change default parameters

debug translation
BHS: Fix previous commit.
2026-10-30 03:20:41 +01:00 · 2024-10-07 17:52:14 +02:00 · 2024-10-07 17:30:52 +02:00 · 2024-10-07 15:34:28 +02:00 · 2024-10-07 15:26:40 +02:00 · 2024-10-07 14:26:49 +02:00
495 changed files with 19437 additions and 12675 deletions
@@ -270,6 +270,7 @@ 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

@@ -645,3 +646,233 @@ TSWLatexianTemp*
 *.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
@@ -1,5 +1,5 @@
 # .gitlab-ci.yml -- Pamhyr gitlab-ci
-# Copyright (C) 2023  INRAE
+# 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
@@ -20,6 +20,8 @@ stages:
  - test
  - build
  - package
+  - hash
+  - antivirus
  - release

 #############
@@ -27,9 +29,9 @@ stages:
 #############

 variables:
-  MAGE_VERSION: "v8.3.3"
+  MAGE_8_VERSION: "v8.3.6"

-dl-mage-doc:
+dl-mage8-doc:
  stage: downloads
  tags:
    - linux
@@ -38,46 +40,48 @@ dl-mage-doc:
  script:
    - mkdir -p doc
    - cd doc
-    - curl -L -o mage8.pdf https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_VERSION/downloads/documents/Mage-8_Documentation.pdf
+    - curl -L -o mage8.pdf https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/documents/Mage-8_Documentation.pdf
  artifacts:
    paths:
      - doc/mage8.pdf

-dl-mage-linux:
+dl-mage8-linux:
  stage: downloads
  tags:
    - linux
  rules:
    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
  script:
-    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_VERSION/downloads/packages/mage_linux.tgz
-    - mkdir -p mage-linux
-    - cd mage-linux
-    - tar xvf ../mage.tgz
+    - curl -L -o mage8.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/packages/mage_linux.tgz
+    - mkdir -p mage8-linux
+    - cd mage8-linux
+    - tar xvf ../mage8.tgz
  artifacts:
    paths:
-      - mage-linux/mage
-      - mage-linux/mage_extraire
-      - mage-linux/mailleurTT
-      - mage-linux/libbief.so
+      - mage8-linux/mage
+      - mage8-linux/mage_as7
+      - mage8-linux/mage_extraire
+      - mage8-linux/mailleurTT
+      - mage8-linux/libbief.so

-dl-mage-windows:
+dl-mage8-windows:
  stage: downloads
  tags:
    - linux
  rules:
    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
  script:
-    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_VERSION/downloads/packages/mage_windows.tgz
-    - mkdir -p mage-windows
-    - cd mage-windows
-    - tar xvf ../mage.tgz
+    - curl -L -o mage8.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/packages/mage_windows.tgz
+    - mkdir -p mage8-windows
+    - cd mage8-windows
+    - tar xvf ../mage8.tgz
  artifacts:
    paths:
-      - mage-windows/mage.exe
-      - mage-windows/mage_extraire.exe
-      - mage-windows/mailleurTT.exe
-      - mage-windows/libbief.dll
+      - mage8-windows/mage.exe
+      - mage8-windows/mage_as7.exe
+      - mage8-windows/mage_extraire.exe
+      - mage8-windows/mailleurTT.exe
+      - mage8-windows/libbief.dll

 #############
 # CONFIGURE #
@@ -148,23 +152,22 @@ test-pep8:
 # 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-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
@@ -221,9 +224,9 @@ build-linux:
  rules:
    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
  needs:
-    - job: dl-mage-linux
+    - job: dl-mage8-linux
      artifacts: true
-    - job: dl-mage-doc
+    - job: dl-mage8-doc
      artifacts: true
    - job: set-version
      artifacts: true
@@ -231,8 +234,8 @@ build-linux:
      artifacts: true
    - job: build-developers-doc
      artifacts: true
-    - job: build-users-doc
-      artifacts: true
+    # - job: build-users-doc
+    #   artifacts: true
    - job: build-td
      artifacts: true
  script:
@@ -248,28 +251,32 @@ build-linux:
    - pyinstaller -y --paths linux-venv/lib/python3.8/site-packages ../src/pamhyr.py
    # Create directory
    - mkdir -p pamhyr
-    - mkdir -p pamhyr/pamhyr
-    - mkdir -p pamhyr/pamhyr/_internal
+    - mkdir -p pamhyr/_internal
    # Copy Pamhyr info
-    - cp -v ../VERSION pamhyr/pamhyr/_internal/
-    - cp -v ../AUTHORS pamhyr/pamhyr/_internal/
-    - cp -v ../LICENSE pamhyr/pamhyr/_internal/
-    - cp -v ../src/motd.txt pamhyr/pamhyr/_internal/
+    - cp -v ../VERSION pamhyr/_internal/
+    - cp -v ../AUTHORS pamhyr/_internal/
+    - cp -v ../LICENSE pamhyr/_internal/
+    - cp -v ../src/motd.txt pamhyr/_internal/
    # Copy mage
-    - mkdir -p pamhyr/mage
-    - cp -v ../mage-linux/* pamhyr/mage/
+    - mkdir -p pamhyr/mage8
+    - cp -v ../mage8-linux/* pamhyr/mage8/
    # 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/_internal/View
-    - mkdir -p pamhyr/pamhyr/_internal/View/ui
-    - mkdir -p pamhyr/pamhyr/_internal/View/ui/Widgets
-    - cp -r ../src/View/ui/*.ui pamhyr/pamhyr/_internal/View/ui/
-    - cp -r ../src/View/ui/ressources/ pamhyr/pamhyr/_internal/View/ui
-    - cp -r ../src/View/ui/Widgets/*.ui pamhyr/pamhyr/_internal/View/ui/Widgets
+    - mkdir -p pamhyr/_internal/View
+    - mkdir -p pamhyr/_internal/View/ui
+    - mkdir -p pamhyr/_internal/View/ui/Widgets
+    - cp -r ../src/View/ui/*.ui pamhyr/_internal/View/ui/
+    - cp -r ../src/View/ui/ressources/ pamhyr/_internal/View/ui
+    - cp -r ../src/View/ui/Widgets/*.ui pamhyr/_internal/View/ui/Widgets
    # Copy lang
-    - mkdir -p pamhyr/pamhyr/_internal/lang
-    - cp -r ../src/lang/*.qm pamhyr/pamhyr/_internal/lang
+    - mkdir -p pamhyr/_internal/lang
+    - cp -r ../src/lang/*.qm pamhyr/_internal/lang
    # Copy tests cases
    - mkdir -p pamhyr/tests_cases/
    - mkdir -p pamhyr/tests_cases/Saar
@@ -297,10 +304,6 @@ build-linux:
    # Copy TP charriage
    - mkdir -p pamhyr/doc/TP_charriage/
    - cp ../doc/users/TP_charriage/* pamhyr/doc/TP_charriage
-    # Create running script
-    - echo "#!/bin/sh" > pamhyr/Pamhyr2
-    - echo "./pamhyr/pamhyr $@" >> pamhyr/Pamhyr2
-    - chmod u+x pamhyr/Pamhyr2
  artifacts:
    paths:
      - linux/pamhyr
@@ -312,9 +315,9 @@ 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-mage-doc
+    - job: dl-mage8-doc
      artifacts: true
    - job: set-version
      artifacts: true
@@ -322,18 +325,20 @@ build-windows:
      artifacts: true
    - job: build-developers-doc
      artifacts: true
-    - job: build-users-doc
-      artifacts: true
+    # - job: build-users-doc
+    #   artifacts: true
    - job: build-td
      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 --hide-console hide-early -y ..\src\pamhyr.py
    # Create directory
    - mkdir pamhyr
    - dir
@@ -403,6 +408,111 @@ 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 #
 ###########
@@ -419,10 +529,12 @@ tag-release:
      artifacts: true
    - job: windows-package-exe
      artifacts: true
-    - job: build-users-doc
-      artifacts: true
+    # - job: build-users-doc
+    #   artifacts: true
    - job: build-developers-doc
      artifacts: true
+    - job: pkg-hash
+      artifacts: true
  rules:
    - if: $CI_COMMIT_TAG
  artifacts:
@@ -430,33 +542,44 @@ tag-release:
      - linux/pamhyr-gnulinux.tar.xz
      - windows/pamhyr-windows.zip
      - windows/pamhyr-windows.exe
+      - linux/pamhyr-gnulinux.tar.xz.sha256
+      - windows/pamhyr-windows.zip.sha256
+      - windows/pamhyr-windows.exe.sha256
      - doc/dev/documentation.pdf
-      - doc/users/documentation.pdf
+      # - doc/users/documentation.pdf
  script:
    - cd packages
  release:
    name: '$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'
@@ -1,3 +1,3 @@
 Sylvain COULIBALY, INRAE, 2020 - 2022
-Théophile TERRAZ, INRAE, 2022 - 2023
-Pierre-Antoine ROUBY, INRAE, 2023
+Théophile TERRAZ, INRAE, 2022 - 2024
+Pierre-Antoine ROUBY, INRAE, 2023 - 2024
@@ -3,63 +3,38 @@
 Pamhyr is a free and open source graphical user interface for 1D hydro-sedimentary
 modelling of rivers.

+![logo](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/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
-+ Add reservoirs
-+ Add hydraulic structures
-+ Generate initial conditions
-+ Edit river sedimentary layers
+ Define river friction
+ Define reservoirs
+ 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

 Let see the
 [documentation](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home)
+([:fr:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home-fr),
+[:gb:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home-en))
 for more details.

 ## Install

 ### GNU/Linux

-Downloads the [last
-realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
-GNU/Linux binary archive.
-
-```shell
-tar xf pamhyr-gnulinux.tar.xz
-cd pamhyr
-./Pamhyr2
-```
+See documentation:
+- [French :fr:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/fr/Install%20on%20GNULinux)
+- [English :gb:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/en/Install%20on%20GNULinux)

 ### Windows

-Downloads the [last
-realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
-Windows installer or ZIP archive.
-
-### From source code
-
-```shell
-# Get mage
-mkdir mage
-cd mage
-
-curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/v8.3.2/downloads/packages/mage_linux.tgz
-tar xf mage.tgz
-
-cd ..
-
-# Get Pamhyr2 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
-```
+See documentation:
+- [French :fr:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/fr/Install%20on%20Windows)
+- [English :gb:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/en/Install%20on%20Windows)
@@ -1,5 +1,5 @@
 # documentation.org -- Pamhyr developers documentation
-# Copyright (C) 2023  INRAE
+# 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
@@ -369,6 +369,7 @@ of Bar (Listing [[sql-bar]] and [[sql-foo]]).
            CREATE TABLE bar (
              id INTEGER NOT NULL PRIMARY KEY,
              x INTEGER NOT NULL,
+              y INTEGER NOT NULL,
              foo_id INTEGER NOT NULL,
              FOREIGN KEY(foo_id) REFERENCES foo(id),
            )""")
@@ -455,6 +456,15 @@ of Bar (Listing [[sql-bar]] and [[sql-foo]]).
              bar._sql_save(execute, data=data)
 #+end_src

+Let see the results database scheme for Pamhyr2 at version v0.0.7 in
+Figure [[sql_schema]].
+
+#+NAME: sql_schema
+#+ATTR_LATEX: :width 16cm
+#+CAPTION: SQLite database scheme at Pamhyr2 version v0.0.7 (generate with [[https://gitlab.com/Screwtapello/sqlite-schema-diagram]])
+[[./images/schema_v0.0.7.png]]
+
+
 [fn:sqlite] The SQLite web site: https://www.sqlite.org/index.html
 (last access 2023-09-20)

@@ -538,44 +548,44 @@ generic value from optional parameters, for examples:
 #+NAME: window
 #+CAPTION: Example of Pamhyr2 window
 #+begin_src python :python python3 :results output :noweb yes
-    from View.Tools.PamhyrWindow import PamhyrWindow
-    from View.My.Translate import MyTranslate
-    from View.My.Table import MyTableModel
+  from View.Tools.PamhyrWindow import PamhyrWindow
+  from View.My.Translate import MyTranslate
+  from View.My.Table import MyTableModel

-    class MyWindow(PamhyrWindow):
-        _pamhyr_ui = "MyUI"
-        _pamhyr_name = "My window"
+  class MyWindow(PamhyrWindow):
+      _pamhyr_ui = "MyUI"
+      _pamhyr_name = "My window"

-        def __init__(self, my_data=None,
-                     study=None, config=None,
-                     parent=None):
-            self._my_data = my_data
+      def __init__(self, study=None, config=None,
+                   my_data=None,
+                   parent=None):
+          self._my_data = my_data

-            super(MyWindow, self).__init__(
-                # Window title
-                title = self._pamhyr_name + " - " + study.name,
-                # Window standard data
-                study = study, config = config,
-                trad = MyTranslate(),
-                parent = parent,
-                # Activate undo/redo and copy/paste shortcut
-                options = ["undo", "copy"]
-            )
+          super(MyWindow, self).__init__(
+              # Window title
+              title = self._pamhyr_name + " - " + study.name,
+              # Window standard data
+              study = study, config = config,
+              trad = MyTranslate(),
+              parent = parent,
+              # Activate undo/redo and copy/paste shortcut
+              options = ["undo", "copy"]
+          )

-            # Add custom data to hash window computation
-            self._hash_data.append(self._my_data)
+          # Add custom data to hash window computation
+          self._hash_data.append(self._my_data)

-            # Setup custom window components
-            self.setup_table()
-            self.setup_connections()
+          # Setup custom window components
+          self.setup_table()
+          self.setup_connections()

-        def setup_table(self):
-            # Init table(s)...
+      def setup_table(self):
+          # Init table(s)...

-        def setup_connections(self):
-            # Init action connection(s)...
+      def setup_connections(self):
+          # Init action connection(s)...

-        # ...
+      # ...
 #+end_src

 Typically we called method =setup_*=, the method to initialize some
@@ -636,7 +646,7 @@ class AddNodeCommand(QUndoCommand):
        self._node = node

    def undo(self):
-        self._graph.remove_node(self._node.name)
+        self._graph.remove_node(self._node)

    def redo(self):
        self._graph.insert_node(self._node)
@@ -661,11 +671,13 @@ creation, this stack is accessible at =self._undo_stack=.

 *** Plot

-To define a new plot you can create a class who inherit to APlot. The
-creator need threee argument:
+To define a new plot you can create a class who inherit to
+PamhyrPlot. The creator need at leaste five argument:
 - A =canvas= of type =MplCanvas=
+ - A (optional) =trad= of type =PamhyrTranslate=
 - A =data= used in =draw= and =update= to create and update the plot
 - A optional =toolbar= of type =PamhyrToolbar=
+ - A =parent= window
 This class must implement two method =draw= and =update=, the first
 method to draw the plot from scratch, the second to update the plot if
 data has changed.
@@ -673,19 +685,36 @@ data has changed.
 #+begin_src python :python python3 :results output :noweb yes
  from View.Tools.PamhyrPlot import PamhyrPlot

-  class MyPlot(APlot):
-      def __init__(self, canvas=None, data=None, toolbar=None):
+  class MyPlot(PamhyrPlot):
+      def __init__(self, canvas=None, trad=None, toolbar=None
+                   data=None, parent=None):
          super(MyPlot, self).__init__(
              canvas=canvas,
+              trad=trad,
              data=data,
-              toolbar=toolbar
+              toolbar=toolbar,
+              parent=parent
          )

+        self.label_x = self._trad["x"]
+        self.label_y = self._trad["y"]
+
+        # Optional configuration
+        self._isometric_axis = False
+
+        self._auto_relim_update = True
+        self._autoscale_update = True
+
      def draw(self):
          # Draw function code...

-      def update(self, ind = None):
+      def update(self):
          # Update function code...
+
+      def clear(self):
+          # Clear plot values...
+
+      # ...
 #+end_src

 ** Solver
@@ -745,7 +774,7 @@ execute a code on distant computer, for example, over ssh.
                  style=dashed;
                  subgraph cluster021 {
                      label="Solver Classes";
-                      classSolverM7[label="Mage7", fillcolor=6];
+                      //classSolverM7[label="Mage7", fillcolor=6];
                      classSolverM8[label="Mage8", fillcolor=6];
                      classSolverR[label="RubarBE", fillcolor=6];
                  }
@@ -828,7 +857,7 @@ solver and get results:
 - (2.1) The solver read the input file(s)
 - (2.2) The solver compute results and write it to solver output
   file(s)
- - (3) Pamhyr2 create a Reuslts
+ - (3) Pamhyr2 create a =Results= object
 - (3.1) The Pamhyr2 solver class read solver output file(s) and
   complete Results with readed data

@@ -958,8 +987,16 @@ different methods:

 ** Unit tests

-The unit tests is actually not implemented in Pamhyr2, it is a *work
-in progress*.
+A very small part of Pamhyr2 has unit test. This part is limited to the Model.
+
+#+begin_src shell
+  python3 -m venv test
+  . test test/bin/activate
+  pip3 install -U -r ./full-requirements.txt
+
+  cd src/
+  python3 -Walways -m unittest discovert -v -t .
+#+end_src

 ** The debug mode

@@ -970,14 +1007,14 @@ line:
 ./Pamhyr2 debug
 #+end_src

-This mode add some log and add two action in main window menu:
-"About/Debug" open a window with Python Repl in current Python
-environement, and "About/Debug SQLite" who open the application
+This mode add some log and add two action in main window menu: "About
+> Debug" open a window with Python Repl in current Python
+environement, and "About > Debug SQLite" who open the application
 SQLiteBrowser (if installed) on current Study to explore the study
 data base file.

 #+NAME: debug-repl
-#+ATTR_LATEX: :width 12cm
+#+ATTR_LATEX: :width 14cm
 #+CAPTION: Pamhyr2 debug Python REPL
 [[./images/python-debug-repl.png]]

@@ -1297,7 +1334,7 @@ https://gitlab.irstea.fr/theophile.terraz/pamhyr

 You can improve or add translation for the project. To contribute to
 Pamhyr2 translate, you need to use Qt Linguist[fn:qt-linguist]. Open
-Qt-linguist and edite the translation ({{{file(.ts)}}}) file, finally,
+Qt-linguist and edit the translation ({{{file(.ts)}}}) file, finally,
 commit the new version of file and make a merge request.

 If you want add a new language, edit the script
@@ -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.irstea.fr/theophile.terraz/pamhyr/
+#+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.irstea.fr/theophile.terraz/pamhyr/
+#+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}
@@ -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
@@ -1,4 +1,6 @@
 #! /bin/sh

+pdflatex -no-shell-escape step-by-step.tex
 pdflatex -no-shell-escape step-by-step.tex
 pdflatex -no-shell-escape pas-a-pas.tex
+pdflatex -no-shell-escape pas-a-pas.tex
@@ -1,2 +0,0 @@
-0:00:00:00	15
-0:00:01:00	15
@@ -1,25 +0,0 @@
-**************** SINGULARITES **********************
-*BieSec Nb Longueur  Cote dev Cote charg Coef deb            Impression         
-*===---===----------==========----------==========----------------------------- 
-*****************************************************
-* Bief n°  1
-*****************************************************
-* Ouvrage au pk 36270.0  seuil_aval
-*SeuilR type D
-D  1  36270.00    18.250    15.500     0.000     0.400 99999.000 seuil palplanches
-* Ouvrage au pk 31875.0  PontRS101
-*OrificeR type O
-O  1  31875.00     9.660    18.710    21.890     0.400  9999.000 
-*SeuilR type D
-D  1  31875.00    14.000    22.890     0.000     0.400 99999.000 
-* Ouvrage au pk 34335.0  PontThivencelle
-*SeuilR type D
-D  1  34335.00    13.000    21.740     0.000     0.400 99999.000 
-*OrificeR type O
-O  1  34335.00     9.070    17.280    20.740     0.400  9999.000 
-*****************************************************
-* Bief n°  3
-*****************************************************
-* Ouvrage au pk 0.0  Orifice
-*OrificeR type O
-*O  3     0.000     6.000    19.000    19.001     0.400    20.000 Clapet_001
@@ -1,2 +0,0 @@
-0:00:00:00	4
-0:00:01:00	4
@@ -1,24 +0,0 @@
-16,03	0
-16,13	1,29
-16,23	3,64
-16,33	6,7
-16,43	10,31
-16,53	14,41
-16,63	18,94
-16,73	23,87
-16,83	29,16
-16,93	34,79
-17,03	40,75
-17,13	47,01
-17,23	53,57
-17,33	60,4
-17,43	67,5
-17,53	74,86
-17,63	82,47
-17,73	90,33
-17,83	98,41
-17,93	106,73
-18,03	115,26
-18,13	124,01
-18,23	132,98
-18,33	142,14
@@ -80,7 +80,7 @@ RiverLy, Hydraulique des rivi

 \begin{center}
 \begin{tabular}{lll}
-Autors : & Pierre-Antoine Rouby & pierre-antoine.rouby@inrae.fr\tabularnewline
+Auteurs : & Pierre-Antoine Rouby & pierre-antoine.rouby@inrae.fr\tabularnewline
 & Théophile TERRAZ & theophile.terraz@inrae.fr\tabularnewline
 & Lionel Pénard & lionel.penard@inrae.fr\tabularnewline

@@ -110,43 +110,64 @@ Autors : & Pierre-Antoine Rouby & pierre-antoine.rouby@inrae.fr\tabularnewline

 Pamhyr2 peut être téléchargé ici : \url{https://gitlab.irstea.fr/theophile.terraz/pamhyr}.

+Si vous arrivez sur une fenêtre de connexion, cliquez sur "parcourir la liste des dépôts publics" et cherchez l'URL donnée plus haut.
+Utilisez le bouton de téléchargement GNU Linux ou Windows en fonction de votre système.
+
 \begin{center}
 \includegraphics[width=15cm]{img/dl.png}
 \par\end{center}

-
-Utilisez le bouton de téléchargement GNU Linux ou Windows en fonction de votre système. Sous Windows, lancez le programme d'installation. Sous Linux, décompressez l'archive et lancez Pamhyr2.
-
+Décompressez l'archive et lancez Pamhyr2.

 \section{Créer une première étude}

-Dans la fenêtre principale, cliquez sur \texttt{[Fichier] => [Nouvelle étude]} pour créer une nouvelle étude. Choisissez un nom, par exemple Hogneau, et validez
+Dans la fenêtre principale, cliquez sur \texttt{[Fichier] => [Nouvelle étude]} pour créer une nouvelle étude.
+Choisissez un nom, par exemple \textit{Hogneau}, et validez.

-Cliquez sur \texttt{[Réseau] => [Editer le réseau]} pour créer les biefs de votre rivière. Dans cette fenêtre, vous devez définir un graphe orienté qui représente les biefs de votre réseau fluvial : les arêtes sont les biefs et les n½uds sont soit des conditions limites amont, soit des conditions limites aval, soit des jonctions entre biefs.
-Appuyez sur le bouton \includegraphics[width=0.5cm]{img/gtk_add.png} pour entrer dans le mode \textit{Ajout}. Créez deux n½uds en cliquant dans la zone grise de la fenêtre, et créez un lien en cliquant à nouveau sur chaque n½ud. Appuyez à nouveau sur \includegraphics[width=0.5cm]{img/gtk_add.png} pour quitter le mode \textit{Ajout}. Vous avez créé votre premier bief, avec un n½ud amont et un n½ud aval. Dans la partie inférieure de la fenêtre \textit{Editer le réseau hydrographique}, vous pouvez renommer les n½uds et les biefs. Comme le bief que vous avez créé est automatiquement sélectionné, toutes les étapes suivantes s'appliqueront à ce bief. La fenêtre doit se présenter comme suit :
+\begin{center}
+\includegraphics[width=15cm]{img/NEWSTUDY.png}
+\par\end{center}

+Pendant que vous travaillez sur votre étude, n'oubliez pas de sauvegarder régulièrement, à l'aide du bouton \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/save.png} de la fenêtre principale.
+
+\section{Créer la structure de la rivière}
+
+Cliquez sur \texttt{[Réseau] => [Éditer le réseau]} ou sur l'icône \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/network.png} pour créer la structure de votre rivière.
+Nous voici dans la fenêtre \textit{Réseau}.
+Dans cette fenêtre, nous allons définir un graphe orienté qui représente les biefs de notre réseau fluvial : les arêtes sont les biefs, les n½uds sont soit des conditions limites amont, soit des conditions limites aval, soit des jonctions entre biefs.
+Un bief par défaut existe dans la nouvelle étude.
+Pour les besoins de ce tutoriel, nous allons le supprimer :
+cliquez sur le bouton \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/del.png} pour entrer dans le mode \textit{Suppression} puis cliquez sur les n½uds.
+Nous voilà repartis sur une fenêtre vierge.
+Appuyez sur le bouton \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} pour entrer dans le mode \textit{Ajout}. Créez deux n½uds en cliquant dans la zone grise de la fenêtre, et créez un lien en cliquant à nouveau sur chaque n½ud.
+Appuyez à nouveau sur \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} pour quitter le mode \textit{Ajout}.
+Vous avez créé votre premier bief, avec un n½ud amont et un n½ud aval.
+Dans la partie inférieure de la fenêtre \textit{Réseau}, vous pouvez renommer les n½uds et les biefs.
+Comme le bief que nous avons créé est automatiquement sélectionné, toutes les étapes suivantes s'appliqueront à ce bief.
+La fenêtre doit se présenter comme suit :

 \begin{center}
 \includegraphics[width=15cm]{img/network.png}
 \par\end{center}

+Fermez la fenêtre \textit{Réseau}.

-Fermer la fenêtre \textit{Editer le réseau}.
-
-
-\section{Editer la géometrie de la rivière}
-
-Cliquez sur \texttt{[Géometrie] => [Editer la géometrie]} pour définir la géométrie du bief sélectionné. Cliquez sur le bouton \texttt{[Importer]} et sélectionnez le fichier \texttt{Data/Bief\_1.st}. Vous devriez voir :
+\section{Éditer la géométrie de la rivière}

+Cliquez sur \texttt{[Géométrie] => [Éditer la géométrie]} ou sur l'icône \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/geometry.png} pour définir la géométrie du bief sélectionné.
+Pour Importer une géométrie depuis un fichier, cliquez sur le bouton \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/import.png}.
+Sélectionnez le fichier \texttt{Data/Bief\_1.st}.
+Vous devriez voir :

 \begin{center}
 \includegraphics[width=15cm]{img/Geo.png}
 \par\end{center}

+Le panneau de gauche contient une liste de toutes les sections en travers avec leur nom et leur abscisse longitudinale (PK).
+Dans le graphique en haut à gauche, vous pouvez voir la vue de dessus de la rivière; dans le panneau en haut à droite, la coupe longitudinale de la rivière et dans le graphique en bas, vous pouvez voir la section en travers sélectionnée (bleu) ainsi que la suivante (pointillés violets) et la précédente (pointillés noirs).
+Vous pouvez vous déplacer dans la liste des sections en cliquant dans le tableau ou sur les sections dans les deux vues du haut.

-Le panneau de gauche contient une liste de toutes les sections en travers avec leur nom et leur abscisse longitudinale (PK). Dans le graphique en haut à gauche, vous pouvez voir la vue de dessus de la rivière, dans le panneau en haut à droite, la coupe longitudinale de la rivière et dans le graphique en bas, vous pouvez voir la section en travers sélectionnée (bleu) ainsi que la suivante (pointillés violets) et la précédente (pointillés noirs). Vous pouvez vous déplacer dans la liste des sections en cliquant dans le tableau ou à l'aide de l'ascenseur situé entre le tableau et les graphiques.
-
-Vous pouvez éditer la section en travers sélectionnée en cliquant sur l'icône \includegraphics[width=0.5cm]{"img/edit.png"}.
+Vous pouvez éditer la section en travers sélectionnée en cliquant sur l'icône \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"}.

 Sélectionnez la section en travers nommée \textit{PontRD101m} et ouvrez la fenêtre d'édition. Vous devriez voir :

@@ -154,145 +175,268 @@ S
 \includegraphics[width=15cm]{img/editsect.png}
 \par\end{center}

+Sur le panneau de gauche se trouve la liste de tous les points de la section, avec leurs coordonnées, leur nom et leur abscisse transversale.
+La coordonnée Z du point le plus haut est inscrite en bleu et celle du point le plus bas en rouge. Les points peuvent avoir un nom.
+Si un point portant le même nom existe dans toutes les sections d'un bief, il forme une ligne longitudinale (ou ligne directrice).
+Par exemple, nous avons ici \textit{rg} et \textit{rd} qui représentent la rive gauche et la rive droite du lit mineur.

-Sur le panneau de gauche se trouve la liste de tous les points de la section, avec leurs coordonnées, leur nom et leur abscisse transversale. La coordonnée Z du point le plus haut est inscrite en bleu et celle du point le plus bas en rouge. Les points peuvent avoir un nom. Si un point portant le même nom existe dans toutes les sections d'un bief, il forme une ligne longitudinale (ou ligne directrice). Par exemple, nous avons ici \textit{rg} et \textit{rd} qui représentent la rive gauche et la rive droite du lit mineur.
+Sur le graphique figure une projection de la section en travers.
+Vous pouvez utiliser \texttt{[clic droit]} pour afficher une ligne d'eau fictive et visualiser des données géométriques utiles.
+Vous pouvez ensuite enlever cette ligne avec \texttt{[clic molette]}.
+Vous pouvez maintenant fermer la fenêtre d'édition de la section en travers.

-Sur le graphique figure une projection de la section en travers. Vous pouvez utiliser \texttt{[ctrl + clic]} pour sélectionner un point dans le tracé et \texttt{[maj + clic]} pour sélectionner une ligne d'eau et visualiser des données géométriques utiles. Vous pouvez fermer la fenêtre d'édition de la section en travers et la fenêtre d'édition de la géométrie.
+Revenons à la fenêtre \textit{Géométrie}.
+Le jeu de sections importé est inégalement espacé, ce qui peut entraîner des difficultés de calcul.
+Nous allons utiliser l'outil de maillage pour interpoler des nouvelles sections entre les sections trop espacées.
+Cliquez sur \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/meshing.png"}.
+Dans la fenêtre \textit{Maillage}, vous avez accès à quelques options basiques.
+L'option \textit{Limites} vous permet de définir deux sections entre lesquelles le maillage sera effectué.
+L'option \textit{Lignes directrices pour le calcul des distances} permet de spécifier au mailleur les points sur lesquels calculer les distances entre les sections.
+La distance sera la moyenne des deux distances entre les points de chaque sections qui portent ces lignes directrices.
+Pour ne choisir qu'une seule ligne, rentrez simplement deux fois la même valeur.
+Il existe toujours au moins deux lignes directrices : les deux extrémités des sections, nommés \textit{un} et \textit{np}, même si les points correspondants ne portent pas de nom.
+Les options \textit{Paramètres} permettent de définir l'interval souhaité entre les nouvelles sections, et la méthode d'interpolation.
+Choisissez les options suivantes, et cliquez sur \texttt{[OK]} :

-\section{Editer les conditions aux limites}
+\begin{center}
+\includegraphics[width=15cm]{img/maillage.png}
+\par\end{center}

-Dans la fenêtre principale, cliquez sur \texttt{[Hydraulique] => [Conditions aux limites et apports ponctuels]} :
+% L'option d'interpolation \textit{Spline} modifie les longueurs longitudinales.
+% Les abscices en long (Pk) des sections sont donc obsolètes.
+% Pour les recalculer, cliquez sur \texttt{[Mise à jour des PK]} dans la fenêtre \textit{Géométrie}.
+% Vous êtes maintenant dans la fenêtre \textit{Mise à jour des PK}.
+% Vous pouvez choisir la section d'origine pour le calcul des PK, ainsi que la valeur du PK à cette section.
+% Le choix des deux lignes directrices sert à calculer les distances entre sections, comme dans la fenêtre \textit{Maillage}.
+% L'orientation vous permet de choisir dans quelle direction les PK seront croissants.
+% Cette option n'a pas d'impact sur les résultats du calcul hydraulique.
+% Choisissez les options suivantes, et cliquez sur \texttt{[OK]} :
+%
+% \begin{center}
+% \includegraphics[width=15cm]{img/mjpk.png}
+% \par\end{center}
+
+La fenêtre \textit{Géométrie} doit maintenant ressembler à ça :
+
+\begin{center}
+\includegraphics[width=15cm]{img/Geo2.png}
+\par\end{center}
+
+
+\section{Éditer les conditions aux limites}
+
+Dans la fenêtre principale, cliquez sur \texttt{[Hydraulique] => [Conditions aux limites et apports ponctuels]} ou sur l'icône \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/boundary_condition.png"}.
+Vous arrivez sur la fenêtre \textit{Conditions aux limites} :

 \begin{center}
 \includegraphics[width=15cm]{img/boundary.png}
 \par\end{center}

-
- Utilisez le bouton \textit{ajouter} en haut à gauche de la fenêtre pour ajouter une condition limite pour le liquide.
- Sur la nouvelle ligne, on peut cliquer pour sélectionner la ligne entière, et double-cliquer pour sélectionner la cellule.
- Sélectionnez la cellule \textit{Type} pour donner un nom à la condition limite. Ici, nous définirons le débit mesuré lors de la crue de février 2002. Vous pouvez nommer cette condition limite "crue2002".
- Sélectionner la cellule \textit{Type} et utiliser la combo box pour mettre une loi Q(t).
- Sélectionnez la cellule \textit{Noeud} et attribuez cette condition au noeud amont.
- Les noms des noeuds sont rappelés dans le réseau du panneau de droite.
- Sélectionnez maintenant la ligne entière et cliquez sur le bouton d'édition \includegraphics[width=0.5cm]{"img/edit.png"}. Vous avez ouvert la fenêtre \textit{Éditer les conditions aux limites}.
- Dans un éditeur de texte, ouvrez le fichier \texttt{Données/Fevrier\_2002.txt}. Copiez le contenu du fichier (par exemple avec \textit{ctrl+a} puis \textit{ctrl+c}) et collez-le dans le panneau gauche de la fenêtre \textit{Éditer les conditions aux limites} avec \textit{ctrl+v}. Vous pouvez maintenant voir la courbe de débit :
+Utilisez le bouton \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} en haut à gauche de la fenêtre pour ajouter une condition limite pour le liquide.
+Nous pouvons cliquer sur la nouvelle ligne pour sélectionner la ligne en entier, et double-cliquer pour sélectionner une seule cellule.
+Ici, nous définirons le débit mesuré lors de la crue de février 2002.
+Sélectionnez la cellule \textit{Nom} pour donner un nom à la condition limite par exemple "crue2002".
+Sélectionner la cellule \textit{Type} et utiliser la combo box pour mettre une loi \textit{Q(t)} : débit en fonction du temps (hydrogramme).
+Sélectionnez la cellule \textit{N½ud} et attribuez cette condition au n½ud amont.
+Les noms des n½uds sont rappelés dans le panneau de droite, avec une vue du réseau.
+Sélectionnez maintenant la ligne entière et cliquez sur le bouton d'édition \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"}.
+Vous avez ouvert la fenêtre \textit{Éditer les conditions aux limites}.
+Dans un éditeur de texte, ouvrez le fichier \texttt{data/Fevrier\_2002.txt}.
+Copiez le contenu du fichier (par exemple avec \textit{ctrl+a} puis \textit{ctrl+c}) et collez-le dans le panneau de gauche de la fenêtre \textit{Éditer les conditions aux limites} avec \textit{ctrl+v}.
+Vous pouvez maintenant voir la courbe de débit :

 \begin{center}
 \includegraphics[width=15cm]{img/fev2002.png}
 \par\end{center}

-
-Fermer cette fenêtre. Revenir sur la fenêtre \textit{Conditions aux limites}. Ajouter une nouvelle ligne, lui donner un nom, lui donner le type \textit{Z(T)} et l'associer au noeud aval du réseau. Ouvrez la fenêtre \textit{Éditer les conditions aux limites} (\includegraphics[width=0.5cm]{"img/edit.png"}). Ajoutez deux lignes. Dans la première, entrez le temps : 0.00.00 et Z : 15.000.
-Dans la seconde, saisissez le temps : 1.00.00 et Z : 15.000. Cela crée une côte constante de l'eau en aval. Pour le calcul, Mage extrapolera continuellement l'élévation de l'eau.
+Fermez cette fenêtre. Revenez sur la fenêtre \textit{Conditions aux limites}.
+Ajoutez une nouvelle ligne, donnez lui un nom, donnez lui le type \textit{Z(T)} (limnigramme) et associez là au n½ud aval du réseau.
+Ouvrez la fenêtre d'édition des conditions aux limites (\includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"}).
+Ajoutez deux lignes et rentrez les valeurs suivantes :
+\begin{center}
+\begin{tabular}{|c|c|}
+\hline
+temps & cote \\ \hline
+0.00.00 & 15.000\\ \hline
+1.00.00 & 15.000\\ \hline
+\end{tabular}\\
+\par\end{center}
+Cela crée une cote constante de l'eau en aval.
+Pour le calcul, le solveur extrapolera continûment l'élévation de l'eau si le temps de la simulation dépasse le dernier point de la courbe.
 Vous pouvez fermer les fenêtres \textit{Éditer les conditions aux limites} et \textit{Conditions aux limites}.

+% Fermer cette fenêtre.
+% Revenez sur la fenêtre \textit{Conditions aux limites}.
+% Ajoutez une nouvelle ligne, donnez lui un nom, donnez lui le type \textit{Q(Z)} (courbe de tarage) et associez-la au noeud aval du réseau.
+% Cette condition limite se trouve au niveau d'un seuil.
+% A cet endroit, l'écoulement passe d'un régime fluvial à un régime torentiel.
+% Nous allons donc calculer une courbe de tarage qui correspond au régime critique de l'écoulement au niveau du seuil.
+% Sélectionnez la condition limite et ouvrez la fenêtre \textit{Éditer les conditions aux limites} :  (\includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"}).
+% Dans la fenêtre \textit{Éditer les conditions aux limites} cliquez sur \texttt{[Générer régime critique]} pour générer cette courbe.
+% Cliquez ensuite sur \texttt{[Rendre croissant]} pour suprimer les points de la courbe qui ne sont pas strictement croissants.
+% Vous pouvez fermer les fenêtres \textit{Éditer les conditions aux limites} et \textit{Conditions aux limites}.
+
 \section{Créer les conditions initiales}

-Dans la fenêtre principale, cliquez sur \texttt{[Hydraulique] => [Conditions initiales]}.
-Si vous ne connaissez pas les conditions initiales de la côte de l'eau et du débit de la rivière, vous pouvez utiliser les boutons \texttt{[Générer une hauteur minimale]} ou \texttt{[Générer un débit constant]} pour laisser Pamhyr2 estimer une condition initiale à l'aide de la formule de Manning-Strickler.
-Cliquez sur \texttt{[Générer à partir du débit]} et saisissez un débit de $4 m^3$ dans la fenêtre contextuelle pour générer une condition initiale de hauteur d'eau basée sur la formule de Manning-Strickler et un débit uniforme de $4 m^3$. Vous devriez voir :
+Dans la fenêtre principale, cliquez sur \texttt{[Hydraulique] => [Conditions initiales]} ou sur le raccourci \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/boundary_condition.png"}.
+Pour démarrer, le code de calcul hydraulique a besoin de connaître le débit et la cote de la surface libre de la rivière en tout point à l'instant initial.
+Si vous ne connaissez pas ces conditions initiales, vous pouvez utiliser les boutons \texttt{[Générer une profondeur uniforme]}, \texttt{[Générer un débit uniforme]} ou \texttt{[Générer une cote uniforme]} pour laisser Pamhyr2 estimer une condition initiale.
+Cliquez sur \texttt{[Générer un débit uniforme]} et saisissez un débit de 4 m$^3$/s dans la fenêtre contextuelle, et cochez \texttt{[Générer une profondeur]} pour générer une condition initiale de hauteur d'eau basée sur la formule de Manning-Strickler pour le débit donné.
+Vous devriez voir :


 \begin{center}
 \includegraphics[width=15cm]{img/ic.png}
 \par\end{center}

+% Vous pouvez également utiliser \texttt{[Générer une cote uniforme]} et saisir une cote de 21 m à l'amont et à l'aval avec un débit nul.
+% Cela revient à créer une bassine et à laisser le solveur la vider pour trouver un écoulement initial satisfaisant.

-Fermer la fenêtre \textit{Conditions initiales}
+Lors des prochaines simulations, vous pourrez utiliser l'état final de la simulation précédente comme état initial.
+Pour cela, cliquez sur \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/import.png} et retrouvez le résultat sous forme de fichier \textit{.BIN}.
+Ce fichier de résultats se trouve normalement dans le sous-dossier \texttt{\_PAMHYR\_/Hogneau/default-mage}.
+
+Fermer la fenêtre \textit{Conditions initiales}.


-\section{Editer les coefficients de frottement}
-
-Dans la fenêtre principale, cliquez sur \texttt{[Hydraulique] => [Editer les frottements]}.
-Vous devez d'abord définir des jeux de coefficients de Strickler. Cliquez sur \includegraphics[width=0.5cm]{"img/edit.png"} pour ouvrir la fenêtre \textit{Strickler}. Vous pouvez y créer des couples de coefficients de Strickler, le premier pour le lit mineur, le second pour le lit moyen. Cliquez quatre fois sur \textit{add} pour créer quatre nouveaux couples. Donnez-leur les valeurs suivantes :
+\section{Éditer les coefficients de frottement}

+Nous allons maintenant définir les coefficients de frottement du fond de la rivière.
+Dans la fenêtre principale, cliquez sur \texttt{[Hydraulique] => [Éditer les frottements]} ou sur l'icône \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/friction.png"}.
+Dans un premier temps, vous devez définir des jeux de coefficients de Strickler.
+Cliquez sur \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"} pour ouvrir la fenêtre \textit{coefficients de Strickler}.
+Vous pouvez y créer des couples de coefficients de Strickler, le premier pour le lit mineur, le second pour le lit moyen.
+Cliquez quatre fois sur \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} pour créer quatre nouveaux couples.
+Donnez-leur les valeurs suivantes :

 \begin{center}
 \includegraphics[width=15cm]{img/K.png}
 \par\end{center}

+Vous pouvez utiliser le bouton \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/sort_A-Z.png} pour trier les couples par ordre alphadétique.
+Fermez la fenêtre \textit{Strickler}.

-Fermez la fenêtre \textit{Strickler}. Dans la fenêtre \textit{Editer les frottements}, ajoutez quatre lignes avec le bouton \includegraphics[width=0.5cm]{img/gtk_add.png} pour créer quatre zones de frottement. Chaque zone est définie par un PK \textit{début} et de \textit{fin} PK et un couple \textit{begin} et \textit{end} couple de Strickler. Les couples de coefficients de Strickler à l'intérieur d'une zone sont interpolés à partir des couples \textit{begin} et \textit{end}. Dans notre cas, nous utiliserons des coefficients constants par zone. Définissez les zones comme suit :
-
+Dans la fenêtre \textit{Éditer les frottements}, ajoutez quatre lignes avec le bouton \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} pour créer quatre zones de frottement.
+Chaque zone est définie par un PK de \textit{début} et de \textit{fin} associés à un couple de coefficients de Strickler.
+% Les couples de coefficients de Strickler à l'intérieur d'une zone sont interpolés à partir des couples \textit{début} et \textit{fin}.
+% Dans notre cas, nous utiliserons des coefficients uniformes par zone.
+Définissez les zones comme suit :

 \begin{center}
 \includegraphics[width=15cm]{img/frictions.png}
 \par\end{center}

-
-La zone sélectionnée est surlignée en bleu. Fermez la fenêtre \textit{Editer les frottements}.
-
+La zone sélectionnée est surlignée en bleu.
+Vous pouvez maintenant fermer la fenêtre \textit{Éditer les frottements}.

 \section{Modélisation des ouvrages hydrauliques}

-Parfois, il peut y avoir des sections en travers dans lesquelles les équations de Saint-Venant ne peuvent pas être utilisées pour modéliser l'écoulement de l'eau. Dans ce cas, nous devons définir une autre loi pour relier la côte de l'eau et le débit. C'est le cas, par exemple, au niveau des ponts lorsque la hauteur d'eau est trop élevée, ce qui entraîne un écoulement en charge. Pamhyr2 permet de définir différents ouvrages hydrauliques avec des lois paramétrables. Dans notre cas, on doit représenter un seuil et deux ponts comme ouvrages hydrauliques.
-Dans la fenêtre principale, cliquez sur \texttt{[Hydraulique] => [Ouvrages hydrauliques]} pour ouvrir la fenêtre des ouvrages hydrauliques. Cliquez trois fois sur le bouton \includegraphics[width=0.5cm]{img/gtk_add.png} pour créer trois ouvrages hydrauliques. Chaque structure peut avoir un nom et doit avoir une portée et un PK. Définissez-les comme suit :
-
+Parfois, il peut y avoir des sections en travers dans lesquelles les équations de Saint-Venant ne peuvent pas être utilisées pour modéliser l'écoulement de l'eau.
+Dans ce cas, nous devons définir une autre loi pour relier la cote de l'eau et le débit.
+C'est le cas, par exemple, au niveau des ponts lorsque la hauteur d'eau est trop élevée et que l'écoulement passe en charge.
+Pamhyr2 permet de définir différents ouvrages hydrauliques avec des lois paramétrables.
+Dans notre cas, nous allons devoir modéliser deux ponts et un seuil par des ouvrages hydrauliques.
+Dans la fenêtre principale, cliquez sur \texttt{[Hydraulique] => [Ouvrages hydrauliques]} pour ouvrir la fenêtre des ouvrages hydrauliques.
+Cliquez trois fois sur le bouton \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/add.png"} pour créer trois ouvrages hydrauliques.
+% Cliquez deux fois sur le bouton \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/add.png"} pour créer deux ouvrages hydrauliques.
+Chaque structure peut avoir un nom et doit avoir un bief et un PK.
+Définissez-les comme suit :

 \begin{center}
 \includegraphics[width=15cm]{img/hs.png}
 \par\end{center}

-
-Sélectionnez le seuil aval et cliquez sur \includegraphics[width=0.5cm]{"img/edit.png"} pour modifier les lois de cette ouvrage. Les ouvrages hydrauliques sont composés d'ouvrages hydrauliques élémentaires. Vous pouvez combiner les lois de plusieurs ouvrages hydrauliques élémentaires pour créer votre ouvrage. Pour ce seuil, nous n'avons besoin que d'un ouvrage hydraulique élémentaire de type déversoir. Cliquez sur \includegraphics[width=0.5cm]{img/gtk_add.png} pour ajouter un nouvel ouvrage hydraulique élémentaire, donnez-lui le type \textit{seuil} et configurez-le comme suit :
-
+Sélectionnez le seuil aval et cliquez sur \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"} pour modifier les lois de cet ouvrage. Les ouvrages hydrauliques sont composés d'ouvrages hydrauliques élémentaires. Vous pouvez combiner les lois de plusieurs ouvrages hydrauliques élémentaires pour créer votre ouvrage. Pour ce seuil, nous n'avons besoin que d'un ouvrage hydraulique élémentaire de type déversoir. Cliquez sur \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/add.png"} pour ajouter un nouvel ouvrage hydraulique élémentaire, donnez-lui le type \textit{Déversoir rectangulaire} et configurez-le comme suit :

 \begin{center}
-\includegraphics[width=15cm]{img/seuil.png}
+\includegraphics[width=15cm]{img/Seuil.png}
 \par\end{center}

-
 Retournez à la fenêtre \textit{Ouvrages hydrauliques}.

-Sélectionnez le pont RS101 et cliquez sur \includegraphics[width=0.5cm]{"img/edit.png"} pour éditer les lois de cet ouvrage. Un pont peut être modélisé comme une combinaison d'un orifice pour l'écoulement sous le pont et d'un déversoir pour l'écoulement au-dessus du pont. Créez deux ouvrages hydrauliques élémentaires et définissez-les comme suit :
+Sélectionnez le pont RD101 et cliquez sur \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"} pour éditer les lois de cet ouvrage.
+% Les ouvrages hydrauliques sont composés d'ouvrages hydrauliques élémentaires.
+% Vous pouvez combiner les lois de plusieurs ouvrages hydrauliques élémentaires pour créer votre ouvrage.
+Un pont peut être modélisé comme une combinaison d'un orifice pour l'écoulement sous le pont et d'un déversoir pour l'écoulement au-dessus du pont.
+Créez deux ouvrages hydrauliques élémentaires à l'aide du bouton \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} et définissez-les comme suit :

 \begin{center}
-\includegraphics[width=15cm]{img/seuilRS101.png}
+\includegraphics[width=15cm]{img/SeuilRD101.png}

-\includegraphics[width=15cm]{img/orificeRS101.png}
+\includegraphics[width=15cm]{img/OrificeRD101.png}
 \par\end{center}

-
 Revenez à la fenêtre \textit{Ouvrages hydrauliques} et appliquez la même procédure pour le pont de Thivencelle :

-\begin{center}
-\includegraphics[width=15cm]{img/orificeThivencelle.png}
+% \begin{center}
+% \includegraphics[width=15cm]{img/SeuilThivencelle.png}
+%
+% \includegraphics[width=15cm]{img/OrificeThivencelle.png}
+% \par\end{center}

-\includegraphics[width=15cm]{img/seuilThivencelle.png}
+\begin{center}
+  \begin{tabular}{|c|c|}
+  \hline
+  \multicolumn{2}{|c|}{Orifice Thivencelle} \\ \hline
+  Largeur & 9.07 \\ \hline
+  cote & 17.28\\ \hline
+  cote de mise en charge & 20.74\\ \hline
+  coefficient de débit & 0.4\\ \hline
+  cote de mise en charge maximale & 9999.999\\ \hline
+  \end{tabular}
+  \hspace{1cm}
+  \begin{tabular}{|c|c|}
+  \hline
+  \multicolumn{2}{|c|}{Seuil Thivencelle} \\ \hline
+  Largeur & 13.0 \\ \hline
+  cote & 21.74\\ \hline
+  coefficient de débit & 0.4\\ \hline
+  \end{tabular}\\
 \par\end{center}


 Vous pouvez maintenant fermer les fenêtres \textit{Ouvrages hydrauliques}.
+Si vous réouvrez la fenêtre \textit{Géométrie} vous pouvez voir apparaitre la position des ouvrages hydrauliques sur la vue longitudinale.

 \section{Paramètres du solveur}

 Dans la fenêtre principale, cliquez sur \texttt{[Exécuter] => [Parameters numériques des solveurs]}.
-Dans la fenêtre \textit{Paramètres du solveur}, sélectionnez l'onglet \textit{Mage v8}. Réglez les paramètres du solveur comme suit :
-
-
-\begin{center}
-\includegraphics[width=15cm]{img/param.png}
-\par\end{center}
-
-
+Dans la fenêtre \textit{Paramètres du solveur}, sélectionnez l'onglet \texttt{[Mage v8]}.
+Ces paramètres pilotent le comportement du solveur numérique.
+la valeur 999:99:00:00 du temps final indique au solveur de s'arrêter lorsqu'il a atteint un régime permanent.
+Vous pouvez changer la fréquence d'écriture des résultats dans la ligne \textit{Pas de temps d'écriture dans le fichier .BIN}.
+Une valeur inférieure à 1 seconde indique que la valeur de la ligne  \textit{Pas de temps d'écriture dans le fichier .TRA} s sera prise à la place.
+% En effet, durant la montée du pic de crue, le solveur a besoin de réduire le pas de temps suffisament pour permettre la convergence des itérations.
+Pour accélérer les calculs et pour aider le solveur à démarer, nous allons l'autoriser à dégrader la précision, à l'aide des facteurs de réduction de la précision.
+Les précisions internes du solveur sont de 10$^{-9}$.
+Cette précision est multipliée par le facteur de réduction de la précision : un facteur de 1000 ramènera donc la précision à 10$^{-5}$.
+Pour utiliser ce facteur de réduction de la précision, il faut donner un \textit{nombre d'itérations à précision maximum} inférieur au \textit{nombre maximum d'itérations} : le solveur va d'abord tenter de converger avec un certain nombre d'itératons à la précision maximum avant de basculer sur une précision dégradée pour le reste des itérations.
+Dans notre cas, c'est nécessaire pour lancer le solveur à partir de la condition initiale calculée par Pamhyr2.
+rentrez 1000 dans les trois lignes \textit{facteurs de réduction de la précision}, rentrez 99 pour le \textit{Nombre d'itérations} et 5 pour le \textit{nombre d'itérations à la précision maximum}.
+Gardez les autres paramètres du solveur par défaut.
 Fermer la fenêtre \textit{Paramètres du solveur}.

 \section{Lancer la simulation}

 Dans la fenêtre principale, cliquez sur \texttt{[Exécuter] => [Lancer le solveur]}.
-Sélectionnez \textit{Defaut-Mage - (Mage8)} et cliquez sur le bouton \textit{Exécuter}.
-Deux fenêtres s'ouvrent : la fenêtre \textit{check list} et la fenêtre \textit{Log du solveur}.
-La fenêtre \textit{Check list} donne quelques indications sur la validité de votre modèle, et la fenêtre \textit{Log du solveur} affiche les résultats du solveur.
-À partir de la fenêtre \textit{Log du solveur}, vous pouvez réexécuter le calcul, et vous pouvez cliquer sur le bouton \textit{Résultats} pour ouvrir la fenêtre \textit{Résultats}.
+Sélectionnez \textit{Defaut-Mage - (Mage8)} et cliquez sur le bouton \textit{Lancer}.
+La fenêtre \textit{Log du solveur} s'ouvre.
+Cette fenêtre affiche les sorties texte du solveur.
+À partir de la fenêtre \textit{Log du solveur}, vous pouvez réexécuter le calcul en cliquant sur l'icône \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/run.png}, et vous pouvez cliquer sur le bouton \textit{Résultats} pour ouvrir la fenêtre \textit{Résultats}.

 \section{Visualiser les résultats}

-il est aussi possible d'ouvrir la fenêtre \textit{Résultats} si vous avez fermé la fenêtre \textit{Log du solveur}, en cliquant sur \texttt{[Résultats] => [Visualiser les derniers résultats]} à partir de la fenêtre principale. Le panneau supérieur vous permet de sélectionner le bief, le panneau inférieur gauche vous permet de sélectionner une section en travers dans ce bief. Les trois diagrammes sur la droite montrent le bief et la section en travers de la même manière que dans la fenêtre \textit{Géométrie}. Vous pouvez utiliser le curseur du bas pour visualiser la côte de l'eau à différents pas de temps.
+il est aussi possible d'ouvrir la fenêtre \textit{Résultats} si vous avez fermé la fenêtre \textit{Log du solveur}, en cliquant sur \texttt{[Résultats] => [Visualiser les derniers résultats]} à partir de la fenêtre principale.
+Le panneau supérieur vous permet de sélectionner le bief, le panneau inférieur gauche vous permet de sélectionner une section dans ce bief.
+Les trois diagrammes sur la droite montrent le bief et la section en travers de la même manière que dans la fenêtre \textit{Géométrie}.
+Vous pouvez utiliser le curseur du bas pour visualiser les résultats à différents pas de temps.
+Les croix rouges dans les deux vues du haut correspondent aux points ou l'eau déborde de la géométrie au moins une fois dans la simulation.
+En pratique il n'y a pas de perte de volume par débordement en dehors du modèle, car le solveur ajoute un mur virtuel aux extrémités des sections.
 Pour visualiser le débit, passez à l'onglet \textit{Hydrogramme}.
-Pour créer des tracés 2D personnalisés, cliquez sur le bouton \includegraphics[width=0.5cm]{img/gtk_add.png} en haut à gauche de la fenêtre. Sélectionnez les valeurs que vous voulez sur les axes $X$ et $Y$ et cliquez sur \textit{OK}.
-Vous pouvez maintenant voir un nouvel onglet avec le tracé 2D personnalisé dans le panneau droit de la fenêtre \textit{Results}.
-
-
+Pour créer des tracés 2D personnalisés, cliquez sur le bouton \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} en haut à gauche de la fenêtre.
+Sélectionnez les valeurs que vous voulez sur les axes $X$ et $Y$ et cliquez sur \texttt{[OK]}.
+Vous pouvez maintenant voir un nouvel onglet avec le tracé 2D personnalisé dans le panneau droit de la fenêtre \textit{Résultats}.
+Le bouton \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/export.png} vous permet d'exporter les résultats au format CSV pour une utilisation en dehors de Pamhyr2.

 \pagebreak{}
 \end{document}
@@ -112,9 +112,28 @@ Use the GNU Linux or the Windows download button depending on your system. On wi
 \section{Create your first study}

 On the main windows, click on \texttt{[Files] => [New Study]} to create a new study.
+Give it a name, for example \textit{Hogneau}, and validate.

-Click on \texttt{[River Network] => [Edit River Network]} to create the reaches of your river. In this window, you must define an oriented graph that represents the reaches of your river network: the edges are the reaches and the nodes are either upstream boundary conditions, downstream boundary conditions or junctions.
-Press the \includegraphics[width=0.5cm]{img/gtk_add.png} to enter the \textit{add} mode. Create two nodes by clicking in the grey zone of the window, and create a link by clicking again on each node. press \includegraphics[width=0.5cm]{img/gtk_add.png} again to exit the \textit{add} mode. You created your first reach, with an upstream node and a downstream node. In the lower part of the \textit{Edit River Network} window you can rename the nodes and the reaches. As the reach you created is automaticaly selected, all the next steps will apply to this reach. The window should look like that:
+\begin{center}
+\includegraphics[width=15cm]{img/NEWSTUDY.png}
+\par\end{center}
+
+During study, don't forget to save periodicaly your work, using the \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/save.png} button on the main window.
+
+\section{Create the structure of the river}
+
+Click on \texttt{[River Network] => [Edit River Network]} or on the \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/network.png} shortcut to create the structure of your river.
+In this window, you must define an oriented graph that represents the reaches of your river network: the edges are the reaches and the nodes are either upstream boundary conditions, downstream boundary conditions or junctions.
+A default reach exists in a new study.
+For this tutorial, we will delete it:
+click on the  \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/del.png} button to enter the \textit{Delete} mode, then click on the nodes.
+We can now start with an empty window.
+Press the \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} to enter the \textit{Add} mode. Create two nodes by clicking in the grey zone of the window, and create a link by clicking again on each node.
+Press \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} again to exit the \textit{Add} mode.
+You created your first reach, with an upstream node and a downstream node.
+In the lower part of the \textit{Edit River Network} window you can rename the nodes and the reaches.
+As the reach you created is automaticaly selected, all the next steps will apply to this reach.
+The window should look like that:

 \begin{center}
 \includegraphics[width=15cm]{img/network.png}
@@ -125,15 +144,19 @@ Close the \textit{Edit River Network} window.

 \section{Edit the river geometry}

-Click on \texttt{[Geometry] => [Edit Geometry]} to define the geometry of the selected bief. Click on the \texttt{[Import]} button and select the file \texttt{Data/Bief\_1.st}. You should see:
+Click on \texttt{[Geometry] => [Edit Geometry]} or on the \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/geometry.png} shortcut to define the geometry of the selected reach.
+Click on the \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/import.png} button and select the file \texttt{Data/Bief\_1.st}.
+You should see:

 \begin{center}
 \includegraphics[width=15cm]{img/Geo.png}
 \par\end{center}

-On the left panel is a list of all the cross sections with their name and longitudinal abscisa. In the top left plot you can see the top view of the river, on the top right panel the longitudinal cross-section of the river and in the bottom plot you can see the selected cross-section (blue) along with the next one (dashed purple) and previous one (dashed black). You can move in the section list using the slider at the very right of the window.
+On the left panel is a list of all the cross sections with their name and longitudinal abscisa.
+In the top left plot you can see the top view of the river, on the top right panel the longitudinal cross-section of the river and in the bottom plot you can see the selected cross-section (blue) along with the next one (dashed purple) and previous one (dashed black).
+You can move in the section list using the right table or by clicking on the sections on one of the two upper plot.

-You can edit the selected cross section by clicking on the \includegraphics[width=0.5cm]{"img/edit.png"} icon.
+You can edit the selected cross section by clicking on the \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"} icon.

 select the cross section named \textit{PontRD101m} and open the edition window. You should see:

@@ -141,58 +164,100 @@ select the cross section named \textit{PontRD101m} and open the edition window.
 \includegraphics[width=15cm]{img/editsect.png}
 \par\end{center}

-On the left panel is the list of all the points of the section, with their coordinates, their name and their transversal absisa. The Z coordinate of the highest point is written in blue and the lowest in red. Points can have a name. If a point with the same name exists in every section in a reach, it forms a longitudinal line. For example, here we have \textit{rg} and \textit{rd} which represent the left bank and the right bank of the main chanel.
+On the left panel is the list of all the points of the section, with their coordinates, their name and their transversal absisa.
+The Z coordinate of the highest point is written in blue and the lowest in red.
+Points can have a name.
+If a point with the same name exists in every section in a reach, it forms a longitudinal line.
+For example, here we have \textit{rg} and \textit{rd} which represent the left bank and the right bank of the main chanel.

-On the plot is a projection of the cross section. You can use \texttt{[ctrl + click]} to select a point in the plot and \texttt{[shift + click]} to select a water line and visualize usefull geometric data. You can close the cross section edition window and the geometry edition window.
+On the plot is a projection of the cross section. You can click on a point to select it in the plot and \texttt{[right click]} to draw a water line and visualize usefull geometric data.
+You can then remove this line with \texttt{[scroll wheel click]}.
+You can close the cross section edition window and the geometry edition window.
+
+% TODO mesh

 \section{Edit the boundary conditions}

-From the main window, click on \texttt{[Hydraulics] => [Boundary conditions and punctual contributions]}.You should see:
+From the main window, click on \texttt{[Hydraulics] => [Boundary conditions and punctual contributions]} or on \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/boundary_condition.png"}.
+You are now on the \textit{Boundary conditions} window:

 \begin{center}
 \includegraphics[width=15cm]{img/boundary.png}
 \par\end{center}

- Use the \textit{add} button on the top left of the window to add a liquid boundary condition.
+ Use the \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} button on the top left of the window to add a liquid boundary condition.
 On the new line, click to select the whole line, double click to select the cell.
- Select the \textit{Type} cell to give a name to the boundary condition. here, we will define the flow discharge mesured during the february 2002 flood. You can name this boundary condition "flood2002".
- Select the \textit{Type} cell and use the combo box to put a Q(t) law.
+ Select the \textit{Type} cell to give a name to the boundary condition.
+ Here, we will define the flow discharge mesured during the february 2002 flood.
+ You can name this boundary condition "flood2002".
+ Select the \textit{Type} cell and use the combo box to put a \textit{Q(t)} law.
 Select the \textit{Node} cell and atribute this condition to the upstream node.
- Names of the nodes are recalled in network in the right panel.
- Now select the whole line and click on the edit button \includegraphics[width=0.5cm]{"img/edit.png"}. You opened the \textit{Edit Boundary Conditions} window.
- On a text editor, open the \texttt{Data/Fevrier\_2002.txt} file. Copy the content of the file (for example with \textit{ctrl+a ctrl+c}) and paste it in the left panel of the \textit{Edit Boundary Conditions} window with \textit{ctrl+v}. You can now see the flow discharge curve:
+ Names of the nodes are recalled in the right panel with the network view.
+ Now select the whole line and click on the edit button \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"}.
+ You opened the \textit{Edit Boundary Conditions} window.
+ In a text editor, open the \texttt{Data/Fevrier\_2002.txt} file.
+ Copy the content of the file (for example with \textit{ctrl+a ctrl+c}) and paste it in the left panel of the \textit{Edit Boundary Conditions} window with \textit{ctrl+v}.
+ You can now see the flow discharge curve:

 \begin{center}
 \includegraphics[width=15cm]{img/fev2002.png}
 \par\end{center}

-Close this window. Go back on the \textit{Boundary Conditions} window. Add a new line, give it a name, give it the textit{Z(T)} type and associate it to the downstream node of the network. Open the \textit{Edit Boundary Conditions} window (\includegraphics[width=0.5cm]{"img/edit.png"}). Add two lines. In the first one, enter time: 0.00.00 and Z: 15.000.
-On the second one, time: 1.00.00 and Z: 15.000. It creates a constant downstream water elevation. For the computaion, Mage will extrapolate continuously the water elevation, that's why we only need to define one hour.
+Close this window.
+Go back on the \textit{Boundary Conditions} window.
+Add a new line, give it a name, give it the textit{Q(Z)} type (rating curve) and associate it to the downstream node of the network.
+This downstream boundary condition corresponds to a weir.
+There, the river transition from a fluvial flow to a torrential flow.
+This allows us to compute a rating curve corresponding to the critical flow located over the weir.
+Open the \textit{Edit Boundary Conditions} window (\includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"}).
+In the \textit{Edit boundary conditions} window click on \texttt{[Générer régime critique]} to comput the said rating curve.
+Click on \texttt{[Make increasing]} to remove the points of the curve that are not strictly increasing.
 You can close the the \textit{Edit Boundary Conditions} and the \textit{Boundary Conditions} window.

 \section{Create initial conditions}

-From the main window, click on \texttt{[Hydraulics] => [Initial conditions]}.
-If you don't know the initial conditions in water elevation and flow discharge of the river, you can use \texttt{[Generate minimal height]} or \texttt{[Generate from discharge]} buttons to let Pamhyr2 estimate an initial condition using the Manning-Strickler formula.
-Click on \texttt{[Generate from discharge]} and enter a discharge of $4 m^3$ in the pop-up window to generate an initial water height condition based on the Manning-Strickler formula and a uniform discharge of $4 m^3$. You should see:
+From the main window, click on \texttt{[Hydraulics] => [Initial conditions]} or on the \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/boundary_condition.png"} shortcut.
+To start, the numerical solver needs to know the water elevation and the discharge at every cross-section of the river.
+If you don't know the initial water elevation and flow discharge conditions of the river, you can use the \texttt{[Generate minimal depth]}, \texttt{[Generate from discharge]} or \texttt{[Generate elevation]} buttons to let Pamhyr2 estimate an initial condition using the Manning-Strickler formula.
+Click on \texttt{[Generate from discharge]} and enter a discharge of $4 m^3$ in the pop-up window, and check the \texttt{[Generate depth]} to generate an initial water elevation condition based on the Manning-Strickler formula.
+You should see:

 \begin{center}
 \includegraphics[width=15cm]{img/ic.png}
 \par\end{center}

+You can alternately use \texttt{[Generate elevation]} to enter a constant elevation of $21 m$ (upstream and downstream) associated with a null discharge.
+The goal is to create a lake and to let the solver drain it to find a suitable initial state.
+
+In your next simulations, you can use the final timestep of the previous simulation as an initial condition.
+To do that, click on \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/import.png} and find the results contained in a \textit{.BIN} file.
+This file should be in the sub-directory \textit{\_PAMHYR\_/Hogneau/default-mage}.
+
 Close the \textit{Initial conditions} window.


 \section{Edit friction coefficients}

-From the main window, click on \texttt{[Hydraulics] => [Edit friction]}.
-You fist have to define sets of Strickler coefficients. Click on \includegraphics[width=0.5cm]{"img/edit.png"} to open the \textit{Strickler} window. Here you can create couples of Strickler coefficients, the first one for the minor bed, the second one for the medium bed. Click on \textit{add} four times to create four new couple. Give them the folowing values:
+We will now define the friction coefficients of the bottom of the river.
+From the main window, click on \texttt{[Hydraulics] => [Edit friction]} or on the \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/friction.png"} shortcut.
+You have to define sets of Strickler coefficients first.
+Click on \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"} to open the \textit{Strickler} window.
+Here you can create couples of Strickler coefficients, the first one for the minor bed, the second one for the medium bed.
+Click on \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} four times to create four new couples.
+Give them the folowing values:

 \begin{center}
 \includegraphics[width=15cm]{img/K.png}
 \par\end{center}

-Close the \textit{Strickler} window. On the \textit{Edit friction} window, add four lines with the button \includegraphics[width=0.5cm]{img/gtk_add.png} to create four friction zones. Each zone is defined by a \textit{begin} and \textit{end} KP and a \textit{begin} and \textit{end} Strickler couple. The strickler coefficient couples inside a zone are interpolated from the \textit{begin} and \textit{end} couples. In our case, we will use constant coefficients per zone. Set the zones as follow:
+You can use the \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/sort_A-Z.png} button to sort the couples by alphabetical order.
+Close the \textit{Strickler} window.
+
+On the \textit{Edit friction} window, add four lines with the button \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} to create four friction zones.
+Each zone is defined by a \textit{begin} and \textit{end} KP associated with a \textit{begin} and \textit{end} Strickler couple.
+The strickler coefficient couples inside a zone are interpolated from the \textit{begin} and \textit{end} couples.
+In our case, we will use uniform coefficients per zone.
+Set the zones as follow:

 \begin{center}
 \includegraphics[width=15cm]{img/frictions.png}
@@ -200,50 +265,53 @@ Close the \textit{Strickler} window. On the \textit{Edit friction} window, add f

 The selected zone is highlighted in blue. Close the \textit{Edit friction} window.

-
 \section{Model hydraulic structures}

-Sometimes there can be cross-sections in which Shallow water equations can not be used to model the water flow. In that case, we have to define an other law to link the water elevation and the flow discharge. This is the case, for example, under bridges when the water elevation is too high, leading to a flow in charge. Pamhyr2 enables to define various hydraulic structures with laws that can be parametrized. In our case, a weir and two bridges have to be represented as hydraulic structures.
-From the main window, click on \texttt{[Hydraulics] => [Hydraulic structures]} to open the hydraulic structures window. Click tree times on the \includegraphics[width=0.5cm]{img/gtk_add.png} button to create three hydraulic structures. Each structure can have a name and must have a reach and a KP. Set them as follow:
+Sometimes there can be cross-sections in which Shallow water equations can not be used to model the water flow.
+In that case, we have to define an other law to link the water elevation and the flow discharge.
+This is the case, for example, under bridges when the water elevation is too high, leading to a flow in charge.
+Pamhyr2 enables to define various hydraulic structures with laws that can be parametrized.
+In our case, two bridges have to be represented as hydraulic structures.
+From the main window, click on \texttt{[Hydraulics] => [Hydraulic structures]} to open the hydraulic structures window.
+Click two times on the \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} button to create two hydraulic structures.
+Each structure can have a name and must have a reach and a KP.
+Set them as follow:

 \begin{center}
 \includegraphics[width=15cm]{img/hs.png}
 \par\end{center}

-Select the downstream weir and click on \includegraphics[width=0.5cm]{"img/edit.png"} to edit the laws of this structure. Hydraulic structures are composed of basic hydraulic structures. You can combine the laws of several basic hydraulic structures to setup your structure. For this weir, we only need a weir basic hydraulic structure. Click on \includegraphics[width=0.5cm]{img/gtk_add.png} to add a new basic hydraulic structure, give it the \textit{weir} type and set it up as folow:
+Select the RD101 bridge and click on \includegraphics[width=0.5cm]{"../../../src/View/ui/ressources/edit.png"} to edit the laws of this structure.
+Hydraulic structures are composed of basic hydraulic structures.
+You can combine the laws of several basic hydraulic structures to setup your structure.
+A bridge can be modeled as a combination of an orifice for the flow under the bridge and a weir for the flow over the bridge.
+Create two basic hydraulic structures with the button \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} and set them as folow:

 \begin{center}
-\includegraphics[width=15cm]{img/seuil.png}
-\par\end{center}
+\includegraphics[width=15cm]{img/seuilRD101.png}

-Go back to the \textit{hydraulic structures} window.
-
-Select the RS101 bridge and click on \includegraphics[width=0.5cm]{"img/edit.png"} to edit the laws of this structure. A bridge can be modeled as a combination of an orifice for the flow under the bridge and a weir for the flow over the bridge. Create two basic hydraulic structures and set them as folow:
-
-\begin{center}
-\includegraphics[width=15cm]{img/seuilRS101.png}
-
-\includegraphics[width=15cm]{img/orificeRS101.png}
+\includegraphics[width=15cm]{img/orificeRD101.png}
 \par\end{center}

 Go back to the \textit{hydraulic structures} window and aply the same procedure for the Thivencelle bridge:

 \begin{center}
-\includegraphics[width=15cm]{img/orificeThivencelle.png}
-
 \includegraphics[width=15cm]{img/seuilThivencelle.png}
+
+\includegraphics[width=15cm]{img/orificeThivencelle.png}
 \par\end{center}

 You can now close the \textit{hydraulic structures} windows.
+If you open the \textit{geometry} window you can see the structure position in the longitudinal view.

 \section{Solver parameters}

 From the main window, click on \texttt{[Execute] => [Numerical parameters for solvers]}.
-In the window \textit{solver parameters} select the \textit{Mage v8} tab. Set the solver parameters as follow:
+In the window \textit{solver parameters} select the \textit{Mage v8} tab.
+Set the minimul timestep to 0.1. and keep the default values for the other parameters.
+We need a smaller minimum timester because the solver needs to reduce the timestep in order to converge during the steep increase of discharge at the begining of the flood.

-\begin{center}
-\includegraphics[width=15cm]{img/param.png}
-\par\end{center}
+% TODO precision

 Close the \textit{solver parameters} window.

@@ -251,17 +319,23 @@ Close the \textit{solver parameters} window.

 From the main window, click on \texttt{[Execute] => [Run solver]}.
 Select \textit{Defaut-Mage - (Mage8)} anc click on the \textit{Run} button.
-It will open two windows: the \textit{Check list} window and the \textit{Solver log} window.
-The \textit{Check list} window gives som hints about the validity of your model, and the \textit{Solver log} window displays the outputs of the solver.
-From the \textit{Solver log} window you can re-run the computation, and from the textit{Solver log} window you can click on the \textit{Results} button to open the \textit{Results} window.
+It will open the \textit{Solver log} window.
+The \textit{Solver log} window displays the outputs of the solver.
+From the \textit{Solver log} window you can re-run the computation with the button \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/run.png}, and you can click on the \textit{Results} button to open the \textit{Results} window.

 \section{Visualize the results}

-If you closed the \textit{Solver log} window, you can click on \texttt{[Results] => [Visualize last results]} from the main window to open the \textit{Results} window. The top lets panel let you select your reach, the bottom left panel lets you select a cross-section in that reach. the three plots on the right show the reach and the cross-section the same way than in the \textit{Geometry} window. You can use the bottom slider to visualize the water elevation at different timesteps.
+If you closed the \textit{Solver log} window, you can click on \texttt{[Results] => [Visualize last results]} from the main window to open the \textit{Results} window.
+The top left panel let you select your reach, the bottom left panel lets you select a cross-section in that reach.
+the three plots on the right show the reach and the cross-section the same way than in the \textit{Geometry} window.
+You can use the bottom slider to visualize the results at different timesteps.
+The red crosses in the graphs corresponds to sections where the water level exceeds the limits of the geometry at least one time during the simulation.
+This does not corresponds to water leaks, as the solver artificialy adds a virtual wall at both ends of the cross-sections geometry.
 To visualize the flow discharge, switch to the \textit{Hydrograph} tab.
-To create custom 2D plots, click on the \includegraphics[width=0.5cm]{img/gtk_add.png} button on the top left of the window. Select the values you want on the $X$ and $Y$ axis and click on \textit{OK}.
+To create custom 2D plots, click on the \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/add.png} button on the top left of the window.
+Select the values you want on the $X$ and $Y$ axis and click on \texttt{[OK]}.
 You can now see a new tab with the custom 2D plot in the right panel of the \textit{Results} window.
-
+The button \includegraphics[width=0.5cm]{../../../src/View/ui/ressources/export.png} allows you to export your results to a CSV file if you want to post-process them outside Pamhyr2.

 \pagebreak{}
 \end{document}
@@ -4,9 +4,11 @@ PyQt5-sip==12.12.2
 PyQtWebEngine==5.15.6
 QScintilla>=2.14.1
 pyqtgraph>=0.12.1
-matplotlib>=3.4.1
+matplotlib>=3.7.1
 numpy>=1.24.2
 colorama>=0.4.3
 pyinstaller>=5.11.0
 shapely>=2.0.1
 lxml>=4.9.3
+platformdirs>=4.2.0
+pyshp>=2.3.1
@@ -0,0 +1,21 @@
+#! /bin/bash
+set +x
+
+OPTS="-r -a -i"
+
+if [ "$1" == "builds" ]; then
+    FILES="../windows/ ../linux/"
+else
+    FILES="../windows/pamhyr-windows.exe ../windows/pamhyr-windows.zip ../linux/pamhyr-gnulinux.tar.xz"
+fi
+
+clamscan $OPTS $FILES | tee clamav.log
+
+RES=$(cat clamav.log | grep "Infected files: 0")
+if [ -z "$RES" ]; then
+    echo "Infected files"
+    exit -1
+else
+    echo "OK"
+    exit 0
+fi
@@ -0,0 +1,3 @@
+@echo off
+
+start cmd /c pamhyr.exe debug
@@ -0,0 +1,3 @@
+#! /bin/sh
+
+./pamhyr debug
@@ -16,34 +16,35 @@ rem along with this program.  If not, see <https://www.gnu.org/licenses/>.

@ECHO ON

-mkdir pamhyr\pamhyr\_internal
-xcopy /s /e /y dist\pamhyr pamhyr\pamhyr
+mkdir pamhyr\_internal
+xcopy /s /e /y dist\pamhyr pamhyr

 rem Copy data
-mkdir pamhyr\pamhyr\_internal\lang
-mkdir pamhyr\pamhyr\_internal\View\ui\ressources
-mkdir pamhyr\pamhyr\_internal\View\ui\Widgets
+mkdir pamhyr\_internal\lang
+mkdir pamhyr\_internal\View\ui\ressources
+mkdir pamhyr\_internal\View\ui\Widgets

 rem UI
-copy /y ..\src\View\ui\ressources\ pamhyr\pamhyr\_internal\View\ui\ressources
-copy /y ..\src\View\ui\Widgets\*.ui pamhyr\pamhyr\_internal\View\ui\Widgets
-copy /y ..\src\View\ui\*.ui pamhyr\pamhyr\_internal\View\ui\
+copy /y ..\src\View\ui\ressources\ pamhyr\_internal\View\ui\ressources
+copy /y ..\src\View\ui\Widgets\*.ui pamhyr\_internal\View\ui\Widgets
+copy /y ..\src\View\ui\*.ui pamhyr\_internal\View\ui\

 rem Lang
-copy /y ..\src\lang\*.qm pamhyr\pamhyr\_internal\lang\
+copy /y ..\src\lang\*.qm pamhyr\_internal\lang\

 rem Information
-copy /y ..\VERSION pamhyr\pamhyr\_internal
-copy /y ..\AUTHORS pamhyr\pamhyr\_internal
-copy /y ..\LICENSE pamhyr\pamhyr\_internal
-copy /y ..\src\motd.txt pamhyr\pamhyr\_internal
+copy /y ..\VERSION pamhyr\_internal
+copy /y ..\AUTHORS pamhyr\_internal
+copy /y ..\LICENSE pamhyr\_internal
+copy /y ..\src\motd.txt pamhyr\_internal

 rem MAGE
-mkdir pamhyr\mage
-copy /y ..\mage-windows\mage.exe pamhyr\mage\
-copy /y ..\mage-windows\mage_extraire.exe pamhyr\mage\
-copy /y ..\mage-windows\mailleurTT.exe pamhyr\mage\
-copy /y ..\mage-windows\libbief.dll pamhyr\mage\
+mkdir pamhyr\mage8
+copy /y ..\mage8-windows\mage.exe pamhyr\mage8\
+copy /y ..\mage8-windows\mage_as7.exe pamhyr\mage8\
+copy /y ..\mage8-windows\mage_extraire.exe pamhyr\mage8\
+copy /y ..\mage8-windows\mailleurTT.exe pamhyr\mage8\
+copy /y ..\mage8-windows\libbief.dll pamhyr\mage8\

 rem Copy tests_cases
 mkdir pamhyr\tests_cases
@@ -3,9 +3,10 @@
 !define LIC_NAME "LICENSE"
 !define APP_NAME "PAMHYR"

+Icon "pamhyr\_internal\View\ui\ressources\icon.ico"
 Name "Pamhyr2"
 OutFile "pamhyr-windows.exe"
-LicenseData "pamhyr\pamhyr\_internal\LICENSE"
+LicenseData "pamhyr\_internal\LICENSE"
 LicenseText "I Agree"

 RequestExecutionLevel admin
@@ -41,12 +42,12 @@ SectionEnd
 Section "Start Menu Shortcuts"
  CreateDirectory "$SMPROGRAMS\Pamhyr2"
  CreateShortcut "$SMPROGRAMS\Pamhyr2\Uninstall.lnk" "$INSTDIR\uninstall.exe"
-  CreateShortcut "$SMPROGRAMS\Pamhyr2\Pamhyr2.lnk" "$INSTDIR\pamhyr\pamhyr.exe"
+  CreateShortcut "$SMPROGRAMS\Pamhyr2\Pamhyr2.lnk" "$INSTDIR\pamhyr.exe"
 SectionEnd

 Section "Desktop Shortcuts"
  SetShellVarContext all
-  CreateShortcut "$desktop\Pamhyr2.lnk" "$instdir\pamhyr\pamhyr.exe"
+  CreateShortcut "$desktop\Pamhyr2.lnk" "$instdir\pamhyr.exe"
 SectionEnd

 Section "Uninstall"
@@ -4,9 +4,11 @@ PyQt5-sip==12.12.2
 #PyQtWebEngine==5.15.6
 QScintilla>=2.14.1
 pyqtgraph>=0.12.1
-matplotlib>=3.4.1
+matplotlib>=3.7.1
 numpy>=1.24.2
 colorama>=0.4.3
 pyinstaller>=5.11.0
 shapely>=2.0.1
 lxml>=4.9.3
+platformdirs>=4.2.0
+pyshp>=2.3.1
@@ -1,5 +1,5 @@
 # Checker.py -- Pamhyr abstract checker class
-# Copyright (C) 2023  INRAE
+# 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
@@ -16,23 +16,53 @@

 # -*- coding: utf-8 -*-

+import logging
+
 from enum import Enum

+from Modules import Modules
 from Model.Except import NotImplementedMethodeError

+logger = logging.getLogger()
+

 class STATUS(Enum):
-    UNKNOWN = -1
    OK = 0
    WARNING = 1
    ERROR = 2
+    UNKNOWN = 999
+
+    def __eq__(self, y):
+        return self.value == y.value
+
+    def __gt__(self, y):
+        return self.value > y.value
+
+    def __or__(self, y):
+        v = [self, y]
+        r = self.OK
+
+        if self.UNKNOWN in v:
+            r = self.UNKNOWN
+        if self.ERROR in v:
+            r = self.ERROR
+        if self.WARNING in v:
+            r = self.WARNING
+
+        logger.debug(f"CHECKER: STATUS: {self} | {y} = {r}")
+        return r


 class AbstractModelChecker(object):
    def __init__(self):
        self._name = ""
        self._description = ""
+        self._solver = "study"
+        self._modules = Modules.NONE

+        self.reset()
+
+    def reset(self):
        self._status = STATUS.UNKNOWN
        self._summary = "Unknown"

@@ -62,6 +92,21 @@ class AbstractModelChecker(object):
    def is_error(self):
        return self._status == STATUS.ERROR

+    # Basic check
+    def basic_check(self, study):
+        if study is None:
+            self._status = STATUS.ERROR
+            self._summary = "invalid_study"
+            return False
+
+        river = study.river
+        if river is None:
+            self._status = STATUS.ERROR
+            self._summary = "no_river_found"
+            return False
+
+        return True
+
    # Abstract function

    def _run(self, study):
@@ -1,5 +1,5 @@
 # Mage.py -- Pamhyr MAGE checkers
-# Copyright (C) 2023  INRAE
+# 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
@@ -23,6 +23,8 @@ from tools import flatten, timer

 from PyQt5.QtCore import QCoreApplication

+from Modules import Modules
+
 from Checker.Checker import AbstractModelChecker, STATUS
 from Checker.Study import StudyGeometryChecker

@@ -30,7 +32,7 @@ _translate = QCoreApplication.translate


 class MageNetworkGraphChecker(AbstractModelChecker):
-    def __init__(self, connectivity=True):
+    def __init__(self, connectivity=True, version="mage8"):
        super(MageNetworkGraphChecker, self).__init__()

        self._mode_conn = connectivity
@@ -44,6 +46,8 @@ class MageNetworkGraphChecker(AbstractModelChecker):
            "Checker", f"Mage network graph {mode} checker")
        self._description = _translate(
            "Checker", "Check if the network graph is valid")
+        self._solver = version
+        self._modules = Modules.NETWORK

    @timer
    def _connectivity(self, summary, status, graph):
@@ -199,15 +203,18 @@ class MageNetworkGraphChecker(AbstractModelChecker):


 class MageGeometryGuideLineChecker(StudyGeometryChecker):
-    def __init__(self):
+    def __init__(self, version="mage8"):
        super(MageGeometryGuideLineChecker, self).__init__()

-        self._name = _translate("Checker", "Mage geometry guide line checker")
+        self._name = _translate("Checker", "Mage geometry guideline checker")
        self._description = _translate(
            "Checker",
-            "Check if exists geometry guide line is correctly defined \
-for each reaches of the study"
+            "Check if exists geometry guidelines are correctly defined \
+for each reach"
        )
+        self._solver = version
+        self._modules = Modules.GEOMETRY
+
        self._reachs = []

    def run(self, study):
@@ -234,7 +241,7 @@ for each reaches of the study"
            for profile in profiles:
                if not profile.has_standard_named_points():
                    self._status = STATUS.WARNING
-                    self._summary = "no_standard_guileline_defined"
+                    self._summary = "no_standard_guideline_defined"
                    return False

        for gl in gls[1:]:
@@ -1,5 +1,5 @@
 # Study.py -- Pamhyr study checkers
-# Copyright (C) 2023  INRAE
+# 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
@@ -17,33 +17,34 @@
 # -*- coding: utf-8 -*-

 import time
+import logging
+from functools import reduce

 from PyQt5.QtCore import QCoreApplication

+from Modules import Modules
 from Checker.Checker import AbstractModelChecker, STATUS

 _translate = QCoreApplication.translate

+logger = logging.getLogger()
+

 class StudyNetworkReachChecker(AbstractModelChecker):
    def __init__(self):
        super(StudyNetworkReachChecker, self).__init__()

-        self._name = _translate("Checker", "Study network reach checker")
+        self._name = _translate("Checker", "Study reach network checker")
        self._description = _translate(
-            "Checker", "Check if exists at least one reach for study")
+            "Checker", "Check if exists at least one reach exists"
+        )
+        self._modules = Modules.NETWORK

    def run(self, study):
-        if study is None:
-            self._status = STATUS.ERROR
-            self._summary = "invalid_study"
+        if not self.basic_check(study):
            return False

        river = study.river
-        if river is None:
-            self._status = STATUS.ERROR
-            self._summary = "no_river_found"
-            return False

        edges = list(filter(lambda e: e.is_enable(), river.edges()))
        if len(edges) == 0:
@@ -62,7 +63,10 @@ class StudyGeometryChecker(AbstractModelChecker):

        self._name = _translate("Checker", "Study geometry checker")
        self._description = _translate(
-            "Checker", "Check if exists geometry for each reach of study")
+            "Checker", "Check if the geometry of each reach exists"
+        )
+        self._modules = Modules.GEOMETRY
+
        self._reachs = []

    def run(self, study):
@@ -71,16 +75,10 @@ class StudyGeometryChecker(AbstractModelChecker):
        summary = "ok"
        status = STATUS.OK

-        if study is None:
-            self._status = STATUS.ERROR
-            self._summary = "invalid_study"
+        if not self.basic_check(study):
            return False

        river = study.river
-        if river is None:
-            self._status = STATUS.ERROR
-            self._summary = "no_river_found"
-            return False

        edges = river.enable_edges()
        if len(edges) == 0:
@@ -100,6 +98,124 @@ class StudyGeometryChecker(AbstractModelChecker):
        return ok


+class StudyInitialConditionsChecker(AbstractModelChecker):
+    def __init__(self):
+        super(StudyInitialConditionsChecker, self).__init__()
+
+        self._name = _translate("Checker", "Study initial conditions checker")
+        self._description = _translate(
+            "Checker", "Check initial conditions for each node of study"
+        )
+        self._modules = Modules.INITIAL_CONDITION
+
+    def run(self, study):
+        ok = True
+        nerror = 0
+        self._summary = "ok"
+        self._status = STATUS.OK
+
+        if not self.basic_check(study):
+            return False
+
+        for reach in study.river.enable_edges():
+            ok &= self.check_reach(study, reach.reach)
+
+        return ok
+
+    def check_reach(self, study, reach):
+        ok = True
+        river = study.river
+
+        if reach not in river.initial_conditions:
+            self._summary = "missing_initial_condition_defined"
+            self._status = STATUS.WARNING
+            return ok
+
+        ic = river.initial_conditions[reach]
+        len_ic = len(ic)
+        len_reach = len(reach)
+
+        if len_ic < len_reach:
+            self._summary = "initial_condition_missing_profile"
+            self._status = STATUS.WARNING
+
+        if len_ic > len_reach:
+            self._summary = "more_initial_condition_than_profile"
+            self._status = STATUS.ERROR
+            ok = False
+
+        return ok
+
+
+class StudyBoundaryConditionChecker(AbstractModelChecker):
+    def __init__(self):
+        super(StudyBoundaryConditionChecker, self).__init__()
+
+        self._name = _translate("Checker", "Study boundary conditions checker")
+        self._description = _translate(
+            "Checker", "Check boundary conditions for each node of study"
+        )
+        self._modules = Modules.BOUNDARY_CONDITION
+
+    def run(self, study):
+        ok = True
+        nerror = 0
+        self._summary = "ok"
+        self._status = STATUS.OK
+
+        if not self.basic_check(study):
+            return False
+
+        ok = self.check_liquid(study)
+
+        return ok
+
+    def check_liquid(self, study):
+        river = study.river
+
+        bcs = river.boundary_condition.get_tab('liquid')
+        if len(bcs) == 0:
+            self._status = STATUS.ERROR
+            self._summary = "no_boundary_condition_defined"
+            return False
+
+        upstream, downstream = reduce(
+            lambda acc, n: (
+                acc[0] + [n] if river.is_upstream_node(n) else acc[0],
+                acc[1] + [n] if river.is_downstream_node(n) else acc[1],
+            ),
+            filter(
+                lambda n: river.is_enable_node(n),
+                river.nodes()
+            ),
+            ([], [])
+        )
+
+        bcs_nodes = set(map(lambda bc: bc.node, bcs))
+
+        upstream_ok = self.check_liquid_all_node_has_bc(
+            bcs_nodes, upstream
+        )
+        downstream_ok = self.check_liquid_all_node_has_bc(
+            bcs_nodes, downstream
+        )
+
+        ok = upstream_ok and downstream_ok
+
+        if not ok:
+            self._status = STATUS.ERROR
+            self._summary = "no_boundary_condition_at_boundary_node"
+
+        return ok
+
+    def check_liquid_all_node_has_bc(self, bcs_nodes, nodes):
+        return reduce(
+            lambda acc, n: (acc and (n in bcs_nodes)),
+            nodes,
+            True
+        )
+
+
 class DummyOK(AbstractModelChecker):
    def __init__(self):
        super(DummyOK, self).__init__()
@@ -1,5 +1,5 @@
 # AMeshingTool.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -1,5 +1,5 @@
 # Mage.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -30,7 +30,7 @@ from ctypes import (
 )
 from PyQt5.QtCore import QProcess

-from tools import logger_color_red, logger_color_reset
+from tools import logger_color_red, logger_color_reset, logger_exception
 from Meshing.AMeshingTool import AMeshingTool

 logger = logging.getLogger()
@@ -65,6 +65,10 @@ class MeshingWithMage(AMeshingTool):
            )
        )

+    @classmethod
+    def _path(cls):
+        return cls._exe_path()
+
    def _init_c_init_bief_from_geo_file(self):
        self._c_init_bief_from_geo_file = getattr(
            self._bief_lib, 'c_init_bief_from_geo_file'
@@ -274,15 +278,27 @@ class MeshingWithMageMailleurTT(AMeshingTool):
        return os.path.abspath(
            os.path.join(
                os.path.dirname(__file__),
-                "..", "..", "..", "mage", f"mailleurTT{ext}"
+                "..", "..", "mage8", f"mailleurTT{ext}"
            )
        )

+    @classmethod
+    def _path(cls):
+        return cls._exe_path()
+
    ###########
    # Meshing #
    ###########

-    def meshing(self, reach, step: float = 50):
+    def meshing(self, reach,
+                step: float = 50,
+                limites=[-1, -1],
+                origin=0,
+                directrices=['un', 'np'],
+                lplan: bool = False,
+                lm: int = 3,
+                linear: bool = False,
+                origin_value=0.0):
        if reach is None or len(reach.profiles) == 0:
            return reach

@@ -294,19 +310,132 @@ class MeshingWithMageMailleurTT(AMeshingTool):
            proc = QProcess()
            proc.setWorkingDirectory(tmp)

-            logger.debug(f"mailleurTT '{st_file}, {m_file}, {str(step)}'")
+            # Mage section index start at 1
+            origin += 1
+            limites[0] += 1
+            limites[1] += 1
+
+            lplan = 1 if lplan else 0
+            linear = 1 if linear else 0
+
+            logger.info(
+                f"! {self._exe_path()} " +
+                f"{st_file} {m_file} " +
+                f"mesh " +
+                f"{str(step)} " +
+                f"{limites[0]} {limites[1]} " +
+                f"{directrices[0]} {directrices[1]} " +
+                f"{lplan} {lm} {linear} " +
+                f"{origin} "
+            )
            proc.start(
-                self._exe_path(), [st_file, m_file, str(step)]
+                self._exe_path(),
+                list(
+                    map(
+                        str,
+                        [
+                            st_file, m_file,
+                            "mesh", step,
+                            limites[0], limites[1],
+                            directrices[0], directrices[1],
+                            lplan, lm, linear, origin, origin_value
+                        ]
+                    )
+                )
            )
            proc.waitForFinished()

-            errors = proc.readAllStandardError()
-            if len(errors) != 0:
+            if proc.exitCode() != 0:
+                logger.error(
+                    f"{logger_color_red()}" +
+                    f"MailleurTT error: {proc.exitCode()}" +
+                    f"{logger_color_reset()}"
+                )
+                outputs = proc.readAllStandardOutput()
+                logger.debug(outputs)
+
+                errors = proc.readAllStandardError()
                logger.error(
                    f"{logger_color_red()}{errors}{logger_color_reset()}"
                )
-            else:
-                self.import_m_file(reach, m_file)
+                return reach
+
+            self.import_m_file(reach, m_file)
+            return reach
+
+    def update_rk(self, reach,
+                  step: float = 50,
+                  limites=[-1, -1],
+                  origin=0,
+                  directrices=['un', 'np'],
+                  lplan: bool = False,
+                  lm: int = 3,
+                  linear: bool = False,
+                  origin_value=0.0,
+                  orientation=0):
+        if reach is None or len(reach.profiles) == 0:
+            return reach
+
+        with tempfile.TemporaryDirectory() as tmp:
+            logger.debug(f"temp file: {tmp}")
+            st_file = self.export_reach_to_st(reach, tmp)
+            m_file = st_file.rsplit(".ST", 1)[0] + ".M"
+
+            proc = QProcess()
+            proc.setWorkingDirectory(tmp)
+
+            # Mage section indices start at 1
+            origin += 1
+            limites[0] += 1
+            limites[1] += 1
+
+            lplan = 1 if lplan else 0
+            linear = 1 if linear else 0
+
+            logger.info(
+                f"! {self._exe_path()} " +
+                f"{st_file} {m_file} " +
+                f"update_kp " +
+                f"{str(step)} " +
+                f"{limites[0]} {limites[1]} " +
+                f"{directrices[0]} {directrices[1]} " +
+                f"{orientation} {lm} {linear} " +
+                f"{origin} " +
+                f"{origin_value} "
+            )
+            proc.start(
+                self._exe_path(),
+                list(
+                    map(
+                        str,
+                        [
+                            st_file, m_file,
+                            "update_kp", step,
+                            limites[0], limites[1],
+                            directrices[0], directrices[1],
+                            orientation, lm, linear, origin, origin_value
+                        ]
+                    )
+                )
+            )
+            proc.waitForFinished()
+
+            if proc.exitCode() != 0:
+                logger.error(
+                    f"{logger_color_red()}" +
+                    f"MailleurTT error: {proc.exitCode()}" +
+                    f"{logger_color_reset()}"
+                )
+                outputs = proc.readAllStandardOutput()
+                logger.debug(outputs)
+
+                errors = proc.readAllStandardError()
+                logger.error(
+                    f"{logger_color_red()}{errors}{logger_color_reset()}"
+                )
+                return reach
+
+            self.import_m_file(reach, m_file)
            return reach

    def export_reach_to_st(self, reach, tmp):
@@ -318,7 +447,9 @@ class MeshingWithMageMailleurTT(AMeshingTool):
        return tmp_st

    def import_m_file(self, reach, m):
-        reach.purge()
-
-        logger.debug(f"meshing: Import geometry from {m}")
-        reach.import_geometry(m)
+        if os.path.exists(m):
+            reach.purge()
+            logger.debug(f"meshing: Import geometry from {m}")
+            reach.import_geometry(m)
+        else:
+            logger.error(f"meshing: Meshed geometry file {m} do not exists")
@@ -1,5 +1,5 @@
 # __init__.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -1,5 +1,5 @@
 # test_Model.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -25,9 +25,10 @@ from Model.Saved import SavedStatus
 from Model.Study import Study
 from Model.River import River

-from Meshing.Mage import MeshingWithMage
+from Meshing.Mage import MeshingWithMage, MeshingWithMageMailleurTT

 mage_mesher = os.path.exists(MeshingWithMage._lib_path())
+mage_mesher_TT = os.path.exists(MeshingWithMageMailleurTT._exe_path())


 class MeshingTestCase(unittest.TestCase):
@@ -35,3 +36,8 @@ class MeshingTestCase(unittest.TestCase):
    def test_create_meshingtool_mage(self):
        mesher = MeshingWithMage()
        self.assertNotEqual(mesher, None)
+
+    @unittest.skipIf(not mage_mesher_TT, "mailleurTT is not available")
+    def test_create_meshingtool_mageTT(self):
+        mesher = MeshingWithMageMailleurTT()
+        self.assertNotEqual(mesher, None)
@@ -0,0 +1,178 @@
+# AddFile.py -- Pamhyr
+# Copyright (C) 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 -*-
+
+from functools import reduce
+
+from tools import trace, timer
+
+from Model.Tools.PamhyrDB import SQLSubModel
+from Model.Except import NotImplementedMethodeError
+
+
+class AddFile(SQLSubModel):
+    _sub_classes = []
+    _id_cnt = 0
+
+    def __init__(self, id: int = -1, enabled=True,
+                 name="", path="", text="",
+                 status=None):
+        super(AddFile, self).__init__()
+
+        if id == -1:
+            self.id = AddFile._id_cnt
+        else:
+            self.id = id
+
+        self._status = status
+
+        self._enabled = enabled
+        self._name = f"File {self.id}" if name == "" else name
+        self._path = path
+        self._text = text
+
+        AddFile._id_cnt = max(id, AddFile._id_cnt+1)
+
+    def __getitem__(self, key):
+        value = None
+
+        if key == "enabled":
+            value = self._enabled
+        elif key == "name":
+            value = self._name
+        elif key == "path":
+            value = self._path
+        elif key == "text":
+            value = self._text
+
+        return value
+
+    def __setitem__(self, key, value):
+        if key == "enabled":
+            self._enabled = value
+        elif key == "name":
+            self._name = value
+        elif key == "path":
+            self._path = value
+        elif key == "text":
+            self._text = value
+
+        self._status.modified()
+
+    @property
+    def enabled(self):
+        return self._enabled
+
+    @enabled.setter
+    def enabled(self, enabled):
+        self._enabled = enabled
+        self._status.modified()
+
+    def is_enabled(self):
+        return self._enabled
+
+    @property
+    def name(self):
+        return self._name
+
+    @name.setter
+    def name(self, name):
+        self._name = name
+        self._status.modified()
+
+    @property
+    def path(self):
+        return self._path
+
+    @path.setter
+    def path(self, path):
+        self._path = path
+        self._status.modified()
+
+    @property
+    def text(self):
+        return self._text
+
+    @text.setter
+    def text(self, text):
+        self._text = text
+        self._status.modified()
+
+    @classmethod
+    def _db_create(cls, execute):
+        execute("""
+          CREATE TABLE additional_files(
+            id INTEGER NOT NULL PRIMARY KEY,
+            enabled BOOLEAN NOT NULL,
+            name TEXT NOT NULL,
+            path TEXT NOT NULL,
+            text TEXT NOT NULL
+          )
+        """)
+
+        return cls._create_submodel(execute)
+
+    @classmethod
+    def _db_update(cls, execute, version):
+        major, minor, release = version.strip().split(".")
+        if major == minor == "0":
+            if int(release) < 8:
+                cls._db_create(execute)
+
+        return True
+
+    @classmethod
+    def _db_load(cls, execute, data=None):
+        new = []
+
+        table = execute(
+            "SELECT id, enabled, name, path, text " +
+            "FROM additional_files"
+        )
+
+        for row in table:
+            it = iter(row)
+
+            id = next(it)
+            enabled = (next(it) == 1)
+            name = next(it)
+            path = next(it)
+            text = next(it)
+
+            f = cls(
+                id=id, enabled=enabled, name=name, path=path, text=text,
+                status=data['status']
+            )
+
+            new.append(f)
+
+        return new
+
+    def _db_save(self, execute, data=None):
+        sql = (
+            "INSERT INTO " +
+            "additional_files(id, enabled, name, path, text) " +
+            "VALUES (" +
+            f"{self.id}, {self._enabled}, " +
+            f"'{self._db_format(self._name)}', " +
+            f"'{self._db_format(self._path)}', " +
+            f"'{self._db_format(self._text)}'" +
+            ")"
+        )
+        execute(sql)
+
+        return True
@@ -0,0 +1,56 @@
+# AddFileList.py -- Pamhyr
+# Copyright (C) 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 -*-
+
+from tools import trace, timer
+
+from Model.Except import NotImplementedMethodeError
+from Model.Tools.PamhyrList import PamhyrModelList
+from Model.AdditionalFile.AddFile import AddFile
+
+
+class AddFileList(PamhyrModelList):
+    _sub_classes = [AddFile]
+
+    @classmethod
+    def _db_load(cls, execute, data=None):
+        new = cls(status=data["status"])
+
+        new._lst = AddFile._db_load(execute, data)
+
+        return new
+
+    def _db_save(self, execute, data=None):
+        ok = True
+
+        # Delete previous data
+        execute("DELETE FROM additional_files")
+
+        for af in self._lst:
+            ok &= af._db_save(execute, data)
+
+        return ok
+
+    @property
+    def files(self):
+        return self.lst
+
+    def new(self, index):
+        n = AddFile(status=self._status)
+        self.insert(index, n)
+        self._status.modified()
+        return n
@@ -1,5 +1,5 @@
 # BoundaryCondition.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -18,7 +18,12 @@

 import logging

-from tools import trace, timer, old_pamhyr_date_to_timestamp
+from tools import (
+    trace, timer,
+    old_pamhyr_date_to_timestamp,
+    date_iso_to_timestamp,
+    date_dmy_to_timestamp,
+)

 from Model.Tools.PamhyrDB import SQLSubModel
 from Model.Except import NotImplementedMethodeError
@@ -189,6 +194,10 @@ class BoundaryCondition(SQLSubModel):
    @classmethod
    def time_convert(cls, data):
        if type(data) is str:
+            if data.count("-") == 2:
+                return date_iso_to_timestamp(data)
+            if data.count("/") == 2:
+                return date_dmy_to_timestamp(data)
            if data.count(":") == 3:
                return old_pamhyr_date_to_timestamp(data)
            if data.count(":") == 2:
@@ -200,6 +209,9 @@ class BoundaryCondition(SQLSubModel):

    @property
    def name(self):
+        if self._name == "":
+            return f"B{self.id + 1}"
+
        return self._name

    @name.setter
@@ -303,6 +315,9 @@ class BoundaryCondition(SQLSubModel):
            self._data.sort(reverse=_reverse, key=key)
        self._status.modified()

+    def index(self, bc):
+        self._data.index(bc)
+
    def get_i(self, index):
        return self.data[index]

@@ -356,3 +371,15 @@ class BoundaryCondition(SQLSubModel):
            d = self._data
            d[index], d[prev] = d[prev], d[index]
            self._status.modified()
+
+    def reach(self, river):
+        r = []
+        if self._node is not None:
+            if river is not None:
+                for edge in river.edges():
+                    if edge.node1.name == self._node.name:
+                        r.append(edge.reach)
+                    if edge.node2.name == self._node.name:
+                        r.append(edge.reach)
+
+        return r
@@ -1,5 +1,5 @@
 # BoundaryConditionList.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -1,5 +1,5 @@
 # BoundaryConditionTypes.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -1,5 +1,5 @@
 # Except.py -- Pamhyr model exceptions
-# Copyright (C) 2023  INRAE
+# 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
@@ -21,7 +21,7 @@ from PyQt5.QtCore import (
 )

 from PyQt5.QtWidgets import (
-    QApplication, QMessageBox,
+    QApplication, QMessageBox, QLabel,
 )

 _translate = QCoreApplication.translate
@@ -34,6 +34,7 @@ _translate = QCoreApplication.translate
 def exception_message_box(exception):
    msg = QMessageBox()
    msg.setIcon(QMessageBox.Critical)
+    msg.findChild(QLabel, "qt_msgbox_label").setFixedWidth(384)

    msg.setText("Exception :")
    msg.setInformativeText(f"{exception}")
@@ -1,5 +1,5 @@
 # Friction.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -22,19 +22,31 @@ from tools import trace, timer

 from Model.Tools.PamhyrDB import SQLSubModel

+from numpy import interp
+
 logger = logging.getLogger()


 class Friction(SQLSubModel):
-    def __init__(self, name: str = "", status=None):
+    _id_cnt = 0
+
+    def __init__(self, id: int = -1, name: str = "",
+                 status=None):
        super(Friction, self).__init__()

        self._status = status

+        if id == -1:
+            self.id = Friction._id_cnt
+        else:
+            self.id = id
+
+        Friction._id_cnt = max(self.id, Friction._id_cnt+1)
+
        self._name = name
        self._edge = None
-        self._begin_kp = 0.0
-        self._end_kp = 0.0
+        self._begin_rk = 0.0
+        self._end_rk = 0.0
        self._begin_strickler = None
        self._end_strickler = None

@@ -42,13 +54,13 @@ class Friction(SQLSubModel):
    def _db_create(cls, execute):
        execute("""
          CREATE TABLE friction(
-            id INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT,
-            ind INTERGER NOT NULL,
-            begin_kp REAL NOT NULL,
-            end_kp REAL NOT NULL,
+            id INTEGER NOT NULL PRIMARY KEY,
+            ind INTEGER NOT NULL,
+            begin_rk REAL NOT NULL,
+            end_rk REAL NOT NULL,
            reach INTEGER NOT NULL,
-            begin_strickler INTERGER,
-            end_strickler INTERGER,
+            begin_strickler INTEGER NOT NULL,
+            end_strickler INTEGER NOT NULL,
            FOREIGN KEY(reach) REFERENCES river_reach(id),
            FOREIGN KEY(begin_strickler) REFERENCES stricklers(id),
            FOREIGN KEY(end_strickler) REFERENCES stricklers(id)
@@ -59,6 +71,13 @@ class Friction(SQLSubModel):

    @classmethod
    def _db_update(cls, execute, version):
+        major, minor, release = version.strip().split(".")
+        if major == minor == "0":
+            if int(release) < 11:
+                execute("ALTER TABLE friction " +
+                        "RENAME COLUMN begin_kp TO begin_rk")
+                execute("ALTER TABLE friction RENAME COLUMN end_kp TO end_rk")
+
        return True

    @classmethod
@@ -70,28 +89,30 @@ class Friction(SQLSubModel):
        stricklers = data["stricklers"].stricklers

        table = execute(
-            "SELECT ind, begin_kp, end_kp, begin_strickler, end_strickler " +
+            "SELECT id, ind, begin_rk, end_rk, " +
+            "begin_strickler, end_strickler " +
            f"FROM friction WHERE reach = {reach.id}"
        )

        for row in table:
-            ind = row[0]
+            id = row[0]
+            ind = row[1]
            # Get stricklers
-            if int(row[3]) == -1:
+            if int(row[4]) == -1:
                bs = None
            else:
-                bs = next(filter(lambda s: s.id == row[3], stricklers))
+                bs = next(filter(lambda s: s.id == row[4], stricklers))

-            if int(row[4]) == -1:
+            if int(row[5]) == -1:
                es = None
            else:
-                es = next(filter(lambda s: s.id == row[4], stricklers))
+                es = next(filter(lambda s: s.id == row[5], stricklers))

            # Create friction
            sec = cls(status=status)
            sec.edge = reach
-            sec.begin_kp = row[1]
-            sec.end_kp = row[2]
+            sec.begin_rk = row[2]
+            sec.end_rk = row[3]
            sec.begin_strickler = bs
            sec.end_strickler = es

@@ -112,10 +133,11 @@ class Friction(SQLSubModel):

        execute(
            "INSERT INTO " +
-            "friction(ind, begin_kp, end_kp, " +
+            "friction(id, ind, begin_rk, end_rk, " +
            "reach, begin_strickler, end_strickler) " +
            "VALUES (" +
-            f"{ind}, {self._begin_kp}, {self._end_kp}, " +
+            f"{self.id}, {ind}, " +
+            f"{self._begin_rk}, {self._end_rk}, " +
            f"{self._edge.id}, " +
            f"{b_s_id}, {e_s_id}" +
            ")"
@@ -144,10 +166,10 @@ class Friction(SQLSubModel):
    def edge(self, edge):
        self._edge = edge
        if (edge is not None and
-            self._begin_kp == 0.0 and
-                self._end_kp == 0.0):
-            self._begin_kp = self._edge.reach.get_kp_min()
-            self._end_kp = self._edge.reach.get_kp_max()
+            self._begin_rk == 0.0 and
+                self._end_rk == 0.0):
+            self._begin_rk = self._edge.reach.get_rk_min()
+            self._end_rk = self._edge.reach.get_rk_max()
        self._status.modified()

    def has_edge(self):
@@ -155,47 +177,54 @@ class Friction(SQLSubModel):

    def has_coefficient(self):
        return (
-            self._begin_strickler is not None and
-            self._end_strickler is not None
+            self._begin_strickler is not None
        )

    def is_full_defined(self):
        return self.has_edge() and self.has_coefficient()

    @property
-    def begin_kp(self):
-        return self._begin_kp
+    def begin_rk(self):
+        return self._begin_rk

-    @begin_kp.setter
-    def begin_kp(self, begin_kp):
+    @begin_rk.setter
+    def begin_rk(self, begin_rk):
        if self._edge is None:
-            self._begin_kp = begin_kp
+            self._begin_rk = begin_rk
        else:
-            _min = self._edge.reach.get_kp_min()
-            _max = self._edge.reach.get_kp_max()
+            _min = self._edge.reach.get_rk_min()
+            _max = self._edge.reach.get_rk_max()

-            if _min <= begin_kp <= _max:
-                self._begin_kp = begin_kp
+            if _min <= begin_rk <= _max:
+                self._begin_rk = begin_rk

        self._status.modified()

    @property
-    def end_kp(self):
-        return self._end_kp
+    def end_rk(self):
+        return self._end_rk

-    @end_kp.setter
-    def end_kp(self, end_kp):
+    @end_rk.setter
+    def end_rk(self, end_rk):
        if self._edge is None:
-            self._end_kp = end_kp
+            self._end_rk = end_rk
        else:
-            _min = self._edge.reach.get_kp_min()
-            _max = self._edge.reach.get_kp_max()
+            _min = self._edge.reach.get_rk_min()
+            _max = self._edge.reach.get_rk_max()

-            if _min <= end_kp <= _max:
-                self._end_kp = end_kp
+            if _min <= end_rk <= _max:
+                self._end_rk = end_rk

        self._status.modified()

+    def __contains__(self, rk):
+        return self.contains_rk(rk)
+
+    def contains_rk(self, rk):
+        return (
+            self._begin_rk <= rk <= self._end_rk
+        )
+
    @property
    def begin_strickler(self):
        return self._begin_strickler
@@ -207,9 +236,28 @@ class Friction(SQLSubModel):

    @property
    def end_strickler(self):
-        return self._end_strickler
+        # return self._end_strickler
+        return self._begin_strickler

    @end_strickler.setter
    def end_strickler(self, strickler):
        self._end_strickler = strickler
        self._status.modified()
+
+    def get_friction(self, rk):
+        if not self.contains_rk(rk):
+            return None
+
+        minor = self.begin_strickler.minor
+        medium = self.begin_strickler.medium
+
+        # minor = interp(rk,
+        #                [self.begin_rk, self.end_rk],
+        #                [self.begin_strickler.minor,
+        #                 self.end_strickler.minor])
+        # medium = interp(rk,
+        #                 [self.begin_rk, self.end_rk],
+        #                 [self.begin_strickler.medium,
+        #                  self.end_strickler.medium])
+
+        return minor, medium
@@ -1,5 +1,5 @@
 # FrictionList.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -44,7 +44,7 @@ class FrictionList(PamhyrModelList):
            logger.info(f"Update friction TABLE from {version}")
            cls._db_update_0_0_1(execute, version)

-        return True
+        return cls._update_submodel(execute, version)

    @classmethod
    def _db_load(cls, execute, data=None):
@@ -1,5 +1,5 @@
 # Point.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -1,5 +1,5 @@
 # PointXY.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -1,5 +1,5 @@
 # PointXYZ.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -47,7 +47,7 @@ class PointXYZ(Point, SQLSubModel):
            z INTEGER NOT NULL,
            profile INTEGER NOT NULL,
            sl INTEGER,
-            FOREIGN KEY(profile) REFERENCES profileXYZ(id),
+            FOREIGN KEY(profile) REFERENCES geometry_profileXYZ(id),
            FOREIGN KEY(sl) REFERENCES sedimentary_layer(id)
          )
        """)
@@ -192,6 +192,22 @@ class PointXYZ(Point, SQLSubModel):
    def dist(self, p2):
        return PointXYZ.distance(self, p2)

+    def dist_2d(self, p2):
+        return PointXYZ.distance_2d(self, p2)
+
+    @staticmethod
+    def distance_2d(p1, p2):
+        """Euclidean distance between p1 and p2.
+
+        Args:
+            p1: A XYZ Point
+            p2: A XYZ Point
+
+        Returns:
+            Euclidean 2D distance between the two points
+        """
+        return dist((p1.x, p1.y), (p2.x, p2.y))
+
    @staticmethod
    def distance(p1, p2):
        """Euclidean distance between p1 and p2.
@@ -201,6 +217,14 @@ class PointXYZ(Point, SQLSubModel):
            p2: A XYZ Point

        Returns:
-            Euclidean distance between the two points
+            Euclidean 3D distance between the two points
        """
        return dist((p1.x, p1.y, p1.z), (p2.x, p2.y, p2.z))
+
+    @staticmethod
+    def areatriangle3d(p1, p2, p3):
+        a = PointXYZ.distance(p1, p2)
+        b = PointXYZ.distance(p2, p3)
+        c = PointXYZ.distance(p3, p1)
+        s = (a + b + c) / 2
+        return (s*(s-a) * (s-b)*(s-c)) ** 0.5
@@ -1,5 +1,5 @@
 # Profile.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -19,6 +19,7 @@
 import logging

 from tools import timer
+from shapely import geometry

 from Model.Geometry.Point import Point
 from Model.Except import NotImplementedMethodeError
@@ -30,7 +31,7 @@ class Profile(object):
    _id_cnt = 0

    def __init__(self, id: int = -1, num: int = 0,
-                 kp: float = 0.0, name: str = "",
+                 rk: float = 0.0, name: str = "",
                 code1: int = 0, code2: int = 0,
                 _type: str = "", reach=None,
                 status=None):
@@ -48,7 +49,7 @@ class Profile(object):
        self._num = int(num)
        self._code1 = int(code1)
        self._code2 = int(code2)
-        self._kp = float(kp)
+        self._rk = float(rk)
        self._name = str(name)
        self._reach = reach
        self._sl = None
@@ -135,16 +136,16 @@ class Profile(object):
        return len(self.points)

    @property
-    def kp(self):
+    def rk(self):
        """
        Returns:
            Kilometer point.
        """
-        return self._kp
+        return self._rk

-    @kp.setter
-    def kp(self, value: float):
-        self._kp = float(value)
+    @rk.setter
+    def rk(self, value: float):
+        self._rk = float(value)
        self._status.modified()

    @property
@@ -295,6 +296,11 @@ class Profile(object):
        )
        self._status.modified()

+    @timer
+    def reverse(self):
+        self._points.reverse()
+        self._status.modified()
+
    # Sediment Layers

    def get_sl(self):
@@ -341,3 +347,21 @@ class Profile(object):
    # Abstract method for width approximation
    def get_water_limits(self, z):
        raise NotImplementedMethodeError(self, self.get_water_limits)
+
+    def wet_points(self, z):
+        raise NotImplementedMethodeError(self, self.wet_point)
+
+    def wet_width(self, z):
+        raise NotImplementedMethodeError(self, self.wet_width)
+
+    def wet_perimeter(self, z):
+        raise NotImplementedMethodeError(self, self.wet_perimeter)
+
+    def wet_area(self, z):
+        raise NotImplementedMethodeError(self, self.wet_area)
+
+    def wet_radius(self, z):
+        raise NotImplementedMethodeError(self, self.wet_radius)
+
+    def get_nb_wet_areas(self, z):
+        raise NotImplementedMethodeError(self, self.get_nb_wet_areas)
@@ -1,5 +1,5 @@
 # ProfileXYZ.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -22,6 +22,7 @@ from typing import List
 from functools import reduce

 from tools import timer
+from shapely import geometry

 from Model.Tools.PamhyrDB import SQLSubModel
 from Model.Except import ClipboardFormatError
@@ -40,7 +41,7 @@ class ProfileXYZ(Profile, SQLSubModel):
    def __init__(self,
                 id: int = -1,
                 name: str = "",
-                 kp: float = 0.,
+                 rk: float = 0.,
                 reach=None,
                 num=0,
                 nb_point: int = 0,
@@ -52,7 +53,7 @@ class ProfileXYZ(Profile, SQLSubModel):
            num: The number of this profile
            code1: The interpolation code 1
            code2: The interpolation code 2
-            kp: Kilometer point
+            rk: Kilometer point
            name: The name of profile

        Returns:
@@ -62,7 +63,7 @@ class ProfileXYZ(Profile, SQLSubModel):
            id=id,
            num=num,
            name=name,
-            kp=kp,
+            rk=rk,
            code1=code1, code2=code2,
            _type="XYZ",
            reach=reach,
@@ -77,7 +78,7 @@ class ProfileXYZ(Profile, SQLSubModel):
            ind INTEGER NOT NULL,
            name TEXT,
            reach INTEGER NOT NULL,
-            kp REAL NOT NULL,
+            rk REAL NOT NULL,
            num INTEGER NOT NULL,
            code1 INTEGER NOT NULL,
            code2 INTEGER NOT NULL,
@@ -93,7 +94,8 @@ class ProfileXYZ(Profile, SQLSubModel):
    def _db_update(cls, execute, version):
        major, minor, release = version.strip().split(".")
        if major == minor == "0":
-            if int(release) < 2:
+            rl = int(release)
+            if rl < 2:
                execute(
                    """
                    ALTER TABLE geometry_profileXYZ
@@ -102,6 +104,14 @@ class ProfileXYZ(Profile, SQLSubModel):
                    """
                )

+            if rl < 11:
+                execute(
+                    """
+                    ALTER TABLE geometry_profileXYZ
+                    RENAME COLUMN kp TO rk
+                    """
+                )
+
        return cls._update_submodel(execute, version)

    @classmethod
@@ -111,7 +121,7 @@ class ProfileXYZ(Profile, SQLSubModel):
        reach = data["reach"]

        table = execute(
-            "SELECT id, ind, name, kp, num, code1, code2, sl " +
+            "SELECT id, ind, name, rk, num, code1, code2, sl " +
            "FROM geometry_profileXYZ " +
            f"WHERE reach = {reach.id}"
        )
@@ -120,7 +130,7 @@ class ProfileXYZ(Profile, SQLSubModel):
            id = row[0]
            ind = row[1]
            name = row[2]
-            kp = row[3]
+            rk = row[3]
            num = row[5]
            code1 = row[5]
            code2 = row[6]
@@ -128,7 +138,7 @@ class ProfileXYZ(Profile, SQLSubModel):

            new = cls(
                id=id, num=num,
-                name=name, kp=kp,
+                name=name, rk=rk,
                code1=code1, code2=code2,
                reach=reach,
                status=status
@@ -158,10 +168,10 @@ class ProfileXYZ(Profile, SQLSubModel):
        sql = (
            "INSERT OR REPLACE INTO " +
            "geometry_profileXYZ(id, ind, name, reach, " +
-            "kp, num, code1, code2, sl) " +
+            "rk, num, code1, code2, sl) " +
            "VALUES (" +
            f"{self.id}, {ind}, '{self._db_format(self._name)}', " +
-            f"{self.reach.id}, {self.kp}, {self.num}, " +
+            f"{self.reach.id}, {self.rk}, {self.num}, " +
            f"{self.code1}, {self.code1}, {sl}" +
            ")"
        )
@@ -186,19 +196,19 @@ class ProfileXYZ(Profile, SQLSubModel):
        try:
            if len(header) == 0:
                name = data[0]
-                kp = data[1]
+                rk = data[1]
                reach = data[2]
                status = data[3]

                profile = cls(
                    id=-1,
                    name=name,
-                    kp=kp,
+                    rk=rk,
                    reach=reach,
                    status=status
                )
            else:
-                valid_header = {'name', 'reach', 'kp', 'status'}
+                valid_header = {'name', 'reach', 'rk', 'status'}
                d = {}
                for i, v in enumerate(data):
                    h = header[i].strip().lower().split(' ')[0]
@@ -243,6 +253,15 @@ class ProfileXYZ(Profile, SQLSubModel):

        return point

+    def display_name(self):
+        name = ""
+        if self.name != "":
+            name += f"{self.name} "
+
+        name += f"({self.rk})"
+
+        return name
+
    def x(self):
        return [point.x for point in self.points]

@@ -322,7 +341,7 @@ class ProfileXYZ(Profile, SQLSubModel):
            logger.debug(f"{e}")
            raise IndexError(
                f"Invalid point name: {name} " +
-                f"for profile ({self.id}) kp = {self.kp}"
+                f"for profile ({self.id}) rk = {self.rk}"
            )

    def has_standard_named_points(self):
@@ -373,99 +392,13 @@ class ProfileXYZ(Profile, SQLSubModel):
        """
        return [x for x in lst if not np.isnan(x)]

-    def _first_point_not_nan(self):
-        first_point = self.points[0]
+    def speed(self, q, z):
+        area = self.wet_area(z)

-        for point in self.points:
-            if not point.is_nan():
-                first_point = point
-                break
+        if area == 0:
+            return 0

-        return first_point
-
-    def _last_point_not_nan(self):
-        last_point = self.points[-1]
-
-        for point in self.points[::-1]:
-            if not point.is_nan():
-                last_point = point
-                break
-
-        return last_point
-
-    @timer
-    def get_station(self) -> np.ndarray:
-        """Projection of the points of the profile on a plane.
-
-        Args:
-            profile: The profile
-
-        Returns:
-            Projection of the points of the profile on a plane.
-        """
-        if self.nb_points < 3:
-            return None
-        else:
-            first_named_point = None
-            index_first_named_point = None
-            last_named_point = None
-
-            first_point_not_nan = self._first_point_not_nan()
-            last_point_not_nan = self._last_point_not_nan()
-
-            for index, point in enumerate(self.points):
-                if point.point_is_named():
-                    index_first_named_point = index
-                    first_named_point = point
-                    break
-
-            for point in reversed(self.points):
-                if point.point_is_named():
-                    last_named_point = point
-                    break
-
-            station = []
-            constant = 0.0
-
-            if (first_named_point is not None and
-                    last_named_point is not None):
-                if (first_named_point != last_named_point and
-                        first_named_point.x != last_named_point.x):
-                    vector = Vector1d(first_named_point, last_named_point)
-                    norm_dir_vec = vector.normalized_direction_vector()
-                else:
-                    vector = Vector1d(first_point_not_nan, last_point_not_nan)
-                    norm_dir_vec = vector.normalized_direction_vector()
-
-                for point in self.points:
-                    xi = point.x - first_named_point.x
-                    yi = point.y - first_named_point.y
-                    station_i = (norm_dir_vec[0] * xi +
-                                 norm_dir_vec[1] * yi)
-                    station.append(station_i)
-
-                constant = station[index_first_named_point]
-            elif first_named_point is None:
-                vector = Vector1d(first_point_not_nan, last_point_not_nan)
-                norm_dir_vec = vector.normalized_direction_vector()
-
-                for point in self.points:
-                    xi = point.x - first_point_not_nan.x
-                    yi = point.y - first_point_not_nan.y
-                    station_i = (norm_dir_vec[0] * xi +
-                                 norm_dir_vec[1] * yi)
-                    station.append(station_i)
-
-                z_min = self.z_min()
-                index_profile_z_min = list(
-                    filter(
-                        lambda z: z[1] == z_min,
-                        enumerate(self.z())
-                    )
-                )[0]
-                constant = station[index_profile_z_min[0]]
-
-            return list(map(lambda s: s - constant, station))
+        return q / area

    def width_approximation(self):
        if self.has_standard_named_points():
@@ -477,58 +410,392 @@ class ProfileXYZ(Profile, SQLSubModel):

        return abs(rg.dist(rd))

-    def get_water_limits(self, z):
-        # ====================================================================
-        #  détermination des points limites RG et RD pour un niveau
-        #  d'eau donné
-        #
-        #  irg et ird sont les premiers indices en partant des rives
-        #  gauche et droite qui correspondent à des points sous la
-        #  surface de l'eau ptX et ptY sont les points interpolés où
-        #  le plan d'eau intersecte le profil known_level est le
-        #  niveau d'eau pour lequel on a obtenu irg, ird, ptX et ptY
-        # ====================================================================
+    def wet_width(self, z):
+        start, end = self.get_all_water_limits_ac(z)

-        # initialisation
-        irg = -1
-        ird = -1
+        if len(start) == 0:
+            return 0
+
+        length = 0.0
+        for s, e in zip(start, end):
+            length += abs(s - e)
+        return length
+
+    def wet_perimeter(self, z):
+        lines = self.wet_lines(z)
+
+        if lines is None:
+            return 0
+
+        length = 0.0
+        for line in lines:
+            length += line.length
+        return length
+
+    def wet_area(self, z):
+        lines = self.wet_lines(z)
+
+        if lines is None:
+            return 0
+
+        area = 0.0
+        for line in lines:
+            if len(line.coords) > 2:
+                poly = geometry.Polygon(line)
+                area += poly.area
+        return area
+
+    def wet_radius(self, z):
+        p = self.wet_perimeter(z)
+        a = self.wet_area(z)
+
+        if p == 0:
+            return 0
+
+        return a/p
+
+    def wet_line(self, z):
+        points = self.wet_points(z)
+        if len(points) < 3:
+            return None
+
+        zz = map(lambda p: p.z, points)
+        station = self._get_station(points)
+
+        line = geometry.LineString(list(zip(station, zz)))
+        return line
+
+    def wet_lines(self, z):
+        points = self._points
+        if len(points) < 3:
+            return None
+
+        lines = []
+
+        zz = list(map(lambda p: p.z, points))
+        station = self._get_station(points)
+
+        line = []
+        for i in range(self.number_points-1):
+
+            if zz[i] >= z and zz[i+1] < z:
+                y = np.interp(
+                    z,
+                    [zz[i], zz[i+1]],
+                    [station[i], station[i+1]]
+                )
+                line.append([y, z])
+
+            if zz[i] < z:
+                line.append([station[i], zz[i]])
+
+            if zz[i] <= z and zz[i+1] >= z:
+                y = np.interp(
+                    z,
+                    [zz[i], zz[i+1]],
+                    [station[i], station[i+1]]
+                )
+                line.append([y, z])
+                if len(line) > 2:
+                    lines.append(geometry.LineString(line))
+                line = []
+
+        if zz[self.number_points-1] < z:
+            line.append([station[self.number_points-1], z])
+            if len(line) > 2:
+                lines.append(geometry.LineString(line))
+            line = []
+
+        return lines
+
+    def max_water_depth(self, z):
+        return z - self.z_min()
+
+    def mean_water_depth(self, z):
+        a = self.wet_area(z)
+        w = self.wet_width(z)
+
+        if w == 0:
+            return 0
+
+        return a/w
+
+    def wet_polygon(self, z):
+        points = self.wet_points(z)
+        if len(points) < 3:
+            return None
+
+        zz = map(lambda p: p.z, points)
+        station = self._get_station(points)
+
+        poly = geometry.Polygon(list(zip(station, zz)))
+        return poly
+
+    def wet_points(self, z):
+        left, right = self.get_water_limits(z)
+
+        points = list(filter(lambda p: p.z < z, self._points))
+        points = [left] + points + [right]
+        points = sorted(points, key=lambda p: p.x)
+
+        return points
+
+    def get_nb_wet_areas(self, z):
+
+        n_zones = 0
+        points = self._points
+        if points[0].z <= z:
+            n_zones += 1
+
+        for i in range(self.number_points-1):
+            if points[i].z > z and points[i+1].z <= z:
+                n_zones += 1
+
+        return n_zones
+
+    def get_all_water_limits_ac(self, z):
+        """
+        Determine all water limits for z elevation.
+        """
+
+        points = self._points
+        if len(points) < 3:
+            return None
+
+        zz = list(map(lambda p: p.z, points))
+        station = self._get_station(points)
+
+        start = []
+        if points[0].z <= z:
+            start.append(station[0])
+
+        for i in range(self.number_points-1):
+            if zz[i] > z and zz[i+1] <= z:
+                y = np.interp(
+                    z,
+                    [zz[i], zz[i+1]],
+                    [station[i], station[i+1]]
+                )
+                start.append(y)
+
+        end = []
+        if points[-1].z <= z:
+            end.append(station[-1])
+
+        for i in reversed(range(self.number_points-1)):
+            if zz[i] <= z and zz[i+1] > z:
+                y = np.interp(
+                    z,
+                    [zz[i], zz[i+1]],
+                    [station[i], station[i+1]]
+                )
+                end.append(y)
+
+        if len(start) != len(end):
+            logger.error(f"ERROR in get_all_water_limits_ac")
+            return [], []
+
+        return start, list(reversed(end))
+
+    def get_water_limits(self, z):
+        """
+        Determine left and right limits of water elevation.
+        """
+
+        # Get the index of first point with elevation lesser than water
+        # elevation (for the right and left river side)
+        i_left = -1
+        i_right = -1

        for i in range(self.number_points):
            if self.point(i).z <= z:
-                irg = i
+                i_left = i
+                break

        for i in reversed(range(self.number_points)):
            if self.point(i).z <= z:
-                ird = i
+                i_right = i
+                break

-        # interpolation des points ptX et ptY
-        if (irg < self.number_points - 1):
+        # Interpolate points at river left side
+        if (i_left > 0):
            x = np.interp(
                z,
-                [self.point(irg).z, self.point(irg + 1).z],
-                [self.point(irg).x, self.point(irg + 1).x]
+                [self.point(i_left).z, self.point(i_left - 1).z],
+                [self.point(i_left).x, self.point(i_left - 1).x]
            )
            y = np.interp(
                z,
-                [self.point(irg).z, self.point(irg + 1).z],
-                [self.point(irg).y, self.point(irg + 1).y]
+                [self.point(i_left).z, self.point(i_left - 1).z],
+                [self.point(i_left).y, self.point(i_left - 1).y]
            )
-            ptX = PointXYZ(x, y, z)
+            pt_left = PointXYZ(x, y, z, name="wl_left")
        else:
-            ptX = self.point(0)
-        if (ird > 0):
+            pt_left = self.point(0)
+
+        # Interpolate points at river right side
+        if (i_right < self.number_points - 1):
            x = np.interp(
                z,
-                [self.point(ird-1).z, self.point(ird).z],
-                [self.point(ird-1).x, self.point(ird).x]
+                [self.point(i_right).z, self.point(i_right + 1).z],
+                [self.point(i_right).x, self.point(i_right + 1).x]
            )
            y = np.interp(
                z,
-                [self.point(ird).z, self.point(ird - 1).z],
-                [self.point(ird).y, self.point(ird - 1).y]
+                [self.point(i_right).z, self.point(i_right + 1).z],
+                [self.point(i_right).y, self.point(i_right + 1).y]
            )
-            ptY = PointXYZ(x, y, z)
+            pt_right = PointXYZ(x, y, z, name="wl_right")
        else:
-            ptY = self.point(self.number_points - 1)
+            pt_right = self.point(self.number_points - 1)

-        return ptX, ptY
+        return pt_left, pt_right
+
+    def get_station(self):
+        """Projection of the points of the profile on a plane.
+
+        Args:
+            self: The profile
+
+        Returns:
+            Projection of the points of the profile on a plane.
+        """
+        if self.nb_points < 2:
+            return [0.0]
+        else:
+            return self._get_station(self.points)
+
+    @timer
+    def _get_station(self, points):
+        first_named_point = None
+        index_first_named_point = None
+        last_named_point = None
+
+        first_point_not_nan = self._first_point_not_nan(points)
+        last_point_not_nan = self._last_point_not_nan(points)
+
+        for index, point in enumerate(points):
+            if point.point_is_named():
+                index_first_named_point = index
+                first_named_point = point
+                break
+
+        for point in reversed(points):
+            if point.point_is_named():
+                last_named_point = point
+                break
+
+        station = []
+        constant = 0.0
+
+        if (first_named_point is not None
+                and last_named_point is not None):
+            if (first_named_point != last_named_point
+                    and first_named_point.x != last_named_point.x):
+                vector = Vector1d(first_named_point, last_named_point)
+                norm_dir_vec = vector.normalized_direction_vector()
+            else:
+                vector = Vector1d(first_point_not_nan, last_point_not_nan)
+                norm_dir_vec = vector.normalized_direction_vector()
+
+            for point in points:
+                xi = point.x - first_named_point.x
+                yi = point.y - first_named_point.y
+                station_i = (norm_dir_vec[0] * xi +
+                             norm_dir_vec[1] * yi)
+                station.append(station_i)
+
+            constant = station[index_first_named_point]
+        elif first_named_point is None:
+            vector = Vector1d(first_point_not_nan, last_point_not_nan)
+            norm_dir_vec = vector.normalized_direction_vector()
+
+            for point in points:
+                xi = point.x - first_point_not_nan.x
+                yi = point.y - first_point_not_nan.y
+                station_i = (norm_dir_vec[0] * xi +
+                             norm_dir_vec[1] * yi)
+                station.append(station_i)
+
+            z_min = self.z_min()
+            index_profile_z_min = next(
+                filter(
+                    lambda z: z[1] == z_min,
+                    enumerate(self.z())
+                )
+            )
+            constant = station[index_profile_z_min[0]]
+
+        return list(map(lambda s: s - constant, station))
+
+    def _first_point_not_nan(self, points):
+        first_point = None
+
+        for point in points:
+            if not point.is_nan():
+                first_point = point
+                break
+
+        return first_point
+
+    def _last_point_not_nan(self, points):
+        last_point = None
+
+        for point in reversed(points):
+            if not point.is_nan():
+                last_point = point
+                break
+
+        return last_point
+
+    def purge(self, np_purge):
+        """
+        Remove points to keep at most np_purge points.
+        """
+        if (self.nb_points <= np_purge):
+            return
+
+        nb_named = 2   # we consider the first and last point as named
+        area = [0.0]
+
+        for i in range(1, self.nb_points-1):
+            if self.point(i).point_is_named():
+                area.append(9999999.999)
+                nb_named += 1
+            else:
+                area.append(
+                    PointXYZ.areatriangle3d(
+                        self.point(i-1),
+                        self.point(i),
+                        self.point(i+1))
+                )
+
+        area.append(0.0)
+
+        while self.nb_points > max(np_purge, nb_named):
+            to_rm = np.argmin(area[1:self.nb_points - 1]) + 1
+
+            self.delete_i([to_rm])
+            area.pop(to_rm)
+
+            for i in [to_rm-1, to_rm]:
+                if (i == 0):
+                    continue
+
+                if (i == self.nb_points - 1):
+                    continue
+
+                if self.point(i).point_is_named():
+                    area[i] = 9999999.999
+                else:
+                    area[i] = PointXYZ.areatriangle3d(
+                        self.point(i-1),
+                        self.point(i),
+                        self.point(i+1)
+                    )
+
+    def shift(self, x, y, z):
+        for p in self.points:
+            p.x = p.x + x
+            p.y = p.y + y
+            p.z = p.z + z
@@ -1,5 +1,5 @@
 # Reach.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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
@@ -16,7 +16,9 @@

 # -*- coding: utf-8 -*-

+import os
 import logging
+import shapefile
 import numpy as np

 from time import time
@@ -65,7 +67,7 @@ class Reach(SQLSubModel):

        new._profiles = ProfileXYZ._db_load(
            execute,
-            data=data
+            data=data.copy()
        )

        return new
@@ -111,7 +113,7 @@ class Reach(SQLSubModel):
    def _get_profiles_list(self):
        # Profiles list generator is type (int, Point) with the first
        # element the index of the Point in list
-        logger.info(f"Load profiles from reach {self.name}")
+        logger.debug(f"Load profiles from reach {self.name}")
        return list(
            map(
                lambda p: p[1],
@@ -139,10 +141,10 @@ class Reach(SQLSubModel):
    def profiles(self, profiles):
        self._profiles = profiles

-    def get_profiles_from_kp(self, kp):
+    def get_profiles_from_rk(self, rk):
        return list(
            filter(
-                lambda p: p.kp == kp, self.profiles
+                lambda p: p.rk == rk, self.profiles
            )
        )

@@ -333,18 +335,18 @@ class Reach(SQLSubModel):
            )
        )

-    def get_kp(self):
-        """List of profiles kp
+    def get_rk(self):
+        """List of profiles rk

        Returns:
-            List of profiles kp
+            List of profiles rk
        """
-        return [profile.kp for profile in self.profiles]
+        return [profile.rk for profile in self.profiles]

-    def get_kp_complete_profiles(self):
+    def get_rk_complete_profiles(self):
        return list(
            map(
-                lambda profile: profile.kp,
+                lambda profile: profile.rk,
                filter(
                    lambda profile: len(profile) > 0,
                    self.profiles
@@ -352,18 +354,45 @@ class Reach(SQLSubModel):
            )
        )

-    def get_kp_min(self):
-        if len(self.get_kp()) > 0:
-            return min(self.get_kp())
+    def get_rk_min(self):
+        if len(self.get_rk()) > 0:
+            return min(self.get_rk())
        else:
            return 0.0

-    def get_kp_max(self):
-        if len(self.get_kp()) > 0:
-            return max(self.get_kp())
+    def get_rk_max(self):
+        if len(self.get_rk()) > 0:
+            return max(self.get_rk())
        else:
            return 0.0

+    def inter_profiles_rk(self):
+        profiles = sorted(self.profiles, key=lambda p: p.rk)
+        if len(profiles) == 0:
+            return []
+
+        first = profiles[0]
+        last = profiles[-1]
+
+        res_rk = [first.rk]
+
+        profiles = iter(profiles)
+        previous = next(profiles)
+
+        for profile in profiles:
+            prev = previous.rk
+            curr = profile.rk
+
+            diff = abs(previous.rk - profile.rk)
+
+            new = previous.rk + (diff / 2.0)
+            res_rk.append(new)
+
+            previous = profile
+
+        res_rk.append(last.rk)
+        return res_rk
+
    # Sediment Layers

    def get_sl(self):
@@ -510,7 +539,7 @@ class Reach(SQLSubModel):
    def sort(self, is_reversed: bool = False):
        self.profiles = sorted(
            self.profiles,
-            key=lambda profile: profile.kp,
+            key=lambda profile: profile.rk,
            reverse=is_reversed
        )
        self._status.modified()
@@ -533,8 +562,66 @@ class Reach(SQLSubModel):

    # Import/Export

-    @timer
    def import_geometry(self, file_path_name: str):
+        ext = file_path_name.split(".")
+        if len(ext) > 0:
+            ext = ext[-1].lower()
+
+            if ext in ['st', 'm']:
+                return self.import_geometry_st(file_path_name)
+
+            if ext in ['shp']:
+                return self.import_geometry_shp(file_path_name)
+
+        raise FileFormatError(
+            file_path_name,
+            f"Geometry file extention ('.{ext}') unkown"
+        )
+
+    @timer
+    def import_geometry_shp(self, file_path_name: str):
+        sf = shapefile.Reader(
+            os.path.abspath(file_path_name)
+        )
+
+        if sf.shapeType != shapefile.POLYLINEZ:
+            raise FileFormatError(
+                file_path_name,
+                "Shapefile is not a POLYLINEZ"
+            )
+
+        profiles = []
+
+        for i in range(len(sf)):
+            s_profile = sf.shape(i)
+            z = s_profile.z
+
+            ind = 0
+            points = []
+            for point in s_profile.points:
+                points.append([
+                    point[0],
+                    point[1],
+                    z[ind]
+                ])
+
+                ind += 1
+
+            prof = ProfileXYZ(
+                reach=self, status=self._status
+            )
+            prof.import_points(points)
+
+            profiles.append(prof)
+
+        self.profiles = profiles + self.profiles
+        self._update_profile_numbers()
+        self._recompute_rk()
+
+        return profiles
+
+    @timer
+    def import_geometry_st(self, file_path_name: str):
        """Import a geometry from file (.ST or .st)

        Args:
@@ -548,8 +635,8 @@ class Reach(SQLSubModel):

        try:
            list_profile, list_header = self.read_file_st(str(file_path_name))
-            profile_header = ["num", "code1",
-                              "code2", "nb_point", "kp", "name"]
+            profile_header = ["num", "code1", "code2",
+                              "nb_point", "rk", "name"]

            if list_profile and list_header:
                for ind, profile in enumerate(list_profile):
@@ -623,6 +710,15 @@ class Reach(SQLSubModel):
                                line_is_header = True
                            else:
                                list_point_profile.append(line)
+                        elif len(line) > 4:
+                            x, y, z = line[:3]
+                            if stop_code in x and stop_code in y:
+                                line_is_header = True
+                                list_profile.append(list_point_profile)
+                                list_point_profile = []
+                            else:
+                                line.append("")
+                                list_point_profile.append(line[:3])
                        else:
                            pass

@@ -637,12 +733,12 @@ class Reach(SQLSubModel):
                c1 = f"{profile.code1:>6}"
                c2 = f"{profile.code2:>6}"
                t = f"{len(profile.points):>6}"
-                kp = f"{profile.kp:>12f}"[0:12]
+                rk = f"{profile.rk:>12f}"[0:12]
                pname = profile.name
                if profile.name == "":
                    pname = f"p{profile.id:>3}".replace(" ", "0")

-                st.write(f"{num}{c1}{c2}{t} {kp} {pname}\n")
+                st.write(f"{num}{c1}{c2}{t} {rk} {pname}\n")

                for point in profile.points:
                    x = f"{point.x:<12.4f}"[0:12]
@@ -657,38 +753,44 @@ class Reach(SQLSubModel):
                cnt += 1

    def get_incline(self):
+        if len(self.profiles) == 0:
+            return 0.0
+
        first = self.profile(0)
        last = self.profile(len(self) - 1)

        z_first = first.z_min()
-        kp_first = first.kp
+        rk_first = first.rk

        z_last = last.z_min()
-        kp_last = last.kp
+        rk_last = last.rk

        return (
            (z_last - z_first)
            /
-            (kp_last - kp_first)
+            (rk_last - rk_first)
        )

    def get_incline_mean(self):
        profiles = self.profiles
+        if len(profiles) == 0:
+            return 0.0
+
        previous = profiles[0]

        incline_acc = 0

        for profile in profiles[1:]:
            z_first = previous.z_min()
-            kp_first = previous.kp
+            rk_first = previous.rk

            z_last = profile.z_min()
-            kp_last = profile.kp
+            rk_last = profile.rk

            incline_acc += (
                (z_last - z_first)
                /
-                (kp_last - kp_first)
+                (rk_last - rk_first)
            )

            previous = profile
@@ -697,21 +799,24 @@ class Reach(SQLSubModel):

    def get_incline_median(self):
        profiles = self.profiles
+        if len(profiles) == 0:
+            return 0.0
+
        previous = profiles[0]

        incline_acc = []

        for profile in profiles[1:]:
            z_first = previous.z_min()
-            kp_first = previous.kp
+            rk_first = previous.rk

            z_last = profile.z_min()
-            kp_last = profile.kp
+            rk_last = profile.rk

            incline_acc += [
                (z_last - z_first)
                /
-                (kp_last - kp_first)
+                (rk_last - rk_first)
            ]

            previous = profile
@@ -721,21 +826,27 @@ class Reach(SQLSubModel):

    def get_incline_median_mean(self):
        profiles = self.profiles
+        if len(profiles) == 0:
+            return 0.0
+
        previous = profiles[0]

        incline_acc = []

        for profile in profiles[1:]:
            z_first = previous.z_min()
-            kp_first = previous.kp
+            rk_first = previous.rk

            z_last = profile.z_min()
-            kp_last = profile.kp
+            rk_last = profile.rk
+
+            if (rk_last - rk_first) == 0:
+                continue

            incline_acc += [
                (z_last - z_first)
                /
-                (kp_last - kp_first)
+                (rk_last - rk_first)
            ]

            previous = profile
@@ -743,7 +854,10 @@ class Reach(SQLSubModel):
        incline_acc.sort()

        marge = round(len(incline_acc) * 0.1)
-        incline_set = incline_acc[marge:-marge]
+        if marge > 0:
+            incline_set = incline_acc[marge:-marge]
+        else:
+            incline_set = incline_acc

        logger.debug(f"+{incline_acc}")
        logger.debug(f"-{incline_set}")
@@ -759,3 +873,24 @@ class Reach(SQLSubModel):
        except Exception as e:
            logger_exception(e)
            return 0
+
+    def _recompute_rk(self, offset=0.0):
+        self._recompute_rk_no_gl(offset=offset)
+
+    def _recompute_rk_no_gl(self, offset=0.0):
+        profiles = iter(self.profiles)
+
+        previous = next(profiles)
+        previous.rk = offset
+
+        for profile in profiles:
+            prev_points = previous.points
+            curr_points = profile.points
+
+            dist = (
+                prev_points[0].dist_2d(curr_points[0]) +
+                prev_points[-1].dist_2d(curr_points[-1])
+            ) / 2.0
+
+            profile.rk = previous.rk + dist
+            previous = profile
@@ -1,5 +1,5 @@
 # Vector_1d.py -- Pamhyr
-# Copyright (C) 2023  INRAE
+# 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