.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

@@ -87,6 +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:

.codespellrc

 [codespell]
-skip = *.bib,*.css,*.pdf,*.yaml,*.yml,*/.vale,./.git,./GeoLib/IO/XmlIO/OpenGeoSysSTN.xsd,./Tests/Data,./ThirdParty,./web/content/imprint.md,./web/node_modules,./web/public/imprint/index.html,./web/resources,
-ignore-words-list = ba,bu,ket,nd,pris,strat,sur,theis,
+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": "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
+    }
+  }
 }

.dockerignore

 # .git
 Tests/Data
 _out/images
-ThirdParty/container-maker

.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_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

.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
 

.gitlab-ci.yml

@@ -16,6 +16,8 @@ variables:
   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"
@@ -39,6 +41,9 @@ workflow:
     - 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 $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME"
@@ -46,9 +51,6 @@ workflow:
     - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_PATH == "ogs/ogs"' # master, ogs/ogs repo only
       variables:
         PIPELINE_NAME: "master pipeline"
-    - if: '$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: "bugfix branch $CI_COMMIT_BRANCH pipeline"
 
 include:
   - local: "scripts/ci/extends/*.yml"
@@ -73,6 +75,9 @@ include:
   - 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.*/

.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
-[submodule "ThirdParty/bilke/cmake-modules"]
-	path = ThirdParty/bilke/cmake-modules
-	url = https://github.com/bilke/cmake-modules.git
-[submodule "ThirdParty/collection"]
-	path = ThirdParty/collection
-	url = https://gitlab.opengeosys.org/ogs/libs/collection.git

.guix-channel

-;; This file lets us present this repo as a Guix channel.
-
-(channel
-  (version 0)
-  (directory ".guix/modules"))  ;look for package modules under .guix/modules/
\ No newline at end of file

.guix/modules/ogs-package.scm

-;; This file defines a Guix package.  It can be used to spawn an
-;; interactive development environment:
-;;
-;;   guix shell
-;;
-;; Or it can be used to build Guile from a checkout in an isolated
-;; environment:
-;;
-;;   guix build -f guix.scm
-;;
-;; Likewise, you may cross-compile it:
-;;
-;;   guix build -f guix.scm --target=x86_64-w64-mingw32
-;;
-;; Or may want to build a variant:
-;;   guix build -L $PWD/.guix/modules ogs-petsc-ssd
-
-(define-module (ogs-package)
-  #:use-module (guix)
-  #:use-module (guix packages)
-  #:use-module (guix build-system cmake)
-  #:use-module (guix download)
-  #:use-module (guix git-download)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (gnu packages algebra)
-  #:use-module (gnu packages boost)
-  #:use-module (gnu packages check)
-  #:use-module (gnu packages certs) ; TODO: cpm
-  #:use-module (gnu packages cmake)
-  #:use-module (gnu packages compression)
-  #:use-module (gnu packages cpp)
-  #:use-module (gnu packages image-processing)
-  #:use-module (gnu packages logging)
-  #:use-module (gnu packages maths)
-  #:use-module (gnu packages mpi)
-  #:use-module (gnu packages ninja)
-  #:use-module (gnu packages pretty-print)
-  #:use-module (gnu packages python-xyz)
-  #:use-module (gnu packages python)
-  #:use-module (gnu packages version-control)
-  #:use-module (gnu packages xml)
-  )
-
-(define vcs-file?
-  ;; Return true if the given file is under version control.
-  (or (git-predicate "../..") ; (current-source-directory)
-      (const #t)))            ;not in a Git checkout
-
-(define-public ogs
-  (package
-    (name "ogs")
-    (version "6.4.99-git")
-    (source (local-file "../.." "ogs-checkout"
-                      #:recursive? #t
-                      #:select? vcs-file?
-                      ))
-    (build-system cmake-build-system)
-    (arguments
-     `(#:build-type "Release"
-       #:configure-flags (list
-        ; passing variables works like this
-        ;                  ,(string-append "-DOGS_VERSION=" version)
-        ; TODO: but it is not overwritten in sub-packages...
-                          "-DGUIX_BUILD=ON"
-                          "-DOGS_BUILD_TESTING=OFF"
-                          "-DOGS_USE_EIGEN_UNSUPPORTED=OFF" ; Eigen 3.4.0
-                          "-DOGS_INSTALL_DEPENDENCIES=OFF"  ; handled by guix
-                          "-DOGS_CPU_ARCHITECTURE=OFF"      ; enable guix --tune
-                          )
-       #:cmake ,cmake)) ;for newer CMake version
-    (inputs (list boost
-                  eigen
-                  googletest
-                  hdf5
-                  json-modern-cxx
-                  libxml2
-                  pybind11-2.10.4
-                  python
-                  range-v3
-                  spdlog
-                  zlib
-                  vtk))
-    (native-inputs (list git ninja googletest nss-certs)) ; TODO: cpm
-    (synopsis "OpenGeoSys")
-    (description
-     "Simulation of thermo-hydro-mechanical-chemical (THMC) processes in porous and fractured media")
-    (home-page "https://www.opengeosys.org")
-    (properties '((tunable? . #t)))
-    (license license:bsd-3)))
-
-(define-public ogs-ssd
-  (package
-    (inherit ogs)
-    (name "ogs-ssd")
-    (arguments
-     (substitute-keyword-arguments (package-arguments ogs)
-       ((#:configure-flags flags)
-        `(cons* "-DOGS_BUILD_PROCESSES=SteadyStateDiffusion"
-                ,flags))))
-    (synopsis "OGS with SteadyStateDiffusion only (for faster build testing)")))
-
-(define-public ogs-petsc
-  (package
-    (inherit ogs)
-    (name "ogs-petsc")
-    (inputs (modify-inputs (package-inputs ogs)
-              (prepend openmpi petsc-openmpi)
-              (replace "vtk" vtk-openmpi)
-              (replace "hdf5" hdf5-parallel-openmpi)))
-    (arguments
-     (substitute-keyword-arguments (package-arguments ogs)
-       ((#:configure-flags flags)
-        `(cons* "-DOGS_USE_PETSC=ON"
-                "-DCMAKE_C_COMPILER=mpicc"
-                "-DCMAKE_CXX_COMPILER=mpic++"
-                ,flags))))
-    (synopsis "OGS with PETSc")))
-
-(define-public ogs-petsc-ssd
-  (package
-    (inherit ogs-petsc)
-    (name "ogs-petsc-ssd")
-    (arguments
-     (substitute-keyword-arguments (package-arguments ogs-petsc)
-       ((#:configure-flags flags)
-        `(cons* "-DOGS_BUILD_PROCESSES=SteadyStateDiffusion"
-                ,flags))))
-    (synopsis "OGS with PETSc and SteadyStateDiffusion only (for faster build testing)")))
-
-; #### Releases ####
-(define-public ogs-6.4.4
-  (package
-    (inherit ogs)
-    (name "ogs")
-    (version "6.4.4")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://gitlab.opengeosys.org/ogs/ogs.git")
-                    (commit "d4ca7e627f2fc012bfe434649b797e78e5c2a8f1")
-                    (recursive? #t)))
-              (file-name (git-file-name name version))
-              (sha256
-               ;; Update with `guix hash -rx .`, make sure to have submodules updated!
-               (base32
-                "1f6mcbjx76irf1g0xkh6hgpv4qn2swbiyvlazvlrhjfyxb9bckq9"))))
-    (synopsis "OGS 6.4.4 release")))
-
-(define-public ogs-petsc-6.4.4
-  (package
-    (inherit ogs-petsc)
-    (name "ogs-petsc")
-    (version "6.4.4")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://gitlab.opengeosys.org/ogs/ogs.git")
-                    (commit "d4ca7e627f2fc012bfe434649b797e78e5c2a8f1")
-                    (recursive? #t)))
-              (file-name (git-file-name name version))
-              (sha256
-               ;; Update with `guix hash -rx .`, make sure to have submodules updated!
-               (base32
-                "1f6mcbjx76irf1g0xkh6hgpv4qn2swbiyvlazvlrhjfyxb9bckq9"))))
-    (synopsis "OGS 6.4.4 with PETSc release")))
-
-; #### Dependencies ####
-(define-public vtk-openmpi
-  (package
-    (inherit vtk)
-    (name "vtk-openmpi")
-    (inputs (modify-inputs (package-inputs vtk)
-              (prepend hdf5-parallel-openmpi openmpi)))
-    (arguments
-     (substitute-keyword-arguments (package-arguments vtk)
-       ((#:configure-flags flags)
-        #~(append '("-DVTK_MODULE_ENABLE_VTK_IOParallelXML=YES"
-                "-DVTK_MODULE_ENABLE_VTK_ParallelMPI=YES" "-DVTK_USE_MPI=ON")
-                #$flags))))
-    (synopsis "VTK with OpenMPI support")))
-
-(define pybind11-2.10.4
-      (package
-        (inherit pybind11)
-        (version "2.10.4")
-        (source (origin
-                  (method git-fetch)
-                  (uri (git-reference
-                    (url "https://github.com/pybind/pybind11")
-                    (commit (string-append "v" version))))
-                  (sha256
-                   (base32
-                    "0rbcfvl7y472sykzdq3vrkw83kar0lpzhk3wq9yj9cdydl8cpfcz"))))))
-;; return package
-ogs
-
-;; TODO: add this to web page
-;  ## Using the ogs repo as a Guix channel (as a user of ogs)
-;
-;  Add the following to `~/.config/guix/channels.scm`:
-;
-;  ```scheme
-;  (append (list (channel
-;                  (name 'ogs)
-;                  (url "https://gitlab.opengeosys.org/ogs/ogs.git")
-;                  (branch "master"))) %default-channels)
-;  ```
-;
-;  Run `guix pull`.
-;
-;  Then you can install the ogs package:
-;
-;  ```bash
-;  guix install ogs@6.4.4
-;  # OR, e.g.
-;  guix install ogs-petsc@6.4.4
-;  ```

.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>
@@ -49,7 +56,7 @@ 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>
+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>
@@ -85,3 +92,10 @@ 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

.pre-commit-config.yaml

@@ -4,7 +4,9 @@ repos:
     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
@@ -19,70 +21,84 @@ repos:
       - id: fix-byte-order-marker
         exclude: "^Documentation/.vale/.*"
       - id: mixed-line-ending
-        exclude: ".*\\.vtu"
+        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/mwouts/jupytext
-    rev: v1.14.5
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
     hooks:
-      - id: jupytext
-        args: [--pipe, black]
-        additional_dependencies:
-          - black==23.1.0 # Matches black hook
-        exclude: "web/.*"
+      - id: nbqa-black
+        additional_dependencies: [jupytext, black==23.1.0]
   - repo: https://github.com/codespell-project/codespell
     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: v0.33.0
+    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
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.262"
+        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
-        files: "Applications/Python/.*"
+        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
   #

Applications/ApplicationsLib/CMakeLists.txt

@@ -7,10 +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 MeshToolsLib 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)
@@ -18,7 +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 MeshToolsLib nlohmann_json::nlohmann_json)
+    target_link_libraries(
+        ApplicationsLib PRIVATE MeshToolsLib nlohmann_json::nlohmann_json
+    )
 endif()
 
 if(OGS_USE_LIS)
@@ -36,7 +47,6 @@ target_compile_definitions(
 # 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)
-    target_link_libraries(ApplicationsLib PRIVATE ogs_embedded_python)
     set_target_properties(
         ApplicationsLib PROPERTIES CXX_VISIBILITY_PRESET hidden
     )

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
@@ -19,6 +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)
@@ -28,9 +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);
@@ -40,8 +40,9 @@ struct LinearSolverLibrarySetup final
     {
         NumLib::cleanupGlobalMatrixProviders();
         PetscFinalize();
-        MPI_Finalize();
     }
+
+    BaseLib::MPI::Setup mpi_setup;
 };
 }    // ApplicationsLib
 #elif defined(USE_LIS)
@@ -67,7 +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();

Applications/ApplicationsLib/ProjectData.h

@@ -4,7 +4,7 @@
  * \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
@@ -32,6 +32,11 @@
 #include <pybind11/embed.h>
 #endif
 
+namespace GeoLib
+{
+struct NamedRaster;
+}
+
 namespace MeshLib
 {
 class Mesh;
@@ -89,7 +94,7 @@ public:
 
     ProcessLib::TimeLoop& getTimeLoop() { return *_time_loop; }
 
-    MeshLib::Mesh* getMesh(std::string const& mesh_name) const;
+    MeshLib::Mesh& getMesh(std::string const& mesh_name) const;
 
     std::map<int, std::shared_ptr<MaterialPropertyLib::Medium>> const&
     getMedia() const
@@ -138,6 +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;
 

Applications/ApplicationsLib/Simulation.cpp

@@ -3,7 +3,7 @@
  * \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
@@ -115,13 +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()
@@ -139,7 +139,7 @@ bool Simulation::executeTimeStep()
     return false;
 }
 
-MeshLib::Mesh* Simulation::getMesh(std::string const& name)
+MeshLib::Mesh& Simulation::getMesh(std::string const& name)
 {
     return project_data->getMesh(name);
 }

Applications/ApplicationsLib/Simulation.h

@@ -3,7 +3,7 @@
  * \brief  Declaration 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
@@ -38,12 +38,12 @@ public:
         bool nonfatal, std::string const& outdir, std::string const& mesh_dir,
         std::string const& script_dir, bool write_prj);
 
-    double currentTime() const;
-    double endTime() const;
+    OGS_EXPORT_SYMBOL double currentTime() const;
+    OGS_EXPORT_SYMBOL double endTime() const;
     OGS_EXPORT_SYMBOL bool executeTimeStep();
     OGS_EXPORT_SYMBOL bool executeSimulation();
     OGS_EXPORT_SYMBOL void outputLastTimeStep() const;
-    OGS_EXPORT_SYMBOL MeshLib::Mesh* getMesh(std::string const& name);
+    OGS_EXPORT_SYMBOL MeshLib::Mesh& getMesh(std::string const& name);
 
     OGS_EXPORT_SYMBOL std::optional<ApplicationsLib::TestDefinition>
     getTestDefinition() const;