debug custom plots

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
@@ -20,45 +20,68 @@ stages:
   - test
   - build
   - package
+  - hash
+  - antivirus
   - release
 
 #############
 # DOWNLOADS #
 #############
 
-dl-mage-linux:
+variables:
-  stage: downloads
+  MAGE_8_VERSION: "v8.3.6"
-  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/v8.3.0/downloads/packages/mage_linux.tgz
-    - mkdir -p mage-linux
-    - cd mage-linux
-    - tar xvf ../mage.tgz
-  artifacts:
-    paths:
-      - mage-linux/mage
-      - mage-linux/mage_extraire
-      - mage-linux/mailleurPF
 
-dl-mage-windows:
+dl-mage8-doc:
   stage: downloads
   tags:
     - linux
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   script:
-    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/v8.3.0/downloads/packages/mage_windows.tgz
+    - mkdir -p doc
-    - mkdir -p mage-windows
+    - cd doc
-    - cd mage-windows
+    - curl -L -o mage8.pdf https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/documents/Mage-8_Documentation.pdf
-    - tar xvf ../mage.tgz
   artifacts:
     paths:
-      - mage-windows/mage.exe
+      - doc/mage8.pdf
-      - mage-windows/mage_extraire.exe
+
-      - mage-windows/mailleurPF.exe
+dl-mage8-linux:
+  stage: downloads
+  tags:
+    - linux
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - curl -L -o mage8.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/packages/mage_linux.tgz
+    - mkdir -p mage8-linux
+    - cd mage8-linux
+    - tar xvf ../mage8.tgz
+  artifacts:
+    paths:
+      - mage8-linux/mage
+      - mage8-linux/mage_as7
+      - mage8-linux/mage_extraire
+      - mage8-linux/mailleurTT
+      - mage8-linux/libbief.so
+
+dl-mage8-windows:
+  stage: downloads
+  tags:
+    - linux
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
+  script:
+    - curl -L -o mage8.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$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 #
@@ -129,7 +152,24 @@ test-pep8:
 # BUILD #
 #########
 
-build-users-doc:
+# 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
@@ -137,13 +177,13 @@ 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:
@@ -184,7 +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
@@ -192,7 +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
@@ -207,28 +251,32 @@ build-linux:
     - pyinstaller -y --paths linux-venv/lib/python3.8/site-packages ../src/pamhyr.py
     # Create directory
     - mkdir -p pamhyr
-    - mkdir -p pamhyr/pamhyr
+    - mkdir -p pamhyr/_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/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
@@ -237,17 +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
@@ -259,7 +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
@@ -267,16 +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
@@ -346,6 +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 #
 ###########
@@ -362,10 +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: $CI_COMMIT_TAG
   artifacts:
@@ -373,33 +542,44 @@ tag-release:
       - linux/pamhyr-gnulinux.tar.xz
       - windows/pamhyr-windows.zip
       - windows/pamhyr-windows.exe
+      - linux/pamhyr-gnulinux.tar.xz.sha256
+      - windows/pamhyr-windows.zip.sha256
+      - windows/pamhyr-windows.exe.sha256
       - doc/dev/documentation.pdf
-      - doc/users/documentation.pdf
+      # - doc/users/documentation.pdf
   script:
     - cd packages
   release:
     name: '$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/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 +1,4 @@
+#! /bin/sh
+
+pdflatex -no-shell-escape step-by-step.tex
+pdflatex -no-shell-escape pas-a-pas.tex

doc/users/Tuto1/data/Cote_canal

@@ -1,2 +0,0 @@
-0:00:00:00	15
-0:00:01:00	15

doc/users/Tuto1/data/Hogneau.SIN

@@ -1,25 +0,0 @@
-**************** SINGULARITES **********************
-*BieSec Nb Longueur  Cote dev Cote charg Coef deb            Impression         
-*===---===----------==========----------==========----------------------------- 
-*****************************************************
-* Bief n°  1
-*****************************************************
-* Ouvrage au pk 36270.0  seuil_aval
-*SeuilR type D
-D  1  36270.00    18.250    15.500     0.000     0.400 99999.000 seuil palplanches
-* Ouvrage au pk 31875.0  PontRS101
-*OrificeR type O
-O  1  31875.00     9.660    18.710    21.890     0.400  9999.000 
-*SeuilR type D
-D  1  31875.00    14.000    22.890     0.000     0.400 99999.000 
-* Ouvrage au pk 34335.0  PontThivencelle
-*SeuilR type D
-D  1  34335.00    13.000    21.740     0.000     0.400 99999.000 
-*OrificeR type O
-O  1  34335.00     9.070    17.280    20.740     0.400  9999.000 
-*****************************************************
-* Bief n°  3
-*****************************************************
-* Ouvrage au pk 0.0  Orifice
-*OrificeR type O
-*O  3     0.000     6.000    19.000    19.001     0.400    20.000 Clapet_001

doc/users/Tuto1/data/Q_permanent

@@ -1,2 +0,0 @@
-0:00:00:00	4
-0:00:01:00	4

doc/users/Tuto1/data/Seuil_aval_23m

@@ -1,24 +0,0 @@
-16,03	0
-16,13	1,29
-16,23	3,64
-16,33	6,7
-16,43	10,31
-16,53	14,41
-16,63	18,94
-16,73	23,87
-16,83	29,16
-16,93	34,79
-17,03	40,75
-17,13	47,01
-17,23	53,57
-17,33	60,4
-17,43	67,5
-17,53	74,86
-17,63	82,47
-17,73	90,33
-17,83	98,41
-17,93	106,73
-18,03	115,26
-18,13	124,01
-18,23	132,98
-18,33	142,14