git: Update 'full-requirement.txt'.

(cherry picked from commit 674247db09)

.gitignore

@@ -1,6 +1,7 @@
 ### CUSTOM ###
 
 *.exe
+*.msi
 *.tar.xz
 *.zip
 *.spec
@@ -8,16 +9,47 @@
 *.class
 
 tmp
+mage8
+adists
 
+*.tar
 *.tar.*
+*.tgz
 *.zip
 
+*.html
+*.pdf
+*.odt
+
+!doc/**/*.pdf
+
+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
+
+mage8/
+adists/
+rubarbe/
+
+linux/
+windows/
+
+install/
+
 ### END CUSTOM ###
 
 # Created by https://www.toptal.com/developers/gitignore/api/python
@@ -249,6 +281,7 @@ flycheck_*.el
 
 
 # End of https://www.toptal.com/developers/gitignore/api/emacs
+
 # Created by https://www.toptal.com/developers/gitignore/api/qt
 # Edit at https://www.toptal.com/developers/gitignore?templates=qt
 
@@ -309,3 +342,548 @@ 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
+
+# Created by https://www.toptal.com/developers/gitignore/api/intellij
+# Edit at https://www.toptal.com/developers/gitignore?templates=intellij
+
+### Intellij ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# SonarLint plugin
+.idea/sonarlint/
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### Intellij Patch ###
+# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
+
+# *.iml
+# modules.xml
+# .idea/misc.xml
+# *.ipr
+
+# Sonarlint plugin
+# https://plugins.jetbrains.com/plugin/7973-sonarlint
+.idea/**/sonarlint/
+
+# SonarQube Plugin
+# https://plugins.jetbrains.com/plugin/7238-sonarqube-community-plugin
+.idea/**/sonarIssues.xml
+
+# Markdown Navigator plugin
+# https://plugins.jetbrains.com/plugin/7896-markdown-navigator-enhanced
+.idea/**/markdown-navigator.xml
+.idea/**/markdown-navigator-enh.xml
+.idea/**/markdown-navigator/
+
+# Cache file creation bug
+# See https://youtrack.jetbrains.com/issue/JBR-2257
+.idea/$CACHE_FILE$
+
+# CodeStream plugin
+# https://plugins.jetbrains.com/plugin/12206-codestream
+.idea/codestream.xml
+
+# Azure Toolkit for IntelliJ plugin
+# https://plugins.jetbrains.com/plugin/8053-azure-toolkit-for-intellij
+.idea/**/azureSettings.xml
+
+# End of https://www.toptal.com/developers/gitignore/api/intellij
+
+# Created by https://www.toptal.com/developers/gitignore/api/visualstudiocode
+# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+.ionide
+
+# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode
+
+# Created by https://www.toptal.com/developers/gitignore/api/linux
+# Edit at https://www.toptal.com/developers/gitignore?templates=linux
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+# End of https://www.toptal.com/developers/gitignore/api/linux
+
+# Created by https://www.toptal.com/developers/gitignore/api/macos
+# Edit at https://www.toptal.com/developers/gitignore?templates=macos
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### macOS Patch ###
+# iCloud generated files
+*.icloud
+
+# End of https://www.toptal.com/developers/gitignore/api/macos
+
+# Created by https://www.toptal.com/developers/gitignore/api/windows
+# Edit at https://www.toptal.com/developers/gitignore?templates=windows
+
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# End of https://www.toptal.com/developers/gitignore/api/windows

.gitlab-ci.yml

@@ -1,5 +1,5 @@
 # .gitlab-ci.yml -- Pamhyr gitlab-ci
-# Copyright (C) 2023  INRAE
+# Copyright (C) 2023-2025  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
@@ -16,55 +16,138 @@
 
 stages:
   - downloads
-  - build
+  - configure
   - test
+  - build
   - package
+  - hash
+  - antivirus
   - release
 
+#########################
+# PYINSTALLER VARIABLES #
+#########################
+
+variables:
+  HIDDEN_IMPORTS: "--hiddenimport rasterio --collect-submodules rasterio"
+
 #############
 # DOWNLOADS #
 #############
 
-dl-mage-linux:
+variables:
+  MAGE_8_VERSION: "permalink/latest"
+  ADISTS_VERSION: "permalink/latest"
+  RUBAR_VERSION: "permalink/latest"
+
+dl-mage8-doc:
   stage: downloads
   tags:
     - linux
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   script:
-    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/Test6/downloads/packages/mage_linux.tgz
+    - mkdir -p doc
-    - mkdir -p mage-linux
+    - cd doc
-    - cd mage-linux
+    - curl -L -o mage8.pdf https://forge.inrae.fr/river-hydraulics/mage/-/releases/$MAGE_8_VERSION/downloads/documents/Mage-8_Documentation.pdf
-    - tar xvf ../mage.tgz
   artifacts:
     paths:
-      - mage-linux/mage
+      - doc/mage8.pdf
-      - mage-linux/mage_extraire
-      - mage-linux/mailleurPF
 
-dl-mage-windows:
+dl-mage8-linux:
   stage: downloads
   tags:
     - linux
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   script:
-    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/Test6/downloads/packages/mage_windows.tgz
+    - curl -L -o mage8.tgz https://forge.inrae.fr/river-hydraulics/mage/-/releases/$MAGE_8_VERSION/downloads/packages/mage_linux.tgz
-    - mkdir -p mage-windows
+    - mkdir -p mage8-linux
-    - cd mage-windows
+    - cd mage8-linux
-    - tar xvf ../mage.tgz
+    - tar xvf ../mage8.tgz
   artifacts:
     paths:
-      - mage-windows/mage.exe
+      - mage8-linux/mage
-      - mage-windows/mage_extraire.exe
-      - mage-windows/mailleurPF.exe
 
-#########
+dl-mage8-windows:
-# BUILD #
+  stage: downloads
-#########
+  tags:
+    - linux
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - curl -L -o mage8.tgz https://forge.inrae.fr/river-hydraulics/mage/-/releases/$MAGE_8_VERSION/downloads/packages/mage_windows.tgz
+    - mkdir -p mage8-windows
+    - cd mage8-windows
+    - tar xvf ../mage8.tgz
+  artifacts:
+    paths:
+      - mage8-windows/mage.exe
+
+dl-adists-linux:
+  stage: downloads
+  tags:
+    - linux
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - mkdir -p adists-linux
+    - cd adists-linux
+    - curl -L -o adists https://forge.inrae.fr/river-hydraulics/adists/-/releases/$ADISTS_VERSION/downloads/executables/adists
+  artifacts:
+    paths:
+      - adists-linux/adists
+
+dl-adists-windows:
+  stage: downloads
+  tags:
+    - linux
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - mkdir -p adists-windows
+    - cd adists-windows
+    - curl -L -o adists.exe https://forge.inrae.fr/river-hydraulics/adists/-/releases/$ADISTS_VERSION/downloads/executables/adists_win64.exe
+  artifacts:
+    paths:
+      - adists-windows/adists.exe
+
+dl-rubar-linux:
+  stage: downloads
+  tags:
+    - linux
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - mkdir -p rubar-linux
+    - cd rubar-linux
+    - curl -L -o rubar.tgz https://forge.inrae.fr/river-hydraulics/rubarbe/-/releases/$RUBAR_VERSION/downloads/packages/rubar_linux.tgz
+    - tar xf rubar.tgz
+  artifacts:
+    paths:
+      - rubar-linux/rubarbe
+
+dl-rubar-windows:
+  stage: downloads
+  tags:
+    - linux
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - mkdir -p rubar-windows
+    - cd rubar-windows
+    - curl -L -o rubar.tgz https://forge.inrae.fr/river-hydraulics/rubarbe/-/releases/$RUBAR_VERSION/downloads/packages/rubar_windows.tgz
+    - tar xf rubar.tgz
+  artifacts:
+    paths:
+      - rubar-windows/rubarbe.exe
+
+#############
+# CONFIGURE #
+#############
 
 set-version:
-  stage: build
+  stage: configure
   tags:
     - linux
   script:
@@ -75,7 +158,7 @@ set-version:
       - VERSION
 
 build-lang:
-  stage: build
+  stage: configure
   tags:
     - linux
   script:
@@ -85,27 +168,132 @@ build-lang:
     paths:
       - src/lang/*.qm
 
-build-users-doc:
+#########
+# TESTS #
+#########
+
+unittest:
+  stage: test
+  tags:
+    - linux
+  needs:
+    - job: set-version
+      artifacts: true
+  script:
+    - python3.12 -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
+    - python3.12 -m unittest discover -t .
+
+test-pep8:
+  stage: test
+  tags:
+    - linux
+  needs:
+    - job: set-version
+      artifacts: true
+    - job: unittest
+  script:
+    # Setup virtual env
+    - python3.12 -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 --exclude="*_to_*.py" ./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-td:
   stage: build
   tags:
     - linux
+  needs:
+    - job: set-version
+      artifacts: true
   script:
-    - cd ./doc/users/
+    - cd ./doc/users/TP_Hydraulique_Hogneau/
     - ./build.sh
   artifacts:
     paths:
-      - doc/users/documentation.pdf
+      - doc/users/TP_Hydraulique_Hogneau/step-by-step.pdf
+      - doc/users/TP_Hydraulique_Hogneau/pas-a-pas.pdf
+      - doc/users/TP_Hydraulique_Hogneau/Tuto-2-fr.pdf
+      - doc/users/TP_Hydraulique_Hogneau/data/
+  allow_failure: true
+
+build-td-2:
+  stage: build
+  tags:
+    - linux
+  needs:
+    - job: set-version
+      artifacts: true
+  script:
+    - cd ./doc/users/TP_AdisTS_Vieux_Rhone/
+    - ./build.sh
+  artifacts:
+    paths:
+      - doc/users/TP_AdisTS_Vieux_Rhone/pas-a-pas.pdf
+      - doc/users/TP_AdisTS_Vieux_Rhone/data/
+      - doc/users/TP_AdisTS_Vieux_Rhone/Sujet.pdf
+      - doc/users/TP_AdisTS_Vieux_Rhone/Vieux_Rhone_TP_AdisTS.pamhyr
+  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
+    - python3.12 -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
@@ -114,7 +302,13 @@ build-linux:
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   needs:
-    - job: dl-mage-linux
+    - job: dl-adists-linux
+      artifacts: true
+    - job: dl-rubar-linux
+      artifacts: true
+    - job: dl-mage8-linux
+      artifacts: true
+    - job: dl-mage8-doc
       artifacts: true
     - job: set-version
       artifacts: true
@@ -122,51 +316,90 @@ build-linux:
       artifacts: true
     - job: build-developers-doc
       artifacts: true
-    - job: build-users-doc
+    # - job: build-users-doc
+    #   artifacts: true
+    - job: build-td
+      artifacts: true
+    - job: build-td-2
       artifacts: true
   script:
     - mkdir -p linux
     - cd linux
     # Setup virtual env
-    - python3 -m venv linux-venv
+    - python3.12 -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
+    - pyinstaller -y $HIDDEN_IMPORTS --paths linux-venv/lib/python3.12/site-packages ../src/pamhyr.py
     # Create directory
     - mkdir -p pamhyr
-    - mkdir -p pamhyr/pamhyr
+    - mkdir -p pamhyr/_internal
     # Copy Pamhyr info
-    - cp -v ../VERSION pamhyr/pamhyr/
+    - cp -v ../VERSION pamhyr/_internal/
-    - cp -v ../AUTHORS pamhyr/pamhyr/
+    - cp -v ../AUTHORS pamhyr/_internal/
-    - cp -v ../LICENSE pamhyr/pamhyr/
+    - cp -v ../LICENSE pamhyr/_internal/
+    - cp -v ../src/motd.txt pamhyr/_internal/
     # Copy mage
-    - mkdir -p pamhyr/mage
+    - mkdir -p pamhyr/mage8
-    - cp -v ../mage-linux/* pamhyr/mage/
+    - cp -v ../mage8-linux/* pamhyr/mage8/
+    # Copy adists
+    - mkdir -p pamhyr/adists
+    - cp -v ../adists-linux/* pamhyr/adists/
+    # Copy rubar
+    - mkdir -p pamhyr/rubar
+    - cp -v ../rubar-linux/* pamhyr/rubar/
     # Copy Pamhyr
-    - cp -r dist/pamhyr pamhyr/
+    - cp -r dist/pamhyr/* pamhyr/
+    # Pamhyr script to force x11
+    - echo '#!/usr/bin/env bash' > pamhyr/pamhyr-x11
+    - echo "" >> pamhyr/pamhyr-x11
+    - echo "GDK_BACKEND=x11 ./pamhyr $@" >> pamhyr/pamhyr-x11
+    - chmod +x pamhyr/pamhyr-x11
     # Copy Pamhyr resources
-    - mkdir -p pamhyr/pamhyr/View
+    - mkdir -p pamhyr/_internal/View
-    - mkdir -p pamhyr/pamhyr/View/ui
+    - mkdir -p pamhyr/_internal/View/ui
-    - mkdir -p pamhyr/pamhyr/View/ui/Widgets
+    - mkdir -p pamhyr/_internal/View/ui/Widgets
-    - cp -r ../src/View/ui/*.ui pamhyr/pamhyr/View/ui/
+    - cp -r ../src/View/ui/*.ui pamhyr/_internal/View/ui/
-    - cp -r ../src/View/ui/ressources/ pamhyr/pamhyr/View/ui
+    - cp -r ../src/View/ui/ressources/ pamhyr/_internal/View/ui
-    - cp -r ../src/View/ui/Widgets/*.ui pamhyr/pamhyr/View/ui/Widgets
+    - cp -r ../src/View/ui/Widgets/*.ui pamhyr/_internal/View/ui/Widgets
     # Copy lang
-    - mkdir -p pamhyr/pamhyr/lang
+    - mkdir -p pamhyr/_internal/lang
-    - cp -r ../src/lang/*.qm pamhyr/pamhyr/lang
+    - cp -r ../src/lang/*.qm 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/
-    - cp ../doc/users/documentation.pdf pamhyr/doc/Pamhyr2-users.pdf
+    - 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/mage8.pdf pamhyr/doc/mage8.pdf
     - cp ../doc/dev/documentation.pdf pamhyr/doc/Pamhyr2-dev.pdf
-    # Create running script
+    - cp ../doc/dev/documentation.html pamhyr/doc/Pamhyr2-dev.html
-    - echo "#!/bin/sh" > pamhyr/Pamhyr2
+    #- cp ../doc/users/images/* pamhyr/doc/images
-    - echo "./pamhyr/pamhyr $@" >> pamhyr/Pamhyr2
+    - cp -r ../doc/dev/images/* pamhyr/doc/images
-    - chmod u+x pamhyr/Pamhyr2
+    - cp -r ../doc/images/* pamhyr/doc/images
+    # Copy Tuto
+    - mkdir -p pamhyr/doc/TP_Hydraulique_Hogneau/
+    - mkdir -p pamhyr/doc/TP_Hydraulique_Hogneau/data
+    - cp ../doc/users/TP_Hydraulique_Hogneau/Hogneau_Engees2022.pdf pamhyr/doc/TP_Hydraulique_Hogneau/Hogneau_Engees2022.pdf
+    - cp ../doc/users/TP_Hydraulique_Hogneau/step-by-step.pdf pamhyr/doc/TP_Hydraulique_Hogneau/Tuto1-en.pdf
+    - cp ../doc/users/TP_Hydraulique_Hogneau/pas-a-pas.pdf pamhyr/doc/TP_Hydraulique_Hogneau/Tuto1-fr.pdf
+    - cp ../doc/users/TP_Hydraulique_Hogneau/Tuto-2-fr.pdf pamhyr/doc/TP_Hydraulique_Hogneau/Tuto2-fr.pdf
+    - cp ../doc/users/TP_Hydraulique_Hogneau/*.pamhyr pamhyr/doc/TP_Hydraulique_Hogneau/
+    - cp ../doc/users/TP_Hydraulique_Hogneau/data/* pamhyr/doc/TP_Hydraulique_Hogneau/data/
+    - mkdir -p pamhyr/doc/TP_AdisTS_Vieux_Rhone/
+    - mkdir -p pamhyr/doc/TP_AdisTS_Vieux_Rhone/data
+    - cp ../doc/users/TP_AdisTS_Vieux_Rhone/*.pdf pamhyr/doc/TP_AdisTS_Vieux_Rhone/
+    - cp ../doc/users/TP_AdisTS_Vieux_Rhone/data/* pamhyr/doc/TP_AdisTS_Vieux_Rhone/data/
+    - cp ../doc/users/TP_AdisTS_Vieux_Rhone/Vieux_Rhone_TP_AdisTS.pamhyr pamhyr/doc/TP_AdisTS_Vieux_Rhone/Vieux_Rhone_TP_AdisTS.pamhyr
+    # Copy TP charriage
+    - mkdir -p pamhyr/doc/TP_charriage/
+    - cp -r ../doc/users/TP_charriage/* pamhyr/doc/TP_charriage
   artifacts:
     paths:
       - linux/pamhyr
@@ -178,7 +411,13 @@ build-windows:
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   needs:
-    - job: dl-mage-windows
+    - job: dl-mage8-windows
+      artifacts: true
+    - job: dl-adists-windows
+      artifacts: true
+    - job: dl-rubar-windows
+      artifacts: true
+    - job: dl-mage8-doc
       artifacts: true
     - job: set-version
       artifacts: true
@@ -186,15 +425,22 @@ build-windows:
       artifacts: true
     - job: build-developers-doc
       artifacts: true
-    - job: build-users-doc
+    # - job: build-users-doc
+    #   artifacts: true
+    - job: build-td
+      artifacts: true
+    - job: build-td-2
       artifacts: true
   script:
     - mkdir windows
     - cd windows
     # Setup env
+    - python -m pip install -U pip
     - python -m pip install -r ..\requirements.txt
+    - python -m pip install -U -r ..\requirements.txt
     # Run Pyinstaller
-    - pyinstaller -y ..\src\pamhyr.py
+    # - pyinstaller --noconsole -y ..\src\pamhyr.py
+    - pyinstaller -i ../src/View/ui/ressources/icon.ico $HIDDEN_IMPORTS --hide-console hide-early -y ..\src\pamhyr.py
     # Create directory
     - mkdir pamhyr
     - dir
@@ -204,36 +450,6 @@ build-windows:
     paths:
       - windows/pamhyr
 
-#########
-# TESTS #
-#########
-
-# test-windows:
-#   stage: test
-#   tags:
-#     - wine
-#   needs:
-#     - job: set-version
-#       artifacts: true
-#     - job: build-windows
-#       artifacts: true
-#   script:
-#     - cd windows\pamhyr
-#     - pamhyr\pamhyr.exe hello
-
-# test-linux:
-#   stage: test
-#   tags:
-#     - linux
-#   needs:
-#     - job: set-version
-#       artifacts: true
-#     - job: build-linux
-#       artifacts: true
-#   script:
-#     - cd linux/pamhyr
-#     - ./Pamhyr2 hello
-
 ############
 # PACKAGES #
 ############
@@ -248,7 +464,7 @@ linux-package-tar:
     - job: build-linux
       artifacts: true
   rules:
-    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_TAG
   artifacts:
     paths:
       - linux/pamhyr-gnulinux.tar.xz
@@ -266,7 +482,7 @@ windows-package-zip:
     - job: build-windows
       artifacts: true
   rules:
-    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_TAG
   artifacts:
     paths:
       - windows/pamhyr-windows.zip
@@ -284,7 +500,7 @@ windows-package-exe:
     - job: build-windows
       artifacts: true
   rules:
-    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_TAG
   artifacts:
     paths:
       - windows/pamhyr-windows.exe
@@ -294,10 +510,149 @@ windows-package-exe:
     - copy ..\packages\pamhyr.nsi pamhyr.nsi
     - .\make-windows-exe.bat
 
+########
+# HASH #
+########
+
+linux-build-hash:
+  stage: hash
+  tags:
+    - release
+    - linux
+  needs:
+    - job: build-linux
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - cd linux
+    - sha256sum -b pamhyr/pamhyr > pamhyr/pamhyr.sha256
+  artifacts:
+    paths:
+      - linux/pamhyr/pamhyr.sha256
+
+windows-build-hash:
+  stage: hash
+  tags:
+    - release
+    - linux
+  needs:
+    - job: build-windows
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - cd windows
+    - sha256sum -b pamhyr/pamhyr.exe > pamhyr/pamhyr.exe.sha256
+  artifacts:
+    paths:
+      - windows/pamhyr/pamhyr.exe.sha256
+
+pkg-hash:
+  stage: hash
+  tags:
+    - release
+    - linux
+  needs:
+    - job: linux-package-tar
+      artifacts: true
+    - job: windows-package-zip
+      artifacts: true
+    - job: windows-package-exe
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_TAG
+  script:
+    - cd windows
+    - sha256sum -b pamhyr-windows.exe > pamhyr-windows.exe.sha256
+    - sha256sum -b pamhyr-windows.zip > pamhyr-windows.zip.sha256
+    - cd ..
+    - cd linux
+    - sha256sum -b pamhyr-gnulinux.tar.xz > pamhyr-gnulinux.tar.xz.sha256
+  artifacts:
+    paths:
+    - windows/pamhyr-windows.exe.sha256
+    - windows/pamhyr-windows.zip.sha256
+    - linux/pamhyr-gnulinux.tar.xz.sha256
+
+#############
+# ANTIVIRUS #
+#############
+
+build-check-clamav:
+  stage: antivirus
+  tags:
+    - release
+    - linux
+  needs:
+    - job: build-linux
+      artifacts: true
+    - job: build-windows
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - cd packages
+    - ./clamav-scan.sh builds
+  allow_failure: true
+
+pkg-check-clamav:
+  stage: antivirus
+  tags:
+    - release
+    - linux
+  needs:
+    - job: linux-package-tar
+      artifacts: true
+    - job: windows-package-zip
+      artifacts: true
+    - job: windows-package-exe
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_TAG
+  script:
+    - cd packages
+    - ./clamav-scan.sh packages
+  allow_failure: true
+
 ###########
 # RELEASE #
 ###########
 
+shadow-release:
+  stage: release
+  tags:
+    - release
+    - linux
+  needs:
+    - job: linux-package-tar
+      artifacts: true
+    - job: windows-package-zip
+      artifacts: true
+    - job: windows-package-exe
+      artifacts: true
+    # - job: build-users-doc
+    #   artifacts: true
+    - job: build-developers-doc
+      artifacts: true
+    - job: pkg-hash
+      artifacts: true
+  rules:
+    - if: $CI_COMMIT_TAG && $CI_COMMIT_TAG !~ /^v/
+  artifacts:
+    paths:
+      - linux/pamhyr-gnulinux.tar.xz
+      - windows/pamhyr-windows.zip
+      - windows/pamhyr-windows.exe
+      - linux/pamhyr-gnulinux.tar.xz.sha256
+      - windows/pamhyr-windows.zip.sha256
+      - windows/pamhyr-windows.exe.sha256
+      - doc/dev/documentation.pdf
+      # - doc/users/documentation.pdf
+  script:
+    - cd packages
+
+
 tag-release:
   stage: release
   tags:
@@ -310,44 +665,57 @@ tag-release:
       artifacts: true
     - job: windows-package-exe
       artifacts: true
-    - job: build-users-doc
+    # - job: build-users-doc
-      artifacts: true
+    #   artifacts: true
     - job: build-developers-doc
       artifacts: true
+    - job: pkg-hash
+      artifacts: true
   rules:
-    - if: $CI_COMMIT_TAG
+    - if: $CI_COMMIT_TAG =~ /^v/
   artifacts:
     paths:
       - linux/pamhyr-gnulinux.tar.xz
       - windows/pamhyr-windows.zip
       - windows/pamhyr-windows.exe
+      - linux/pamhyr-gnulinux.tar.xz.sha256
+      - windows/pamhyr-windows.zip.sha256
+      - windows/pamhyr-windows.exe.sha256
       - doc/dev/documentation.pdf
-      - doc/users/documentation.pdf
+      # - doc/users/documentation.pdf
   script:
     - cd packages
   release:
     name: '$CI_COMMIT_TAG'
-    description: 'Automatic release from tag $CI_COMMIT_TAG'
+    description: '$CI_COMMIT_TAG_MESSAGE'
     tag_name: '$CI_COMMIT_TAG'
     ref: '$CI_COMMIT_SHA'
     assets:
       links:
+        - name: 'GNU/Linux CHECKSUM SHA256 (tar.xz)'
+          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/linux/pamhyr-gnulinux.tar.xz.sha256'
+          filepath: '/linux/pamhyr-gnulinux.tar.xz.sha256'
+          link_type: 'package'
         - 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 CHECKSUM SHA256 (exe)'
+          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/windows/pamhyr-windows.exe.sha256'
+          filepath: '/windows/pamhyr-windows.exe.sha256'
+          link_type: 'package'
         - 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 CHECKSUM SHA256 (zip)'
+          url: '${CI_PROJECT_URL}/-/jobs/${CI_JOB_ID}/artifacts/raw/windows/pamhyr-windows.zip.sha256'
+          filepath: '/windows/pamhyr-windows.zip.sha256'
+          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'

.idea/.gitignore

@@ -0,0 +1,3 @@
+# Default ignored files
+/shelf/
+/workspace.xml

.idea/inspectionProfiles/profiles_settings.xml

@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

.idea/misc.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Black">
+    <option name="sdkName" value="Python 3.10 (pamhyr)" />
+  </component>
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.10 (pamhyr)" project-jdk-type="Python SDK" />
+</project>

.idea/modules.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/pamhyr.iml" filepath="$PROJECT_DIR$/.idea/pamhyr.iml" />
+    </modules>
+  </component>
+</project>

.idea/pamhyr.iml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/venv" />
+    </content>
+    <orderEntry type="jdk" jdkName="Python 3.10 (pamhyr)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="PyDocumentationSettings">
+    <option name="format" value="PLAIN" />
+    <option name="myDocStringFormat" value="Plain" />
+  </component>
+</module>

.idea/vcs.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+  </component>
+</project>

AUTHORS

@@ -1,3 +1,4 @@
 Sylvain COULIBALY, INRAE, 2020 - 2022
-Théophile TERRAZ, INRAE, 2022 - 2023
+Théophile TERRAZ, INRAE, 2022 - 2024
-Pierre-Antoine ROUBY, INRAE, 2023
+Pierre-Antoine ROUBY, INRAE, 2023 - 2026
+Dylan JEANNIN, INRAE, 2026

README.md

@@ -3,48 +3,39 @@
 Pamhyr is a free and open source graphical user interface for 1D hydro-sedimentary
 modelling of rivers.
 
+![logo](https://gitlab.com/pamhyr/pamhyr2/-/raw/master/src/View/ui/ressources/Pamhyr2_logo.png)
+
 ## Features
 
-+ Edit a complex river hydraulics network
++ Define a complex river hydraulics network
 + Define the river geometry
 + Define boundary conditions
 + Define lateral contribution
-+ Edit river friction
++ Define river friction
-+ Generate initial conditions
++ Define reservoirs
-+ Edit river sedimentary layers
++ Define hydraulic structures
++ Define or generate initial conditions
++ Define river sedimentary layers
 + Save the study in a unique file
 + Run Mage 8 on a study and visualize results
++ Create and edit study alternative scenario tree
+
+Let see the
+[documentation](https://gitlab.com/pamhyr/pamhyr2/-/wikis/home)
+([:fr:](https://gitlab.com/pamhyr/pamhyr2/-/wikis/home-fr),
+[:gb:](https://gitlab.com/pamhyr/pamhyr2/-/wikis/home-en))
+for more details.
 
 ## Install
 
 ### GNU/Linux
 
-Downloads [last
+See documentation:
-realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
+- [French :fr:](https://gitlab.com/pamhyr/pamhyr2/-/wikis/home/fr/Install%20on%20GNULinux)
-GNU/Linux binary archive.
+- [English :gb:](https://gitlab.com/pamhyr/pamhyr2/-/wikis/home/en/Install%20on%20GNULinux)
-
-```shell
-tar xf pamhyr-gnulinux-amd64.tar.xz
-cd pamhyr
-./pamhyr
-```
 
 ### Windows
 
-Downloads [last
+See documentation:
-realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
+- [French :fr:](https://gitlab.com/pamhyr/pamhyr2/-/wikis/home/fr/Install%20on%20Windows)
-Windows installer.
+- [English :gb:](https://gitlab.com/pamhyr/pamhyr2/-/wikis/home/en/Install%20on%20Windows)
-
-### 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

@@ -1,10 +1,23 @@
 #! /bin/sh
 
-# Build the PDF
+FILES="documentation.org scenario.org"
 
-emacs -Q -q -nw --batch                                 \
+for file in $FILES
-      --eval "(require 'org)"                           \
+do
-      --eval "(require 'ox-latex)"                      \
+    echo " PDF  $file"
-      --eval "(load-file \"../tools/setup.el\")"        \
+    emacs -nw --batch                                   \
-      --file ./documentation.org                        \
+          --eval "(require 'org)"                       \
-      -f org-latex-export-to-pdf
+          --eval "(require 'ox-latex)"                  \
+          --eval "(load-file \"../tools/setup.el\")"    \
+          --file ./$file                                \
+          -f org-latex-export-to-pdf                    \
+
+    echo " HTML $file"
+    emacs -nw --batch                                   \
+          --eval "(require 'org)"                       \
+          --eval "(require 'ox-latex)"                  \
+          --eval "(require 'ox-html)"                   \
+          --eval "(load-file \"../tools/setup.el\")"    \
+          --file ./$file                                \
+          -f org-html-export-to-html
+done

doc/dev/scenario.org

@@ -0,0 +1,661 @@
+# senario.org -- Pamhyr developers documentation
+# Copyright (C) 2023-2024  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 -*-
+
+#+STARTUP: indent show2levels
+
+#+INCLUDE: ../tools/macro.org
+#+INCLUDE: ../tools/latex.org
+
+#+TITLE: Scenario implementation in Pamhyr2: \textbf{Preparatory work}
+#+SUBTITLE: Version: {{{version}}}
+#+AUTHOR: {{{INRAE}}}
+
+#+OPTIONS: toc:t
+#+LANGUAGE: UKenglish
+
+#+latex: \newpage
+
+* COMMENT tools
+
+#+begin_src emacs-lisp :export none
+  (add-to-list 'org-structure-template-alist
+               '("p" "#+begin_src python :python python3 :results output\n\n#+end_src"))
+#+end_src
+
+#+RESULTS:
+#+begin_example
+((p #+begin_src python :python python3 :results output
+
+,#+end_src) (d . #+name: graph-XXX
+,#+header: :results drawer
+,#+header: :exports results
+,#+header: :post attr_wrap(width="12cm", data=*this*, name="graph-XXX", caption="Graph XXX", float="t")
+,#+begin_src dot :file "images/graph-XXX.png" :cache no
+digraph {
+        bgcolor="transparent";
+        node[colorscheme=set19,shape=box,style="filled",fillcolor=9];
+}
+,#+end_src) (p . src python :python python3 :results output :noweb yes
+
+src) (t . EXPORT latex
+\begin{table}
+\centering
+\resizebox{0.6\linewidth}{!}{
+
+}
+%\vspace{0.5pt}
+%\caption{Number of tests by errors types}
+\end{table}
+,#+E) (B . src shell :session *shell* :results output :exports both) (a . export ascii) (c . center) (C . comment) (e . example) (E . export) (h . export html) (l . export latex) (q . quote) (s . src) (v . verse))
+#+end_example
+
+#+name: dbg-execute
+#+begin_src python :python python3 :results output :noweb yes
+  def execute(db, query):
+      print(query)
+      return db.execute(query)
+#+end_src
+
+#+RESULTS: dbg-execute
+
+#+name: execute
+#+begin_src python :python python3 :results output :noweb yes
+  def execute(db, query):
+      return db.execute(query)
+#+end_src
+
+#+RESULTS: execute
+
+* Principe
+
+** Scenario
+
+A scenario is defined by a name, a description and a parent
+scenario. If a scenario as no parent, parent value is =None=. So, in
+Pamhyr2 the list of scenario must by a tree with a root defined by a
+default scenarios with no parent.
+
+#+begin_src sql
+  CREATE TABLE scenario(
+    id INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT,
+    name TEXT NOT NULL,           -- Name of the scenario
+    description TEXT NOT NULL,    -- Rich text description
+    parent_id INTEGER REFERENCES scenario(id) -- Recursive references
+                                              -- for parent scenario
+  )
+#+end_src
+
+** Data
+
+Each data is associated with one and only one scenario. This senario
+is defined by the =id=. So, each data structure who can saved in DB
+must add the following lines in table définition:
+
+#+begin_src sql
+  scenario_id INTEGER NOT NULL,
+  FOREIGN KEY(scenario_id) REFERENCES scenario(id)
+#+end_src
+
+To avoid, at least, memory usage exploitation, by default, a scenario
+must saved only the modified data from its parent. This contrains
+require to wrap any data modification to update the data scenario id
+to current scenario id in source code. In addition, we need to modify
+the data loading méthode to take in considération this recursive
+dependencies.
+
+#+CAPTION: Recursive loading method
+#+begin_src python :python python3 :results output :noweb yes
+  def rec_load(cls, db, current_scenario):
+    # Default case, end of recursion
+    if current_scenario is None:
+      return []                   # Default value
+
+    table = db.execute(f"<MY SELECT> WHERE scenario_id = {current_scenario}")
+
+    # If no data for this scenario, recursion
+    if len(table) == 0:
+      parent_id = db.get_parent_id(current_scenario)
+      return cls.rec_load(db, parent_id)
+
+    # Otherelse, parse data and return...
+#+end_src
+
+With this method, modify a data in parent scenario, modify this data
+in child scenario too. Unless is value has been previously modified in
+the child scenario. Deny tree node modification, except for leaf.
+
+This method work, but it dont allow to delete data un child scenarios,
+because if we dont found data for this scenario we search for parent
+scenario. So, we need a condition to stop recursion in case of data
+deletion in child scenario. To stop the recurtion, we can use a dummy
+data flag. By default, this flags is =false=, but if this flags is
+=true= the data is ignored at loading.
+
+So, we can use this flags for each data structure who can saved in DB:
+
+#+begin_src sql
+  is_dummy BOOLEAN,               -- True if this data as been deleted
+#+end_src
+
+Modify the loading method:
+
+#+CAPTION: Recursive loading method with possible dummy data
+#+begin_src python :python python3 :results output :noweb yes
+  def rec_load_2(cls, db, current_scenario):
+    # Default case, end of recursion
+    if current_scenario is None:
+      return []                   # Default value
+
+    table = db.execute(f"<MY SELECT> WHERE scenario_id = {current_scenario}")
+
+    # If no data for this scenario, recursion
+    if len(table) == 0:
+      parent_id = db.get_parent_id(current_scenario)
+      return cls.rec_load(db, parent_id)
+
+    for data in table:
+      if is_dummy(data):
+        continue
+
+      # Otherelse, parse data ...
+
+    # return ...
+#+end_src
+
+#+RESULTS:
+
+And add a data reduction method:
+
+#+caption: Data reduction method for data subtree
+#+begin_src python :python python3 :results output :noweb yes
+  def reduce_change(self):
+       # Get the greater scenario
+       scenar = reduce(
+            lambda acc, x: max(acc, x._scenario),
+            self._values,
+            self._scenario
+       )
+
+       # Apply change on this subtree
+       self._scenario = scenar
+
+       if is_dummy(self):         # There are no more subtree
+          self.values = []
+       else:                      # Update data subtree scenario id
+            for value in self._values:
+                 value.set_scenario(self._scenario)
+            # Dummy data is no more necessary in this subtree
+            self._values = list(
+                 filter(
+                      lambda v: not is_dummy(v),
+                      self._values
+                 )
+            )
+
+       # Keep data id unique for all subtree
+       self.get_new_db_id()
+#+end_src
+
+#+RESULTS:
+
+#+latex: \newpage
+
+* Prototype
+
+** Scenario
+
+#+name: scenario
+#+begin_src python :python python3 :results output :noweb yes
+  class Scenario():
+       def __init__(self, id, name, parent):
+           self._id = id
+           self._name = name
+           self._parent = parent
+
+       @classmethod
+       def create_db(cls, db):
+           execute(
+               db, """
+               CREATE TABLE scenario(
+                 id INTEGER PRIMARY KEY,
+                 name TEXT NOT NULL,
+                 parent_id INTEGER REFERENCES scenario(id)
+               )
+               """
+           )
+
+       @classmethod
+       def load_db(cls, db):
+           cur = execute(
+               db, f"SELECT * FROM scenario"
+           )
+           table = cur.fetchall()
+
+           new = []
+           for values in table:
+               new.append(
+                   cls(
+                       values[0], values[1], values[2],
+                   )
+               )
+
+           return new
+
+       def save(self, db):
+           sid = 'NULL' if self._parent is None else self._parent
+
+           execute(
+               db,
+               "INSERT INTO scenario (id, name, parent_id) " +
+               f"VALUES ({self._id}, '{self._name}', {sid})"
+           )
+
+       def __repr__(self):
+           return f"Scenario {{ {self._id}, {self._name}, parent {self._parent} }}"
+
+       def __str__(self):
+           return f"{self._name}({self._id})"
+#+end_src
+
+#+RESULTS: scenario
+
+** Data
+
+#+name: data-b
+#+begin_src python :python python3 :results output :noweb yes
+  class B():
+      def __init__(self, value, scenario):
+           self._value = value
+           self._scenario = scenario
+           self._dummy = False
+
+      @classmethod
+      def create_db(cls, db):
+          execute(db, """
+            CREATE TABLE b(
+              id INTEGER PRIMARY KEY AUTOINCREMENT,
+              dummy_data BOOLEAN,
+              x INTEGER,
+              a_id INTEGER NOT NULL,
+              scenario_id INTEGER NOT NULL,
+              FOREIGN KEY(a_id) REFERENCES a(id),
+              FOREIGN KEY(scenario_id) REFERENCES scenario(id)
+            )
+          """)
+
+      def save(self, db, a_id):
+          execute(
+              db,
+              "INSERT INTO b (x, dummy_data, a_id, scenario_id) " +
+              f"VALUES ({self._value}, {self._dummy}, {a_id}, {self._scenario})"
+          )
+
+      @classmethod
+      def load_db(cls, db, a_id, senar):
+          if senar is None:
+              return []
+
+          cur = execute(
+              db,
+              "SELECT x, scenario_id, dummy_data FROM b " +
+              f"WHERE scenario_id = {senar} AND a_id = {a_id}"
+          )
+          table = cur.fetchall()
+
+          if len(table) == 0:
+              parent = execute(
+                  db,
+                  f"SELECT parent_id FROM scenario WHERE id = {senar}"
+              ).fetchone()
+
+              return cls.load_db(db, parent[0])
+
+          new = []
+          for values in table:
+              if values[2]:    # Is dummy
+                  continue
+
+              new.append(cls(values[0], values[1]))
+
+          return new
+
+      def set_value(self, value, scenario):
+          self._value = value
+          self._scenario = scenario
+
+      def set_dummy(self, scenario):
+          self._scenario = scenario
+          self._dummy = True
+
+      def __repr__(self):
+          if self._dummy:
+              return ""
+          return f"{self._value}"
+
+      def __str__(self):
+          if self._dummy:
+              return ""
+          return f"{self._value}"
+#+end_src
+
+#+RESULTS: data-b
+
+#+name: data-a
+#+begin_src python :python python3 :results output :noweb yes
+  class A():
+       def __init__(self, id, values, scenario):
+           self._id = id
+           self._values = values
+           self._scenario = scenario
+           self._dummy = False
+
+       @classmethod
+       def create_db(cls, db):
+           execute(db, """
+           CREATE TABLE a(
+             id INTEGER PRIMARY KEY,
+             dummy_data BOOLEAN,
+             scenario_id INTEGER,
+             FOREIGN KEY(scenario_id) REFERENCES scenario(id)
+           )
+           """)
+
+       def save(self, db):
+           self.reduce_change()
+
+           execute(db, f"DELETE FROM a WHERE scenario_id = {self._scenario}")
+           execute(
+               db,
+               "INSERT INTO a (id, dummy_data, scenario_id) " +
+               f"VALUES ({self._id}, {self._dummy}, {self._scenario})"
+           )
+
+           execute(
+                db,
+                "DELETE FROM b " +
+                f"WHERE scenario_id = {self._scenario} " +
+                f"AND a_id = {self._id}"
+           )
+
+           for value in self._values:
+                value.save(db, self._id)
+
+       def reduce_change(self):
+            diff_scenar = reduce(
+                 lambda acc, x: max(acc, x._scenario),
+                 self._values,
+                 self._scenario
+            )
+            print(f" ~> Reduce: {self._scenario} to {diff_scenar}")
+            self._scenario = diff_scenar
+
+            # Reduce new scenario value on each value
+            for value in self._values:
+                 value._scenario = self._scenario
+
+            # Delete useless dummy data
+            self._values = list(
+                 filter(
+                      lambda v: not v._dummy,
+                      self._values
+                 )
+            )
+
+            # HACK: keep id unique
+            self._id = self._id * 100 + diff_scenar
+
+       @classmethod
+       def load_db(cls, db, senar):
+           if senar is None:
+               return []
+
+           cur = execute(
+               db,
+               f"SELECT id, scenario_id, dummy_data FROM a WHERE scenario_id = {senar}"
+           )
+           table = cur.fetchall()
+
+           if len(table) == 0:
+               parent = execute(
+                   db,
+                   f"SELECT parent_id FROM scenario WHERE id = {senar}"
+               ).fetchone()
+
+               return cls.load_db(db, parent[0])
+
+           new = []
+           for values in table:
+               if values[2]:
+                    continue
+
+               bb = B.load_db(db, values[0], senar)
+               new.append(cls(values[0], bb, values[1]))
+
+           return new
+
+       def set_dummy(self, scenario):
+           self._scenario = scenario
+           self._dummy = True
+
+       def add(self, b):
+          self._values.append(b)
+
+       def delete(self, index, scenario):
+            self._values[index].set_dummy(scenario)
+            self._scenario = scenario
+
+       def __repr__(self):
+           if self._dummy:
+               return "{ }"
+           return f"{{ {self._values}, ({self._scenario}) }}"
+
+       def __str__(self):
+           if self._dummy:
+               return "{ }"
+           return f"{{ {list(map(str, self._values))}, ({self._scenario}) }}"
+#+end_src
+
+#+RESULTS: data-a
+
+** Full prototype
+
+#+begin_src python :python python3 :results output :exports both :noweb yes :cache yes
+  from functools import reduce
+
+  def execute(db, query):
+      # print(query)
+      return db.execute(query)
+
+  def get_tree(db):
+      from treelib import Node, Tree
+
+      tree = Tree()
+
+      for senar in db.execute("SELECT * FROM scenario").fetchall():
+          if senar[1] is None:
+              tree.create_node(
+                  str(Scenario(senar[0], senar[1], senar[2])) +
+                  " : " + str(A.load_db(db, senar[0])[0]),
+                  senar[0]
+              )
+          else:
+              tree.create_node(
+                  str(Scenario(senar[0], senar[1], senar[2])) +
+                  " : " + str(A.load_db(db, senar[0])[0]),
+                  senar[0],
+                  parent=senar[2]
+              )
+
+      return tree
+
+  ### --- Scenario ---
+  <<scenario>>
+
+  ### --- class B ---
+  <<data-b>>
+
+  ### --- class A ---
+  <<data-a>>
+
+  ### --- Script ---
+  import sqlite3
+  import pprint
+
+  pp = pprint.PrettyPrinter(width=79, compact=True, depth=6)
+
+  with sqlite3.connect(":memory:") as db:
+      cur = db.cursor()
+
+      Scenario.create_db(cur)
+      A.create_db(cur)
+      B.create_db(cur)
+
+      print("--- Default scenario (s0) ---")
+
+      # One scenario
+
+      s0 = Scenario(0, "s0", None)
+      a0 = A(
+          1,
+          [
+              B(0, s0._id),
+              B(1, s0._id),
+              B(2, s0._id),
+          ],
+          s0._id
+      )
+
+      s0.save(cur)
+      a0.save(cur)
+
+      print("--- New scenario (s1) -- copy without modification ---")
+
+      # New scenario
+
+      s1 = Scenario(1, "s1", s0._id)
+      s1.save(cur)
+
+      print("--- New scenario (s2) -- data modification ---")
+
+      # New scenario 2 with data
+
+      s2 = Scenario(2, "s2", s0._id)
+      s2.save(cur)
+
+      a2 = a0
+      bb = list(map(
+          lambda b: b.set_value(b._value + 1, s2._id),
+          a2._values
+      ))
+
+      a2.save(cur)
+
+      print("--- New scenario (s3) -- delete data ---")
+
+      # New scenario 3 with data
+
+      s3 = Scenario(3, "s3", s0._id)
+      s3.save(cur)
+
+      a3 = A.load_db(cur, s3._id)[0]
+      a3._values[0].set_dummy(s3._id)
+      a3.save(cur)
+
+      print("--- New scenario (s4) -- new data ---")
+
+      s4 = Scenario(4, "s4", s3._id)
+      s4.save(cur)
+
+      a4 = A.load_db(cur, s3._id)[0]
+      a4.add(B(666, s4._id))
+      a4.save(cur)
+
+      print("--- Scenario tree ---")
+
+      tree = get_tree(db)
+      print(tree)
+
+      print("--- Modify s0 data ---")
+
+      aa = A.load_db(db, s0._id)[0]
+      bb = list(map(
+          lambda b: b.set_value(b._value * 100 - 1, s0._id),
+          aa._values
+      ))
+      aa.save(db)
+
+      print("--- Scenario tree ---")
+
+      tree = get_tree(db)
+      print(tree)
+
+      print("--- DB ---")
+
+      ss = db.execute("SELECT * FROM scenario").fetchall()
+      print(f"+ scenario ({len(ss)}):")
+      pp.pprint(ss)
+
+      aa = db.execute("SELECT * FROM a").fetchall()
+      print(f"+ a ({len(aa)}):")
+      pp.pprint(aa)
+
+      bb = db.execute("SELECT * FROM b").fetchall()
+      print(f"+ b ({len(bb)}):")
+      pp.pprint(bb)
+
+#+end_src
+
+#+RESULTS[96c84f23be557425ae2822ef7f174175ef69f9b9]:
+#+begin_example
+--- Default scenario (s0) ---
+ ~> Reduce: 0 to 0
+--- New scenario (s1) -- copy without modification ---
+--- New scenario (s2) -- data modification ---
+ ~> Reduce: 0 to 2
+--- New scenario (s3) -- delete data ---
+ ~> Reduce: 0 to 3
+--- New scenario (s4) -- new data ---
+ ~> Reduce: 3 to 4
+--- Scenario tree ---
+s0(0) : { ['0', '1', '2'], (0) }
+├── s1(1) : { ['0', '1', '2'], (0) }
+├── s2(2) : { ['1', '2', '3'], (2) }
+└── s3(3) : { ['1', '2'], (3) }
+    └── s4(4) : { ['1', '2', '666'], (4) }
+
+--- Modify s0 data ---
+ ~> Reduce: 0 to 0
+--- Scenario tree ---
+s0(0) : { ['-1', '99', '199'], (0) }
+├── s1(1) : { ['-1', '99', '199'], (0) }
+├── s2(2) : { ['1', '2', '3'], (2) }
+└── s3(3) : { ['1', '2'], (3) }
+    └── s4(4) : { ['1', '2', '666'], (4) }
+
+--- DB ---
++ scenario (5):
+[(0, 's0', None), (1, 's1', 0), (2, 's2', 0), (3, 's3', 0), (4, 's4', 3)]
++ a (4):
+[(10000, 0, 0), (10002, 0, 2), (10003, 0, 3), (1000304, 0, 4)]
++ b (14):
+[(1, 0, 0, 100, 0), (2, 0, 1, 100, 0), (3, 0, 2, 100, 0), (4, 0, 1, 10002, 2),
+ (5, 0, 2, 10002, 2), (6, 0, 3, 10002, 2), (7, 0, 1, 10003, 3),
+ (8, 0, 2, 10003, 3), (9, 0, 1, 1000304, 4), (10, 0, 2, 1000304, 4),
+ (11, 0, 666, 1000304, 4), (12, 0, -1, 10000, 0), (13, 0, 99, 10000, 0),
+ (14, 0, 199, 10000, 0)]
+#+end_example

doc/dev/scenarios/presentation.org

@@ -0,0 +1,525 @@
+# presentation.org -- 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 -*-
+
+#+STARTUP: indent hideblocks content beamer
+
+#+TITLE: \textbf{Pamhyr2}
+#+SUBTITLE: Scenarios managements
+
+# #+AUTHOR: Pierre-Antoine Rouby
+#+LATEX_HEADER: \author[Pierre-Antoine Rouby]{\textbf{Pierre-Antoine Rouby}}
+#+EMAIL: pierre-antoine.rouby@inrae.fr
+#+INSTITUTE: INRAE Lyon-Villerbanne, teams River Hydraulics
+#+LATEX_HEADER: \institute{INRAE Lyon-Villerbanne, River Hydraulics team}
+#+DATE: 9th November
+
+#+KEYWORDS: g ui, hydraulics, sedimentary, hydro-sedimentary, 1D modelling, freesoftware, foss
+
+#+OPTIONS: H:2 toc:t num:t author:nil
+#+LATEX_CLASS: beamer
+#+LATEX_CLASS_OPTIONS: [slideopt,A4,showboxes,svgnames,aspectratio=169]
+# #+LATEX_CLASS_OPTIONS: [presentation]
+#+BEAMER_THEME: default
+#+COLUMNS: %45ITEM %10BEAMER_ENV(Env) %10BEAMER_ACT(Act) %4BEAMER_COL(Col)
+
+#+LANGUAGE: fr
+#+LATEX_HEADER: \usepackage[frenchb]{babel}
+
+#+BEGIN_SRC emacs-lisp :results silent :exports none
+  (setq org-latex-pdf-process (list
+    "latexmk -pdflatex='lualatex -shell-escape -interaction nonstopmode' -pdf -f  %f"))
+
+  (add-to-list 'org-latex-packages-alist '("" "minted"))
+  (setq org-latex-listings 'minted)
+  (setq org-src-fontify-natively t)
+
+  (org-add-link-type
+   "cite" 'ebib
+   (lambda (path desc format)
+     (cond
+      ((eq format 'html)
+       (format "(<cite>%s</cite>)" path))
+      ((eq format 'text)
+       (format "[%s]" 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))))))
+#+END_SRC
+
+# 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
+
+#+LATEX_HEADER: \setbeamertemplate{footline}[frame number]
+#+LATEX_HEADER: \setbeamertemplate{headline}{}
+#+LATEX_HEADER: \usepackage{multirow}
+#+LATEX_HEADER: \usepackage{fontawesome5}
+#+LATEX_HEADER: \usepackage{tcolorbox}
+#+LATEX_HEADER: \usepackage{tikz}
+
+#+LATEX_HEADER: \logo{\includegraphics[width=.1\textwidth]{../../../src/View/ui/ressources/Logo-INRAE.png}}
+
+#+LATEX_HEADER: \newcommand{\R}[1]{\rotatebox[origin=c]{90}{#1}}
+
+# Beamer colors
+#+LATEX_HEADER: \setbeamersize{text margin left=0.5cm,text margin right=0.5cm}
+#+LATEX_HEADER: \setbeamerfont{alerted text}{series=\bfseries}
+#+LATEX_HEADER: \setbeamerfont{example text}{series=\bfseries}
+
+#+LATEX_HEADER: \definecolor{inrae_1}{RGB}{102,193,191}
+#+LATEX_HEADER: \definecolor{inrae_2}{RGB}{0,150,152}
+#+LATEX_HEADER: \definecolor{inrae_3}{RGB}{39,86,98}
+
+#+LATEX_HEADER: \setbeamercolor{alerted text}{fg=inrae_1}
+#+LATEX_HEADER: \setbeamercolor{structure}{fg=inrae_2}
+#+LATEX_HEADER: \setbeamercolor{normal text}{fg=inrae_3}
+#+LATEX_HEADER: \setbeamercolor*{author}{fg=inrae_3}
+
+#+LATEX_HEADER: \usepackage[absolute,showboxes,overlay]{textpos}
+
+#+LATEX_HEADER: \TPshowboxesfalse
+#+LATEX_HEADER: \textblockorigin{5mm}{0mm}
+
+# Biblio
+#+LATEX_HEADER: \usepackage{natbib}
+# #+LATEX_HEADER: \bibliographystyle{apalike}
+#+LATEX_HEADER: \setbeamertemplate{bibliography item}{}
+#+LATEX_HEADER: \renewcommand\bibfont{\scriptsize}
+#+LATEX_HEADER: \setbeamertemplate{frametitle continuation}[from second]
+#+LATEX_HEADER: \setbeamercolor*{bibliography entry title}{fg=inrae_3}
+#+LATEX_HEADER: \setbeamercolor*{bibliography entry author}{fg=inrae_3}
+#+LATEX_HEADER: \setbeamercolor*{bibliography entry location}{fg=inrae_3}
+
+#+LATEX_HEADER: \usepackage{bbding}
+#+LATEX_HEADER: \usepackage{pdfpages}
+
+# Renew title page
+#+LATEX_HEADER: \defbeamertemplate*{title page}{customized}[1][]
+#+LATEX_HEADER: {
+# #+LATEX_HEADER:   {
+# #+LATEX_HEADER:     \usebeamerfont{date}\usebeamercolor[fg]{date}
+# #+LATEX_HEADER:     \tikz[overlay,remember picture]
+# #+LATEX_HEADER:     \node[xshift=-1cm,yshift=-1cm,text width=10cm] at (current page.north east) {
+# #+LATEX_HEADER:        7$^{th}$ International Conference\\
+# #+LATEX_HEADER:        8TH-10TH November\\
+# #+LATEX_HEADER:        EDF Lab - CHATOU, FRANCE
+# #+LATEX_HEADER:     }
+# #+LATEX_HEADER:   }
+#+LATEX_HEADER:   {
+#+LATEX_HEADER:     \usebeamerfont{title}\inserttitle\par
+#+LATEX_HEADER:     \usebeamerfont{title}\usebeamercolor[fg]{title}
+#+LATEX_HEADER:   }
+#+LATEX_HEADER:   \bigskip
+#+LATEX_HEADER:   \begin{center}
+#+LATEX_HEADER:     \usebeamerfont{subtitle}\usebeamercolor[fg]{subtitle}
+#+LATEX_HEADER:     {
+#+LATEX_HEADER:       \LARGE\insertsubtitle\par
+#+LATEX_HEADER:     }
+#+LATEX_HEADER:     \bigskip
+#+LATEX_HEADER:     \usebeamerfont{author}\usebeamercolor[fg]{author}\insertauthor\par
+#+LATEX_HEADER:     \bigskip
+#+LATEX_HEADER:     \usebeamerfont{institute}\usebeamercolor[fg]{institute}\insertinstitute\par
+#+LATEX_HEADER:     \bigskip
+#+LATEX_HEADER:     \usebeamerfont{date}\usebeamercolor[fg]{date}\insertdate\par
+#+LATEX_HEADER:     \usebeamercolor[fg]{titlegraphic}\inserttitlegraphic
+#+LATEX_HEADER:   \end{center}
+#+LATEX_HEADER: }
+
+# #+LATEX_HEADER: \newcommand{\tred}[1]{\textcolor{rouge_inrae}{#1}}
+
+#+TODO: TODO WIP TOREVIEW | DONE
+
+#+MACRO: pamhyr \textsc{PAMHyR}
+#+MACRO: pamhyr2 \textsc{Pamhyr2}
+
+#+MACRO: pause \pause
+#+MACRO: framebreak \framebreak
+#+MACRO: no
+# #+MACRO: OK  \checkmark
+#+MACRO: OK  \faIcon{check}
+#+MACRO: bf \textbf{$1}
+
+# #+latex: \frame{\tocpage}
+
+* Problématique
+
+** Problématique
+
+*** Utilisateur
+
+- Définire une version modifier de l'étude (changement dans les
+  données)
+- Comparé des résultats entre une variante et l'étude
+
+{{{pause}}}
+
+**** COMMENT Développeur
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
+
+- Un unique fichier
+- Limité la duplication de donnée à sauvegarder
+- Garder une bonne cohérence entre données et résultats
+
+{{{pause}}}
+
+*** Scénarios
+:PROPERTIES:
+:BEAMER_COL: 1
+:BEAMER_ENV: definition
+:END:
+
+Un scénario est une variate d'une étude.
+
+** Problématique -- Avancer
+
+*** Utilisateur
+
+- Définire une version modifier d'un senarios
+- Comparé des résultats entre plusieurs senarios
+
+{{{pause}}}
+
+**** COMMENT Développeur
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
+
+- Un unique fichier
+- Limité la duplication de donnée à sauvegarder
+- Garder une bonne cohérence entre données et résultats
+
+{{{pause}}}
+
+*** Scénarios
+:PROPERTIES:
+:BEAMER_COL: 1
+:BEAMER_ENV: definition
+:END:
+
+Un scénario peut être l'étude ou une variate d'un autre scénario.
+
+** Problématique -- Encore plus avancer
+
+*** Utilisateur
+
+- Définire un ensemble fini de variante correspondant a un ensemble de
+  valeur pour un(des) paramètre(s) et executer un solveur sur
+  l'ensemble des variantes
+- Pouvoir comparé des metrics sur un ensemble de résultats trop grand
+  pour une comparaisont à la mains
+
+{{{pause}}}
+
+**** COMMENT Développeur
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
+
+- Un unique fichier
+- Limité la duplication de donnée à sauvegarder
+- Garder une bonne cohérence entre données et résultats
+
+{{{pause}}}
+
+*** Scénarios
+:PROPERTIES:
+:BEAMER_COL: 1
+:BEAMER_ENV: definition
+:END:
+
+Un scénario peut être l'étude, une variate d'un scénarios ou un
+ensemble fini de variantes d'un scénarios.
+
+** Problématique -- Encore plus plus avancer
+
+*** Utilisateur
+
+- Définire un ensemble fini de variante correspondant a un ensemble de
+  valeur pour un(des) paramètre(s) et faire un nombre fini de tirage
+  aléatoire dans ces paramètre pour executer un solveur ces paramètres
+- Pouvoir comparé des metrics sur un ensemble de résultats trop grand
+  pour une comparaisont à la mains
+
+{{{pause}}}
+
+*** Scénarios
+:PROPERTIES:
+:BEAMER_COL: 1
+:BEAMER_ENV: definition
+:END:
+
+Un scénario peut être l'étude, une variate d'un scénarios ou un
+ensemble fini ou un tirage aléatoire dans un ensemble de variantes
+d'un scénarios.
+
+** Problématique -- Développeur
+
+*** Développeur
+
+- Permetre a l'utilisateur de *garder une bonne cohérence entre
+  données et résultats* de façon claire
+- Permetre a l'utilisateur de *géré les scénarios* de façon claire
+  (représentation graphique)
+- Garder *un unique fichier* (=.pamhyr=)
+- *Limité la duplication* de donnée à sauvegarder
+- Permetre à l'utilisateur de garder les *résultats pertinant* sans
+  exploser la mémoire de l'ordinateur
+
+* Proposition
+
+** Proposition -- Concept
+
+*** {{{no}}}
+\vspace{-1.2cm}
+**** Deux type de scénarios
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
+
+- Scénarios simple
+- Scénarios d'éxecution d'ensemble
+
+{{{pause}}}
+
+**** Scénarios simple
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
+
+Est composer:
+- d'un identifiant unique
+- d'un nom (définie par l'utilisateur)
+- d'une description (définie par l'utilisateur)
+- d'un parent (définie par l'utilisateur)
+
+{{{pause}}}
+
+\vspace{-0.5cm}
+
+*** Scénarios d'ensembles
+
+**** {{{no}}}
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
+\vspace{-1cm}
+Est composer:
+- d'un identifiant unique
+- d'un nom (définie par l'utilisateur)
+- d'une description (définie par l'utilisateur)
+- d'un parent (définie par l'utilisateur)
+- d'un ou plusieurs ensemble de valeur
+
+**** {{{no}}}
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
+\vspace{-0.5cm}
+Un ensemble de valeurs est definie par:
+- une valeurs de départ
+- une valeurs de fin
+- un pas de valeur
+- un élément d'origine (élément définie dans l'étude)
+- une fonctions (modification de l'élément à l'aide d'une valeur de
+  l'ensemble)
+
+** Proposition -- Limitation
+
+*** Scénarios simple
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
+
+Si le scénarios est le *parent d'un autre scénarios*, il ne *peut plus
+être modifier* sans risquer des comportement difficilement
+comprehensible pour l'utilisateur.
+
+{{{pause}}}
+
+*** Scénarios d'ensembles
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
+
+- Un scénarios d'ensemble *ne peut pas être parent* d'un autre
+  scénarios
+- Le nombre d'exécution peut très rapidement grossir
+
+** Proposition -- Affichage
+
+#+name: graph-scenarios
+#+header: :results drawer
+#+header: :exports results
+#+header: :post attr_wrap(width="7cm", data=*this*, name="graph-scenarios", caption="Exemple of scenarios graph", float="t")
+#+begin_src dot :file "images/graph-scenarios.png" :cache no
+  digraph {
+        bgcolor="transparent";
+        node[colorscheme=pastel19,shape=ellipse,style="filled",fillcolor=9];
+
+        b[fillcolor=2];
+
+        aa[shape=box,fillcolor=2];
+        aa2[label="aa'", shape=box, fillcolor=2];
+        ad[shape=box, fillcolor=2];
+        re[shape=box, fillcolor=2];
+        rf[shape=box, fillcolor=2];
+
+        default -> a;
+        default -> b;
+        default -> c;
+
+        a -> aa;
+        a -> aa2;
+        a -> f -> rf;
+        c -> d -> ad;
+        c -> e -> re;
+  }
+#+end_src
+
+#+RESULTS[80ed2484b9cc71143f800ff23c10846fd04697c3]: graph-scenarios
+:results:
+#+CAPTION[]: Exemple of scenarios graph
+#+NAME: graph-scenarios
+#+ATTR_LATEX: :width 7cm :float t
+[[file:images/graph-scenarios.png]]
+:end:
+
+* Solution technique
+
+** Technique -- scénarios
+
+#+begin_src sql
+  CREATE TABLE scenario(
+    id INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT,
+    name TEXT NOT NULL,           -- Name of the scenario
+    description TEXT NOT NULL,    -- Rich text description
+    parent_id INTEGER REFERENCES scenario(id) -- Recursive references
+                                              -- for parent scenario
+  )
+#+end_src
+
+** Technique -- Données -- Enregistrement
+
+#+begin_src sql
+  -- Unique ID (Must be unused, to delete)
+  id INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT,
+  -- New ID (not unique)
+  pamhyr_id INTEGER NOT NULL,
+  -- (Optional) Flag for set there is no data in this scenario and
+  -- ignore parent scenario
+  dummy BOOLEAN NOT NULL,
+  -- Corresponding scenario
+  scenario_id INTEGER NOT NULL,
+  PRIMARY KEY(pamhyr_id, scenario_id),
+  FOREIGN KEY(scenario_id) REFERENCES scenario(id),
+#+end_src
+
+** Technique -- Données -- Chargement
+
+#+begin_src python :python python3 :results output :noweb yes
+  def load(cls, db, current_scenario):
+    # Default case, end of recursion
+    if current_scenario is None:
+      return []                   # Default value
+
+    table = db.execute(f"<MY SELECT> WHERE scenario_id = {current_scenario}")
+
+    # If no data for this scenario, recursion
+    if len(table) == 0:
+      parent_id = db.get_parent_id(current_scenario)
+      return cls.load(db, parent_id)
+
+    # Otherelse, parse data and return...
+#+end_src
+
+** Technique -- Données -- Modification
+
+#+begin_src python :python python3 :results output :noweb yes
+  def set_modified(self, current_scenario):
+      self.scenario = current_scenario
+#+end_src
+
+#+begin_src python :python python3 :results output :noweb yes
+  def delete(self, current_scenario):
+      self.deleted = True
+      self.set_modified(current_scenario)
+#+end_src
+
+** Technique -- Exécution d'ensemble
+
+#+begin_src sql
+  CREATE TABLE range_set(
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    start REAL NOT NULL,          -- Range start
+    end REAL NOT NULL,            -- Range end
+    step REAL NOT NULL,           -- Range step
+    generator_name TEXT NOT NULL, -- Generator function name (ex:
+                                  -- 'minor_strickler')
+    original_data_id INTEGER,     -- (optional) Ref to data who apply
+                                  -- this range (ex: a strickler id)
+    scenario_id INTEGER NOT NULL,
+    FOREIGN KEY(scenario_id) REFERENCES scenario(id)
+  )
+#+end_src
+
+* Sauvegarde des résultats
+
+** Sauvegarde des résultats
+
+*** Scénarios simple
+
+Sauvegarde d'un seul résultats complet par scénarios (et par solver).
+
+*** Scénarios d'ensemble
+
+Sauvegarde de metrics récupéré sur un ensemble de résultats (pas de
+sauvegarde de tous les résultats) ou certain résultats particuliers.
+
+* Question & remarque
+
+** Question & remarque
+
+- Solution satisfaisante ?
+- Cas d'usage intéressent non couvert ?
+- Contre exemple ?
+- Meilleur solution ?

doc/paper/2023/simhydro/presentation/presentation.org

@@ -0,0 +1,487 @@
+# presentation.org -- 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 -*-
+
+#+STARTUP: indent hideblocks content beamer
+
+#+TITLE: SimHydro 2023
+#+SUBTITLE: \textbf{Pamhyr2}: a graphical user interface for 1D hydro-sedimentary modelling of rivers
+
+# #+AUTHOR: Pierre-Antoine Rouby
+#+LATEX_HEADER: \author[Pierre-Antoine Rouby]{\textbf{Pierre-Antoine Rouby$^{*}$}, Benoît Camenen, Lionel Pénard, Léa Kieffer, Théophile Terraz\\\texttt{<pierre-antoine.rouby@inrae.fr>}^{*}}
+#+EMAIL: pierre-antoine.rouby@inrae.fr
+#+INSTITUTE: INRAE Lyon-Villerbanne, teams River Hydraulics
+#+LATEX_HEADER: \institute{INRAE Lyon-Villerbanne, River Hydraulics team}
+#+DATE: 9th November
+
+#+KEYWORDS: g ui, hydraulics, sedimentary, hydro-sedimentary, 1D modelling, freesoftware, foss
+
+#+OPTIONS: H:2 toc:t num:t author:nil
+#+LATEX_CLASS: beamer
+#+LATEX_CLASS_OPTIONS: [slideopt,A4,showboxes,svgnames,aspectratio=169]
+# #+LATEX_CLASS_OPTIONS: [presentation]
+#+BEAMER_THEME: default
+#+COLUMNS: %45ITEM %10BEAMER_ENV(Env) %10BEAMER_ACT(Act) %4BEAMER_COL(Col)
+
+#+LANGUAGE: fr
+#+LATEX_HEADER: \usepackage[frenchb]{babel}
+
+#+BEGIN_SRC emacs-lisp :results silent :exports none
+  (setq org-latex-pdf-process (list
+    "latexmk -pdflatex='lualatex -shell-escape -interaction nonstopmode' -pdf -f  %f"))
+
+  (add-to-list 'org-latex-packages-alist '("" "minted"))
+  (setq org-latex-listings 'minted)
+  (setq org-src-fontify-natively t)
+
+  (org-add-link-type
+   "cite" 'ebib
+   (lambda (path desc format)
+     (cond
+      ((eq format 'html)
+       (format "(<cite>%s</cite>)" path))
+      ((eq format 'text)
+       (format "[%s]" 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))))))
+#+END_SRC
+
+#+LATEX_HEADER: \setbeamertemplate{footline}[frame number]
+#+LATEX_HEADER: \setbeamertemplate{headline}{}
+#+LATEX_HEADER: \usepackage{multirow}
+#+LATEX_HEADER: \usepackage{fontawesome5}
+#+LATEX_HEADER: \usepackage{tcolorbox}
+#+LATEX_HEADER: \usepackage{tikz}
+
+#+LATEX_HEADER: \logo{\includegraphics[width=.1\textwidth]{../../../../../src/View/ui/ressources/Logo-INRAE.png}}
+
+#+LATEX_HEADER: \newcommand{\R}[1]{\rotatebox[origin=c]{90}{#1}}
+
+# Beamer colors
+#+LATEX_HEADER: \setbeamersize{text margin left=0.5cm,text margin right=0.5cm}
+#+LATEX_HEADER: \setbeamerfont{alerted text}{series=\bfseries}
+#+LATEX_HEADER: \setbeamerfont{example text}{series=\bfseries}
+
+#+LATEX_HEADER: \definecolor{inrae_1}{RGB}{102,193,191}
+#+LATEX_HEADER: \definecolor{inrae_2}{RGB}{0,150,152}
+#+LATEX_HEADER: \definecolor{inrae_3}{RGB}{39,86,98}
+
+#+LATEX_HEADER: \setbeamercolor{alerted text}{fg=inrae_1}
+#+LATEX_HEADER: \setbeamercolor{structure}{fg=inrae_2}
+#+LATEX_HEADER: \setbeamercolor{normal text}{fg=inrae_3}
+#+LATEX_HEADER: \setbeamercolor*{author}{fg=inrae_3}
+
+#+LATEX_HEADER: \usepackage[absolute,showboxes,overlay]{textpos}
+
+#+LATEX_HEADER: \TPshowboxesfalse
+#+LATEX_HEADER: \textblockorigin{5mm}{0mm}
+
+# Biblio
+#+LATEX_HEADER: \usepackage{natbib}
+# #+LATEX_HEADER: \bibliographystyle{apalike}
+#+LATEX_HEADER: \setbeamertemplate{bibliography item}{}
+#+LATEX_HEADER: \renewcommand\bibfont{\scriptsize}
+#+LATEX_HEADER: \setbeamertemplate{frametitle continuation}[from second]
+#+LATEX_HEADER: \setbeamercolor*{bibliography entry title}{fg=inrae_3}
+#+LATEX_HEADER: \setbeamercolor*{bibliography entry author}{fg=inrae_3}
+#+LATEX_HEADER: \setbeamercolor*{bibliography entry location}{fg=inrae_3}
+
+#+LATEX_HEADER: \usepackage{bbding}
+#+LATEX_HEADER: \usepackage{pdfpages}
+
+# Renew title page
+#+LATEX_HEADER: \defbeamertemplate*{title page}{customized}[1][]
+#+LATEX_HEADER: {
+# #+LATEX_HEADER:   {
+# #+LATEX_HEADER:     \usebeamerfont{date}\usebeamercolor[fg]{date}
+# #+LATEX_HEADER:     \tikz[overlay,remember picture]
+# #+LATEX_HEADER:     \node[xshift=-1cm,yshift=-1cm,text width=10cm] at (current page.north east) {
+# #+LATEX_HEADER:        7$^{th}$ International Conference\\
+# #+LATEX_HEADER:        8TH-10TH November\\
+# #+LATEX_HEADER:        EDF Lab - CHATOU, FRANCE
+# #+LATEX_HEADER:     }
+# #+LATEX_HEADER:   }
+#+LATEX_HEADER:   {
+#+LATEX_HEADER:     \usebeamerfont{title}\inserttitle\par
+#+LATEX_HEADER:     \usebeamerfont{title}\usebeamercolor[fg]{title}
+#+LATEX_HEADER:     \large New modeling paradigms for water issues?\par
+#+LATEX_HEADER:   }
+#+LATEX_HEADER:   \bigskip
+#+LATEX_HEADER:   \begin{center}
+#+LATEX_HEADER:     \usebeamerfont{subtitle}\usebeamercolor[fg]{subtitle}
+#+LATEX_HEADER:     {
+#+LATEX_HEADER:       \LARGE\insertsubtitle\par
+#+LATEX_HEADER:     }
+#+LATEX_HEADER:     \bigskip
+#+LATEX_HEADER:     \usebeamerfont{author}\usebeamercolor[fg]{author}\insertauthor\par
+#+LATEX_HEADER:     \bigskip
+#+LATEX_HEADER:     \usebeamerfont{institute}\usebeamercolor[fg]{institute}\insertinstitute\par
+#+LATEX_HEADER:     \bigskip
+#+LATEX_HEADER:     \usebeamerfont{date}\usebeamercolor[fg]{date}\insertdate\par
+#+LATEX_HEADER:     \usebeamercolor[fg]{titlegraphic}\inserttitlegraphic
+#+LATEX_HEADER:   \end{center}
+#+LATEX_HEADER: }
+
+# #+LATEX_HEADER: \newcommand{\tred}[1]{\textcolor{rouge_inrae}{#1}}
+
+#+TODO: TODO WIP TOREVIEW | DONE
+
+#+MACRO: pamhyr \textsc{PAMHyR}
+#+MACRO: pamhyr2 \textsc{Pamhyr2}
+
+#+MACRO: pause \pause
+#+MACRO: framebreak \framebreak
+#+MACRO: no
+# #+MACRO: OK  \checkmark
+#+MACRO: OK  \faIcon{check}
+#+MACRO: bf \textbf{$1}
+
+# #+latex: \frame{\tocpage}
+
+* 1D hydro-sedimentary simulation at INRAE
+** COMMENT 1D river flow simulation
+*** INRAE (Lyon-Villerbanne)
+
+- Mage [fn:: Mage: https://gitlab.irstea.fr/jean-baptiste.faure/mage]
+- RubarBE [fn:: RubarBE:
+  https://gitlab.irstea.fr/theophile.terraz/rubarbe]
+
+*** Other project
+
+- Mascaret [fn:: OpenTeleMac: http://www.opentelemac.org]
+- HEC-RAS [fn:: HEC-RAS:
+  https://www.hec.usace.army.mil/software/hec-ras]
+- Mike 11 [fn:: Mike11:
+  https://www.mikepoweredbydhi.com/products/mike-11]
+
+** {{{pamhyr}}}
+#+BEGIN_EXPORT latex
+\tikz[overlay,remember picture]
+\node[xshift=-4cm,yshift=4cm] at (current page.south east) {
+  \includegraphics[width=7cm]{../images/PAMHyR.png}
+};
+#+END_EXPORT
+
+{{{pamhyr}}} developed at INRAE in Java since the end of 90s
+
+*** Features
+- Graphical user interface
+- Define and edit complexe 1D river models
+- Run a solver
+- Visualize simulation results
+
+*** Compatibility
+- 2 solvers *Mage and RubarBE*
+# - Multi-reaches (Only for Mage)
+- Multi-platform (Linux / Windows)
+
+** {{{pamhyr}}}
+#+BEGIN_EXPORT latex
+\tikz[overlay,remember picture]
+\node[xshift=-4cm,yshift=4cm] at (current page.south east) {
+  \includegraphics[width=7cm]{../images/PAMHyR.png}
+};
+#+END_EXPORT
+
+*** Conception issues
+- Monolingual French
+- Interface too different for each solver
+- Impossible to undo an action
+
+*** Huge technical debts
+- Out dated technologies (UML $\to$ Java)
+- Unmaintained library
+- Unstable development process
+
+Hard to maintain or add features to the interface
+
+(No modification since 2016)
+
+* Presentation of {{{pamhyr2}}}
+** {{{Pamhyr2}}} - Needs - General constraints
+
+Create a new version of {{{pamhyr}}} called {{{pamhyr2}}}
+
+{{{pause}}}
+
+*** Constraints for users experience
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
++ *User friendly*
++ *Multi platform* (at least Linux and Windows)
++ *Multi language* (at least English and French)
++ *Multi solver* (as much as possible, at least Mage and
+  RubarBE)
++ *Single save file* per study
+
+{{{pause}}}
+
+*** Constraints for developers experience
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
+- *Common used* code library and tools
+# - *Modular* and *flexible* code
+- *Clear* architecture
+- *Free and open sources software* (FOSS)
+
+** {{{Pamhyr2}}} - Needs - Features
+# #+BEGIN_EXPORT latex
+# \tikz[overlay,remember picture]
+# \node[xshift=-5cm,yshift=-2cm] at (current page.north east) {
+#   \includegraphics[width=6cm]{../images/geometry_saar.png}
+# };
+# #+END_EXPORT
+
+**** {{{no}}}
+:PROPERTIES:
+:BEAMER_COL: 0.30
+:BEAMER_ENV: block
+:END:
+- Define and edit data
+  + River network
+  + Geometry
+  + Boundary conditions
+  + Friction
+  + Initial conditions
+  + *Sedimentary layers*
+- User meshed geometry
+- Run a solver
+- Display results
+  + Default visualisation
+  + *Customized visualisation*
+
+**** {{{no}}}
+:PROPERTIES:
+:BEAMER_COL: 0.70
+:BEAMER_ENV: block
+:END:
+[[../images/geometry_saar.png]]
+
+** {{{pamhyr2}}} - Technical choices
+#+BEGIN_EXPORT latex
+\tikz[overlay,remember picture]
+\node[xshift=-9.3cm,yshift=-4cm] at (current page.north east) {
+  \includegraphics[width=6.3cm]{../images/BC.png}
+};
+#+END_EXPORT
+
+*** Technologies
+:PROPERTIES:
+:BEAMER_COL: 0.60
+:BEAMER_ENV: block
+:END:
+- *Python*
+- *PyQt*
+- Qt Designer
+- Qt Linguist
+- *Matplotlib*
+- SQLite (as =*.pamhyr=)
+- *GPLv3* license (strong copyleft)
+
+*** Architecture
+:PROPERTIES:
+:BEAMER_COL: 0.35
+:BEAMER_ENV: block
+:END:
+- Qt Model/View
+- Multiple solvers configuration
+- *Unified interface*, as much as possible
+
+** {{{pamhyr2}}} - State of the project
+#+BEGIN_EXPORT latex
+\tikz[overlay,remember picture]
+\node[xshift=-4.5cm,yshift=-2.5cm] at (current page.north east) {
+  \includegraphics[width=8cm]{../images/apply_sedi.png}
+};
+#+END_EXPORT
+
+*** {{{no}}}
+:PROPERTIES:
+:BEAMER_COL: 0.40
+:BEAMER_ENV: block
+:END:
+
+\vspace{-1.5cm}
+
+\begin{center}
+\emph{Last version:} \texttt{v0.0.3}
+\end{center}
+
+{{{pause}}}
+
+#+latex: \begin{center}
+#+latex: \resizebox{0.9\columnwidth}{!}{
+# #+caption: Tools by methods
+#+name: tab:current-state
+#+attr_latex: :align |l|c|
+|---------------------------------+-----------------|
+| {{{bf(Features)}}}              | {{{bf(State)}}} |
+|---------------------------------+-----------------|
+| Create save and load study      | {{{OK}}}        |
+| *Undo/Redo actions*             | {{{OK}}}        |
+| Edit river network              | {{{OK}}}        |
+| Edit geometry                   | {{{OK}}}        |
+| Edit boundary conditions        | {{{OK}}}        |
+| Edit lateral contributions      | {{{OK}}}        |
+| Edit frictions (Stricklers)     | {{{OK}}}        |
+| Edit initial conditions         | {{{OK}}}        |
+| *Edit sedimentary layers*       | {{{OK}}}        |
+| Edit hydraulics structures      |                 |
+| Edit suspended sediment         |                 |
+| Edit polluant                   |                 |
+| Use meshing tool                | WIP             |
+| Run a solver                    | {{{OK}}}        |
+| Read and display results        | {{{OK}}}        |
+| Customize results visualisation | WIP             |
+| Generic solver input/output     |                 |
+|---------------------------------+-----------------|
+#+latex: }
+#+latex: \end{center}
+
+{{{pause}}}
+
+*** {{{no}}}
+:PROPERTIES:
+:BEAMER_COL: 0.60
+:BEAMER_ENV: block
+:END:
+
+\vspace{2.5cm}
+
+#+latex: \begin{center}
+#+latex: \resizebox{0.8\columnwidth}{!}{
+# #+caption: Tools by methods
+#+name: tab:current-state-solver
+#+attr_latex: :align |l|c|c|c|
+|----------------------------+----------------+-------------------+--------------------|
+| {{{bf(Usage)}}}            | {{{bf(Mage)}}} | {{{bf(RubarBE)}}} | {{{bf(Mascaret)}}} |
+|----------------------------+----------------+-------------------+--------------------|
+| *Hydraulics* (mono reach)  | {{{OK}}}       |                   | {{{OK}}}           |
+| *Hydraulics* (multi reach) | {{{OK}}}       |                   |                    |
+| *Bed load evolution*       | {{{OK}}}       |                   |                    |
+|----------------------------+----------------+-------------------+--------------------|
+#+latex: }
+#+latex: \end{center}
+
+# #+LaTeX: \vspace{0.3cm}
+
+#+latex: \begin{center}
+#+latex: \resizebox{0.6\columnwidth}{!}{
+# #+caption: Tools by methods
+#+name: tab:current-state-package
+#+attr_latex: :align |l|c|c|
+|--------------------+---------------------+-------------------|
+| {{{bf(Packages)}}} | {{{bf(GNU/Linux)}}} | {{{bf(Windows)}}} |
+|--------------------+---------------------+-------------------|
+| Archive (tar/zip)  | {{{OK}}}            | {{{OK}}}          |
+| Installer          |                     | {{{OK}}}          |
+|--------------------+---------------------+-------------------|
+#+latex: }
+#+latex: \end{center}
+
+* Future work and perspective
+** Future work
+#+BEGIN_EXPORT latex
+\tikz[overlay,remember picture]
+\node[xshift=-4.8cm,yshift=-3.8cm] at (current page.north east) {
+  \includegraphics[width=8.7cm]{../images/results_hydro.png}
+};
+#+END_EXPORT
+
+*** Next step
+- *Meshing tools integration*
+- *Custom results visualisation*
+  + Python + matplotlib script
+- RubarBE integration
+- Hydraulics structures
+- Unified graphics theme
+
+*** Open questions
+- Generic solver input/output (HDF5? CGNS? SQLite?)
+- GNU/Linux packages (Pip? Conda? Guix? Deb?)
+
+** Contribution
+#+LaTeX: \begin{center}
+\faIcon{gitlab} https://gitlab.com/pamhyr/pamhyr2/
+#+LaTeX: \end{center}
+
+*** For users
+:PROPERTIES:
+:BEAMER_COL: 0.45
+:BEAMER_ENV: block
+:END:
+- Try {{{pamhyr2}}}
+- Report bug
+- Propose improvement
+- Improve translation
+- Improve user documentation
+- Improve tests cases examples
+- /Find better project name/
+
+*** For developers
+:PROPERTIES:
+:BEAMER_COL: 0.45
+:BEAMER_ENV: block
+:END:
+- Add new solver / features
+- Improve sources code
+- Improve developers documentation
+- Improve unit tests
+
+# * Conclusion
+** Thanks for listening
+# #+BEGIN_EXPORT latex
+# \tikz[overlay,remember picture]
+# \node[xshift=-6cm,yshift=-1.5cm,text width=10cm] at (current page.north east) {
+#    {\small\emph{\alert{Journées de la modélisation 1D hydro-sédimentaire} (in french) -}
+#    \emph{30 \& 31 janvier 2024, INRAE Villeurbanne - }
+#    \emph{Information and inscription: }\texttt{<benoit.camenen@inrae.fr>}}
+# };
+# #+END_EXPORT
+
+#+LaTeX: \begin{center}
+\faIcon{gitlab} https://gitlab.com/pamhyr/pamhyr2/
+#+LaTeX: \end{center}
+
+#+LaTeX: \begin{center}
+/*Journées de la modélisation 1D hydro-sédimentaire*/ (in French)
+#+LaTeX: \\
+/30 & 31 janvier 2024/, INRAE Villeurbanne
+#+LaTeX: \\
+Information and registration: =<benoit.camenen@inrae.fr>=
+#+LaTeX: \end{center}
+
+- {{{pamhyr2}}} developers:
+  + =<pierre-antoine.rouby@inrae.fr>=,
+  + =<theophile.terraz@inrae.fr>=
+- Mage/RubarBE developer:
+  + =<theophile.terraz@inrae.fr>=
+
+# #+LaTeX: \vspace{0.5cm}
+# #+LaTeX: \begin{center}
+# #+LaTeX: {\Large
+# *Thanks for listening*
+# #+LaTeX: }
+# #+LaTeX: \end{center}

doc/tools/PamhyrDoc.cls

@@ -11,7 +11,8 @@
 \usepackage[absolute]{textpos}
 \usepackage{titlesec}
 \usepackage{amssymb}
-\usepackage{tcolorbox}
+\usepackage[minted,xparse,breakable]{tcolorbox}
+\usepackage{pmboxdraw}
 
 \usepackage{enumitem}
 \setlist[enumerate]{itemsep=-0.5em}
@@ -133,6 +134,7 @@
 \setminted[c]{fontsize=\footnotesize,encoding=utf8,linenos}
 \setminted[c++]{breaklines,fontsize=\footnotesize,encoding=utf8,linenos}
 \setminted[python]{breaklines,fontsize=\footnotesize,encoding=utf8,linenos}
+\setminted[sql]{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}
@@ -140,7 +142,7 @@
 \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]}%
+\BeforeBeginEnvironment{minted}{\begin{tcolorbox}[breakable, boxsep=0pt, left=0.1cm, right=0.1cm, arc=0pt, boxrule=0.5pt, colback=white]}%
 \AfterEndEnvironment{minted}{\end{tcolorbox}}%
 
 \makeatletter
@@ -155,9 +157,13 @@
 %%
 
 %% FIXME: Delete me for the first realease
-\usepackage{draftwatermark}
+%% \usepackage{draftwatermark}
-\SetWatermarkLightness{0.8}
+%% \SetWatermarkLightness{0.8}
-\SetWatermarkAngle{25}
+%% \SetWatermarkAngle{25}
-\SetWatermarkScale{3}
+%% \SetWatermarkScale{3}
-\SetWatermarkFontSize{1cm}
+%% \SetWatermarkFontSize{1cm}
-\SetWatermarkText{Work in progress}
+%% \SetWatermarkText{Work in progress}
+
+%% Icons
+
+\usepackage{fontawesome5}

doc/tools/macro.org

@@ -17,11 +17,15 @@
 # -*- coding: utf-8 -*-
 
 # Constant name
-#+MACRO: oldPamhyr     PAMHyR
+#+MACRO: pamhyr        \textsc{PAMHyR}
-#+MACRO: Pamhyr        Pamhyr2
+#+MACRO: pamhyr2       \textsc{Pamhyr2}
-#+MACRO: Mage          Mage
+#+MACRO: mage          \textsc{Mage}
-#+MACRO: Rubarbe       RubarBE
+#+MACRO: mage7         \textsc{Mage7}
-#+MACRO: Inrae         INRAE
+#+MACRO: mage8         \textsc{Mage8}
+#+MACRO: rubarbe       \textsc{RubarBE}
+#+MACRO: adists        \textsc{AdisTS}
+#+MACRO: mascaret      \textsc{Mascaret}
+#+MACRO: inrae         INRAE
 #+MACRO: latex         \LaTeX
 
 # Information
@@ -35,6 +39,16 @@
 #+MACRO: cite          [cite:$1]
 #+MACRO: biblio        \bibliography{documentation}
 
+# Icons
+#+MACRO: bulb \faIcon{lightbulb}
+#+MACRO: OK  \faIcon{check}
+
+#+MACRO: linux  \faIcon{linux}
+#+MACRO: windows  \faIcon{windows}
+
+#+MACRO: python  \faIcon{python}
+#+MACRO: java  \faIcon{java}
+
 # Wrapper
 #+NAME: attr_wrap
 #+HEADER: :var width="\\textwidth"

doc/users/TP_AdisTS_Vieux_Rhone/Biblio.bib

@@ -0,0 +1,68 @@
+
+@article{camenen_simple_2007,
+	title = {Simple and {General} {Formula} for the {Settling} {Velocity} of {Particles}},
+	volume = {133},
+	language = {en},
+	number = {2},
+	urldate = {2025-01-23},
+	journal = {Journal of Hydraulic Engineering},
+	author = {Camenen, Benoit},
+	month = feb,
+	year = {2007},
+	pages = {229-233},
+}
+
+@article{meyer-peter_formulas_1948,
+	address = {Stockholm, Sweden},
+	title = {Formulas for bed-load transport.},
+	journal = {Report on Second Meeting of IAHR},
+	author = {Meyer-Peter, E and Mueller, R},
+	year = {1948},
+	pages = {39-64},
+}
+
+@article{elder_dispersion_1959,
+	title = {The dispersion of marked fluid in turbulent shear flow},
+	volume = {5},
+	issn = {0022-1120, 1469-7645},
+	language = {en},
+	number = {04},
+	urldate = {2025-01-23},
+	journal = {Journal of Fluid Mechanics},
+	author = {Elder, J. W.},
+	month = may,
+	year = {1959},
+	pages = {544},
+}
+
+@article{fischer_discussion_1975,
+	title = {Discussion of Simple Method for Predicting Dispersion in Streams},
+	volume = {101},
+	issn = {0090-3914, 2690-2435},
+	language = {en},
+	number = {3},
+	urldate = {2025-01-23},
+	journal = {Journal of the Environmental Engineering Division},
+	author = {Fischer, Hugo B},
+	month = mar,
+	year = {1975},
+	pages = {453-455},
+}
+
+@article{iwasa_predicting_1991,
+	address = {Hong Kong},
+	title = {Predicting longitudinal dispersion coefficient in open channel flows},
+	journal = {roc. Int. Symp. of Environmental Hydraulics},
+	author = {Iwasa, Y and Aya, S},
+	year = {1991},
+	pages = {505-510},
+}
+
+@book{soulsby_dynamics_1997,
+	address = {London},
+	edition = {Thomas Telford},
+	title = {Dynamics of {Marine} {Sands}: {A} {Manual} for {Practical} {Applications}},
+	urldate = {2025-01-23},
+	author = {Soulsby, Richard},
+	year = {1997},
+}

doc/users/TP_AdisTS_Vieux_Rhone/Sujet.tex

@@ -0,0 +1,175 @@
+
+%% LyX 2.0.2 created this file.  For more info, see http://www.lyx.org/.
+%% Do not edit unless you really know what you are doing.
+\documentclass[12pt,french]{article}
+\usepackage[T1]{fontenc}
+\usepackage[latin9]{inputenc}
+\usepackage{geometry}
+\geometry{verbose,tmargin=2cm,bmargin=2cm,lmargin=2cm,rmargin=2cm,headheight=2cm,headsep=2cm,footskip=2cm}
+\usepackage{textcomp}
+\usepackage{graphicx}
+\usepackage{hyperref}
+\usepackage[frenchb]{babel}
+
+\makeatletter
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LyX specific LaTeX commands.
+\newcommand{\noun}[1]{\textsc{#1}}
+%% Because html converters don't know tabularnewline
+\providecommand{\tabularnewline}{\\}
+
+\makeatother
+
+\usepackage{babel}
+\addto\extrasfrench{%
+   \providecommand{\og}{\leavevmode\flqq~}%
+   \providecommand{\fg}{\ifdim\lastskip>\z@\unskip\fi~\frqq}%
+}
+
+\begin{document}
+\includegraphics[width=5cm]{img/Logo-INRAE_Transparent.png}
+
+~
+
+~
+
+~
+
+\begin{center}
+
+TP AdisTS - Pamhyr2\\
+Version : Janvier 2025
+
+\par\end{center}
+
+~
+
+~
+
+\begin{center}
+
+\textbf{\LARGE Modélisation 1D du transport sédimentaire :  } \\
+\textbf{\LARGE Cas du Vieux-Rhône de Miribel-Jonage}\\
+\textbf{\LARGE (Lyon, France)}
+
+\par\end{center}{\LARGE \par}
+
+~
+\begin{center}
+	\includegraphics[width=17cm]{img/Garde.jpeg}
+	\par\end{center}
+~
+
+\begin{center}
+{\large INRAE Lyon-Grenoble Auvergne-Rhône-Alpes}
+\par\end{center}{\large \par}
+
+\begin{center}
+
+RiverLy, Hydraulique des rivières
+
+\par\end{center}
+
+~
+
+\begin{center}
+\begin{tabular}{lll}
+Auteur : & Dorian Hernandez & dorian.hernandez@inrae.fr\tabularnewline
+	     & Théophile Terraz & theophile.terraz@inrae.fr\tabularnewline
+
+\end{tabular}
+\par\end{center}
+
+~
+
+
+\pagebreak{}
+
+\begin{center}
+\tableofcontents{}
+\par\end{center}
+
+~
+
+\pagebreak{}
+
+% \section{Introduction}
+%
+% TODO
+%
+% \pagebreak{}
+
+
+\section{Contexte de l'étude - le colmatage du Vieux-Rhône}
+
+Le champ de captage de Crépieux-Charmy est un site de pompage d'eau potable alimentant 97 \% de la ville de Lyon. Situé au nord-est de la ville, il est en contact hydraulique avec trois chenaux du Rhône. Le canal de Miribel au Nord, dont les débits varient entre 89 (débit réservé) et 2400 ~$m³/s$ (Crue extrême), le canal de Jonage au sud, imposant un débit quasi constant de 600 ~$m³/s$ pour alimenter la centrale de Cusset, et un Vieux-Rhône qui traverse le site. Les fortes variations hydrauliques le long de Miribel, ainsi que le débit constant le long de Jonage mènent à un dépôt général des sédiments fins et grossiers le long du Vieux-Rhône, avec la création d'un remous important causé par Jonage.
+
+\begin{center}
+\includegraphics[width=15cm]{img/Intro.jpeg}
+\par\end{center}
+
+Eau du grand Lyon, le gérant du champ de captage, souhaite identifier les zones de dépôts de sédiments fin le long du Vieux-Rhône, cause principale de colmatage, impactant les performances de pompage de l'eau dans les nappes. 
+
+
+\begin{center}
+\includegraphics[width=15cm]{img/Champ_captant.jpeg}
+\par\end{center}
+
+Pour cela, une campagne expérimentale visant à identifier les zones colmatés du Vieux-Rhône a été réalisée et a mis en avant une hétérogénéité du site. Notamment, une forte zone de dépôts de grossier est présente en amont. Tandis qu'une présence plus importante de fines et sables dans la zone aval (zone de remous de Jonage) a été observée, ainsi qu'un colmatage plus important.
+
+\begin{center}
+	\includegraphics[width=15cm]{img/Grossier_sable.jpeg}
+\par\end{center}
+
+En parallèle, un modèle numérique hydraulique 1D a été élaboré sous Pamhyr2 afin d'analyser l'écoulement sur le site. Les résultats numériques mettent alors bien en avant le remous généré par Jonage, ainsi qu'une diminution de la vitesse de l'écoulement à partir du point kilométrique (PK) 1000, fin de la zone amont.
+
+\begin{center}
+	\includegraphics[width=15cm]{img/Simu.jpeg}
+	\par\end{center}
+
+\section{Objectifs de l'étude}
+
+Le modèle numérique 1D représente actuellement la partie hydraulique du système. L'objectif du TP est alors de mettre en donnée la partie sédimentaire (fines) du modèle, afin d'effectuer des calculs à l'aide de AdisTS , et in-fine, identifier les zones de dépôt et d'érosion des sédiments fins le long du Vieux-Rhône selon différents scénarios hydraulique. Les différentes étapes seront alors : 
+
+\begin{itemize}
+	\item Mettre en données le modèle Pamhyr2 du Vieux-Rhône pour le solveur AdisTS.
+	\item Lancer des calculs Mage - AdisTS pour différents scénarios hydrauliques.
+	\item Interpréter et discuter les résultats obtenus (comportement hydro-sédimentaire du site, impacts des débits, impact d'une crue, limites du modèle, etc..)
+\end{itemize}
+
+\section{Données fournies}
+
+\textbf{Le modèle numérique du Vieux-Rhône}
+
+Fichier \textit{Vieux\_Rhone\_TP\_AdisTS.pamhyr}.\\
+
+\textbf{Les scénarios hydrauliques}
+
+Quatre scénarios hydrauliques sont à analyser  (voir les conditions initiales hydraulique) : 
+
+\begin{itemize}
+	\item Le premier correspond à un débit constant de 25~$m³/s$
+	\item Le deuxième consiste en une faible montée en débit puis à une redescente (25 - 50 - 25~$m³/s)$.
+	\item Le troisième correspondant à une plus forte montée en débit (25 - 100 - 25~$m³/s)$.
+	\item Le dernier correspond à une crue (25 - 600 - 25~$m3/s)$.\\
+\end{itemize}
+
+\textbf{Propriétés des sédiments}
+
+Nous considérerons 2 classes de sédiments de types sable naturel, correspondant à une classe de Fines (limon) de diamètre moyen 63 microns et une classe de Sable de 500 microns. Les deux classes auront une masse volumique de 2650~$kg/m³$, et une porosité de 0,45 pourra être choisie. Leurs concentrations constantes en amont (conditions aux limites amont) seront de 60 $mg/l$ pour les fines et 30 $mg/l$ pour les sables. Nous considérerons dans un premier temps qu'il n'y a aucun dépôt initial de ces deux classes de sédiments et que la concentration initiale en sédiments dans le bief est nulle.\\
+
+\textbf{Documentation}
+
+\begin{itemize}
+	\item Un tutoriel guidé de mise en données : Pas-a-pas.pdf.
+	\item Un guide utilisateur de AdisTS : adis-TS\_usage.pdf
+	\item Un guide de conception de AdisTS : adis-TS\_conception.pdf
+\end{itemize}
+
+\section{Bonus}
+
+Ajouter une épaisseur initiale de sédiments \textit{Sables} au fond de 1 $cm$ et relancer un calcul avec le scénario 1.
+
+
+\pagebreak{}
+\end{document}

doc/users/TP_AdisTS_Vieux_Rhone/build.sh

@@ -0,0 +1,8 @@
+#! /bin/sh
+
+pdflatex -no-shell-escape pas-a-pas.tex
+bibtex pas-a-pas.aux
+pdflatex -no-shell-escape pas-a-pas.tex
+pdflatex -no-shell-escape pas-a-pas.tex
+pdflatex -no-shell-escape Sujet.tex
+pdflatex -no-shell-escape Sujet.tex