.clang-tidy

 ---
-Checks: '-*,clang-diagnostic-*,clang-analyzer-*,cppcoreguidelines-pro-type-member-init, *explicit-conversions*, google-explicit-constructor, google-readability-braces-around-statements, modernize-loop-convert, modernize-use-default-member-init, modernize-use-emplace, modernize-use-using, readability-braces-around-statements, readability-else-after-return, readability-named-parameter, *readability-namespace-comments, *readability-inconsistent-*, readability-redundant-member-init, readability-simplify-boolean-expr, readability-string-compare'
+Checks: >
+  -*
+  ,clang-diagnostic-*,
+  clang-analyzer-*,
+  cppcoreguidelines-pro-type-member-init,
+  *explicit-conversions*,
+  google-explicit-constructor,
+  google-readability-braces-around-statements,
+  modernize-loop-convert,
+  modernize-use-default-member-init,
+  modernize-use-emplace,
+  modernize-use-using,
+  readability-braces-around-statements,
+  readability-else-after-return,
+  readability-named-parameter,
+  *readability-namespace-comments,
+  *readability-inconsistent-*,
+  readability-redundant-member-init,
+  readability-simplify-boolean-expr,
+  readability-string-compare
 
-WarningsAsErrors: ''
-HeaderFilterRegex: '.*'
+WarningsAsErrors: ""
+HeaderFilterRegex: ".*"
 AnalyzeTemporaryDtors: false
-FormatStyle:     file
+FormatStyle: file
 CheckOptions:
-  - key:             google-readability-braces-around-statements.ShortStatementLines
-    value:           '1'
-  - key:             hicpp-braces-around-statements.ShortStatementLines
-    value:           '1'
-  - key:             readability-braces-around-statements.ShortStatementLines
-    value:           '1'
+  - key: google-readability-braces-around-statements.ShortStatementLines
+    value: "1"
+  - key: hicpp-braces-around-statements.ShortStatementLines
+    value: "1"
+  - key: readability-braces-around-statements.ShortStatementLines
+    value: "1"

.cmake-format.yaml

@@ -45,7 +45,6 @@ parse:
         WRAPPER_ARGS: +
         REQUIREMENTS: +
         PYTHON_PACKAGES: +
-        VIS: +
 
     ogstest:
       pargs:
@@ -58,28 +57,6 @@ parse:
         RUNTIME: 1
         WRAPPER: +
 
-    meshtest:
-      pargs:
-        nargs: "*"
-        flags:
-          - NONE
-      spelling: MeshTest
-      kwargs:
-        EXECUTABLE: 1
-        PATH: 1
-        NAME: 1
-        WRAPPER: 1
-        RUNTIME: 1
-        WORKING_DIRECTORY: 1
-        EXECUTABLE_ARGS: +
-        DATA: +
-        DIFF_DATA:
-          pargs:
-            tags:
-              - cmdline
-        WRAPPER_ARGS: +
-        REQUIREMENTS: +
-
     cpmaddpackage:
       pargs:
         nargs: "*"
@@ -110,6 +87,7 @@ parse:
         HTTP_PASSWORD: 1
         EXCLUDE_FROM_ALL: 1
         OPTIONS: +
+        PATCH_COMMAND: +
     cpmfindpackage:
       pargs:
         nargs: "*"

.codeclimate.yml

 version: "2"
 exclude_patterns:
-  - "ThirdParty/"
   - "Tests/"
 plugins:
   duplication:

.codespellexclude

@@ -11,3 +11,4 @@ Malcom, M.A.M.(2018).Analysis of underground excavations in argillaceous hard
             Stoffverhaltens von Salzgestein in Abh{\"a}ngigkeit von der Zeit und der
             Temperatur auf der Grundlage von Laborversuchen mit begleitenden kontinuumsmechanischen
             Berechnungen nach der Methode der finiten Elemente}'
+- _Dupuit J. Mouvement de l’eau a travers le terrains permeables. C. R. Hebd. Seances Acad. Sci., 45:92–96, 1857._

.codespellrc

 [codespell]
-skip = ./.git,./Tests/Data,./ThirdParty,*.yml,*.bib,./web/content/imprint.md,./GeoLib/IO/XmlIO/OpenGeoSysSTN.xsd
-ignore-words-list = Theis,nd,theis,strat
+skip = *.bib,*.css,*.pdf,*.yaml,*.yml,*.vtu,*/.vale,./.git,./GeoLib/IO/XmlIO/OpenGeoSysSTN.xsd,./Tests/Data,./web/content/imprint.md,./web/node_modules,./web/public/imprint/index.html,./web/resources,CITATION.cff,
+ignore-words-list = ba,bu,ket,nd,pris,strat,sur,theis,ot,Jupyter,testrunner
 exclude-file = .codespellexclude
+uri-ignore-words-list = *

.devcontainer.json

+{
+  "name": "ogs-gcc-dev",
+  "image": "mcr.microsoft.com/devcontainers/cpp",
+  "mounts": [
+    "source=devcontainer-cpm-cache,target=/opt/cpm,type=volume",
+    "source=devcontainer-ccache-cache,target=/opt/ccache,type=volume",
+    "source=${localWorkspaceFolder}/../build,target=${containerWorkspaceFolder}/../build,type=bind"
+  ],
+  "features": {
+    "common": {},
+    "ghcr.io/devcontainers/features/python:1": {},
+    "ghcr.io/devcontainers/features/common-utils:2": {
+      "configureZshAsDefaultShell": true
+    }
+  }
+}

.editorconfig

@@ -8,5 +8,5 @@ indent_size = 4
 [*.{md,pandoc}]
 trim_trailing_whitespace = false
 
-[*.{json,yml,yaml,toml,html,css,js,scss}]
+[*.{json,yml,yaml,toml,html,css,js,scss,md}]
 indent_size = 2

.github/workflows/msvc-code-analysis.yml

+on: push
+
+env:
+  # Path to the CMake build directory.
+  build: "${{ github.workspace }}/build"
+  config: "Debug"
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: windows-2019
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Configure CMake
+        run: cmake -B ${{ env.build }} -DCMAKE_BUILD_TYPE=${{ env.config }} -DOGS_USE_UNITY_BUILDS=OFF -DOGS_BUILD_TESTING=OFF -DOGS_ENABLE_ELEMENT_PRISM=OFF -DOGS_ENABLE_ELEMENT_PYRAMID=OFF -DOGS_MAX_ELEMENT_DIM=2
+
+      # Build is not required unless generated source files are used
+      # - name: Build CMake
+      #   run: cmake --build ${{ env.build }} --config ${{ env.config }}
+
+      - name: Run MSVC Code Analysis
+        uses: microsoft/msvc-code-analysis-action@v0.1.0
+        # Provide a unique ID to access the sarif output path
+        id: run-analysis
+        with:
+          cmakeBuildDirectory: ${{ env.build }}
+          buildConfiguration: ${{ env.config }}
+          # Ruleset file that will determine what checks will be run
+          ruleset: NativeRecommendedRules.ruleset
+          # Paths to ignore analysis of CMake targets and includes
+          ignoredPaths: build/_deps
+
+      # Upload SARIF file to GitHub Code Scanning Alerts
+      - name: Upload SARIF to GitHub
+        uses: github/codeql-action/upload-sarif@v1
+        with:
+          sarif_file: ${{ steps.run-analysis.outputs.sarif }}
+
+      # Upload SARIF file as an Artifact to download and view
+      - name: Upload SARIF as an Artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: sarif-file
+          path: ${{ steps.run-analysis.outputs.sarif }}

.gitignore

@@ -3,6 +3,7 @@
 *.sw[op]
 tags
 .ExternalData_*
+.DS_Store
 
 # CLion IDE project files
 *.iml
@@ -11,18 +12,32 @@ tags
 # Visual Studio Code project files
 .vscode
 
-# Conan package manager
-conanbuildinfo.cmake
-conaninfo.txt
-CMakeLists.txt.user*
-
 *.pyc
 .venv
 
 Tests/**/*.md5
 Tests/Data/Parabolic/HT/InvalidProjectFiles/*.prj
+Tests/Data/_out
 web/.netlify
 
 CMakeUserPresets.json
+scripts/cmake/vtk-*.patch
 
 .snakemake
+
+# clangd and other language servers' caches
+.cache
+.ccls-cache
+
+# VS Code devcontainer
+/.cpm
+nohup.out
+
+/Documentation/.vale
+
+# Python build
+/_skbuild
+*.egg-info/
+/wheelhouse
+.ipynb_checkpoints
+/Applications/Python/_version.py

.gitlab-ci.yml

 stages:
   - preparation
   - build
+  - test
   - check
   - release
   - package
@@ -8,43 +9,75 @@ stages:
 variables:
   # Build config
   BUILD_TYPE: Release
-  BUILD_PROCESSES: "" # Empty string: builds all processes
   BUILD_TESTS: "true"
   BUILD_CTEST: "true"
+  CTEST_ARGS: "" # If not empty supply arguments to select tests
+  CTEST_TIMEOUT: "" # in minutes
+  CPU_TARGET: ivybridge # envinf1 has oldest cpu
+  ARTIFACTS_PAGES_URL: https://$CI_PROJECT_ROOT_NAMESPACE.$CI_PAGES_DOMAIN/-/$CI_PROJECT_NAME/-/jobs/$CI_JOB_ID/artifacts
+  PIPELINE_NAME: "Default pipeline name"
+  # by default skip performance tests, they can be enabled on isolated test machines
+  OGS_PERFORMANCE_TESTS_ALLOWED_TO_FAIL: true
 
 workflow:
+  name: "$PIPELINE_NAME"
   rules:
     # Disable CI for non-MR user-scoped pipelines
-    - if: '$CI_MERGE_REQUEST_IID == null && $CI_PROJECT_NAMESPACE != "ogs"'
+    - if: '$CI_MERGE_REQUEST_IID == null && $CI_PROJECT_PATH != "ogs/ogs"'
       when: never
-    - if: '$CI_MERGE_REQUEST_LABELS =~ /.*(workflow::paused|ci skip).*/'
+    - if: "$CI_MERGE_REQUEST_LABELS =~ /.*(workflow::paused|ci::skip).*/"
       when: never
-    - if: $CI_MERGE_REQUEST_IID                         # merge requests
-    - if: $CI_COMMIT_TAG                                # tags, ogs/ogs repo only
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH       # master, ogs/ogs repo only
-    - if: $CI_COMMIT_BRANCH =~ /^v[0-9]\.[0-9]\.[0-9]/  # release branches, e.g. v6.x.x
+    - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::web only.*/
+      variables:
+        PIPELINE_NAME: "web only MR pipeline: $CI_MERGE_REQUEST_SOURCE_PROJECT_PATH $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME"
+        BUILD_TESTS: "false"
+        CTEST_INCLUDE_REGEX: "nb-"
+    - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::linux only.*/
+      variables:
+        PIPELINE_NAME: "linux only MR pipeline: $CI_MERGE_REQUEST_SOURCE_PROJECT_PATH $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME"
+    - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::mac only.*/
+      variables:
+        PIPELINE_NAME: "mac only MR pipeline: $CI_MERGE_REQUEST_SOURCE_PROJECT_PATH $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME"
+    - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::win only.*/
+      variables:
+        PIPELINE_NAME: "win only MR pipeline: $CI_MERGE_REQUEST_SOURCE_PROJECT_PATH $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME"
+    - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::guix only.*/
+      variables:
+        PIPELINE_NAME: "guix only MR pipeline: $CI_MERGE_REQUEST_SOURCE_PROJECT_PATH $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME"
+    - if: $CI_MERGE_REQUEST_IID # merge requests
+      variables:
+        PIPELINE_NAME: "MR pipeline: $CI_MERGE_REQUEST_SOURCE_PROJECT_PATH $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME"
+    - if: $CI_COMMIT_TAG # tags, ogs/ogs repo only
+    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_PATH == "ogs/ogs"' # master, ogs/ogs repo only
+      variables:
+        PIPELINE_NAME: "master pipeline"
 
 include:
-  - local: 'scripts/ci/extends/*.yml'
-  - local: '/scripts/ci/jobs/meta.yml'
-  - local: '/scripts/ci/jobs/ci_images.yml'
-  - local: '/scripts/ci/jobs/pre-commit.yml'
-  # jobs, can be indiviually disabled for testing
-  - local: '/scripts/ci/jobs/build-linux.yml'
-  - local: '/scripts/ci/jobs/build-linux-petsc.yml'
-  - local: '/scripts/ci/jobs/build-linux-frontend.yml'
-  - local: '/scripts/ci/jobs/build-docs.yml'
-  - local: '/scripts/ci/jobs/build-win.yml'
-  - local: '/scripts/ci/jobs/build-mac.yml'
-  # - template: 'Code-Quality.gitlab-ci.yml' # see !3053
-  - local: '/scripts/ci/jobs/code-quality.yml'
-  - local: '/scripts/ci/jobs/code-coverage.yml'
-  - local: '/scripts/ci/jobs/build-gui-linux.yml'
-  - local: '/scripts/ci/jobs/build-gui-win.yml'
-  - local: '/scripts/ci/jobs/build-gui-mac.yml'
-  - local: '/scripts/ci/jobs/check-header.yml'
-  - local: '/scripts/ci/jobs/clang-sanitizer.yml'
-  - local: '/scripts/ci/jobs/clang-tidy.yml'
-  - local: '/scripts/ci/jobs/web.yml'
-  - local: '/scripts/ci/jobs/container.yml'
-  - local: '/scripts/ci/jobs/release.yml'
+  - local: "scripts/ci/extends/*.yml"
+  - local: "/scripts/ci/pipelines/regular.yml"
+    rules:
+      - if: $CI_PIPELINE_SOURCE != "schedule" && $CI_MERGE_REQUEST_LABELS !~ /.*ci::\w* only.*/
+  - local: "/scripts/ci/pipelines/web.yml"
+    rules:
+      - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::web only?($|,)/
+  - local: "/scripts/ci/pipelines/web-fast.yml"
+    rules:
+      - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::web only \(fast.*/
+  - local: "/scripts/ci/pipelines/scheduled.yml"
+    rules:
+      - if: '$CI_PIPELINE_SOURCE == "schedule"'
+  - local: "/scripts/ci/pipelines/linux.yml"
+    rules:
+      - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::linux only.*/
+  - local: "/scripts/ci/pipelines/mac.yml"
+    rules:
+      - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::mac only.*/
+  - local: "/scripts/ci/pipelines/win.yml"
+    rules:
+      - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::win only.*/
+  - local: "/scripts/ci/pipelines/guix.yml"
+    rules:
+      - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::guix only.*/
+  - local: "/scripts/ci/jobs/build-wheels.yml"
+    rules:
+      - if: $CI_MERGE_REQUEST_LABELS =~ /.*ci::wheels only.*/

.gitlab/CODEOWNERS

+^[CMake]
+*.cmake @bilke
+CMakeLists.txt @bilke
+
+[Documentation] @ogs/docs-team
+Documentation
+web/content

.gitlab/route-map.yml

+# Hugo pages
+- source: /web/content/(.+?)/index\.md/
+  public: '../\1.html'

.gitmodules

-[submodule "ThirdParty/container-maker"]
-	path = ThirdParty/container-maker
-	url = https://gitlab.opengeosys.org/ogs/container-maker.git
-[submodule "ThirdParty/ogs6py"]
-	path = ThirdParty/ogs6py
-	url = https://github.com/joergbuchwald/ogs6py.git

.mailmap

+Alireza Hassanzadegan <a.hassanzadegan@gmail.com> AlirezaBGE <a.hassanzadegan@gmail.com>
+Aqeel Chaudhry <Aqeel.Chaudhry@ifgt.tu-freiberg.de> aachaudhry <aqeel318@gmail.com>
 Carolin Helbig <carolin.helbig@ufz.de>
 Chaofan Chen <chaofan.chen@ufz.de>
+Chaofan Chen <chaofan.chen@ufz.de> <cchaofan1311@gmail.com>
+Christian Silbermann <christian.silbermann@ifgt.tu-freiberg.de> cbsilver <christian.silbermann@ifgt.tu-freiberg.de>
 Christoph Lehmann <christoph.lehmann@ufz.de> <chleh@users.noreply.github.com>
-Dmitri Naumov <dmitri.naumov@ufz.de> <github@naumov.de>
-Dmitri Naumov <dmitri.naumov@ufz.de> Dmitrij Naumov <dmitrij@naumov.de>
-Dmitri Naumov <dmitri.naumov@ufz.de> Dmitry Yu. Naumov <dmitri.naumov@ufz.de>
-Francesco Parisio <francesco.parisio@ufz.de>
-Francesco Parisio <francesco.parisio@ufz.de> fparisio <francesco.parisio@protonmail.com>
+Dmitri Naumov <dmitri-jurievic.naumov@ifgt.tu-freiberg.de> <github@naumov.de>
+Dmitri Naumov <dmitri-jurievic.naumov@ifgt.tu-freiberg.de> Dmitrij Naumov <dmitrij@naumov.de>
+Dmitri Naumov <dmitri-jurievic.naumov@ifgt.tu-freiberg.de> Dmitry Yu. Naumov <dmitri.naumov@ufz.de>
+Dmitri Naumov <dmitri-jurievic.naumov@ifgt.tu-freiberg.de> <dmitri.naumov@ufz.de>
+Dmitri Naumov <dmitri-jurievic.naumov@ifgt.tu-freiberg.de> <Dmitri-Jurievic.Naumov@ifgt.tu-freiberg.de>
+Dominik Kern <dominik.kern1@ifgt.tu-freiberg.de> <dominik.kern.ifgt@gmail.com>
+Eric Simo <eric.simo@bge.de> ericsimo <kuateric>
+Florian Zill <florian.zill@ufz.de> Florian Krupsack <florian.krupsack@ufz.de>
+Florian Zill <florian.zill@ufz.de> FZill <48240078+FZill@users.noreply.github.com>
+Florian Zill <florian.zill@ufz.de> FZill <florian.zill@ufz.de>
+Francesco Parisio <francesco.parisio@ufz.de> <francesco.parisio@protonmail.com>
 Haibing Shao <haibing.shao@ufz.de> <36633245+HBShaoUFZ@users.noreply.github.com>
 Haibing Shao <haibing.shao@ufz.de> HBShaoUFZ
+Jaime Garibay <jaimegaribay.1@gmail.com> garibay-j <jaimegaribay.1@gmail.com>
 Jan Thiedau <jan.thiedau@bgr.de> <44462589+ThieJan@users.noreply.github.com>
+Jan Thiedau <jan.thiedau@bgr.de> Jan Thiedau <Jan.Thiedau@bgr.de>
+Jan Thiedau <jan.thiedau@bgr.de> ThieJan <jan.thiedau@bgr.de>
+Jasper Bathmann <jasper.bathmann@ufz.de>
+Jeremie Lagraviere <jeremie.lagraviere@gmail.com>
+Johannes Boog <johannes.boog@ufz.de> <johannesboog@yahoo.de>
+Jörg Buchwald <joerg.buchwald@ufz.de> joerg <joerg.buchwald@ufz.de>
+Jörg Buchwald <joerg.buchwald@ufz.de> joerg <joerg@debian>
+Jörg Buchwald <joerg.buchwald@ufz.de> joergbuchwald <44933043+joergbuchwald@users.noreply.github.com>
+Jörg Buchwald <joerg.buchwald@ufz.de> joergbuchwald <joerg.buchwald@ufz.de>
 Karsten Rink <karsten.rink@ufz.de>
 Keita Yoshioka <keita.yoshioka@ufz.de>
-Lars Bilke <lars.bilke@ufz.de> <bilke@users.noreply.github.com> <larsbilke83@googlemail.com>
+Keita Yoshioka <keita.yoshioka@ufz.de> <32516139+KeitaYoshioka@users.noreply.github.com>
+Lars Bilke <lars.bilke@ufz.de> <bilke@users.noreply.github.com> <lars@bilke.info>
+Lars Bilke <lars.bilke@ufz.de> Lars Bilke <lars@bilke.info>
+Lars Bilke <lars.bilke@ufz.de> Lars Bilke <larsbilke83@googlemail.com>
+Marc Walther <marc.walther@ufz.de>
+Mostafa Mollaali <mostafa.mollaali@ufz.de> MostafaMollaali <m.molaali@gmail.com>
 Myles English <mylesenglish@gmail.com>
 Norbert Grunwald <norbert.grunwald@ufz.de> <n.g.boettcher@gmail.com>
-Norihiro Watanabe <norihiro.w@gmail.com> <norihiro.watanabe@aist.go.jp> <norihiro.watanabe@ufz.de>
-OGS Bot <larsbilke@web.de>
+Norbert Grunwald <norbert.grunwald@ufz.de> <Norbert.Grunwald@ufz.de>
+Norihiro Watanabe <norihiro.watanabe@ufz.de> <norihiro.watanabe@aist.go.jp>
+Norihiro Watanabe <norihiro.watanabe@ufz.de> <norihiro.w@gmail.com>
+OGS Bot[bot] <no-email> git@dev2 <lars.bilke@ufz.de>
+OGS Bot[bot] <no-email> GitLab Runner <ci@opengeosys.org>
+OGS Bot[bot] <no-email> OGS Bot <larsbilke@web.de>
+OGS Bot[bot] <no-email> OGS Bot <larsbilke@web.de>
+OGS Bot[bot] <no-email> ogsbot <larsbilke@web.de>
+Renchao Lu <renchao.lu@ufz.de> <renchao.lu@gmail.com>
+Renchao Lu <renchao.lu@ufz.de> <lur@modmon128.intranet.ufz.de>
+Renchao Lu <renchao.lu@ufz.de> renchao.lu <renchao.lu@ufz.de>
+Reza Taher Dang Koo <reza.taherdangkoo@ifgt.tu-freiberg.de> rezataherdangkoo <reza.taherdangkoo@gmail.com>
+Shuang Chen <shuang.chen@bgr.de> <gechenshuang88@gmail.com>
+Shuang Chen <shuang.chen@bgr.de> Shuang Chen <shuang.chen@ufz.de>
+Tengfei Deng <Tengfei.Deng@doktorand.tu-freiberg.de> tengfeideng <54792615+tengfeideng@users.noreply.github.com>
+Tengfei Deng <Tengfei.Deng@doktorand.tu-freiberg.de> tengfeideng <dengtengfei2016@hotmail.com>
 Thomas Fischer <thomas.fischer@ufz.de> <123_tom_dabei@web.de> <Thomas.Fischer@ufz.de>
-Thomas Fischer <thomas.fischer@ufz.de> Tom Fischer <Thomas.Fischer@ufz.de>
-Wenqing Wang <wenqing.wang@ufz.de>
-Yonghui Huang <huangyh56@gmail.com>
-Yonghui Huang <huangyh56@gmail.com> Yonghui56 <huangyh56@gmail.com>
-Yonghui Huang <huangyh56@gmail.com> Yonghui <huangyh56@gmial.com>
+Thomas Fischer <thomas.fischer@ufz.de> <Thomas.Fischer@ufz.de>
+Thomas Kalbacher <thomas.kalbacher@ufz.de> Thomas-TK <thomas.kalbacher@ufz.de>
+Thomas Nagel <thomas.nagel@ufz.de> <nagelt@tcd.ie>
+Thomas Nagel <thomas.nagel@ufz.de> nagelt <thomas.nagel@ufz.de>
+Thomas Nagel <thomas.nagel@ufz.de> tnagel <thomas.nagel@ufz.de>
+Thomas Nagel <thomas.nagel@ufz.de> <thomas.nagel@ifgt.tu-freiberg.de>
 Tianyuan Zheng <ichbinzty@gmail.com>
-Jasper Bathmann <jasper.bathmann@ufz.de>
-Renchao Lu <renchao.lu@gmail.com>
-Thomas Nagel <thomas.nagel@ufz.de>
-Marc Walther <marc.walther@ufz.de>
+Tobias Meisel <tobias.meisel@ufz.de> <tobias.meisel@web.de>
+Tobias Meisel <tobias.meisel@ufz.de>
+Tuanny Cajuhi <Tuanny.Cajuhi@bgr.de> tcajuhi <trmcajuhi@gmail.com>
+Vanessa Montoya <vanessa.montoya@ufz.de> montoyag <vanemonto@hotmail.com>
+Vanessa Montoya <vanessa.montoya@ufz.de> montoyav <vanessa.montoya@ufz.de>
+Wanlong Cai <cccwl828@gmail.com> Wanlong <cccwl828@gmail.com>
+Wanlong Cai <cccwl828@gmail.com> WanlongCai <wanlong.cai@ufz.de>
+Wenqing Wang <wenqing.wang@ufz.de>
 Xing-Yuan Miao <miaoxingyuan@live.cn> <xing-yuan.miao@ufz.de>
-Xing-Yuan Miao <miaoxingyuan@live.cn> xymiao
 Xing-Yuan Miao <miaoxingyuan@live.cn> xingyuanmiao <xingyuanmiao@users.noreply.github.com>
+Xing-Yuan Miao <miaoxingyuan@live.cn> xymiao
+Yonghui Huang <huangyh56@gmail.com>
+Yonghui Huang <huangyh56@gmail.com> Yonghui <huangyh56@gmial.com>
+Yonghui Huang <huangyh56@gmail.com> Yonghui56 <huangyh56@gmail.com>
+Zhang Ning <zhangning737@gmail.com> Rooney <43574869+zhangning737@users.noreply.github.com>
+Zhang Ning <zhangning737@gmail.com> zhangning737 <zhangning737@gmail.com>
+dependabot[bot] <no-email> dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
+dependabot[bot] <no-email> dependabot[bot] <dependabot[bot]@users.noreply.github.com>
+Robert Habel <Robert.Habel@student.tu-freiberg.de> Robert Habel <robert.habel@student.tu-freiberg.de>
+Linda Günther <linda.guenther@student.tu-freiberg.de> Linda Günther <Linda.Guenther@student.tu-freiberg.de>
+Sophia Einspänner <sophia.einspaenner@student.tu-freiberg.de> Sophia Einspänner <Sophia.Einspaenner@student.tu-freiberg.de>
+Jakob Randow <jakob.randow@web.de> jrandow <jakob.randow@htwk-leipzig.de>
+Jakob Randow <jakob.randow@web.de> jrandow <jakob.randow@web.de>
+Olaf Kolditz <olaf.kolditz@ufz.de>
+Falko Vehling <falko.vehling@ufz.de>
+Julian Heinze <julian.heinze@ufz.de>
+Tao You <hhutyou@126.com>
+Matthes Kantzenbach <m.kantzenbach@outlook.de>
+Feliks K. Kiszkurno <feliks-kuba.kiszkurno@ufz.de>
+Philipp Selzer <philipp.selzer@ufz.de>
+Philipp Selzer <philipp.selzer@ufz.de> <Philipp.Selzer@gmx.net>
+Joy Brato Shil <joybroto6@gmail.com>
+Frieder Loer <frieder.loer@ufz.de>
+Eike Radeisen <eike.radeisen@bgr.de>
+Maximilian Dörnbrack <maximilian.doernbrack@ufz.de> <maximlian.doernbrack@ufz.de>
+Kristof Kessler <kristof.kessler@bgr.de> <mail@kristofkessler.com>
\ No newline at end of file

web/content/.markdownlint.yaml → .markdownlint.yaml

@@ -3,3 +3,5 @@ default: true
 line-length: false
 no-inline-html: false
 no-duplicate-heading: false
+first-line-h1: false
+no-bare-urls: false

.markdownlintignore

+web/content/releases/
+web/content/docs/devguide/packages/mfront/index.md
+Documentation/.vale/

.pre-commit-config.yaml

 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.4.0
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md, --markdown-linebreak-ext=pandoc]
-        exclude: "^ThirdParty/.*|^Tests/Data/.*|^web/static/images/xsd"
+        # Tests/Python/res/test_docu_scripts/ contain improper white spaces on
+        # purpose: such whitespace errors should be tested, there.
+        exclude: "^Tests/Data/.*|^Tests/Python/res/test_docu_scripts/|^web/static|^Documentation/.vale/.*|.*\\.patch"
       - id: check-added-large-files
         args: [--maxkb 1024]
       - id: check-merge-conflict
       - id: check-xml
+        exclude: '^Tests/Data/.*\.xml'
       - id: check-yaml
         exclude: "^scripts/ci/.*|.cmake-format.yaml"
       - id: check-toml
-  - repo: local
-    hooks:
-      - id: git-diff-check
-        name: Run git diff --check
-        entry: git diff --check --cached -- ':!*.md' ':!*.pandoc' ':!*.asc' ':!*.dat' ':!*.ts'
-        language: system
-        exclude: "ThirdParty/*|Tests/Data/*|web/static/images/xsd"
-        stages: [commit, manual]
-      - id: file-extensions
-        name: Check file extensions
-        entry: scripts/hooks/pre-commit-file-extensions.sh
-        language: system
-        files: '.*\.cpp'
-        stages: [commit, manual]
-  - repo: https://github.com/ambv/black
-    rev: 20.8b1
+      - id: check-executables-have-shebangs
+      - id: check-shebang-scripts-are-executable
+      - id: check-json
+      - id: fix-byte-order-marker
+        exclude: "^Documentation/.vale/.*"
+      - id: mixed-line-ending
+        exclude: ".*\\.vtu|.*@@"
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
     hooks:
       - id: black
-        exclude: "ThirdParty|LinearMFront/generate_ref.py"
+        exclude: "LinearMFront/generate_ref.py"
+  # Run black on markdown notebooks
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
+    hooks:
+      - id: nbqa-black
+        additional_dependencies: [jupytext, black==23.1.0]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.0.0
+    rev: v2.2.2
     hooks:
       - id: codespell
-        exclude: 'ThirdParty/.*|Tests/Data/.*|.*\.ya?ml|.*\.bib|^web/content/imprint.md|^GeoLib/IO/XmlIO/OpenGeoSysSTN.xsd|^Applications/FileIO/Legacy/OGSIOVer4.cpp'
+        exclude: 'Tests/Data/.*|.*\.ya?ml|.*\.bib|^web/content/imprint.md|^GeoLib/IO/XmlIO/OpenGeoSysSTN.xsd|^Applications/FileIO/Legacy/OGSIOVer4.cpp|^scripts/cmake/CPM.cmake|Documentation/.vale/.*|.*\.ipynb|.*\.svg|^GeoLib/predicates.c'
   - repo: https://github.com/cheshirekow/cmake-format-precommit
     rev: v0.6.13
     hooks:
       - id: cmake-format
         additional_dependencies: ["cmakelang[YAML]"]
         args: [--config=.cmake-format.yaml]
-        exclude: "scripts/cmake/jedbrown/.*|PackagingMacros.cmake|conan.cmake|CPM.cmake|FindFilesystem.cmake|ConanSetup.cmake|Tests.cmake"
+        exclude: "CPM.cmake|FindFilesystem.cmake|FindMKL.cmake|JSONParser.cmake|Tests.cmake|FindTFEL.cmake|FindMFrontGenericInterface.cmake"
       - id: cmake-lint
         additional_dependencies: ["cmakelang[YAML]"]
-        exclude: "scripts/cmake/jedbrown/.*|PackagingMacros.cmake|conan.cmake|CPM.cmake|FindFilesystem.cmake|ConanSetup.cmake|BuildExternalProject.cmake"
+        exclude: "CPM.cmake|FindFilesystem.cmake|FindMKL.cmake|JSONParser.cmake|BuildExternalProject.cmake|FindTFEL.cmake|FindMFrontGenericInterface.cmake"
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.42.0
+    hooks:
+      - id: markdownlint
+        language_version: 22.11.0
   - repo: local
     hooks:
+      - id: git-diff-check
+        name: Run git diff --check
+        entry: git diff --check --cached -- ':!*.md' ':!*.pandoc' ':!*.asc' ':!*.dat' ':!*.ts'
+        language: system
+        exclude: "Tests/Data/.*|web/static/images/xsd"
+        stages: [pre-commit, manual]
+      - id: file-extensions
+        name: Check file extensions
+        entry: scripts/hooks/pre-commit-file-extensions.sh
+        language: system
+        files: '.*\.cpp'
+        stages: [pre-commit, manual]
       - id: git-clang-format
         name: git-clang-format
         entry: bash -c 'if command -v git-clang-format &> /dev/null; then git clang-format; else exit 0; fi'
         language: system
         pass_filenames: false
         files: \.(h|cpp)$
+  - repo: https://github.com/errata-ai/vale
+    rev: v2.24.4
+    hooks:
+      - id: vale
+        name: vale sync
+        pass_filenames: false
+        args: [sync]
+      - id: vale
+        args: [--output=line, --minAlertLevel=error]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.9.9"
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--output-format=full]
+  # A variant of the ruff hook above that automatically applies proposed fixes.
+  # Runs only manually.
+  # Run this hook (and all other manual hooks if any) with:
+  # pre-commit run --hook-stage manual
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.9.9"
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--output-format=full, --fix, --exit-non-zero-on-fix]
+        stages: [manual]
+  # Enable on demand, run with
+  #     pre-commit run --all-files clang-format
+  #
+  # - repo: https://github.com/pocc/pre-commit-hooks
+  #   rev: master
+  #   hooks:
+  #     - id: clang-format
+  #       args: ["-i"]

.vale.ini

+# Vale configuration file.
+#
+# For more information, see https://vale.sh/docs/topics/config
+StylesPath = Documentation/.vale
+Vocab = ogs
+MinAlertLevel = suggestion
+Packages = Hugo
+
+[*.md]
+BasedOnStyles = Vale, write-good, ogs
+Vale.Spelling = None
+write-good.ThereIs = None
+write-good.Passive = None
+write-good.TooWordy = None
+write-good.Weasel = None
+write-good.E-Prime = None
+
+TokenIgnores = \
+(\{\{[%<][^>]+[%>]\}\}), \
+(.*?\{\{[%<]?/.*[%>]\}\}), \
+; (\\ref\s\S+(\s"\S*")?), \
+; (\\subpage\s\S*), \
+; (\\copydoc\s\S*), \
+(\$[^\n$]+\$), \
+(\\\S*|\{\S*\}), \
+(\w*\set\sal), \
+({{<\s?(rel)?ref (.*)>}})
+
+# https://regex101.com/r/QWLhgT/1 helped me generating this one:
+BlockIgnores = (?s) *(\$\$.*?\$\$)

Applications/ApplicationsLib/CMakeLists.txt

@@ -7,38 +7,61 @@ ogs_add_library(ApplicationsLib ${LIB_SOURCES})
 
 target_link_libraries(
     ApplicationsLib
-    PUBLIC BaseLib GeoLib NumLib
+    PUBLIC
+        BaseLib
+        GeoLib
+        NumLib
+        $<$<AND:$<BOOL:${OGS_USE_PETSC}>,$<TARGET_EXISTS:VTK::ParallelMPI>>:VTK::ParallelMPI>
+        $<$<AND:$<NOT:$<BOOL:${OGS_BUILD_WHEEL}>>,$<BOOL:${OGS_BUILD_CLI}>>:ogs_embedded_python>
     PRIVATE CMakeInfoLib
             MathLib
             MeshLib
             MeshGeoToolsLib
-            $<$<BOOL:${OGS_USE_PYTHON}>:pybind11::pybind11>
-            $<$<BOOL:${OGS_USE_PETSC}>:petsc>
+            MeshToolsLib
+            $<$<BOOL:${OGS_USE_PETSC}>:PkgConfig::PETSC>
+            pybind11::module
 )
 
 if(OGS_BUILD_CLI OR OGS_BUILD_UTILS OR OGS_BUILD_TESTING)
     target_link_libraries(
-        ApplicationsLib
-        PUBLIC Processes
-        PRIVATE ParameterLib ProcessLib
+        ApplicationsLib PUBLIC Processes PRIVATE ParameterLib ProcessLib
     )
 elseif(OGS_BUILD_GUI)
-    target_link_libraries(ApplicationsLib PRIVATE nlohmann_json)
+    target_link_libraries(
+        ApplicationsLib PRIVATE MeshToolsLib nlohmann_json::nlohmann_json
+    )
 endif()
 
 if(OGS_USE_LIS)
     target_include_directories(ApplicationsLib PUBLIC ${LIS_INCLUDE_DIR})
 endif()
 
-target_compile_definitions(ApplicationsLib PUBLIC $<$<BOOL:${USE_LIS}>:USE_LIS>)
+target_compile_definitions(
+    ApplicationsLib PUBLIC $<$<BOOL:${USE_LIS}>:USE_LIS>
+    PRIVATE $<$<BOOL:${OGS_USE_INSITU}>:OGS_USE_INSITU>
+)
+
+# ~~~
+# Prevent warning:
+# warning: ‘ProjectData’ declared with greater visibility than the type of its field ‘ProjectData::_py_scoped_interpreter’
+# see https://pybind11.readthedocs.io/en/stable/faq.html#someclass-declared-with-greater-visibility-than-the-type-of-its-field-someclass-member-wattributes
+# ~~~
+if(NOT OGS_BUILD_WHEEL AND OGS_BUILD_CLI)
+    set_target_properties(
+        ApplicationsLib PROPERTIES CXX_VISIBILITY_PRESET hidden
+    )
+endif()
 
 # Set cpp definitions if the cmake option is enabled for the given process.
-foreach(process ${_processes_list})
-    if(OGS_BUILD_PROCESS_${process})
-        string(TOUPPER "OGS_BUILD_PROCESS_${process}" EnableProcess)
-        set_property(
-            TARGET ApplicationsLib APPEND PROPERTY COMPILE_DEFINITIONS
-                                                   ${EnableProcess}
-        )
-    endif()
+foreach(process ${_enabled_processes})
+    string(TOUPPER "OGS_BUILD_PROCESS_${process}" EnableProcess)
+    set_property(
+        TARGET ApplicationsLib APPEND PROPERTY COMPILE_DEFINITIONS
+                                               ${EnableProcess}
+    )
 endforeach()
+
+target_precompile_headers(
+    ApplicationsLib PRIVATE [["BaseLib/Error.h"]] [["BaseLib/ConfigTree.h"]]
+    [["BaseLib/Logging.h"]]
+)