remove GL doublons

.gitignore

@@ -19,8 +19,6 @@ tmp
 *.pdf
 *.odt
 
-!doc/**/*.pdf
-
 doc/dev/images/auto_*
 doc/dev/documentation.*
 !doc/dev/*.org
@@ -270,7 +268,6 @@ 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
 
@@ -646,233 +643,3 @@ 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) 2023-2024  INRAE
+# 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
@@ -20,68 +20,45 @@ stages:
   - test
   - build
   - package
-  - hash
-  - antivirus
   - release
 
 #############
 # DOWNLOADS #
 #############
 
-variables:
+dl-mage-linux:
-  MAGE_8_VERSION: "v8.3.6"
-
-dl-mage8-doc:
   stage: downloads
   tags:
     - linux
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   script:
-    - mkdir -p doc
+    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/v8.3.0/downloads/packages/mage_linux.tgz
-    - cd doc
+    - mkdir -p mage-linux
-    - curl -L -o mage8.pdf https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/$MAGE_8_VERSION/downloads/documents/Mage-8_Documentation.pdf
+    - cd mage-linux
+    - tar xvf ../mage.tgz
   artifacts:
     paths:
-      - doc/mage8.pdf
+      - mage-linux/mage
+      - mage-linux/mage_extraire
+      - mage-linux/mailleurPF
 
-dl-mage8-linux:
+dl-mage-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_linux.tgz
+    - curl -L -o mage.tgz https://gitlab.irstea.fr/jean-baptiste.faure/mage/-/releases/v8.3.0/downloads/packages/mage_windows.tgz
-    - mkdir -p mage8-linux
+    - mkdir -p mage-windows
-    - cd mage8-linux
+    - cd mage-windows
-    - tar xvf ../mage8.tgz
+    - tar xvf ../mage.tgz
   artifacts:
     paths:
-      - mage8-linux/mage
+      - mage-windows/mage.exe
-      - mage8-linux/mage_as7
+      - mage-windows/mage_extraire.exe
-      - mage8-linux/mage_extraire
+      - mage-windows/mailleurPF.exe
-      - 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 #
@@ -152,24 +129,7 @@ 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
@@ -177,13 +137,13 @@ build-td:
     - job: set-version
       artifacts: true
   script:
-    - cd ./doc/users/Tuto1/
+    - cd ./doc/users/
     - ./build.sh
   artifacts:
     paths:
-      - doc/users/Tuto1/step-by-step.pdf
+      - doc/users/documentation.pdf
-      - doc/users/Tuto1/pas-a-pas.pdf
+      - doc/users/documentation.html
-      - doc/users/Tuto1/data/
+      - doc/users/images/
   allow_failure: true
 
 build-developers-doc:
@@ -224,9 +184,7 @@ build-linux:
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   needs:
-    - job: dl-mage8-linux
+    - job: dl-mage-linux
-      artifacts: true
-    - job: dl-mage8-doc
       artifacts: true
     - job: set-version
       artifacts: true
@@ -234,9 +192,7 @@ 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
@@ -251,32 +207,28 @@ build-linux:
     - pyinstaller -y --paths linux-venv/lib/python3.8/site-packages ../src/pamhyr.py
     # Create directory
     - mkdir -p pamhyr
-    - mkdir -p pamhyr/_internal
+    - mkdir -p pamhyr/pamhyr
+    - mkdir -p pamhyr/pamhyr/_internal
     # Copy Pamhyr info
-    - cp -v ../VERSION pamhyr/_internal/
+    - cp -v ../VERSION pamhyr/pamhyr/_internal/
-    - cp -v ../AUTHORS pamhyr/_internal/
+    - cp -v ../AUTHORS pamhyr/pamhyr/_internal/
-    - cp -v ../LICENSE pamhyr/_internal/
+    - cp -v ../LICENSE pamhyr/pamhyr/_internal/
-    - cp -v ../src/motd.txt pamhyr/_internal/
+    - cp -v ../src/motd.txt pamhyr/pamhyr/_internal/
     # Copy mage
-    - mkdir -p pamhyr/mage8
+    - mkdir -p pamhyr/mage
-    - cp -v ../mage8-linux/* pamhyr/mage8/
+    - cp -v ../mage-linux/* pamhyr/mage/
     # 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/_internal/View
+    - mkdir -p pamhyr/pamhyr/_internal/View
-    - mkdir -p pamhyr/_internal/View/ui
+    - mkdir -p pamhyr/pamhyr/_internal/View/ui
-    - mkdir -p pamhyr/_internal/View/ui/Widgets
+    - mkdir -p pamhyr/pamhyr/_internal/View/ui/Widgets
-    - cp -r ../src/View/ui/*.ui pamhyr/_internal/View/ui/
+    - cp -r ../src/View/ui/*.ui pamhyr/pamhyr/_internal/View/ui/
-    - cp -r ../src/View/ui/ressources/ pamhyr/_internal/View/ui
+    - cp -r ../src/View/ui/ressources/ pamhyr/pamhyr/_internal/View/ui
-    - cp -r ../src/View/ui/Widgets/*.ui pamhyr/_internal/View/ui/Widgets
+    - cp -r ../src/View/ui/Widgets/*.ui pamhyr/pamhyr/_internal/View/ui/Widgets
     # Copy lang
-    - mkdir -p pamhyr/_internal/lang
+    - mkdir -p pamhyr/pamhyr/_internal/lang
-    - cp -r ../src/lang/*.qm pamhyr/_internal/lang
+    - cp -r ../src/lang/*.qm pamhyr/pamhyr/_internal/lang
     # Copy tests cases
     - mkdir -p pamhyr/tests_cases/
     - mkdir -p pamhyr/tests_cases/Saar
@@ -285,25 +237,17 @@ 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 -r ../doc/dev/images/* pamhyr/doc/images
+    - cp ../doc/dev/images/* pamhyr/doc/images
-    - cp -r ../doc/images/* pamhyr/doc/images
+    - cp ../doc/images/* pamhyr/doc/images
-    # Copy Tuto
+    # Create running script
-    - mkdir -p pamhyr/doc/Tuto1/
+    - echo "#!/bin/sh" > pamhyr/Pamhyr2
-    - mkdir -p pamhyr/doc/Tuto1/data
+    - echo "./pamhyr/pamhyr $@" >> pamhyr/Pamhyr2
-    - cp ../doc/users/Tuto1/Hogneau_Engees2022.pdf pamhyr/doc/Tuto1/Hogneau_Engees2022.pdf
+    - chmod u+x pamhyr/Pamhyr2
-    - 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
@@ -315,9 +259,7 @@ build-windows:
   rules:
     - if: $CI_COMMIT_BRANCH == 'ci-test' || $CI_COMMIT_BRANCH == 'master' || $CI_COMMIT_TAG
   needs:
-    - job: dl-mage8-windows
+    - job: dl-mage-windows
-      artifacts: true
-    - job: dl-mage8-doc
       artifacts: true
     - job: set-version
       artifacts: true
@@ -325,20 +267,16 @@ 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 --noconsole -y ..\src\pamhyr.py
+    - pyinstaller -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
@@ -408,111 +346,6 @@ 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 #
 ###########
@@ -529,11 +362,9 @@ tag-release:
       artifacts: true
     - job: windows-package-exe
       artifacts: true
-    # - job: build-users-doc
+    - job: build-users-doc
-    #   artifacts: true
-    - job: build-developers-doc
       artifacts: true
-    - job: pkg-hash
+    - job: build-developers-doc
       artifacts: true
   rules:
     - if: $CI_COMMIT_TAG
@@ -542,44 +373,33 @@ tag-release:
       - linux/pamhyr-gnulinux.tar.xz
       - windows/pamhyr-windows.zip
       - windows/pamhyr-windows.exe
-      - linux/pamhyr-gnulinux.tar.xz.sha256
-      - windows/pamhyr-windows.zip.sha256
-      - windows/pamhyr-windows.exe.sha256
       - doc/dev/documentation.pdf
-      # - doc/users/documentation.pdf
+      - doc/users/documentation.pdf
   script:
     - cd packages
   release:
     name: '$CI_COMMIT_TAG'
-    description: '$CI_COMMIT_TAG_MESSAGE'
+    description: 'Automatic release from tag $CI_COMMIT_TAG'
     tag_name: '$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 - 2024
+Théophile TERRAZ, INRAE, 2022 - 2023
-Pierre-Antoine ROUBY, INRAE, 2023 - 2024
+Pierre-Antoine ROUBY, INRAE, 2023

README.md

@@ -3,38 +3,48 @@
 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
 
-+ Define a complex river hydraulics network
++ Edit a complex river hydraulics network
 + Define the river geometry
 + Define boundary conditions
 + Define lateral contribution
-+ Define river friction
++ Edit river friction
-+ Define reservoirs
++ Generate initial conditions
-+ Define hydraulic structures
++ Edit river sedimentary layers
-+ 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
 
-See documentation:
+Downloads [last
-- [French :fr:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/fr/Install%20on%20GNULinux)
+realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
-- [English :gb:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/en/Install%20on%20GNULinux)
+GNU/Linux binary archive.
+
+```shell
+tar xf pamhyr-gnulinux-amd64.tar.xz
+cd pamhyr
+./pamhyr
+```
 
 ### Windows
 
-See documentation:
+Downloads [last
-- [French :fr:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/fr/Install%20on%20Windows)
+realease](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/releases/permalink/latest)
-- [English :gb:](https://gitlab.irstea.fr/theophile.terraz/pamhyr/-/wikis/home/en/Install%20on%20Windows)
+Windows installer.
+
+### From source code
+
+```shell
+# Get source code
+git clone https://gitlab.irstea.fr/theophile.terraz/pamhyr/
+cd pamhyr
+
+# Install dependencies
+pip3 install -r requirements.txt
+
+# Run pamhyr
+./src/pamhyr.py
+```

doc/dev/documentation.org

@@ -1,5 +1,5 @@
 # documentation.org -- Pamhyr developers documentation
-# Copyright (C) 2023-2024  INRAE
+# 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
@@ -369,7 +369,6 @@ 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),
             )""")
@@ -456,15 +455,6 @@ 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)
 
@@ -556,8 +546,8 @@ generic value from optional parameters, for examples:
         _pamhyr_ui = "MyUI"
         _pamhyr_name = "My window"
 
-      def __init__(self, study=None, config=None,
+        def __init__(self, my_data=None,
-                   my_data=None,
+                     study=None, config=None,
                      parent=None):
             self._my_data = my_data
 
@@ -646,7 +636,7 @@ class AddNodeCommand(QUndoCommand):
         self._node = node
 
     def undo(self):
-        self._graph.remove_node(self._node)
+        self._graph.remove_node(self._node.name)
 
     def redo(self):
         self._graph.insert_node(self._node)
@@ -671,13 +661,11 @@ creation, this stack is accessible at =self._undo_stack=.
 
 *** Plot
 
-To define a new plot you can create a class who inherit to
+To define a new plot you can create a class who inherit to APlot. The
-PamhyrPlot. The creator need at leaste five argument:
+creator need threee 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.
@@ -685,36 +673,19 @@ data has changed.
 #+begin_src python :python python3 :results output :noweb yes
   from View.Tools.PamhyrPlot import PamhyrPlot
 
-  class MyPlot(PamhyrPlot):
+  class MyPlot(APlot):
-      def __init__(self, canvas=None, trad=None, toolbar=None
+      def __init__(self, canvas=None, data=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):
+      def update(self, ind = None):
           # Update function code...
-
-      def clear(self):
-          # Clear plot values...
-
-      # ...
 #+end_src
 
 ** Solver
@@ -774,7 +745,7 @@ 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];
                   }
@@ -857,7 +828,7 @@ 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 =Results= object
+ - (3) Pamhyr2 create a Reuslts
  - (3.1) The Pamhyr2 solver class read solver output file(s) and
    complete Results with readed data
 
@@ -987,16 +958,8 @@ different methods:
 
 ** Unit tests
 
-A very small part of Pamhyr2 has unit test. This part is limited to the Model.
+The unit tests is actually not implemented in Pamhyr2, it is a *work
-
+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
 
@@ -1007,14 +970,14 @@ line:
 ./Pamhyr2 debug
 #+end_src
 
-This mode add some log and add two action in main window menu: "About
+This mode add some log and add two action in main window menu:
-> Debug" open a window with Python Repl in current Python
+"About/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 14cm
+#+ATTR_LATEX: :width 12cm
 #+CAPTION: Pamhyr2 debug Python REPL
 [[./images/python-debug-repl.png]]
 
@@ -1334,7 +1297,7 @@ 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 edit the translation ({{{file(.ts)}}}) file, finally,
+Qt-linguist and edite 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

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

@@ -1,4 +0,0 @@
-#! /bin/sh
-
-pdflatex -no-shell-escape step-by-step.tex
-pdflatex -no-shell-escape pas-a-pas.tex

doc/users/Tuto1/data/Cote_canal

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

doc/users/Tuto1/data/Hogneau.SIN

@@ -0,0 +1,25 @@
+**************** 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

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

doc/users/Tuto1/data/Seuil_aval_23m

@@ -0,0 +1,24 @@
+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