Compare revisions

02a16832 · 36e05335 · e4798935 · 026f922b · 0f761877 · 988b3450
--- a/.clang-tidy
+++ b/.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"
--- a/.cmake-format.yaml
+++ b/.cmake-format.yaml
@@ -57,28 +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: "*"
@@ -109,6 +87,7 @@ parse:
        HTTP_PASSWORD: 1
        EXCLUDE_FROM_ALL: 1
        OPTIONS: +
+        PATCH_COMMAND: +
    cpmfindpackage:
      pargs:
        nargs: "*"

--- a/.codeclimate.yml
+++ b/.codeclimate.yml
 version: "2"
 exclude_patterns:
-  - "ThirdParty/"
  - "Tests/"
 plugins:
  duplication:

--- a/.codespellexclude
+++ b/.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._
--- a/.codespellrc
+++ b/.codespellrc
 [codespell]
-skip = ./.git,./Tests/Data,./ThirdParty,*.yml,*.bib,./web/content/imprint.md,./GeoLib/IO/XmlIO/OpenGeoSysSTN.xsd
-ignore-words-list = ket,nd,strat,theis,ba,sur
+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 = *
--- a/.devcontainer.json
+++ b/.devcontainer.json
 {
-	"name": "ogs-gcc-dev",
-	"image": "registry.opengeosys.org/ogs/ogs/vscode:latest",
-	"postStartCommand": "nohup bash -c 'cd web; yarn; yarn build; hugo server &'",
-	"forwardPorts": [
-		1313
-	],
-	"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"
-	],
-	"customizations": {
-		"vscode": {
-			"extensions": [
-				"ms-vscode.cmake-tools",
-				"ms-vscode.cpptools"
-			]
-		}
-	},
-	"remoteUser": "vscode",
-	"features": {
-		"common": {}
-	}
+  "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
+    }
+  }
 }
--- a/.dockerignore
+++ b/.dockerignore
 # .git
 Tests/Data
 _out/images
-ThirdParty/container-maker
--- a/.github/workflows/msvc-code-analysis.yml
+++ b/.github/workflows/msvc-code-analysis.yml
@@ -15,7 +15,7 @@ jobs:
        uses: actions/checkout@v2

      - name: Configure CMake
-        run: cmake -B ${{ env.build }} -DCMAKE_BUILD_TYPE=${{ env.config }} -DOGS_BUILD_PROCESS_TH2M=OFF -DOGS_USE_PYTHON=OFF -DOGS_USE_UNITY_BUILDS=OFF -DOGS_BUILD_TESTING=OFF -DOGS_ENABLE_ELEMENT_PRISM=OFF -DOGS_ENABLE_ELEMENT_PYRAMID=OFF -DOGS_MAX_ELEMENT_DIM=2
+        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

--- a/.gitignore
+++ b/.gitignore
@@ -12,11 +12,6 @@ tags
 # Visual Studio Code project files
 .vscode

-# Conan package manager
-conanbuildinfo.cmake
-conaninfo.txt
-CMakeLists.txt.user*
-
 *.pyc
 .venv

@@ -26,6 +21,7 @@ Tests/Data/_out
 web/.netlify

 CMakeUserPresets.json
+scripts/cmake/vtk-*.patch

 .snakemake


--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
 stages:
  - preparation
  - build
+  - test
  - check
  - release
  - package
@@ -10,58 +11,73 @@ variables:
  BUILD_TYPE: Release
  BUILD_TESTS: "true"
  BUILD_CTEST: "true"
-  CTEST_INCLUDE_REGEX: "" # Regex is given via ctest -R [regex]
-  CTEST_EXCLUDE_REGEX: "" # Regex is given via ctest -E [regex]
+  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 && $CI_PROJECT_PATH != "ogs/ogs"'
      when: never
-    - if: "$CI_MERGE_REQUEST_LABELS =~ /.*(workflow::paused|ci skip).*/"
+    - if: "$CI_MERGE_REQUEST_LABELS =~ /.*(workflow::paused|ci::skip).*/"
      when: never
+    - if: $CI_MERGE_REQUEST_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 && $CI_PROJECT_PATH == "ogs/ogs"' # master, ogs/ogs repo only
-    - if: '$CI_COMMIT_BRANCH =~ /^v[0-9]\.[0-9]\.[0-9]/ && $CI_PROJECT_PATH == "ogs/ogs"' # release branches, e.g. v6.x.x
+      variables:
+        PIPELINE_NAME: "master pipeline"

 include:
  - local: "scripts/ci/extends/*.yml"
-  - local: "/scripts/ci/jobs/meta.yml"
-  - local: "/scripts/ci/jobs/ci_images.yml"
-  # jobs, can be indiviually disabled for testing
-  - local: "/scripts/ci/jobs/pre-commit.yml"
-  - 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"
-  - local: "/scripts/ci/jobs/build-container.yml"
-  - local: "/scripts/ci/jobs/jupyter.yml"
-  - 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/jobs/package.yml"
-  - local: "/scripts/ci/jobs/trigger.yml"
-
-# child pipelines
-wheels:
-  stage: build
-  needs: []
-  trigger:
-    include: /scripts/ci/jobs/build-wheels.yml
-  rules:
-    - if: $CI_COMMIT_TAG
-    - when: manual
-      allow_failure: true
+  - 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.*/
--- a/.gitlab/CODEOWNERS
+++ b/.gitlab/CODEOWNERS
+^[CMake]
+*.cmake @bilke
+CMakeLists.txt @bilke
+
+[Documentation] @ogs/docs-team
+Documentation
+web/content
--- a/.gitmodules
+++ b/.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
--- a/.mailmap
+++ b/.mailmap
@@ -2,11 +2,14 @@ Alireza Hassanzadegan <a.hassanzadegan@gmail.com> AlirezaBGE <a.hassanzadegan@gm
 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>
+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>
@@ -27,21 +30,25 @@ 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> KeitaYoshioka <32516139+KeitaYoshioka@users.noreply.github.com>
+Keita Yoshioka <keita.yoshioka@ufz.de>
+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> <Norbert.Grunwald@ufz.de>
-Norihiro Watanabe <norihiro.watanabe@aist.go.jp> <norihiro.w@gmail.com> <norihiro.watanabe@ufz.de>
+Norbert Grunwald <norbert.grunwald@ufz.de> <n.g.boettcher@gmail.com>
+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> <lur@modmon128.intranet.ufz.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>
@@ -49,13 +56,15 @@ 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>
+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>
 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>
@@ -78,3 +87,15 @@ Sophia Einspänner <sophia.einspaenner@student.tu-freiberg.de> Sophia Einspänne
 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
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
 repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.4.0
    hooks:
      - id: trailing-whitespace
        args: [--markdown-linebreak-ext=md, --markdown-linebreak-ext=pandoc]
-        exclude: "^ThirdParty/.*|^Tests/Data/.*|^web/static|^Documentation/.vale/.*"
+        # 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
@@ -18,53 +21,89 @@ repos:
      - id: fix-byte-order-marker
        exclude: "^Documentation/.vale/.*"
      - id: mixed-line-ending
-        exclude: ".*\\.vtu"
+        exclude: ".*\\.vtu|.*@@"
  - repo: https://github.com/psf/black
-    rev: 22.3.0
+    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: v2.1.0
+    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|^scripts/cmake/CPM.cmake|Documentation/.vale/.*'
+        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: v0.31.1
+    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: "ThirdParty/*|Tests/Data/*|web/static/images/xsd"
-        stages: [commit, manual]
+        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: [commit, manual]
+        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: Check spelling with vale
-        entry: bash -c 'if command -v vale &> /dev/null; then vale sync; VALE_MIN_ALERT_LEVEL=error scripts/ci/helper/run-vale; else exit 0; fi'
+        name: vale sync
        pass_filenames: false
-        language: system
+        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"]
--- a/.vale.ini
+++ b/.vale.ini
@@ -9,7 +9,7 @@ Packages = Hugo
 [*.md]
 BasedOnStyles = Vale, write-good, ogs
 Vale.Spelling = None
-write-good.ThereIs = suggestion
+write-good.ThereIs = None
 write-good.Passive = None
 write-good.TooWordy = None
 write-good.Weasel = None
@@ -21,7 +21,10 @@ TokenIgnores = \
 ; (\\ref\s\S+(\s"\S*")?), \
 ; (\\subpage\s\S*), \
 ; (\\copydoc\s\S*), \
-(\$+[^\n$]+\$+), \
 (\$[^\n$]+\$), \
 (\\\S*|\{\S*\}), \
-(\w*\set\sal)
+(\w*\set\sal), \
+({{<\s?(rel)?ref (.*)>}})
+
+# https://regex101.com/r/QWLhgT/1 helped me generating this one:
+BlockIgnores = (?s) *(\$\$.*?\$\$)
--- a/Applications/ApplicationsLib/CMakeLists.txt
+++ b/Applications/ApplicationsLib/CMakeLists.txt
@@ -7,11 +7,19 @@ ogs_add_library(ApplicationsLib ${LIB_SOURCES})

 target_link_libraries(
    ApplicationsLib
-    PUBLIC BaseLib GeoLib NumLib
-           $<$<TARGET_EXISTS:VTK::ParallelMPI>:VTK::ParallelMPI>
-    PRIVATE CMakeInfoLib MathLib MeshLib MeshGeoToolsLib
-            $<$<BOOL:${OGS_USE_PYTHON}>:pybind11::pybind11>
-            $<$<BOOL:${OGS_USE_PETSC}>:petsc>
+    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
+            MeshToolsLib
+            $<$<BOOL:${OGS_USE_PETSC}>:PkgConfig::PETSC>
+            pybind11::module
 )

 if(OGS_BUILD_CLI OR OGS_BUILD_UTILS OR OGS_BUILD_TESTING)
@@ -19,7 +27,9 @@ if(OGS_BUILD_CLI OR OGS_BUILD_UTILS OR OGS_BUILD_TESTING)
        ApplicationsLib PUBLIC Processes PRIVATE ParameterLib ProcessLib
    )
 elseif(OGS_BUILD_GUI)
-    target_link_libraries(ApplicationsLib PRIVATE nlohmann_json::nlohmann_json)
+    target_link_libraries(
+        ApplicationsLib PRIVATE MeshToolsLib nlohmann_json::nlohmann_json
+    )
 endif()

 if(OGS_USE_LIS)
@@ -28,10 +38,20 @@ endif()

 target_compile_definitions(
    ApplicationsLib PUBLIC $<$<BOOL:${USE_LIS}>:USE_LIS>
-                           $<$<BOOL:${OGS_USE_PYTHON}>:OGS_USE_PYTHON>
    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 ${_enabled_processes})
    string(TOUPPER "OGS_BUILD_PROCESS_${process}" EnableProcess)
@@ -41,5 +61,7 @@ foreach(process ${_enabled_processes})
    )
 endforeach()

-target_precompile_headers(ApplicationsLib PRIVATE [["BaseLib/Error.h"]]
-    [["BaseLib/ConfigTree.h"]] [["BaseLib/Logging.h"]])
+target_precompile_headers(
+    ApplicationsLib PRIVATE [["BaseLib/Error.h"]] [["BaseLib/ConfigTree.h"]]
+    [["BaseLib/Logging.h"]]
+)
--- a/Applications/ApplicationsLib/LinearSolverLibrarySetup.h
+++ b/Applications/ApplicationsLib/LinearSolverLibrarySetup.h
 /**
+ * \file
 * \copyright
- * Copyright (c) 2012-2023, OpenGeoSys Community (http://www.opengeosys.org)
+ * Copyright (c) 2012-2025, OpenGeoSys Community (http://www.opengeosys.org)
 *            Distributed under a Modified BSD License.
 *              See accompanying file LICENSE.txt or
 *              http://www.opengeosys.org/project/license
@@ -18,6 +19,7 @@
 /// The default implementation is empty providing polymorphic behaviour when
 /// using this class.

+#include "BaseLib/MPI.h"
 #include "NumLib/DOF/GlobalMatrixProviders.h"

 #if defined(USE_PETSC)
@@ -27,9 +29,8 @@ namespace ApplicationsLib
 {
 struct LinearSolverLibrarySetup final
 {
-    LinearSolverLibrarySetup(int argc, char* argv[])
+    LinearSolverLibrarySetup(int argc, char* argv[]) : mpi_setup(argc, argv)
    {
-        MPI_Init(&argc, &argv);
        char help[] = "ogs6 with PETSc \n";
        PetscInitialize(&argc, &argv, nullptr, help);
        MPI_Comm_set_errhandler(PETSC_COMM_WORLD, MPI_ERRORS_RETURN);
@@ -39,8 +40,9 @@ struct LinearSolverLibrarySetup final
    {
        NumLib::cleanupGlobalMatrixProviders();
        PetscFinalize();
-        MPI_Finalize();
    }
+
+    BaseLib::MPI::Setup mpi_setup;
 };
 }    // ApplicationsLib
 #elif defined(USE_LIS)
@@ -66,7 +68,22 @@ namespace ApplicationsLib
 {
 struct LinearSolverLibrarySetup final
 {
-    LinearSolverLibrarySetup(int /*argc*/, char* /*argv*/[]) {}
+    LinearSolverLibrarySetup(int /*argc*/, char* /*argv*/[])
+    {
+#ifdef _OPENMP
+        const char* omp_num_threads_env = std::getenv("OMP_NUM_THREADS");
+        if (omp_num_threads_env)
+        {
+            INFO("OMP_NUM_THREADS is set to: {:s}", omp_num_threads_env);
+        }
+        else
+        {
+            WARN("OMP_NUM_THREADS is not set, falling back to: {:d}",
+                 omp_get_max_threads());
+        }
+#endif
+        INFO("Eigen use {:d} threads", Eigen::nbThreads());
+    }
    ~LinearSolverLibrarySetup()
    {
        NumLib::cleanupGlobalMatrixProviders();

--- a/Applications/ApplicationsLib/ProjectData.cpp
+++ b/Applications/ApplicationsLib/ProjectData.cpp
--- a/Applications/ApplicationsLib/ProjectData.h
+++ b/Applications/ApplicationsLib/ProjectData.h
 /**
+ * \file
 * \author Karsten Rink
 * \date   2010-08-25
 *
 * \copyright
- * Copyright (c) 2012-2023, OpenGeoSys Community (http://www.opengeosys.org)
+ * Copyright (c) 2012-2025, OpenGeoSys Community (http://www.opengeosys.org)
 *            Distributed under a Modified BSD License.
 *              See accompanying file LICENSE.txt or
 *              http://www.opengeosys.org/project/license
@@ -18,6 +19,7 @@
 #include <string>

 #include "BaseLib/ConfigTree-fwd.h"
+#include "BaseLib/ExportSymbol.h"
 #include "ChemistryLib/ChemicalSolverInterface.h"
 #include "MaterialLib/MPL/Medium.h"
 #include "MathLib/InterpolationAlgorithms/PiecewiseLinearInterpolation.h"
@@ -26,6 +28,15 @@
 #include "ProcessLib/Process.h"
 #include "ProcessLib/ProcessVariable.h"

+#ifdef OGS_EMBED_PYTHON_INTERPRETER
+#include <pybind11/embed.h>
+#endif
+
+namespace GeoLib
+{
+struct NamedRaster;
+}
+
 namespace MeshLib
 {
 class Mesh;
@@ -83,6 +94,14 @@ public:

    ProcessLib::TimeLoop& getTimeLoop() { return *_time_loop; }

+    MeshLib::Mesh& getMesh(std::string const& mesh_name) const;
+
+    std::map<int, std::shared_ptr<MaterialPropertyLib::Medium>> const&
+    getMedia() const
+    {
+        return _media;
+    }
+
 private:
    /// Parses the process variables configuration and creates new variables for
    /// each variable entry passing the corresponding subtree to the process
@@ -124,6 +143,7 @@ private:
        const std::string& output_directory);

    std::vector<std::unique_ptr<MeshLib::Mesh>> _mesh_vec;
+    std::vector<GeoLib::NamedRaster> _named_rasters;
    std::vector<std::unique_ptr<ProcessLib::Process>> _processes;
    std::vector<ProcessLib::ProcessVariable> _process_variables;

@@ -144,9 +164,8 @@ private:
    std::map<std::string,
             std::unique_ptr<MathLib::PiecewiseLinearInterpolation>>
        _curves;
-};

-/// Parses a comma separated list of integers.
-/// Such lists occur in the medium definition in the OGS prj file.
-/// Error messages in this function refer to this specific purpose.
-std::vector<int> splitMaterialIdString(std::string const& material_id_string);
+#ifdef OGS_EMBED_PYTHON_INTERPRETER
+    std::optional<pybind11::scoped_interpreter> _py_scoped_interpreter;
+#endif
+};
--- a/Applications/ApplicationsLib/Simulation.cpp
+++ b/Applications/ApplicationsLib/Simulation.cpp
 /**
- * \brief  Implementation of class Simulation
 * \file
+ * \brief  Implementation of class Simulation
 *
 * \copyright
- * Copyright (c) 2012-2023, OpenGeoSys Community (http://www.opengeosys.org)
+ * Copyright (c) 2012-2025, OpenGeoSys Community (http://www.opengeosys.org)
 *            Distributed under a Modified BSD License.
 *              See accompanying file LICENSE.txt or
 *              http://www.opengeosys.org/project/license
@@ -21,6 +21,7 @@
 #include "BaseLib/ConfigTreeUtil.h"
 #include "BaseLib/FileTools.h"
 #include "BaseLib/PrjProcessing.h"
+#include "MeshLib/Mesh.h"
 #include "NumLib/NumericsConfig.h"
 #include "ProcessLib/TimeLoop.h"

@@ -100,7 +101,7 @@ void Simulation::initializeDataStructures(
    INFO("Initialize processes.");
    for (auto& p : project_data->getProcesses())
    {
-        p->initialize();
+        p->initialize(project_data->getMedia());
    }

    // Check intermediately that config parsing went fine.
@@ -114,13 +115,13 @@ void Simulation::initializeDataStructures(
 double Simulation::currentTime() const
 {
    auto const& time_loop = project_data->getTimeLoop();
-    return time_loop.currentTime();
+    return time_loop.currentTime()();
 }

 double Simulation::endTime() const
 {
    auto const& time_loop = project_data->getTimeLoop();
-    return time_loop.endTime();
+    return time_loop.endTime()();
 }

 bool Simulation::executeTimeStep()
@@ -128,11 +129,21 @@ bool Simulation::executeTimeStep()
    auto& time_loop = project_data->getTimeLoop();
    if (time_loop.currentTime() < time_loop.endTime())
    {
-        return time_loop.executeTimeStep();
+        auto const result = time_loop.executeTimeStep();
+        if (time_loop.calculateNextTimeStep())
+        {
+            time_loop.outputLastTimeStep();
+        }
+        return result;
    }
    return false;
 }

+MeshLib::Mesh& Simulation::getMesh(std::string const& name)
+{
+    return project_data->getMesh(name);
+}
+
 bool Simulation::executeSimulation()
 {
    INFO("Solve processes.");
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