
+
+            return 0
+        except Exception as e:
+            logger.error(str(e))
+            return 1

src/Scripts/Run.py

@@ -0,0 +1,113 @@
+# Run.py -- Pamhyr
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+import os
+import logging
+
+from queue import Queue
+
+from PyQt5.QtCore import QProcess
+
+from Scripts.AScript import AScript
+from Model.Study import Study
+
+logger = logging.getLogger()
+
+
+class ScriptRun(AScript):
+    name = "Run"
+    description = "Run solver on Pamhyr2 a study"
+
+    def usage(self):
+        logger.info(
+            f"Usage : {self._args[0]} {self._args[1]} " +
+            "<SOLVER> <STUDY>"
+        )
+
+    def run(self):
+        if len(self._args) < 4:
+            return 1
+
+        command = self._args[1]
+        solver_name = self._args[2]
+        study_file = os.path.abspath(
+            self._args[3]
+        )
+
+        try:
+            solver = next(
+                filter(
+                    lambda solver: solver.name == solver_name,
+                    self._conf.solvers
+                )
+            )
+        except Exception as e:
+            logger.error(f"No solver found: {e}")
+            return 2
+
+        study = Study.open(study_file)
+
+        self._solver = solver
+        self._study = study
+
+        logger.info(
+            f"Run {solver.name} ({solver.type}) " +
+            "on study '{study.name}' ({study_file})"
+        )
+
+        # Workdir
+        workdir = os.path.join(
+            os.path.dirname(study.filename),
+            "_PAMHYR_",
+            study.name.replace(" ", "_"),
+            solver.name.replace(" ", "_")
+        )
+        os.makedirs(workdir, exist_ok=True)
+        logger.info(f"Set working dir to {workdir}")
+
+        # Preparate process
+        p = QProcess(None)
+        p.setWorkingDirectory(workdir)
+
+        self._q = Queue()
+
+        # Export and Run
+        logger.info(f"~Export~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
+        solver.export(study, workdir, qlog=self._q)
+
+        while self._q.qsize() != 0:
+            s = self._q.get()
+            logger.info(s)
+
+        if command == "run":
+            logger.info(f"~Run~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
+            solver.run(
+                study,
+                process=p,
+                output_queue=self._q
+            )
+            p.waitForFinished()
+
+        logger.info(f"~End~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
+
+        return 0
+
+
+class ScriptExport(ScriptRun):
+    name = "Export"
+    description = "Export Pamhyr2 study for solver"

src/Scripts/plot_3DST.py

@@ -1,68 +0,0 @@
-# plot_3DST.py -- Pamhyr
-# Copyright (C) 2023  INRAE
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-# -*- coding: utf-8 -*-
-
-# a lancer depuis src
-import sys
-from matplotlib import pyplot as plt
-from Model.Geometry.Reach import Reach
-from numpy import mean
-
-def set_axes_equal(ax):
-    '''Make axes of 3D plot have equal scale so that spheres appear as spheres,
-    cubes as cubes, etc..  This is one possible solution to Matplotlib's
-    ax.set_aspect('equal') and ax.axis('equal') not working for 3D.
-
-    Input
-      ax: a matplotlib axis, e.g., as output from plt.gca().
-    '''
-
-    x_limits = ax.get_xlim3d()
-    y_limits = ax.get_ylim3d()
-    z_limits = ax.get_zlim3d()
-
-    x_range = abs(x_limits[1] - x_limits[0])
-    x_middle = mean(x_limits)
-    y_range = abs(y_limits[1] - y_limits[0])
-    y_middle = mean(y_limits)
-    z_range = abs(z_limits[1] - z_limits[0])
-    z_middle = mean(z_limits)
-
-    # The plot bounding box is a sphere in the sense of the infinity
-    # norm, hence I call half the max range the plot radius.
-    plot_radius = 0.5*max([x_range, y_range, z_range])
-
-    ax.set_xlim3d([x_middle - plot_radius, x_middle + plot_radius])
-    ax.set_ylim3d([y_middle - plot_radius, y_middle + plot_radius])
-    ax.set_zlim3d([z_middle - plot_radius, z_middle + plot_radius])
-
-st_file = sys.argv[1]
-my_reach = Reach(None)
-my_reach.import_geometry(st_file)
-my_reach.compute_guidelines()
-
-ax = plt.figure().add_subplot(projection="3d")
-for x, y, z in zip(my_reach.get_x(), my_reach.get_y(), my_reach.get_z()):
-    ax.plot(x, y, z, color='r', lw=1.)
-for x, y, z in zip(my_reach.get_guidelines_x(), my_reach.get_guidelines_y(), my_reach.get_guidelines_z()):
-    ax.plot(x, y, z, color='b', lw=1.)
-ax.set_xlabel('X')
-ax.set_ylabel('Y')
-ax.set_zlabel('Z')
-plt.tight_layout()
-set_axes_equal(ax)
-plt.show()

src/Solver/ASolver.py

@@ -19,24 +19,32 @@
 import os
 import logging
 
+from tools import timer
+
 try:
+    # Installation allow Unix-like signal
     from signal import SIGTERM, SIGSTOP, SIGCONT
     _signal = True
-except:
+except Exception:
     _signal = False
 
 from enum import Enum
 
 from Model.Except import NotImplementedMethodeError
 
+from Model.Results.Results import Results
+from Model.Results.River.River import River, Reach, Profile
+
 logger = logging.getLogger()
 
+
 class STATUS(Enum):
     NOT_LAUNCHED = -1
     STOPED = 0
     RUNNING = 1
     PAUSED = 5
 
+
 class AbstractSolver(object):
     _type = ""
 
@@ -62,6 +70,9 @@ class AbstractSolver(object):
         self._process = None
         self._output = None
 
+        # Last study running
+        self._study = None
+
     def __str__(self):
         return f"{self._name} : {self._type} : {self._description}"
 
@@ -81,6 +92,7 @@ class AbstractSolver(object):
             ("all_init_time", "000:00:00:00"),
             ("all_final_time", "999:99:00:00"),
             ("all_timestep", "300.0"),
+            ("all_command_line_arguments", ""),
         ]
 
         return lst
@@ -145,9 +157,20 @@ class AbstractSolver(object):
     # Export #
     ##########
 
-    def export(self, study, repertory, qlog = None):
+    def export(self, study, repertory, qlog=None):
         raise NotImplementedMethodeError(self, self.export)
 
+    def cmd_args(self, study):
+        """Return solver command line arguments list
+
+        Returns:
+            Command line arguments list
+        """
+        params = study.river.get_params(self.type)
+        args = params.get_by_key("all_command_line_arguments")
+
+        return args.split(" ")
+
     def input_param(self):
         """Return input command line parameter(s)
 
@@ -156,6 +179,14 @@ class AbstractSolver(object):
         """
         raise NotImplementedMethodeError(self, self.input_param)
 
+    def output_param(self):
+        """Return output command line parameter(s)
+
+        Returns:
+            Returns output parameter(s) string
+        """
+        raise NotImplementedMethodeError(self, self.output_param)
+
     def log_file(self):
         """Return log file name
 
@@ -164,6 +195,15 @@ class AbstractSolver(object):
         """
         raise NotImplementedMethodeError(self, self.log_file)
 
+    ###########
+    # RESULTS #
+    ###########
+
+    @timer
+    def results(self, study, repertory, qlog=None):
+        results = Results(study=study)
+        return results
+
     #######
     # Run #
     #######
@@ -172,11 +212,11 @@ class AbstractSolver(object):
         return os.path.abspath(
             os.path.join(
                 os.path.dirname(__file__),
-                ".."
+                "..", ".."
             )
         )
 
-    def _format_command(self, cmd, path = ""):
+    def _format_command(self, study, cmd, path=""):
         """Format command line
 
         Args:
@@ -187,35 +227,46 @@ class AbstractSolver(object):
             The executable and list of arguments
         """
         # HACK: Works in most case... Trust me i'm an engineer
-
         cmd = cmd.replace("@install_dir", self._install_dir())
-        cmd = cmd.replace("@path", path.replace(" ", "\ "))
+        cmd = cmd.replace("@path", path.replace(" ", "%20"))
         cmd = cmd.replace("@input", self.input_param())
+        cmd = cmd.replace("@output", self.output_param())
         cmd = cmd.replace("@dir", self._process.workingDirectory())
+        cmd = cmd.replace("@args", " ".join(self.cmd_args(study)))
 
         logger.debug(f"! {cmd}")
 
         if cmd[0] == "\"":
             # Command line executable path is between " char
             cmd = cmd.split("\"")
-            exe = cmd[1].replace("\ ", " ")
-            args = "\"".join(cmd[2:]).split(" ")[1:]
+            exe = cmd[1].replace("%20", " ")
+            args = list(
+                filter(
+                    lambda s: s != "",
+                    "\"".join(cmd[2:]).split(" ")[1:]
+                )
+            )
         else:
             # We suppose the command line executable path as no space char
-            cmd = cmd.replace("\ ", "&_&").split(" ")
+            cmd = cmd.replace("\\ ", "&_&").split(" ")
             exe = cmd[0].replace("&_&", " ")
-            args = list(map(lambda s: s.replace("&_&", "\ "), cmd[1:]))
+            args = list(
+                filter(
+                    lambda s: s != "",
+                    map(lambda s: s.replace("&_&", " "), cmd[1:])
+                )
+            )
 
         logger.info(f"! {exe} {args}")
         return exe, args
 
-    def run_input_data_fomater(self):
+    def run_input_data_fomater(self, study):
         if self._cmd_input == "":
-            self._run_next()
+            self._run_next(study)
             return True
 
         cmd = self._cmd_input
-        exe, args = self._format_command(cmd, self._path_input)
+        exe, args = self._format_command(study, cmd, self._path_input)
 
         if not os.path.exists(exe):
             error = f"[ERROR] Path {exe} do not exists"
@@ -228,13 +279,13 @@ class AbstractSolver(object):
 
         return True
 
-    def run_solver(self):
+    def run_solver(self, study):
         if self._cmd_solver == "":
-            self._run_next()
+            self._run_next(study)
             return True
 
         cmd = self._cmd_solver
-        exe, args = self._format_command(cmd, self._path_solver)
+        exe, args = self._format_command(study, cmd, self._path_solver)
 
         if not os.path.exists(exe):
             error = f"[ERROR] Path {exe} do not exists"
@@ -244,17 +295,18 @@ class AbstractSolver(object):
         self._process.start(
             exe, args,
         )
+        self._process.waitForStarted()
 
         self._status = STATUS.RUNNING
         return True
 
-    def run_output_data_fomater(self):
+    def run_output_data_fomater(self, study):
         if self._cmd_output == "":
-            self._run_next()
+            self._run_next(study)
             return True
 
         cmd = self._cmd_output
-        exe, args = self._format_command(cmd, self._path_output)
+        exe, args = self._format_command(study, cmd, self._path_output)
 
         if not os.path.exists(exe):
             error = f"[ERROR] Path {exe} do not exists"
@@ -273,29 +325,32 @@ class AbstractSolver(object):
             for x in s.split('\n'):
                 self._output.put(x)
 
-    def _run_next(self):
+    def _run_next(self, study):
         self._step += 1
         if self._step < len(self._runs):
-            res = self._runs[self._step]()
+            res = self._runs[self._step](study)
             if res is not True:
                 self._output.put(res)
         else:
             self._status = STATUS.STOPED
 
-    def _finished(self, exit_code, exit_status):
+    def _finished(self, study, exit_code, exit_status):
         if self._output is not None:
             self._output.put(exit_code)
 
-        self._run_next()
+        self._run_next(study)
+
+    def run(self, study, process=None, output_queue=None):
+        self._study = study
 
-    def run(self, process = None, output_queue = None):
         if process is not None:
             self._process = process
         if output_queue is not None:
             self._output = output_queue
 
         self._process.readyRead.connect(self._data_ready)
-        self._process.finished.connect(self._finished)
+        self._process.finished.connect(
+            lambda c, s: self._finished(study, c, s))
 
         self._runs = [
             self.run_input_data_fomater,
@@ -304,7 +359,7 @@ class AbstractSolver(object):
         ]
         self._step = 0
         # Run first step
-        res = self._runs[0]()
+        res = self._runs[0](study)
         if res is not True:
             self._output.put(res)
 
@@ -316,14 +371,15 @@ class AbstractSolver(object):
         self._status = STATUS.STOPED
         return True
 
-    def start(self, process = None):
+    def start(self, study, process=None):
         if _signal:
+            # Solver is PAUSED, so continue execution
             if self._status == STATUS.PAUSED:
                 os.kill(self._process.pid(), SIGCONT)
                 self._status = STATUS.RUNNING
                 return True
 
-        self.run(process)
+        self.run(study, process)
         return True
 
     def pause(self):
@@ -331,6 +387,7 @@ class AbstractSolver(object):
             if self._process is None:
                 return False
 
+            # Send SIGSTOP to PAUSED solver
             os.kill(self._process.pid(), SIGSTOP)
             self._status = STATUS.PAUSED
             return True

src/Solver/GenericSolver.py

@@ -20,6 +20,7 @@ from Solver.ASolver import (
     AbstractSolver, STATUS
 )
 
+
 class GenericSolver(AbstractSolver):
     _type = "generic"
 

src/Solver/Mage.py

@@ -17,12 +17,20 @@
 # -*- coding: utf-8 -*-
 
 import os
+import logging
+import numpy as np
 
 from tools import timer
 
 from Solver.ASolver import AbstractSolver
 from Checker.Mage import MageNetworkGraphChecker
 
+from Model.Results.Results import Results
+from Model.Results.River.River import River, Reach, Profile
+
+logger = logging.getLogger()
+
+
 def mage_file_open(filepath, mode):
     f = open(filepath, mode)
 
@@ -32,6 +40,7 @@ def mage_file_open(filepath, mode):
 
     return f
 
+
 class Mage(AbstractSolver):
     _type = "mage"
 
@@ -44,7 +53,6 @@ class Mage(AbstractSolver):
         self._cmd_solver = "@path @input -o @output"
         self._cmd_output = ""
 
-
     @classmethod
     def default_parameters(cls):
         lst = super(Mage, cls).default_parameters()
@@ -54,11 +62,11 @@ class Mage(AbstractSolver):
             ("mage_timestep_tra", "3600"),
             ("mage_timestep_bin", "0"),
             # ("mage_timestep_melissa", "0"),
-            ("mage_implication", "0.70"),
+            ("mage_implicitation", "0.70"),
             ("mage_continuity_discretization", "S"),
             ("mage_qsj_discretization", "B"),
             ("mage_stop_criterion_iterations", "R"),
-            ("mage_iter_type", "0"),
+            ("mage_iteration_type", "0"),
             ("mage_smooth_coef", "0"),
             ("mage_cfl_max", "-1."),
             ("mage_min_height", "0.1"),
@@ -80,8 +88,8 @@ class Mage(AbstractSolver):
     @classmethod
     def checkers(cls):
         lst = [
-            MageNetworkGraphChecker(connectivity = True),
-            MageNetworkGraphChecker(connectivity = False)
+            MageNetworkGraphChecker(connectivity=True),
+            MageNetworkGraphChecker(connectivity=False)
         ]
 
         return lst
@@ -90,19 +98,35 @@ class Mage(AbstractSolver):
     # Export #
     ##########
 
+    def cmd_args(self, study):
+        lst = super(Mage, self).cmd_args(study)
+
+        lst.append("-r")
+
+        return lst
+
     def input_param(self):
-        return "0.REP"
+        name = self._study.name
+        return f"{name}.REP"
+
+    def output_param(self):
+        name = self._study.name
+        return f"{name}.BIN"
 
     def log_file(self):
-        return "0.TRA"
+        name = self._study.name
+        return f"{name}.TRA"
 
     @timer
-    def _export_ST(self, study, repertory, qlog):
+    def _export_ST(self, study, repertory, qlog, name="0"):
         files = []
 
         if qlog is not None:
             qlog.put("Export ST file")
 
+        os.makedirs(os.path.join(repertory, "net"), exist_ok=True)
+        gra_file = f"{name}.GRA"
+
         # Write header
         edges = study.river.edges()
         edges = list(
@@ -117,33 +141,82 @@ class Mage(AbstractSolver):
             if edge._name == "":
                 name = f"Reach_{edge.id}"
 
-            with mage_file_open(os.path.join(repertory, f"{name}.ST"), "w+") as f:
-                files.append(f"{name}.ST")
+            with mage_file_open(
+                    os.path.join(repertory, "net", f"{name}.ST"),
+                    "w+"
+            ) as f:
+                files.append(str(os.path.join("net", f"{name}.ST")))
 
+                cnt_num = 1
                 for profile in edge.reach.profiles:
-                    num = f"{profile.num:>6}"
+                    num = f"{cnt_num:>6}"
                     c1 = f"{profile.code1:>6}"
                     c2 = f"{profile.code2:>6}"
                     t = f"{len(profile.points):>6}"
-                    kp = f"{profile.kp:>13.4f}"
-                    name = profile.name
+                    kp = f"{profile.kp:>12f}"[0:12]
+                    pname = profile.name
+                    if profile.name == "":
+                        # Generate name from profile id prefixed with
+                        # 'p' (and replace space char with '0' char)
+                        pname = f"p{profile.id:>3}".replace(" ", "0")
+                    name = f"{pname:<19}"
 
-                    f.write(f"{num}{c1}{c2}{t}{kp}  {name}\n")
+                    # Generate sediment additional data if available
+                    sediment = ""
+                    if profile.sl is not None:
+                        if not any(filter(lambda f: ".GRA" in f, files)):
+                            files.append(gra_file)
 
+                        # Number of layers
+                        nl = len(profile.sl)
+                        sediment = f" {nl:>3}"
+
+                        # Layers data
+                        for layer in profile.sl.layers:
+                            sediment += (
+                                f" {layer.height:>10} {layer.d50:>10} " +
+                                f"{layer.sigma:>10} " +
+                                f"{layer.critical_constraint:>10}"
+                            )
+
+                    # Profile header line
+                    f.write(f"{num}{c1}{c2}{t} {kp} {name} {sediment}\n")
+                    cnt_num += 1
+
+                    # Points
                     for point in profile.points:
-                        x = f"{point.x:>13.4f}"
-                        y = f"{point.y:>13.4f}"
-                        z = f"{point.z:>13.4f}"
-                        n = point.name
+                        x = f"{point.x:<12f}"[0:12]
+                        y = f"{point.y:<12f}"[0:12]
+                        z = f"{point.z:<12f}"[0:12]
+                        n = f"{point.name:<3}"
 
-                        f.write(f"{x}{y}{z} {n}\n")
+                        # Generate sediment additional data if available
+                        sediment = ""
+                        prev = point.z
+                        if point.sl is not None:
+                            # Number of layers
+                            nl = len(point.sl)
+                            sediment = f"{nl:>3}"
 
+                            # Layers data
+                            for layer in point.sl.layers:
+                                prev = round(prev - layer.height, 5)
+                                sediment += (
+                                    f" {prev:>10} {layer.d50:>10} " +
+                                    f"{layer.sigma:>10} " +
+                                    f"{layer.critical_constraint:>10}"
+                                )
+
+                        # Point line
+                        f.write(f"{x} {y} {z} {n} {sediment}\n")
+
+                    # Profile last line
                     f.write(f"     999.9990     999.9990     999.9990\n")
 
         return files
 
     @timer
-    def _export_BC(self, t, bounds, repertory, qlog):
+    def _export_BC(self, t, bounds, repertory, qlog, name="0"):
         files = []
 
         if len(bounds) == 0:
@@ -152,8 +225,8 @@ class Mage(AbstractSolver):
         if qlog is not None:
             qlog.put(f"Export {t} file")
 
-        with mage_file_open(os.path.join(repertory, f"0.{t}"), "w+") as f:
-            files.append(f"0.{t}")
+        with mage_file_open(os.path.join(repertory, f"{name}.{t}"), "w+") as f:
+            files.append(f"{name}.{t}")
 
             for bound in bounds:
                 name = f"{bound.node.id:3}".replace(" ", "x")
@@ -163,18 +236,25 @@ class Mage(AbstractSolver):
                 f.write(f"*{header[0]:>9}|{header[1]:>10}\n")
 
                 for d in bound.data:
-                    f.write(f"{d[0]:10.3f}{d[1]:10.3f}\n")
+                    v0 = d[0]
+                    v1 = d[1]
+
+                    if t in ["HYD", "QSO", "LIM"]:
+                        v0 /= 60  # Convert first column to minute
+
+                    f.write(f"{v0:10}{v1:10}\n")
 
         return files
 
     @timer
-    def _export_bound_cond(self, study, repertory, qlog):
+    def _export_bound_cond(self, study, repertory, qlog, name="0"):
         files = []
         lst = study.river.boundary_condition
 
         AVA = []
         HYD = []
         LIM = []
+        QSO = []
 
         for tab in ["liquid", "solid", "suspenssion"]:
             for bound in lst.get_tab(tab):
@@ -184,22 +264,28 @@ class Mage(AbstractSolver):
                     HYD.append(bound)
                 elif bound.bctype == "TZ":
                     LIM.append(bound)
+                elif bound.bctype == "SL":
+                    QSO.append(bound)
 
-        files = files + self._export_BC("AVA", AVA, repertory,  qlog)
-        files = files + self._export_BC("HYD", HYD, repertory,  qlog)
-        files = files + self._export_BC("LIM", LIM, repertory,  qlog)
+        files = files + self._export_BC("AVA", AVA, repertory, qlog, name=name)
+        files = files + self._export_BC("HYD", HYD, repertory, qlog, name=name)
+        files = files + self._export_BC("LIM", LIM, repertory, qlog, name=name)
+        files = files + self._export_QSO(QSO, repertory, qlog, name=name)
 
         return files
 
     # @timer
-    # def _export_LC(self, lateral, repertory, qlog):
+    # def _export_LC(self, lateral, repertory, qlog, name="0"):
     #     files = []
 
     #     if qlog is not None:
     #         qlog.put(f"Export LAT file")
 
-    #     with mage_file_open(os.path.join(repertory, f"0.LAT"), "w+") as f:
-    #         files.append(f"0.LAT")
+    #     with mage_file_open(
+    #             os.path.join(repertory, f"{name}.LAT"),
+    #             "w+"
+    #     ) as f:
+    #         files.append(f"{name}.LAT")
 
     #         name = f"{lateral.node.id:3}".replace(" ", "x")
     #         f.write(f"* {lateral.node.name} ({name}) {lateral.bctype}\n")
@@ -208,12 +294,12 @@ class Mage(AbstractSolver):
     #         f.write(f"*{header[0]:>9}|{header[1]:>10}\n")
 
     #         for d in lateral.data:
-    #             f.write(f"{d[0]:10.3f}{d[1]:10.3f}\n")
+    #             f.write(f"{d[0]:1{name}.3f}{d[1]:10.3f}\n")
 
     #     return files
 
     # @timer
-    # def _export_lateral_contrib(self, study, repertory, qlog):
+    # def _export_lateral_contrib(self, study, repertory, qlog, name="0"):
     #     files = []
     #     lst = study.river.lateral_contribution
 
@@ -224,15 +310,15 @@ class Mage(AbstractSolver):
     #     return files
 
     @timer
-    def _export_RUG(self, study, repertory, qlog):
+    def _export_RUG(self, study, repertory, qlog, name="0"):
         files = []
 
         if qlog is not None:
             qlog.put("Export RUG file")
 
         # Write header
-        with mage_file_open(os.path.join(repertory, "0.RUG"), "w+") as f:
-            files.append("0.RUG")
+        with mage_file_open(os.path.join(repertory, f"{name}.RUG"), "w+") as f:
+            files.append(f"{name}.RUG")
 
             edges = study.river.edges()
             edges = list(
@@ -265,14 +351,14 @@ class Mage(AbstractSolver):
         return files
 
     @timer
-    def _export_INI(self, study, repertory, qlog):
+    def _export_INI(self, study, repertory, qlog, name="0"):
         files = []
 
         if qlog is not None:
             qlog.put("Export INI file")
 
         # Write header
-        with mage_file_open(os.path.join(repertory, "0.INI"), "w+") as f:
+        with mage_file_open(os.path.join(repertory, f"{name}.INI"), "w+") as f:
             has_ini = False
             id = 1
             reachs = study.river.edges()
@@ -310,37 +396,67 @@ class Mage(AbstractSolver):
                 id += 1
 
         if has_ini:
-            files.append("0.INI")
+            files.append(f"{name}.INI")
         return files
 
     @timer
-    def _export_REP(self, study, repertory, files, qlog):
+    def _export_REP(self, study, repertory, files, qlog, name="0"):
         if qlog is not None:
             qlog.put("Export REP file")
 
         # Write header
-        with mage_file_open(os.path.join(repertory, f"0.REP"), "w+") as f:
+        with mage_file_open(os.path.join(repertory, f"{name}.REP"), "w+") as f:
             f.write("confirmation=non\n")
 
             for file in files:
                 EXT = file.split('.')[1]
 
-                f.write(f"{EXT} {file}\n")
+                if EXT not in ["ST", "GRA"]:
+                    f.write(f"{EXT} {file}\n")
 
             f.write("* OUTPUT\n")
-            f.write(f"TRA 0.TRA\n")
-            f.write(f"BIN 0.BIN\n")
+            f.write(f"TRA {name}.TRA\n")
+            f.write(f"BIN {name}.BIN\n")
+
+            for file in files:
+                EXT = file.split('.')[1]
+
+                if EXT in ["GRA"]:
+                    f.write(f"{EXT} {file}\n")
 
     @timer
-    def export(self, study, repertory, qlog = None):
-        self._export_ST(study, repertory, qlog)
+    def export(self, study, repertory, qlog=None):
+        self._study = study
+        name = study.name.replace(" ", "_")
+
+        self._export_ST(study, repertory, qlog, name=name)
 
         return True
 
+    ###########
+    # RESULTS #
+    ###########
+
+    def read_bin(self, study, repertory, results, qlog=None, name="0"):
+        return
+
+    @timer
+    def results(self, study, repertory, qlog=None, name="0"):
+        results = Results(
+            study=study,
+            solver=self,
+            repertory=repertory,
+            name=name,
+        )
+        self.read_bin(study, repertory, results, qlog, name=name)
+
+        return results
+
 ##########
 # MAGE 7 #
 ##########
 
+
 class Mage7(Mage):
     _type = "mage7"
 
@@ -359,6 +475,7 @@ class Mage7(Mage):
 # MAGE 8 #
 ##########
 
+
 class Mage8(Mage):
     _type = "mage8"
 
@@ -376,21 +493,43 @@ class Mage8(Mage):
         i = names.index("mage_precision_reduction_factor_Q")
         lst.insert(i+1, ("mage_precision_reduction_factor_r", "1"))
 
+        # Mage parameter for sediment module (added in DB 0.0.4)
+        lst.append(("mage_sediment_masse_volumique", "2650.0"))
+        lst.append(("mage_sediment_angle_repos", "40.0"))
+        lst.append(("mage_sediment_porosity", "0.40"))
+        lst.append(("mage_distance_Han", "0.0"))
+        lst.append(("mage_distance_chargement_d50", "100.0"))
+        lst.append(("mage_distance_chargement_sigma", "100.0"))
+        lst.append(("mage_methode_modification_geometrie", "1"))
+        lst.append(("mage_shields_critique", "1"))
+        lst.append(("mage_shields_correction", "1"))
+        lst.append(("mage_capacite_solide", "1"))
+        lst.append(("mage_pas_de_temps_charriage", "1"))
+        lst.append(("mage_facteur_multiplicateur", "1.0"))
+
         return lst
 
     ##########
     # Export #
     ##########
 
+    def cmd_args(self, study):
+        lst = super(Mage8, self).cmd_args(study)
+
+        if study.river.has_sediment():
+            lst.append("-c=3")
+
+        return lst
+
     @timer
-    def _export_PAR(self, study, repertory, qlog = None):
+    def _export_PAR(self, study, repertory, qlog=None, name="0"):
         files = []
 
         if qlog is not None:
             qlog.put("Export PAR file")
 
-        with mage_file_open(os.path.join(repertory, "0.PAR"), "w+") as f:
-            files.append("0.PAR")
+        with mage_file_open(os.path.join(repertory, f"{name}.PAR"), "w+") as f:
+            files.append(f"{name}.PAR")
 
             params = study.river.get_params(self.type).parameters
             for p in params:
@@ -399,20 +538,25 @@ class Mage8(Mage):
                         .replace("mage_", "")
                 value = p.value
 
-                f.write(f"{name} {value}\n")
+                if name in ["command_line_arguments"]:
+                    continue
 
+                if name == "mage_compute_reach_volume_balance":
+                    value = "O" if value == "y" else "N"
+
+                f.write(f"{name} {value}\n")
 
         return files
 
     @timer
-    def _export_NET(self, study, repertory, qlog = None):
+    def _export_NET(self, study, repertory, qlog=None, name="0"):
         files = []
 
         if qlog is not None:
             qlog.put("Export NET file")
 
-        with mage_file_open(os.path.join(repertory, "0.NET"), "w+") as f:
-            files.append("0.NET")
+        with mage_file_open(os.path.join(repertory, f"{name}.NET"), "w+") as f:
+            files.append(f"{name}.NET")
 
             edges = study.river.edges()
             edges = list(
@@ -431,22 +575,363 @@ class Mage8(Mage):
 
                 n1 = f"{e.node1.id:3}".replace(" ", "x")
                 n2 = f"{e.node2.id:3}".replace(" ", "x")
-                file = name + ".ST"
+                file = os.path.join("net", name + ".ST")
 
                 f.write(f"{id} {n1} {n2} {file}\n")
 
         return files
 
     @timer
-    def export(self, study, repertory, qlog = None):
+    def _export_QSO(self, bounds, repertory, qlog, name="0"):
         files = []
 
-        self._export_ST(study, repertory, qlog)
-        files = files + self._export_PAR(study, repertory, qlog)
-        files = files + self._export_NET(study, repertory, qlog)
-        files = files + self._export_bound_cond(study, repertory, qlog)
-        files = files + self._export_RUG(study, repertory, qlog)
-        files = files + self._export_INI(study, repertory, qlog)
-        self._export_REP(study, repertory, files, qlog)
+        if len(bounds) == 0:
+            return files
+
+        if qlog is not None:
+            qlog.put(f"Export QSO file")
+
+        with mage_file_open(os.path.join(repertory, f"{name}.QSO"), "w+") as f:
+            files.append(f"{name}.QSO")
+
+            for bound in bounds:
+                # File header
+                name = f"{bound.node.id:3}".replace(" ", "x")
+                f.write(f"* {bound.node.name} ({name}) {bound.bctype}\n")
+
+                d50 = bound.d50
+                sigma = bound.sigma
+
+                if len(bound.data) == 0:
+                    f.write(f"${name} {d50} {sigma} default\n")
+                else:
+                    f.write(f"${name} {d50} {sigma}\n")
+
+                # Table header
+                header = bound.header
+                f.write(f"*{header[0]:>9}|{header[1]:>10}\n")
+
+                # Data
+                for d in bound.data:
+                    f.write(f"{d[0]:10.3f}{d[1]:10.3f}\n")
+
+        return files
+
+    @timer
+    def export(self, study, repertory, qlog=None, name="0"):
+        self._study = study
+        name = study.name.replace(" ", "_")
+
+        files = []
+
+        files = self._export_ST(study, repertory, qlog, name=name)
+        files = files + self._export_PAR(study, repertory, qlog, name=name)
+        files = files + self._export_NET(study, repertory, qlog, name=name)
+        files = files + \
+            self._export_bound_cond(study, repertory, qlog, name=name)
+        files = files + self._export_RUG(study, repertory, qlog, name=name)
+        files = files + self._export_INI(study, repertory, qlog, name=name)
+        self._export_REP(study, repertory, files, qlog, name=name)
 
         return True
+
+    ###########
+    # RESULTS #
+    ###########
+
+    @timer
+    def read_bin(self, study, repertory, results, qlog=None, name="0"):
+        fname = os.path.join(repertory, f"{name}.BIN")
+        logger.info(f"read_bin: Start reading '{fname}' ...")
+
+        with mage_file_open(fname, "r") as f:
+            def newline(): return np.fromfile(f, dtype=np.int32, count=1)
+            def endline(): return np.fromfile(f, dtype=np.int32, count=1)
+
+            def read_int(size): return np.fromfile(
+                f, dtype=np.int32, count=size)
+
+            def read_float(size): return np.fromfile(
+                f, dtype=np.float32, count=size)
+
+            def read_float64(size): return np.fromfile(
+                f, dtype=np.float64, count=size)
+
+            # Meta data (1st line)
+            newline()
+
+            data = read_int(3)
+
+            nb_reach = data[0]
+            nb_profile = data[1]
+            mage_version = data[2]
+
+            logger.debug(f"read_bin: nb_reach = {nb_reach}")
+            logger.debug(f"read_bin: nb_profile = {nb_profile}")
+            logger.debug(f"read_bin: mage_version = {mage_version}")
+
+            if mage_version <= 80:
+                msg = (
+                    "Read BIN files: " +
+                    f"Possible incompatible mage version '{mage_version}', " +
+                    "please check your solver configuration..."
+                )
+                logger.warning(msg)
+
+                if qlog is not None:
+                    qlog.put("[WARNING] " + msg)
+
+            results.set("solver_version", f"Mage8 ({mage_version})")
+            results.set("nb_reach", f"{nb_reach}")
+            results.set("nb_profile", f"{nb_profile}")
+
+            endline()
+
+            # Reach information (2nd line)
+            newline()
+
+            reachs = []
+            iprofiles = {}
+            reach_offset = {}
+
+            data = read_int(2*nb_reach)
+
+            for i in range(nb_reach):
+                # Add results reach to reach list
+                r = results.river.add(i)
+                reachs.append(r)
+
+                # ID of first and last reach profiles
+                i1 = data[2*i] - 1
+                i2 = data[2*i+1] - 1
+
+                # Add profile id correspondance to reach
+                key = (i1, i2)
+                iprofiles[key] = r
+
+                # Profile ID offset
+                reach_offset[r] = i1
+
+            logger.debug(f"read_bin: iprofiles = {iprofiles}")
+
+            endline()
+
+            # X (3rd line)
+            newline()
+            _ = read_float(nb_profile)
+            endline()
+
+            # Z and Y (4th line)
+            newline()
+            _ = read_float(3*nb_profile)
+            endline()
+
+            # Data
+            newline()
+
+            def ip_to_r(i): return iprofiles[
+                next(
+                    filter(
+                        lambda k: k[0] <= i <= k[1],
+                        iprofiles
+                    )
+                )
+            ]
+            def ip_to_ri(r, i): return i - reach_offset[r]
+
+            ts = set()
+            end = False
+            while not end:
+                n = read_int(1)[0]
+                timestamp = read_float64(1)[0]
+                key = bytearray(np.fromfile(
+                    f, dtype=np.byte, count=1)).decode()
+                data = read_float(n)
+
+                logger.debug(f"read_bin: timestamp = {timestamp} sec")
+                ts.add(timestamp)
+
+                if key in ["Z", "Q"]:
+                    for i, d in enumerate(data):
+                        # Get reach corresponding to profile ID
+                        reach = ip_to_r(i)
+                        # Get profile id in reach
+                        ri = ip_to_ri(reach, i)
+
+                        # Set data for profile RI
+                        reach.set(ri, timestamp, key, d)
+
+                endline()
+                end = newline().size <= 0
+
+            logger.debug(reachs[0].profiles[0]._data)
+            results.set("timestamps", ts)
+            logger.info(f"read_bin: ... end with {len(ts)} timestamp read")
+
+    @timer
+    def read_gra(self, study, repertory, results, qlog=None, name="0"):
+        if not study.river.has_sediment():
+            return
+
+        fname = os.path.join(repertory, f"{name}.GRA")
+        logger.info(f"read_gra: Start reading '{fname}' ...")
+
+        with mage_file_open(fname, "r") as f:
+            def newline(): return np.fromfile(f, dtype=np.int32, count=1)
+            def endline(): return np.fromfile(f, dtype=np.int32, count=1)
+
+            def read_int(size): return np.fromfile(
+                f, dtype=np.int32, count=size)
+
+            def read_float(size): return np.fromfile(
+                f, dtype=np.float32, count=size)
+
+            def read_float64(size): return np.fromfile(
+                f, dtype=np.float64, count=size)
+
+            # Meta data (1st line)
+            newline()
+
+            data = read_int(3)
+
+            nb_reach = data[0]
+            nb_profile = data[1]
+            mage_version = data[2]
+
+            logger.debug(f"read_gra: nb_reach = {nb_reach}")
+            logger.debug(f"read_gra: nb_profile = {nb_profile}")
+            logger.debug(f"read_gra: mage_version = {mage_version}")
+
+            if mage_version <= 80:
+                msg = (
+                    "Read GRA files: " +
+                    f"Possible incompatible mage version '{mage_version}', " +
+                    "please check your solver configuration..."
+                )
+                logger.warning(msg)
+
+                if qlog is not None:
+                    qlog.put("[WARNING] " + msg)
+
+            results.set("gra_solver_version", f"Mage8 ({mage_version})")
+            results.set("gra_nb_reach", f"{nb_reach}")
+            results.set("gra_nb_profile", f"{nb_profile}")
+
+            endline()
+
+            # Reach information (2nd line)
+            newline()
+
+            reachs = []
+            iprofiles = {}
+            reach_offset = {}
+
+            data = read_int(2*nb_reach)
+
+            for i in range(nb_reach):
+                # Get results reach to reach list
+                r = results.river.reach(i)
+                reachs.append(r)
+
+                # ID of first and last reach profiles
+                i1 = data[2*i] - 1
+                i2 = data[2*i+1] - 1
+
+                # Add profile id correspondance to reach
+                key = (i1, i2)
+                iprofiles[key] = r
+
+                # Profile ID offset
+                reach_offset[r] = i1
+
+            logger.debug(f"read_gra: iprofiles = {iprofiles}")
+
+            endline()
+
+            # X (3rd line)
+            newline()
+            _ = read_float(nb_profile)
+            endline()
+
+            # npts (4th line)
+            newline()
+            _ = read_int(nb_profile)
+            endline()
+
+            # Data
+            def ip_to_r(i): return iprofiles[
+                next(
+                    filter(
+                        lambda k: k[0] <= i <= k[1],
+                        iprofiles
+                    )
+                )
+            ]
+            def ip_to_ri(r, i): return i - reach_offset[r]
+
+            ts = set()
+            ind = 0
+            end = False
+
+            newline()
+            while not end:
+                n = read_int(1)[0]
+                timestamp = read_float64(1)[0]
+
+                logger.debug(f"read_gra: timestamp = {timestamp} sec")
+                ts.add(timestamp)
+
+                endline()
+
+                for i in range(n):
+                    newline()
+                    nsl = read_int(1)[0]
+                    endline()
+
+                    # Get current profile id
+                    reach = ip_to_r(i)
+                    ri = ip_to_ri(reach, i)
+
+                    if nsl > 1:
+                        logger.warning(
+                            "read_gra: " +
+                            "Multiple sediment layers for one profile " +
+                            "is not implemented yet..."
+                        )
+
+                    for j in range(nsl):
+                        newline()
+                        nl = read_int(1)[0]
+                        endline()
+
+                        sl = []
+
+                        for k in range(nl):
+                            newline()
+                            data = read_float64(3)
+                            endline()
+
+                            h = data[0]
+                            d50 = data[1]
+                            sigma = data[2]
+
+                            sl.append((h, d50, sigma))
+
+                        reach.set(ri, timestamp, "sl", sl)
+
+                ind += 1
+                end = newline().size <= 0
+
+            logger.debug(reachs[0].profiles[0]._data)
+            results.set("timestamps", ts)
+            logger.info(f"read_gra: ... end with {len(ts)} timestamp read")
+
+    @timer
+    def results(self, study, repertory, qlog=None):
+        self._study = study
+        name = study.name.replace(" ", "_")
+
+        results = super(Mage8, self).results(study, repertory, qlog, name=name)
+        self.read_gra(study, repertory, results, qlog, name=name)
+
+        return results

src/Solver/Solvers.py

@@ -24,9 +24,9 @@ from Solver.Mage import Mage7, Mage8
 _translate = QCoreApplication.translate
 
 solver_long_name = {
-    "generic": _translate("Solvers", "Generic"),
-    # "mage7": _translate("Solvers", "Mage version 7"),
-    "mage8": _translate("Solvers", "Mage version 8"),
+    "generic": "Generic",
+    # "mage7": "Mage v7",
+    "mage8": "Mage v8",
 }
 
 solver_type_list = {

src/View/About/Window.py

@@ -19,14 +19,18 @@
 import os
 import logging
 
-from View.ASubWindow import ASubWindow
+from View.Tools.PamhyrWindow import PamhyrDialog
 
 from PyQt5.QtCore import QCoreApplication
 
 _translate = QCoreApplication.translate
 logger = logging.getLogger()
 
-class AboutWindow(ASubWindow):
+
+class AboutWindow(PamhyrDialog):
+    _pamhyr_ui = "about"
+    _pamhyr_name = "About"
+
     def _path_file(self, filename):
         return os.path.abspath(
             os.path.join(
@@ -35,10 +39,14 @@ class AboutWindow(ASubWindow):
             )
         )
 
-
-    def __init__(self, title="About", parent=None):
-        super(AboutWindow, self).__init__(name=title, ui="about", parent=parent)
-        self.ui.setWindowTitle(title)
+    def __init__(self, study=None, config=None, parent=None):
+        super(AboutWindow, self).__init__(
+            title=_translate("About", "About"),
+            study=study,
+            config=config,
+            options=[],
+            parent=parent
+        )
 
         # Version
         with open(self._path_file("VERSION"), "r") as f:

src/View/BoundaryCondition/Edit/Plot.py

@@ -16,31 +16,43 @@
 
 # -*- coding: utf-8 -*-
 
+import logging
+
 from datetime import datetime
 
 from tools import timer, trace
-from View.Plot.APlot import APlot
+from View.Tools.PamhyrPlot import PamhyrPlot
 
 from PyQt5.QtCore import (
     QCoreApplication
 )
 
-from View.BoundaryCondition.Edit.translate import *
+from View.BoundaryCondition.Edit.translate import BCETranslate
 
 _translate = QCoreApplication.translate
 
-class Plot(APlot):
-    def __init__(self, canvas=None, data=None,
-                 mode = "time", toolbar=None):
+logger = logging.getLogger()
+
+
+class Plot(PamhyrPlot):
+    def __init__(self, mode="time", data=None,
+                 trad=None, canvas=None, toolbar=None,
+                 parent=None):
         super(Plot, self).__init__(
             canvas=canvas,
+            trad=trad,
             data=data,
-            toolbar=toolbar
+            toolbar=toolbar,
+            parent=parent
         )
 
+        self._table_headers = self._trad.get_dict("table_headers")
         self._mode = mode
 
     def custom_ticks(self):
+        if self.data.header[0] != "time":
+            return
+
         t0 = datetime.fromtimestamp(0)
         nb = len(self.data.data)
         mod = int(nb / 5)
@@ -61,8 +73,8 @@ class Plot(APlot):
                 map(
                     lambda v: str(
                         datetime.fromtimestamp(v[0]) - t0
-                    ).split(",")[0]\
-                    .replace("days", _translate("BoundaryCondition", "days"))\
+                    ).split(",")[0]
+                    .replace("days", _translate("BoundaryCondition", "days"))
                     .replace("day", _translate("BoundaryCondition", "day")),
                     fx
                 )
@@ -77,7 +89,6 @@ class Plot(APlot):
 
         self.canvas.axes.set_xticks(ticks=xx, labels=xt, rotation=45)
 
-
     @timer
     def draw(self):
         self.canvas.axes.cla()
@@ -102,22 +113,22 @@ class Plot(APlot):
         # Plot label
         header = self.data.header
         self.canvas.axes.set_xlabel(
-            table_headers[header[0]], color='black', fontsize=10
+            self._table_headers[header[0]], color='black', fontsize=10
         )
         self.canvas.axes.set_ylabel(
-            table_headers[header[1]], color='black', fontsize=10
+            self._table_headers[header[1]], color='black', fontsize=10
         )
 
         self.canvas.axes.autoscale_view(True, True, True)
         self.canvas.figure.tight_layout()
         self.canvas.figure.canvas.draw_idle()
-        #self.toolbar.update()
+        # self.toolbar.update()
 
         self._init = True
 
     @timer
     def update(self, ind=None):
-        if self._init == False:
+        if not self._init:
             self.draw()
             return
 

src/View/BoundaryCondition/Edit/Table.py

@@ -23,8 +23,7 @@ from datetime import date, time, datetime, timedelta
 
 from tools import trace, timer
 
-from View.ASubWindow import ASubMainWindow, AWidget
-from View.ListedSubWindow import ListedSubWindow
+from View.Tools.PamhyrTable import PamhyrTableModel
 
 from PyQt5.QtCore import (
     Qt, QVariant, QAbstractTableModel,
@@ -47,131 +46,13 @@ from View.BoundaryCondition.Edit.UndoCommand import (
     SortCommand, MoveCommand, PasteCommand,
     DuplicateCommand,
 )
-from View.BoundaryCondition.Edit.translate import *
 
 _translate = QCoreApplication.translate
 
 logger = logging.getLogger()
 
-class ExtendedTimeEdit(AWidget):
-    def __init__(self, parent=None):
-        super(ExtendedTimeEdit, self).__init__(
-            ui="extendedTimeEdit",
-            parent=parent
-        )
-        self.parent = parent
-
-        self.spinBox_days = self.find(QSpinBox, "spinBox_days")
-        self.timeEdit = self.find(QTimeEdit, "timeEdit")
-
-    def set_time(self, time):
-        days = 0
-        stime = time
-
-        # if ',' in time, time format is 'DD days, HH:MM:SS',
-        # otherelse is 'HH:MM:SS'
-        if "," in time:
-            s = time.strip().split(" ")
-            days = int(s[0])
-            stime = s[-1]
-
-        qtime = QTime.fromString(
-            stime,
-            "h:mm:ss"
-        )
-        self.spinBox_days.setValue(days)
-        self.timeEdit.setTime(qtime)
-
-    def get_time(self):
-        days = self.spinBox_days.value()
-        time = self.timeEdit.time().toPyTime()
-        secs = (
-            (time.hour * 3600) +
-            (time.minute * 60) +
-            time.second
-        )
-
-        return timedelta(days=days, seconds=secs)
-
-class ExtendedDateTimeEdit(AWidget):
-    def __init__(self, parent=None):
-        super(ExtendedDateTimeEdit, self).__init__(
-            ui="extendedDateTimeEdit",
-            parent=parent
-        )
-        self.parent = parent
-
-        self.dateTimeEdit = self.find(QDateTimeEdit, "dateTimeEdit")
-
-    def set_time(self, time):
-        qdatetime = QDateTime.fromString(
-            time,
-            "yyyy-MM-dd hh:mm:ss"
-        )
-        self.dateTimeEdit.setDateTime(qdatetime)
-
-    def get_time(self):
-        time = self.dateTimeEdit.dateTime().toPyDateTime()
-        return time
-
-class ExTimeDelegate(QItemDelegate):
-    def __init__(self, data=None, mode="time", parent=None):
-        super(ExTimeDelegate, self).__init__(parent)
-
-        self._data = data
-        self._mode = mode
-
-    def createEditor(self, parent, option, index):
-        if self._mode == "time":
-            self.editor = ExtendedTimeEdit(parent=parent)
-        else:
-            self.editor = ExtendedDateTimeEdit(parent=parent)
-        value = index.data(Qt.DisplayRole)
-        self.editor.set_time(value)
-        logger.debug(str(value))
-        return self.editor
-
-    def setModelData(self, editor, model, index):
-        time = editor.get_time()
-        if self._mode == "time":
-            model.setData(index, int(time.total_seconds()))
-        else:
-            logger.debug(str(time.timestamp()))
-            model.setData(index, int(time.timestamp()))
-        editor.close()
-        editor.deleteLater()
-
-    def updateEditorGeometry(self, editor, option, index):
-        r = QRect(option.rect)
-        if self.editor.windowFlags() & Qt.Popup and editor.parent() is not None:
-            r.setTopLeft(self.editor.parent().mapToGlobal(r.topLeft()))
-        editor.setGeometry(r)
-
-    @pyqtSlot()
-    def currentItemChanged(self):
-        self.commitData.emit(self.sender())
-
-
-class TableModel(QAbstractTableModel):
-    def __init__(self, data=None, mode="time", undo=None):
-        super(QAbstractTableModel, self).__init__()
-        self._headers = data.header
-        self._data = data
-        self._mode = mode
-        self._undo = undo
-
-    def flags(self, index):
-        options = Qt.ItemIsEnabled | Qt.ItemIsSelectable
-        options |= Qt.ItemIsEditable
-
-        return options
-
-    def rowCount(self, parent):
-        return len(self._data)
-
-    def columnCount(self, parent):
-        return len(self._headers)
 
+class TableModel(PamhyrTableModel):
     def data(self, index, role):
         if role == Qt.TextAlignmentRole:
             return Qt.AlignHCenter | Qt.AlignVCenter
@@ -189,7 +70,7 @@ class TableModel(QAbstractTableModel):
             if self._data.get_type_column(column) == float:
                 value = f"{v:.4f}"
             elif self._data.header[column] == "time":
-                if self._mode == "time":
+                if self._opt_data == "time":
                     t0 = datetime.fromtimestamp(0)
                     t = datetime.fromtimestamp(v)
                     value = str(t - t0)
@@ -200,12 +81,6 @@ class TableModel(QAbstractTableModel):
 
         return value
 
-    def headerData(self, section, orientation, role):
-        if role == Qt.ItemDataRole.DisplayRole and orientation == Qt.Orientation.Horizontal:
-            return table_headers[self._headers[section]]
-
-        return QVariant()
-
     def setData(self, index, value, role=Qt.EditRole):
         if not index.isValid() or role != Qt.EditRole:
             return False
@@ -315,12 +190,3 @@ class TableModel(QAbstractTableModel):
 
         self.layoutAboutToBeChanged.emit()
         self.layoutChanged.emit()
-
-
-    def undo(self):
-        self._undo.undo()
-        self.layoutChanged.emit()
-
-    def redo(self):
-        self._undo.redo()
-        self.layoutChanged.emit()

src/View/BoundaryCondition/Edit/UndoCommand.py

@@ -16,6 +16,8 @@
 
 # -*- coding: utf-8 -*-
 
+import logging
+
 from copy import deepcopy
 from tools import trace, timer
 
@@ -25,6 +27,9 @@ from PyQt5.QtWidgets import (
 
 from Model.BoundaryCondition.BoundaryCondition import BoundaryCondition
 
+logger = logging.getLogger()
+
+
 class SetDataCommand(QUndoCommand):
     def __init__(self, data, index, column, new_value):
         QUndoCommand.__init__(self)
@@ -42,6 +47,33 @@ class SetDataCommand(QUndoCommand):
     def redo(self):
         self._data._set_i_c_v(self._index, self._column, self._new)
 
+
+class SetMetaDataCommand(QUndoCommand):
+    def __init__(self, data, column, new_value):
+        QUndoCommand.__init__(self)
+
+        self._data = data
+        self._column = column
+        if self._column == "d50":
+            self._old = self._data.d50
+        elif self._column == "sigma":
+            self._old = self._data.sigma
+
+        self._new = float(new_value)
+
+    def undo(self):
+        if self._column == "d50":
+            self._data.d50 = self._old
+        elif self._column == "sigma":
+            self._data.sigma = self._old
+
+    def redo(self):
+        if self._column == "d50":
+            self._data.d50 = self._new
+        elif self._column == "sigma":
+            self._data.sigma = self._new
+
+
 class AddCommand(QUndoCommand):
     def __init__(self, data, index):
         QUndoCommand.__init__(self)
@@ -59,6 +91,7 @@ class AddCommand(QUndoCommand):
         else:
             self._data.insert(self._index, self._new)
 
+
 class DelCommand(QUndoCommand):
     def __init__(self, data, rows):
         QUndoCommand.__init__(self)
@@ -78,6 +111,7 @@ class DelCommand(QUndoCommand):
     def redo(self):
         self._data.delete_i(self._rows)
 
+
 class SortCommand(QUndoCommand):
     def __init__(self, data, _reverse):
         QUndoCommand.__init__(self)