change default parameters

work on tuto1

.gitignore

@@ -19,6 +19,8 @@ tmp
 *.pdf
 *.odt
 
+!doc/**/*.pdf
+
 doc/dev/images/auto_*
 doc/dev/documentation.*
 !doc/dev/*.org
@@ -268,6 +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
 
@@ -643,3 +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

.gitlab-ci.yml

@@ -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
@@ -16,55 +16,79 @@
 
 stages:
   - downloads
-  - build
+  - configure
   - test
+  - build
   - package
+  - hash
+  - antivirus
   - release
 
 #############
 # DOWNLOADS #
 #############
 
-dl-mage-linux:
+variables:
+  MAGE_8_VERSION: "v8.3.6"
+
+dl-mage8-doc:
   stage: downloads
   tags:
     - linux
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   script:
-    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/Test6/downloads/packages/mage_linux.tgz
+    - mkdir -p doc
-    - mkdir -p mage-linux
+    - cd doc
-    - cd mage-linux
+    - curl -L -o mage8.pdf https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/documents/Mage-8_Documentation.pdf
-    - tar xvf ../mage.tgz
   artifacts:
     paths:
-      - mage-linux/mage
+      - doc/mage8.pdf
-      - mage-linux/mage_extraire
-      - mage-linux/mailleurPF
 
-dl-mage-windows:
+dl-mage8-linux:
   stage: downloads
   tags:
     - linux
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   script:
-    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/Test6/downloads/packages/mage_windows.tgz
+    - curl -L -o mage8.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/packages/mage_linux.tgz
-    - mkdir -p mage-windows
+    - mkdir -p mage8-linux
-    - cd mage-windows
+    - cd mage8-linux
-    - tar xvf ../mage.tgz
+    - tar xvf ../mage8.tgz
   artifacts:
     paths:
-      - mage-windows/mage.exe
+      - mage8-linux/mage
-      - mage-windows/mage_extraire.exe
+      - mage8-linux/mage_as7
-      - mage-windows/mailleurPF.exe
+      - mage8-linux/mage_extraire
+      - mage8-linux/mailleurTT
+      - mage8-linux/libbief.so
 
-#########
+dl-mage8-windows:
-# BUILD #
+  stage: downloads
-#########
+  tags:
+    - linux
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - curl -L -o mage8.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/packages/mage_windows.tgz
+    - mkdir -p mage8-windows
+    - cd mage8-windows
+    - tar xvf ../mage8.tgz
+  artifacts:
+    paths:
+      - mage8-windows/mage.exe
+      - mage8-windows/mage_as7.exe
+      - mage8-windows/mage_extraire.exe
+      - mage8-windows/mailleurTT.exe
+      - mage8-windows/libbief.dll
+
+#############
+# CONFIGURE #
+#############
 
 set-version:
-  stage: build
+  stage: configure
   tags:
     - linux
   script:
@@ -75,7 +99,7 @@ set-version:
       - VERSION
 
 build-lang:
-  stage: build
+  stage: configure
   tags:
     - linux
   script:
@@ -85,7 +109,67 @@ build-lang:
     paths:
       - src/lang/*.qm
 
-build-users-doc:
+#########
+# TESTS #
+#########
+
+unittest:
+  stage: test
+  tags:
+    - linux
+  needs:
+    - job: set-version
+      artifacts: true
+  script:
+    - python3 -m venv venv
+    - . venv/bin/activate
+    - pip3 install -U pip
+    - pip3 install -r ./full-requirements.txt
+    - pip3 install -U -r ./full-requirements.txt
+    - cd src
+    - python3 -m unittest discover -t .
+
+test-pep8:
+  stage: test
+  tags:
+    - linux
+  needs:
+    - job: set-version
+      artifacts: true
+    - job: unittest
+  script:
+    # Setup virtual env
+    - python3 -m venv venv
+    - . venv/bin/activate
+    - pip3 install -U pip
+    - pip3 install -r ./requirements.txt
+    - pip3 install -U -r ./requirements.txt
+    - pip3 install pycodestyle
+    - pycodestyle --exclude="*_to_*.py" ./src
+  allow_failure: true
+
+#########
+# BUILD #
+#########
+
+# build-users-doc:
+#   stage: build
+#   tags:
+#     - linux
+#   needs:
+#     - job: set-version
+#       artifacts: true
+#   script:
+#     - cd ./doc/users/
+#     - ./build.sh
+#   artifacts:
+#     paths:
+#       - doc/users/documentation.pdf
+#       - doc/users/documentation.html
+#       - doc/users/images/
+#   allow_failure: true
+
+build-td:
   stage: build
   tags:
     - linux
@@ -93,13 +177,14 @@ build-users-doc:
     - job: set-version
       artifacts: true
   script:
-    - cd ./doc/users/
+    - cd ./doc/users/Tuto1/
     - ./build.sh
   artifacts:
     paths:
-      - doc/users/documentation.pdf
+      - doc/users/Tuto1/step-by-step.pdf
-      - doc/users/documentation.html
+      - doc/users/Tuto1/pas-a-pas.pdf
-      - doc/users/images/
+      - doc/users/Tuto1/data/
+  allow_failure: true
 
 build-developers-doc:
   stage: build
@@ -113,6 +198,12 @@ build-developers-doc:
     - ./build.sh
     # Create html documentation
     - cd ../../src
+    - python3 -m venv doc-venv
+    - . doc-venv/bin/activate
+    - pip3 install -U pip
+    - pip3 install -r ../full-requirements.txt
+    - pip3 install -U -r ../full-requirements.txt
+    - pip3 install pdoc3
     - pdoc --html .
     # Create archive
     - tar cf html.tar ./html
@@ -124,6 +215,7 @@ build-developers-doc:
       - doc/dev/documentation.html
       - doc/dev/html.tar
       - doc/dev/images/
+  allow_failure: true
 
 build-linux:
   stage: build
@@ -132,7 +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-mage8-doc
       artifacts: true
     - job: set-version
       artifacts: true
@@ -140,7 +234,9 @@ build-linux:
       artifacts: true
     - job: build-developers-doc
       artifacts: true
-    - job: build-users-doc
+    # - job: build-users-doc
+    #   artifacts: true
+    - job: build-td
       artifacts: true
   script:
     - mkdir -p linux
@@ -148,32 +244,39 @@ build-linux:
     # Setup virtual env
     - python3 -m venv linux-venv
     - . linux-venv/bin/activate
+    - pip3 install -U pip
+    - pip3 install -r ../requirements.txt
     - pip3 install -U -r ../requirements.txt
     # Run Pyinstaller
     - pyinstaller -y --paths linux-venv/lib/python3.8/site-packages ../src/pamhyr.py
     # Create directory
     - mkdir -p pamhyr
-    - mkdir -p pamhyr/pamhyr
+    - mkdir -p pamhyr/_internal
-    - mkdir -p pamhyr/pamhyr/_internal
     # Copy Pamhyr info
-    - cp -v ../VERSION pamhyr/pamhyr/_internal/
+    - cp -v ../VERSION pamhyr/_internal/
-    - cp -v ../AUTHORS pamhyr/pamhyr/_internal/
+    - cp -v ../AUTHORS pamhyr/_internal/
-    - cp -v ../LICENSE pamhyr/pamhyr/_internal/
+    - cp -v ../LICENSE pamhyr/_internal/
+    - cp -v ../src/motd.txt pamhyr/_internal/
     # Copy mage
-    - mkdir -p pamhyr/mage
+    - mkdir -p pamhyr/mage8
-    - cp -v ../mage-linux/* pamhyr/mage/
+    - cp -v ../mage8-linux/* pamhyr/mage8/
     # Copy 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/_internal/View
-    - mkdir -p pamhyr/pamhyr/_internal/View/ui
+    - mkdir -p pamhyr/_internal/View/ui
-    - mkdir -p pamhyr/pamhyr/_internal/View/ui/Widgets
+    - mkdir -p pamhyr/_internal/View/ui/Widgets
-    - cp -r ../src/View/ui/*.ui pamhyr/pamhyr/_internal/View/ui/
+    - cp -r ../src/View/ui/*.ui pamhyr/_internal/View/ui/
-    - cp -r ../src/View/ui/ressources/ pamhyr/pamhyr/_internal/View/ui
+    - cp -r ../src/View/ui/ressources/ pamhyr/_internal/View/ui
-    - cp -r ../src/View/ui/Widgets/*.ui pamhyr/pamhyr/_internal/View/ui/Widgets
+    - cp -r ../src/View/ui/Widgets/*.ui pamhyr/_internal/View/ui/Widgets
     # Copy lang
-    - mkdir -p pamhyr/pamhyr/_internal/lang
+    - mkdir -p pamhyr/_internal/lang
-    - cp -r ../src/lang/*.qm pamhyr/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
@@ -182,17 +285,25 @@ build-linux:
     - mkdir -p pamhyr/doc/
     - mkdir -p pamhyr/doc/images/
     - mkdir -p pamhyr/doc/html/
-    - cp ../doc/users/documentation.pdf pamhyr/doc/Pamhyr2-users.pdf
+    # - cp ../doc/users/documentation.pdf pamhyr/doc/Pamhyr2-users.pdf
-    - cp ../doc/users/documentation.html pamhyr/doc/Pamhyr2-users.html
+    # - cp ../doc/users/documentation.html pamhyr/doc/Pamhyr2-users.html
+    - cp ../doc/mage8.pdf pamhyr/doc/mage8.pdf
     - cp ../doc/dev/documentation.pdf pamhyr/doc/Pamhyr2-dev.pdf
     - cp ../doc/dev/documentation.html pamhyr/doc/Pamhyr2-dev.html
     #- cp ../doc/users/images/* pamhyr/doc/images
-    - cp ../doc/dev/images/* pamhyr/doc/images
+    - cp -r ../doc/dev/images/* pamhyr/doc/images
-    - cp ../doc/images/* pamhyr/doc/images
+    - cp -r ../doc/images/* pamhyr/doc/images
-    # Create running script
+    # Copy Tuto
-    - echo "#!/bin/sh" > pamhyr/Pamhyr2
+    - mkdir -p pamhyr/doc/Tuto1/
-    - echo "./pamhyr/pamhyr $@" >> pamhyr/Pamhyr2
+    - mkdir -p pamhyr/doc/Tuto1/data
-    - chmod u+x pamhyr/Pamhyr2
+    - cp ../doc/users/Tuto1/Hogneau_Engees2022.pdf pamhyr/doc/Tuto1/Hogneau_Engees2022.pdf
+    - cp ../doc/users/Tuto1/step-by-step.pdf pamhyr/doc/Tuto1/Tuto1-en.pdf
+    - cp ../doc/users/Tuto1/pas-a-pas.pdf pamhyr/doc/Tuto1/Tuto1-fr.pdf
+    - cp ../doc/users/Tuto1/*.pamhyr pamhyr/doc/Tuto1/
+    - cp ../doc/users/Tuto1/data/* pamhyr/doc/Tuto1/data/
+    # Copy TP charriage
+    - mkdir -p pamhyr/doc/TP_charriage/
+    - cp ../doc/users/TP_charriage/* pamhyr/doc/TP_charriage
   artifacts:
     paths:
       - linux/pamhyr
@@ -204,7 +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-mage8-doc
       artifacts: true
     - job: set-version
       artifacts: true
@@ -212,15 +325,20 @@ build-windows:
       artifacts: true
     - job: build-developers-doc
       artifacts: true
-    - job: build-users-doc
+    # - job: build-users-doc
+    #   artifacts: true
+    - job: build-td
       artifacts: true
   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
@@ -230,36 +348,6 @@ build-windows:
     paths:
       - windows/pamhyr
 
-#########
-# TESTS #
-#########
-
-# test-windows:
-#   stage: test
-#   tags:
-#     - wine
-#   needs:
-#     - job: set-version
-#       artifacts: true
-#     - job: build-windows
-#       artifacts: true
-#   script:
-#     - cd windows\pamhyr
-#     - pamhyr\pamhyr.exe hello
-
-# test-linux:
-#   stage: test
-#   tags:
-#     - linux
-#   needs:
-#     - job: set-version
-#       artifacts: true
-#     - job: build-linux
-#       artifacts: true
-#   script:
-#     - cd linux/pamhyr
-#     - ./Pamhyr2 hello
-
 ############
 # PACKAGES #
 ############
@@ -320,6 +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 #
 ###########
@@ -336,10 +529,12 @@ tag-release:
       artifacts: true
     - job: windows-package-exe
       artifacts: true
-    - job: build-users-doc
+    # - job: build-users-doc
-      artifacts: true
+    #   artifacts: true
     - job: build-developers-doc
       artifacts: true
+    - job: pkg-hash
+      artifacts: true
   rules:
     - if: $CI_COMMIT_TAG
   artifacts:
@@ -347,33 +542,44 @@ tag-release:
       - linux/pamhyr-gnulinux.tar.xz
       - windows/pamhyr-windows.zip
       - windows/pamhyr-windows.exe
+      - linux/pamhyr-gnulinux.tar.xz.sha256
+      - windows/pamhyr-windows.zip.sha256
+      - windows/pamhyr-windows.exe.sha256
       - doc/dev/documentation.pdf
-      - doc/users/documentation.pdf
+      # - doc/users/documentation.pdf
   script:
     - cd packages
   release:
     name: '$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'

AUTHORS

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

README.md

@@ -3,48 +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
++ Define river friction
-+ Generate initial conditions
++ Define reservoirs
-+ Edit river sedimentary layers
++ Define hydraulic structures
++ Define or generate initial conditions
++ Define river sedimentary layers
 + Save the study in a unique file
 + Run Mage 8 on a study and visualize results
 
+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 [last
+See documentation:
-realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
+- [French :fr:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/fr/Install%20on%20GNULinux)
-GNU/Linux binary archive.
+- [English :gb:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/en/Install%20on%20GNULinux)
-
-```shell
-tar xf pamhyr-gnulinux-amd64.tar.xz
-cd pamhyr
-./pamhyr
-```
 
 ### Windows
 
-Downloads [last
+See documentation:
-realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
+- [French :fr:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/fr/Install%20on%20Windows)
-Windows installer.
+- [English :gb:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/en/Install%20on%20Windows)
-
-### From source code
-
-```shell
-# Get source code
-git clone https://gitlab.irstea.fr/theophile.terraz/pamhyr/
-cd pamhyr
-
-# Install dependencies
-pip3 install -r requirements.txt
-
-# Run pamhyr
-./src/pamhyr.py
-```

doc/dev/documentation.org

@@ -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.Tools.PamhyrWindow import PamhyrWindow
-    from View.My.Translate import MyTranslate
+  from View.My.Translate import MyTranslate
-    from View.My.Table import MyTableModel
+  from View.My.Table import MyTableModel
 
-    class MyWindow(PamhyrWindow):
+  class MyWindow(PamhyrWindow):
-        _pamhyr_ui = "MyUI"
+      _pamhyr_ui = "MyUI"
-        _pamhyr_name = "My window"
+      _pamhyr_name = "My window"
 
-        def __init__(self, my_data=None,
+      def __init__(self, study=None, config=None,
-                     study=None, config=None,
+                   my_data=None,
-                     parent=None):
+                   parent=None):
-            self._my_data = my_data
+          self._my_data = my_data
 
-            super(MyWindow, self).__init__(
+          super(MyWindow, self).__init__(
-                # Window title
+              # Window title
-                title = self._pamhyr_name + " - " + study.name,
+              title = self._pamhyr_name + " - " + study.name,
-                # Window standard data
+              # Window standard data
-                study = study, config = config,
+              study = study, config = config,
-                trad = MyTranslate(),
+              trad = MyTranslate(),
-                parent = parent,
+              parent = parent,
-                # Activate undo/redo and copy/paste shortcut
+              # Activate undo/redo and copy/paste shortcut
-                options = ["undo", "copy"]
+              options = ["undo", "copy"]
-            )
+          )
 
-            # Add custom data to hash window computation
+          # Add custom data to hash window computation
-            self._hash_data.append(self._my_data)
+          self._hash_data.append(self._my_data)
 
-            # Setup custom window components
+          # Setup custom window components
-            self.setup_table()
+          self.setup_table()
-            self.setup_connections()
+          self.setup_connections()
 
-        def setup_table(self):
+      def setup_table(self):
-            # Init table(s)...
+          # Init table(s)...
 
-        def setup_connections(self):
+      def setup_connections(self):
-            # Init action connection(s)...
+          # 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
+To define a new plot you can create a class who inherit to
-creator need threee argument:
+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):
+  class MyPlot(PamhyrPlot):
-      def __init__(self, canvas=None, data=None, toolbar=None):
+      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
+A very small part of Pamhyr2 has unit test. This part is limited to the Model.
-in progress*.
+
+#+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:
+This mode add some log and add two action in main window menu: "About
-"About/Debug" open a window with Python Repl in current Python
+> Debug" open a window with Python Repl in current Python
-environement, and "About/Debug SQLite" who open the application
+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

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

@@ -0,0 +1,487 @@
+# presentation.org -- Pamhyr
+# Copyright (C) 2023  INRAE
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# -*- coding: utf-8 -*-
+
+#+STARTUP: indent hideblocks content beamer
+
+#+TITLE: SimHydro 2023
+#+SUBTITLE: \textbf{Pamhyr2}: a graphical user interface for 1D hydro-sedimentary modelling of rivers
+
+# #+AUTHOR: Pierre-Antoine Rouby
+#+LATEX_HEADER: \author[Pierre-Antoine Rouby]{\textbf{Pierre-Antoine Rouby$^{*}$}, Benoît Camenen, Lionel Pénard, Léa Kieffer, Théophile Terraz\\\texttt{<pierre-antoine.rouby@inrae.fr>}^{*}}
+#+EMAIL: pierre-antoine.rouby@inrae.fr
+#+INSTITUTE: INRAE Lyon-Villerbanne, teams River Hydraulics
+#+LATEX_HEADER: \institute{INRAE Lyon-Villerbanne, River Hydraulics team}
+#+DATE: 9th November
+
+#+KEYWORDS: g ui, hydraulics, sedimentary, hydro-sedimentary, 1D modelling, freesoftware, foss
+
+#+OPTIONS: H:2 toc:t num:t author:nil
+#+LATEX_CLASS: beamer
+#+LATEX_CLASS_OPTIONS: [slideopt,A4,showboxes,svgnames,aspectratio=169]
+# #+LATEX_CLASS_OPTIONS: [presentation]
+#+BEAMER_THEME: default
+#+COLUMNS: %45ITEM %10BEAMER_ENV(Env) %10BEAMER_ACT(Act) %4BEAMER_COL(Col)
+
+#+LANGUAGE: fr
+#+LATEX_HEADER: \usepackage[frenchb]{babel}
+
+#+BEGIN_SRC emacs-lisp :results silent :exports none
+  (setq org-latex-pdf-process (list
+    "latexmk -pdflatex='lualatex -shell-escape -interaction nonstopmode' -pdf -f  %f"))
+
+  (add-to-list 'org-latex-packages-alist '("" "minted"))
+  (setq org-latex-listings 'minted)
+  (setq org-src-fontify-natively t)
+
+  (org-add-link-type
+   "cite" 'ebib
+   (lambda (path desc format)
+     (cond
+      ((eq format 'html)
+       (format "(<cite>%s</cite>)" path))
+      ((eq format 'text)
+       (format "[%s]" path))
+      ((eq format 'latex)
+       (if (or (not desc) (equal 0 (search "cite:" desc)))
+           (format "\\cite{%s}" path)
+         (format "\\cite[%s][%s]{%s}"
+                 (cadr (split-string desc ";"))
+                 (car (split-string desc ";"))  path))))))
+#+END_SRC
+
+#+LATEX_HEADER: \setbeamertemplate{footline}[frame number]
+#+LATEX_HEADER: \setbeamertemplate{headline}{}
+#+LATEX_HEADER: \usepackage{multirow}
+#+LATEX_HEADER: \usepackage{fontawesome5}
+#+LATEX_HEADER: \usepackage{tcolorbox}
+#+LATEX_HEADER: \usepackage{tikz}
+
+#+LATEX_HEADER: \logo{\includegraphics[width=.1\textwidth]{../../../../../src/View/ui/ressources/Logo-INRAE.png}}
+
+#+LATEX_HEADER: \newcommand{\R}[1]{\rotatebox[origin=c]{90}{#1}}
+
+# Beamer colors
+#+LATEX_HEADER: \setbeamersize{text margin left=0.5cm,text margin right=0.5cm}
+#+LATEX_HEADER: \setbeamerfont{alerted text}{series=\bfseries}
+#+LATEX_HEADER: \setbeamerfont{example text}{series=\bfseries}
+
+#+LATEX_HEADER: \definecolor{inrae_1}{RGB}{102,193,191}
+#+LATEX_HEADER: \definecolor{inrae_2}{RGB}{0,150,152}
+#+LATEX_HEADER: \definecolor{inrae_3}{RGB}{39,86,98}
+
+#+LATEX_HEADER: \setbeamercolor{alerted text}{fg=inrae_1}
+#+LATEX_HEADER: \setbeamercolor{structure}{fg=inrae_2}
+#+LATEX_HEADER: \setbeamercolor{normal text}{fg=inrae_3}
+#+LATEX_HEADER: \setbeamercolor*{author}{fg=inrae_3}
+
+#+LATEX_HEADER: \usepackage[absolute,showboxes,overlay]{textpos}
+
+#+LATEX_HEADER: \TPshowboxesfalse
+#+LATEX_HEADER: \textblockorigin{5mm}{0mm}
+
+# Biblio
+#+LATEX_HEADER: \usepackage{natbib}
+# #+LATEX_HEADER: \bibliographystyle{apalike}
+#+LATEX_HEADER: \setbeamertemplate{bibliography item}{}
+#+LATEX_HEADER: \renewcommand\bibfont{\scriptsize}
+#+LATEX_HEADER: \setbeamertemplate{frametitle continuation}[from second]
+#+LATEX_HEADER: \setbeamercolor*{bibliography entry title}{fg=inrae_3}
+#+LATEX_HEADER: \setbeamercolor*{bibliography entry author}{fg=inrae_3}
+#+LATEX_HEADER: \setbeamercolor*{bibliography entry location}{fg=inrae_3}
+
+#+LATEX_HEADER: \usepackage{bbding}
+#+LATEX_HEADER: \usepackage{pdfpages}
+
+# Renew title page
+#+LATEX_HEADER: \defbeamertemplate*{title page}{customized}[1][]
+#+LATEX_HEADER: {
+# #+LATEX_HEADER:   {
+# #+LATEX_HEADER:     \usebeamerfont{date}\usebeamercolor[fg]{date}
+# #+LATEX_HEADER:     \tikz[overlay,remember picture]
+# #+LATEX_HEADER:     \node[xshift=-1cm,yshift=-1cm,text width=10cm] at (current page.north east) {
+# #+LATEX_HEADER:        7$^{th}$ International Conference\\
+# #+LATEX_HEADER:        8TH-10TH November\\
+# #+LATEX_HEADER:        EDF Lab - CHATOU, FRANCE
+# #+LATEX_HEADER:     }
+# #+LATEX_HEADER:   }
+#+LATEX_HEADER:   {
+#+LATEX_HEADER:     \usebeamerfont{title}\inserttitle\par
+#+LATEX_HEADER:     \usebeamerfont{title}\usebeamercolor[fg]{title}
+#+LATEX_HEADER:     \large New modeling paradigms for water issues?\par
+#+LATEX_HEADER:   }
+#+LATEX_HEADER:   \bigskip
+#+LATEX_HEADER:   \begin{center}
+#+LATEX_HEADER:     \usebeamerfont{subtitle}\usebeamercolor[fg]{subtitle}
+#+LATEX_HEADER:     {
+#+LATEX_HEADER:       \LARGE\insertsubtitle\par
+#+LATEX_HEADER:     }
+#+LATEX_HEADER:     \bigskip
+#+LATEX_HEADER:     \usebeamerfont{author}\usebeamercolor[fg]{author}\insertauthor\par
+#+LATEX_HEADER:     \bigskip
+#+LATEX_HEADER:     \usebeamerfont{institute}\usebeamercolor[fg]{institute}\insertinstitute\par
+#+LATEX_HEADER:     \bigskip
+#+LATEX_HEADER:     \usebeamerfont{date}\usebeamercolor[fg]{date}\insertdate\par
+#+LATEX_HEADER:     \usebeamercolor[fg]{titlegraphic}\inserttitlegraphic
+#+LATEX_HEADER:   \end{center}
+#+LATEX_HEADER: }
+
+# #+LATEX_HEADER: \newcommand{\tred}[1]{\textcolor{rouge_inrae}{#1}}
+
+#+TODO: TODO WIP TOREVIEW | DONE
+
+#+MACRO: pamhyr \textsc{PAMHyR}
+#+MACRO: pamhyr2 \textsc{Pamhyr2}
+
+#+MACRO: pause \pause
+#+MACRO: framebreak \framebreak
+#+MACRO: no
+# #+MACRO: OK  \checkmark
+#+MACRO: OK  \faIcon{check}
+#+MACRO: bf \textbf{$1}
+
+# #+latex: \frame{\tocpage}
+
+* 1D hydro-sedimentary simulation at INRAE
+** COMMENT 1D river flow simulation
+*** INRAE (Lyon-Villerbanne)
+
+- Mage [fn:: Mage: https://gitlab.irstea.fr/jean-baptiste.faure/mage]
+- RubarBE [fn:: RubarBE:
+  https://gitlab.irstea.fr/theophile.terraz/rubarbe]
+
+*** Other project
+
+- Mascaret [fn:: OpenTeleMac: http://www.opentelemac.org]
+- HEC-RAS [fn:: HEC-RAS:
+  https://www.hec.usace.army.mil/software/hec-ras]
+- Mike 11 [fn:: Mike11:
+  https://www.mikepoweredbydhi.com/products/mike-11]
+
+** {{{pamhyr}}}
+#+BEGIN_EXPORT latex
+\tikz[overlay,remember picture]
+\node[xshift=-4cm,yshift=4cm] at (current page.south east) {
+  \includegraphics[width=7cm]{../images/PAMHyR.png}
+};
+#+END_EXPORT
+
+{{{pamhyr}}} developed at INRAE in Java since the end of 90s
+
+*** Features
+- Graphical user interface
+- Define and edit complexe 1D river models
+- Run a solver
+- Visualize simulation results
+
+*** Compatibility
+- 2 solvers *Mage and RubarBE*
+# - Multi-reaches (Only for Mage)
+- Multi-platform (Linux / Windows)
+
+** {{{pamhyr}}}
+#+BEGIN_EXPORT latex
+\tikz[overlay,remember picture]
+\node[xshift=-4cm,yshift=4cm] at (current page.south east) {
+  \includegraphics[width=7cm]{../images/PAMHyR.png}
+};
+#+END_EXPORT
+
+*** Conception issues
+- Monolingual French
+- Interface too different for each solver
+- Impossible to undo an action
+
+*** Huge technical debts
+- Out dated technologies (UML $\to$ Java)
+- Unmaintained library
+- Unstable development process
+
+Hard to maintain or add features to the interface
+
+(No modification since 2016)
+
+* Presentation of {{{pamhyr2}}}
+** {{{Pamhyr2}}} - Needs - General constraints
+
+Create a new version of {{{pamhyr}}} called {{{pamhyr2}}}
+
+{{{pause}}}
+
+*** Constraints for users experience
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
++ *User friendly*
++ *Multi platform* (at least Linux and Windows)
++ *Multi language* (at least English and French)
++ *Multi solver* (as much as possible, at least Mage and
+  RubarBE)
++ *Single save file* per study
+
+{{{pause}}}
+
+*** Constraints for developers experience
+:PROPERTIES:
+:BEAMER_COL: 0.5
+:BEAMER_ENV: block
+:END:
+- *Common used* code library and tools
+# - *Modular* and *flexible* code
+- *Clear* architecture
+- *Free and open sources software* (FOSS)
+
+** {{{Pamhyr2}}} - Needs - Features
+# #+BEGIN_EXPORT latex
+# \tikz[overlay,remember picture]
+# \node[xshift=-5cm,yshift=-2cm] at (current page.north east) {
+#   \includegraphics[width=6cm]{../images/geometry_saar.png}
+# };
+# #+END_EXPORT
+
+**** {{{no}}}
+:PROPERTIES:
+:BEAMER_COL: 0.30
+:BEAMER_ENV: block
+:END:
+- Define and edit data
+  + River network
+  + Geometry
+  + Boundary conditions
+  + Friction
+  + Initial conditions
+  + *Sedimentary layers*
+- User meshed geometry
+- Run a solver
+- Display results
+  + Default visualisation
+  + *Customized visualisation*
+
+**** {{{no}}}
+:PROPERTIES:
+:BEAMER_COL: 0.70
+:BEAMER_ENV: block
+:END:
+[[../images/geometry_saar.png]]
+
+** {{{pamhyr2}}} - Technical choices
+#+BEGIN_EXPORT latex
+\tikz[overlay,remember picture]
+\node[xshift=-9.3cm,yshift=-4cm] at (current page.north east) {
+  \includegraphics[width=6.3cm]{../images/BC.png}
+};
+#+END_EXPORT
+
+*** Technologies
+:PROPERTIES:
+:BEAMER_COL: 0.60
+:BEAMER_ENV: block
+:END:
+- *Python*
+- *PyQt*
+- Qt Designer
+- Qt Linguist
+- *Matplotlib*
+- SQLite (as =*.pamhyr=)
+- *GPLv3* license (strong copyleft)
+
+*** Architecture
+:PROPERTIES:
+:BEAMER_COL: 0.35
+:BEAMER_ENV: block
+:END:
+- Qt Model/View
+- Multiple solvers configuration
+- *Unified interface*, as much as possible
+
+** {{{pamhyr2}}} - State of the project
+#+BEGIN_EXPORT latex
+\tikz[overlay,remember picture]
+\node[xshift=-4.5cm,yshift=-2.5cm] at (current page.north east) {
+  \includegraphics[width=8cm]{../images/apply_sedi.png}
+};
+#+END_EXPORT
+
+*** {{{no}}}
+:PROPERTIES:
+:BEAMER_COL: 0.40
+:BEAMER_ENV: block
+:END:
+
+\vspace{-1.5cm}
+
+\begin{center}
+\emph{Last version:} \texttt{v0.0.3}
+\end{center}
+
+{{{pause}}}
+
+#+latex: \begin{center}
+#+latex: \resizebox{0.9\columnwidth}{!}{
+# #+caption: Tools by methods
+#+name: tab:current-state
+#+attr_latex: :align |l|c|
+|---------------------------------+-----------------|
+| {{{bf(Features)}}}              | {{{bf(State)}}} |
+|---------------------------------+-----------------|
+| Create save and load study      | {{{OK}}}        |
+| *Undo/Redo actions*             | {{{OK}}}        |
+| Edit river network              | {{{OK}}}        |
+| Edit geometry                   | {{{OK}}}        |
+| Edit boundary conditions        | {{{OK}}}        |
+| Edit lateral contributions      | {{{OK}}}        |
+| Edit frictions (Stricklers)     | {{{OK}}}        |
+| Edit initial conditions         | {{{OK}}}        |
+| *Edit sedimentary layers*       | {{{OK}}}        |
+| Edit hydraulics structures      |                 |
+| Edit suspended sediment         |                 |
+| Edit polluant                   |                 |
+| Use meshing tool                | WIP             |
+| Run a solver                    | {{{OK}}}        |
+| Read and display results        | {{{OK}}}        |
+| Customize results visualisation | WIP             |
+| Generic solver input/output     |                 |
+|---------------------------------+-----------------|
+#+latex: }
+#+latex: \end{center}
+
+{{{pause}}}
+
+*** {{{no}}}
+:PROPERTIES:
+:BEAMER_COL: 0.60
+:BEAMER_ENV: block
+:END:
+
+\vspace{2.5cm}
+
+#+latex: \begin{center}
+#+latex: \resizebox{0.8\columnwidth}{!}{
+# #+caption: Tools by methods
+#+name: tab:current-state-solver
+#+attr_latex: :align |l|c|c|c|
+|----------------------------+----------------+-------------------+--------------------|
+| {{{bf(Usage)}}}            | {{{bf(Mage)}}} | {{{bf(RubarBE)}}} | {{{bf(Mascaret)}}} |
+|----------------------------+----------------+-------------------+--------------------|
+| *Hydraulics* (mono reach)  | {{{OK}}}       |                   | {{{OK}}}           |
+| *Hydraulics* (multi reach) | {{{OK}}}       |                   |                    |
+| *Bed load evolution*       | {{{OK}}}       |                   |                    |
+|----------------------------+----------------+-------------------+--------------------|
+#+latex: }
+#+latex: \end{center}
+
+# #+LaTeX: \vspace{0.3cm}
+
+#+latex: \begin{center}
+#+latex: \resizebox{0.6\columnwidth}{!}{
+# #+caption: Tools by methods
+#+name: tab:current-state-package
+#+attr_latex: :align |l|c|c|
+|--------------------+---------------------+-------------------|
+| {{{bf(Packages)}}} | {{{bf(GNU/Linux)}}} | {{{bf(Windows)}}} |
+|--------------------+---------------------+-------------------|
+| Archive (tar/zip)  | {{{OK}}}            | {{{OK}}}          |
+| Installer          |                     | {{{OK}}}          |
+|--------------------+---------------------+-------------------|
+#+latex: }
+#+latex: \end{center}
+
+* Future work and perspective
+** Future work
+#+BEGIN_EXPORT latex
+\tikz[overlay,remember picture]
+\node[xshift=-4.8cm,yshift=-3.8cm] at (current page.north east) {
+  \includegraphics[width=8.7cm]{../images/results_hydro.png}
+};
+#+END_EXPORT
+
+*** Next step
+- *Meshing tools integration*
+- *Custom results visualisation*
+  + Python + matplotlib script
+- RubarBE integration
+- Hydraulics structures
+- Unified graphics theme
+
+*** Open questions
+- Generic solver input/output (HDF5? CGNS? SQLite?)
+- GNU/Linux packages (Pip? Conda? Guix? Deb?)
+
+** Contribution
+#+LaTeX: \begin{center}
+\faIcon{gitlab} https://gitlab.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}

doc/tools/PamhyrDoc.cls

@@ -11,7 +11,8 @@
 \usepackage[absolute]{textpos}
 \usepackage{titlesec}
 \usepackage{amssymb}
-\usepackage{tcolorbox}
+\usepackage[minted,xparse,breakable]{tcolorbox}
+\usepackage{pmboxdraw}
 
 \usepackage{enumitem}
 \setlist[enumerate]{itemsep=-0.5em}
@@ -133,6 +134,7 @@
 \setminted[c]{fontsize=\footnotesize,encoding=utf8,linenos}
 \setminted[c++]{breaklines,fontsize=\footnotesize,encoding=utf8,linenos}
 \setminted[python]{breaklines,fontsize=\footnotesize,encoding=utf8,linenos}
+\setminted[sql]{breaklines,fontsize=\footnotesize,encoding=utf8,linenos}
 \setminted[shell]{breaklines,fontsize=\footnotesize,encoding=utf8}
 \setminted[scheme]{breaklines,fontsize=\footnotesize,encoding=utf8}
 \setminted[commun-lisp]{breaklines,fontsize=\footnotesize,encoding=utf8}
@@ -140,7 +142,7 @@
 \setminted[llvm]{breaklines,fontsize=\footnotesize,encoding=utf8}
 
 %% Add box arrond of minted
-\BeforeBeginEnvironment{minted}{\begin{tcolorbox}[boxsep=0pt, left=0.1cm, right=0.1cm, arc=0pt, boxrule=0.5pt, colback=white]}%
+\BeforeBeginEnvironment{minted}{\begin{tcolorbox}[breakable, boxsep=0pt, left=0.1cm, right=0.1cm, arc=0pt, boxrule=0.5pt, colback=white]}%
 \AfterEndEnvironment{minted}{\end{tcolorbox}}%
 
 \makeatletter

doc/users/Tuto1/build.sh

@@ -0,0 +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

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+   33140.0000       4.3000      19.0600 
+   33140.0000       6.4000      17.9200 
+   33140.0000      11.3000      17.9200 
+   33140.0000      12.6000      19.1400 rd
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+   33140.0000      19.2000      22.1800 
+     999.9990     999.9990     999.9990 
+    20     0     0    10   33425.0000   
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+   33425.0000       0.5000      21.5300 
+   33425.0000       2.2000      20.1600 
+   33425.0000       3.0000      19.9400 
+   33425.0000       4.8000      18.8200 rg
+   33425.0000       4.9000      18.7500 
+   33425.0000       7.2000      17.8000 
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+   33685.0000       3.3000      19.4200 
+   33685.0000       5.2000      18.5300 rg
+   33685.0000       5.4000      18.4700 
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+   33685.0000      12.9000      18.6500 rd
+   33685.0000      17.6000      21.5300 
+     999.9990     999.9990     999.9990 
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+   33920.0000       0.6000      20.9800 
+   33920.0000       2.6000      19.1300 
+   33920.0000       3.6000      18.9400 
+   33920.0000       5.7000      18.2600 rg
+   33920.0000       5.8000      18.2200 
+   33920.0000       8.5000      17.6000 
+   33920.0000      12.3000      17.6000 
+   33920.0000      13.1000      18.4400 rd
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+   34095.0000       3.8000      18.5900 
+   34095.0000       6.0000      18.0600 rg
+   34095.0000       6.1000      18.0300 
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+   34095.0000      12.5000      17.5300 
+   34095.0000      13.2000      18.2800 rd
+   34095.0000      16.6000      20.9800 
+     999.9990     999.9990     999.9990 
+    24     0     0    10   34295.0000   
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+   34295.0000       0.6000      20.8300 
+   34295.0000       2.4000      18.3500 
+   34295.0000       3.5000      18.1900 
+   34295.0000       5.8000      17.8300 rg
+   34295.0000       6.5000      17.3400 
+   34295.0000       9.5000      17.3600 
+   34295.0000      12.8000      17.4100 
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+   34295.0000      16.1000      21.3600 
+     999.9990     999.9990     999.9990 
+    25     0     0    10   34334.0000   amontPontThivencel
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+   34334.0000       5.8000      17.8300 rg
+   34334.0000       6.5000      17.3400 
+   34334.0000       9.5000      17.3600 
+   34334.0000      12.8000      17.4100 
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+   34334.0000      16.1000      21.1300 
+     999.9990     999.9990     999.9990 
+    26     0     0     9   34335.0000   PontmThivencelle
+   34335.0000       2.9000      22.0000 
+   34335.0000       2.9000      20.7400 
+   34335.0000       2.9000      18.2900 rg
+   34335.0000       6.4000      17.7900 
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+   34335.0000      12.8000      17.2600 
+   34335.0000      12.8000      18.3100 rd
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+   34335.0000      12.8000      22.0000 
+     999.9990     999.9990     999.9990 
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+   34343.0000      12.8000      22.0000 
+     999.9990     999.9990     999.9990 
+    28     0     0    10   34345.0000   avalPontThivencell
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+   34345.0000       2.4000      18.3500 
+   34345.0000       3.5000      18.1900 
+   34345.0000       5.8000      17.8300 rg
+   34345.0000       6.5000      17.3400 
+   34345.0000       9.5000      17.2600 
+   34345.0000      12.8000      17.4100 
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+    29     0     0     7   34405.0000   
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+   34405.0000       9.6000      17.2000 
+   34405.0000      12.8000      17.2200 
+   34405.0000      13.9000      17.8400 rd
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+    30     0     0     7   34535.0000   
+   34535.0000       0.0000      20.5900 
+   34535.0000       2.9000      17.7400 rg
+   34535.0000       6.4000      17.2400 
+   34535.0000       9.6000      17.0300 
+   34535.0000      12.8000      17.0300 
+   34535.0000      13.5000      17.7400 rd
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+    31     0     0     7   34705.0000   
+   34705.0000       0.0000      20.5000 
+   34705.0000       2.9000      17.6100 rg
+   34705.0000       6.4000      17.1100 
+   34705.0000       9.6000      16.8500 
+   34705.0000      12.8000      16.8500 
+   34705.0000      14.0000      18.0000 rd
+   34705.0000      16.2000      20.5300 
+     999.9990     999.9990     999.9990 
+    32     0     0     7   34825.0000   
+   34825.0000       0.0000      20.6200 
+   34825.0000       2.9000      17.5200 rg
+   34825.0000       6.4000      17.0200 
+   34825.0000       9.6000      16.7100 
+   34825.0000      12.8000      16.7100 
+   34825.0000      13.5000      17.5200 rd
+   34825.0000      16.2000      20.5000 
+     999.9990     999.9990     999.9990 
+    33     0     0     7   34995.0000   
+   34995.0000       0.0000      20.3900 
+   34995.0000       2.9000      17.3900 rg
+   34995.0000       6.4000      16.8900 
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+   34995.0000      12.8000      16.5300 
+   34995.0000      13.6000      17.4300 rd
+   34995.0000      16.2000      20.3200 
+     999.9990     999.9990     999.9990 
+    34     0     0     7   35135.0000   
+   35135.0000       0.0000      20.1600 
+   35135.0000       2.9000      17.2900 rg
+   35135.0000       6.4000      16.7900 
+   35135.0000       9.6000      16.4300 
+   35135.0000      12.8000      16.4300 
+   35135.0000      13.9000      17.3700 rd
+   35135.0000      16.2000      20.0600 
+     999.9990     999.9990     999.9990 
+    35     0     0     7   35360.0000   
+   35360.0000       0.0000      19.8600 
+   35360.0000       2.9000      17.1200 rg
+   35360.0000       6.4000      16.6200 
+   35360.0000       9.6000      16.2600 
+   35360.0000      12.8000      16.2600 
+   35360.0000      13.7000      17.1200 rd
+   35360.0000      16.2000      19.4600 
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+    36     0     0     7   35580.0000   
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+   35580.0000       3.0000      16.0900 
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+   35580.0000      20.0000      16.0900 
+   35580.0000      21.0000      17.0300 rd
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+     999.9990     999.9990     999.9990 
+    37     0     0     7   35920.0000   
+   35920.0000       0.0000      20.0000 
+   35920.0000       2.2000      16.0200 rg
+   35920.0000       3.0000      14.5500 
+   35920.0000      11.5000      14.5000 
+   35920.0000      20.0000      14.5500 
+   35920.0000      20.9000      16.0200 rd
+   35920.0000      23.0000      19.5000 
+     999.9990     999.9990     999.9990 
+    38     0     0     7   36270.0000   S1
+   36270.0000       0.0000      20.0000 
+   36270.0000       1.8000      17.0100 rg
+   36270.0000       3.0000      15.0800 
+   36270.0000      11.5000      15.0500 
+   36270.0000      20.0000      15.0800 
+   36270.0000      21.3000      17.0100 rd
+   36270.0000      23.0000      19.5000 
+     999.9990     999.9990     999.9990 
+    39     0     0     7   36271.0000   S1bis
+   36271.0000       0.0000      20.0000 
+   36271.0000       1.8000      17.0100 rg
+   36271.0000       3.0000      13.0800 
+   36271.0000      11.5000      13.0500 
+   36271.0000      20.0000      13.0800 
+   36271.0000      21.3000      17.0100 rd
+   36271.0000      23.0000      19.5000 
+     999.9990     999.9990     999.9990 

doc/users/Tuto1/data/Fevrier_2002

@@ -0,0 +1,25 @@
+0:00:00:00	5,53
+0:11:37:00	5,72
+0:16:17:00	5,82
+0:22:57:00	5,92
+1:00:00:00	6,6
+1:00:57:00	8,04
+1:02:29:00	14,3
+1:04:38:00	24,4
+1:08:48:00	40
+1:11:27:00	46,3
+1:13:47:00	48,8
+1:16:07:00	47,9
+1:17:17:00	44,8
+1:20:23:00	27,8
+1:21:57:00	24,3
+2:01:15:00	19,2
+2:05:15:00	15,8
+2:11:25:00	11,5
+2:11:57:00	11,1
+2:13:17:00	10,5
+2:19:07:00	9,84
+2:23:59:00	8,43
+3:04:51:00	7,02
+3:09:43:00	5,61
+3:14:35:00	5,53

doc/users/Tuto1/data/Hogneau.var

@@ -0,0 +1 @@
+$Clapet_001  clapet

doc/users/Tuto1/data/T_100ans

@@ -0,0 +1,9 @@
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+0:16:00:00	50
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+2:07:27:22	23,3
+5:04:24:58	13,8
+10:03:00:06	9,38
+20:02:19:58	7,29
+30:01:54:37	5,97

doc/users/Tuto1/data/T_10ans

@@ -0,0 +1,10 @@
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+5:03:55:12	9,66
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+27:00:54:00	4,91
+30:01:48:36	4
+31:06:00:00	4

doc/users/Tuto1/pas-a-pas.tex

@@ -0,0 +1,443 @@
+%% LyX 2.0.2 created this file.  For more info, see http://www.lyx.org/.
+%% Do not edit unless you really know what you are doing.
+\documentclass[12pt,french]{article}
+\usepackage[T1]{fontenc}
+\usepackage[latin9]{inputenc}
+\usepackage{geometry}
+\geometry{verbose,tmargin=2cm,bmargin=2cm,lmargin=2cm,rmargin=2cm,headheight=2cm,headsep=2cm,footskip=2cm}
+\usepackage{textcomp}
+\usepackage{graphicx}
+\usepackage{hyperref}
+
+\makeatletter
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LyX specific LaTeX commands.
+\newcommand{\noun}[1]{\textsc{#1}}
+%% Because html converters don't know tabularnewline
+\providecommand{\tabularnewline}{\\}
+
+\makeatother
+
+\usepackage{babel}
+\addto\extrasfrench{%
+   \providecommand{\og}{\leavevmode\flqq~}%
+   \providecommand{\fg}{\ifdim\lastskip>\z@\unskip\fi~\frqq}%
+}
+
+\begin{document}
+\includegraphics[width=5cm]{img/Logo-INRAE_Transparent.png}
+
+~
+
+~
+
+~
+
+\begin{center}
+
+Tutoriel pour Pamhyr2
+
+Janvier 2024
+
+\par\end{center}
+
+~
+
+~
+
+\begin{center}
+
+\textbf{\LARGE Modélisation 1D de la rivière  } \\
+\textbf{\LARGE Hogneau (Nord, France) avec Pamhyr2}
+
+\par\end{center}{\LARGE \par}
+
+~
+
+~
+
+\begin{center}
+{\large INRAE Lyon-Grenoble Auvergne-Rhône-Alpes}
+\par\end{center}{\large \par}
+
+\begin{center}
+
+RiverLy, Hydraulique des rivières
+
+\par\end{center}
+
+~
+
+~
+
+~
+
+~
+
+~
+
+~
+
+\begin{center}
+\begin{tabular}{lll}
+Auteurs : & Pierre-Antoine Rouby & pierre-antoine.rouby@inrae.fr\tabularnewline
+& Théophile TERRAZ & theophile.terraz@inrae.fr\tabularnewline
+& Lionel Pénard & lionel.penard@inrae.fr\tabularnewline
+
+\end{tabular}
+\par\end{center}
+
+~
+
+\pagebreak{}
+
+\begin{center}
+\tableofcontents{}
+\par\end{center}
+
+~
+
+\pagebreak{}
+
+% \section{Introduction}
+%
+% TODO
+%
+% \pagebreak{}
+
+
+\section{Installer Pamhyr2}
+
+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}
+
+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 \textit{Hogneau}, et validez.
+
+\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}.
+
+\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.
+
+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 :
+
+\begin{center}
+\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 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.
+
+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]} :
+
+\begin{center}
+\includegraphics[width=15cm]{img/maillage.png}
+\par\end{center}
+
+% 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 \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}
+
+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]} 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.
+
+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{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}.
+
+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.
+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 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]{"../../../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}
+\par\end{center}
+
+Retournez à la fenêtre \textit{Ouvrages hydrauliques}.
+
+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/SeuilRD101.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/SeuilThivencelle.png}
+%
+% \includegraphics[width=15cm]{img/OrificeThivencelle.png}
+% \par\end{center}
+
+\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 \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{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 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]{../../../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}
+

doc/users/Tuto1/step-by-step.tex

@@ -0,0 +1,342 @@
+%% LyX 2.0.2 created this file.  For more info, see http://www.lyx.org/.
+%% Do not edit unless you really know what you are doing.
+\documentclass[12pt,french]{article}
+\usepackage[T1]{fontenc}
+\usepackage[latin9]{inputenc}
+\usepackage{geometry}
+\geometry{verbose,tmargin=2cm,bmargin=2cm,lmargin=2cm,rmargin=2cm,headheight=2cm,headsep=2cm,footskip=2cm}
+\usepackage{textcomp}
+\usepackage{graphicx}
+\usepackage{hyperref}
+
+\makeatletter
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LyX specific LaTeX commands.
+\newcommand{\noun}[1]{\textsc{#1}}
+%% Because html converters don't know tabularnewline
+\providecommand{\tabularnewline}{\\}
+
+\makeatother
+
+\usepackage{babel}
+\addto\extrasfrench{%
+   \providecommand{\og}{\leavevmode\flqq~}%
+   \providecommand{\fg}{\ifdim\lastskip>\z@\unskip\fi~\frqq}%
+}
+
+\begin{document}
+\includegraphics[width=5cm]{img/Logo-INRAE_Transparent.png}
+
+~
+
+~
+
+~
+
+\begin{center}
+Tutorial for Pamhyr2
+
+January 2024
+\par\end{center}
+
+~
+
+~
+
+\begin{center}
+\textbf{\LARGE 1D Modeling of the Hogneau River (Nord, France)}
+
+using Pamhyr2
+\par\end{center}{\LARGE \par}
+
+~
+
+~
+
+\begin{center}
+{\large INRAE Lyon-Grenoble Auvergne-Rhône-Alpes}
+\par\end{center}{\large \par}
+
+\begin{center}
+RiverLy, river hydraulics
+\par\end{center}
+
+~
+
+~
+
+~
+
+~
+
+~
+
+~
+
+\begin{center}
+\begin{tabular}{lll}
+Authors : & Pierre-Antoine Rouby & pierre-antoine.rouby@inrae.fr\tabularnewline
+& Théophile Terraz & theophile.terraz@inrae.fr\tabularnewline
+& Lionel Pénard & lionel.penard@inrae.fr\tabularnewline
+\end{tabular}
+\par\end{center}
+
+~
+
+\pagebreak{}
+
+\begin{center}
+\tableofcontents{}
+\par\end{center}
+
+~
+
+\pagebreak{}
+
+% \section{Introduction}
+%
+% TODO
+%
+% \pagebreak{}
+
+\section{Install Pamhyr2}
+
+Pamhyr2 can be downloaded from \url{https://gitlab.irstea.fr/theophile.terraz/pamhyr}.
+\begin{center}
+\includegraphics[width=15cm]{img/dl.png}
+\par\end{center}
+
+Use the GNU Linux or the Windows download button depending on your system. On windows, launch the installer. On Linux, unpack the archive and launch Pamhyr2.
+
+
+\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.
+
+\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}
+\par\end{center}
+
+Close the \textit{Edit River Network} window.
+
+
+\section{Edit the river geometry}
+
+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 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]{"../../../src/View/ui/ressources/edit.png"} icon.
+
+select the cross section named \textit{PontRD101m} and open the edition window. You should see:
+
+\begin{center}
+\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 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]} 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 \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 \textit{Q(t)} law.
+ Select the \textit{Node} cell and atribute this condition to the upstream node.
+ 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{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]} 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}
+
+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}
+
+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}
+\par\end{center}
+
+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, 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 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/seuilRD101.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/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 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.
+
+% TODO precision
+
+Close the \textit{solver parameters} window.
+
+\section{Run the simulation}
+
+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 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 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]{../../../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}
+