.clang-format

+---
+Language:        Cpp
+BasedOnStyle:    Google
+
+AccessModifierOffset: -4
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Inline
+BreakBeforeBraces: Allman
+DerivePointerAlignment: false
+ExperimentalAutoDetectBinPacking: true
+IndentWidth:     4
+PointerAlignment: Left
+Standard:        Cpp11
+TabWidth:        4
+UseTab:          Never

.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
+
+WarningsAsErrors: ""
+HeaderFilterRegex: ".*"
+AnalyzeTemporaryDtors: false
+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"

.cmake-format.yaml

+format:
+  tab_size: 4
+  max_subgroups_hwrap: 3
+  dangle_parens: true
+  command_case: "unchanged"
+  line_width: 80
+lint:
+  disabled_codes:
+    - "C0301"
+    - "C0301" # Line to long.
+    - "C0113" # Missing COMMAND for optional dependencies.
+
+parse:
+  vartags:
+    - !!python/tuple
+      - set_property
+      - - cmdline
+  additional_commands:
+    ogs_add_library:
+      pargs:
+        nargs: 2+
+    addtest:
+      pargs:
+        nargs: "*"
+        flags:
+          - DISABLED
+      spelling: AddTest
+      kwargs:
+        EXECUTABLE: 1
+        PATH: 1
+        NAME: 1
+        WRAPPER: 1
+        TESTER: 1
+        ABSTOL: 1
+        RELTOL: 1
+        RUNTIME: 1
+        DEPENDS: 1
+        WORKING_DIRECTORY: 1
+        EXECUTABLE_ARGS: +
+        DATA: +
+        DIFF_DATA:
+          pargs:
+            tags:
+              - cmdline
+        WRAPPER_ARGS: +
+        REQUIREMENTS: +
+        PYTHON_PACKAGES: +
+
+    ogstest:
+      pargs:
+        nargs: "*"
+        flags:
+          - DISABLED
+      spelling: OgsTest
+      kwargs:
+        PROJECTFILE: 1
+        RUNTIME: 1
+        WRAPPER: +
+
+    cpmaddpackage:
+      pargs:
+        nargs: "*"
+        flags: []
+      spelling: CPMAddPackage
+      kwargs: &cpmaddpackagekwargs
+        NAME: 1
+        FORCE: 1
+        VERSION: 1
+        GIT_TAG: 1
+        DOWNLOAD_ONLY: 1
+        GITHUB_REPOSITORY: 1
+        GITLAB_REPOSITORY: 1
+        GIT_REPOSITORY: 1
+        SVN_REPOSITORY: 1
+        SVN_REVISION: 1
+        SOURCE_DIR: 1
+        DOWNLOAD_COMMAND: 1
+        FIND_PACKAGE_ARGUMENTS: 1
+        NO_CACHE: 1
+        GIT_SHALLOW: 1
+        URL: 1
+        URL_HASH: 1
+        URL_MD5: 1
+        DOWNLOAD_NAME: 1
+        DOWNLOAD_NO_EXTRACT: 1
+        HTTP_USERNAME: 1
+        HTTP_PASSWORD: 1
+        EXCLUDE_FROM_ALL: 1
+        OPTIONS: +
+        PATCH_COMMAND: +
+    cpmfindpackage:
+      pargs:
+        nargs: "*"
+        flags: []
+      spelling: CPMFindPackage
+      kwargs: *cpmaddpackagekwargs
+    cpmdeclarepackage:
+      pargs:
+        nargs: "*"
+        flags: []
+      spelling: CPMDeclarePackage
+      kwargs: *cpmaddpackagekwargs
+    packageproject:
+      pargs:
+        nargs: "*"
+        flags: []
+      spelling: packageProject
+      kwargs:
+        NAME: 1
+        VERSION: 1
+        INCLUDE_DIR: 1
+        INCLUDE_DESTINATION: 1
+        BINARY_DIR: 1
+        COMPATIBILITY: 1
+        VERSION_HEADER: 1
+        DEPENDENCIES: +
+    cpmusepackagelock:
+      pargs: 1
+      spelling: CPMUsePackageLock
+    cpmregisterpackage:
+      pargs: 1
+      spelling: CPMRegisterPackage
+    cpmgetpackageversion:
+      pargs: 2
+      spelling: CPMGetPackageVersion
+
+    buildexternalproject:
+      pargs:
+        nargs: "*"
+      spelling: BuildExternalProject
+      kwargs:
+        GIT_REPOSITORY: 1
+        GIT_TAG: 1
+        CONFIGURE_COMMAND: +
+        BUILD_COMMAND: +
+        INSTALL_COMMAND: +
+        BUILD_IN_SOURCE: 1
+        LOG_OUTPUT_ON_FAILURE: 1
+        CMAKE_ARGS: +

.codeclimate.yml

+version: "2"
+exclude_patterns:
+  - "Tests/"
+plugins:
+  duplication:
+    enabled: false

.codespellexclude

+* De Nevers N. Physical and chemical equilibrium for chemical engineers[M].
+        "\tthe command must be run with its full path.\n\n"
+        COO = 10,
+              var dateA = new Date(a.created_at);
+              var dateB = new Date(b.created_at);
+              return dateB - dateA;
+Malcom, M.A.M.(2018).Analysis of underground excavations in argillaceous hard
+    auto Ket = local_K.template block<temperature_size, temperature_size>(
+        Ket.noalias() +=
+        title: '{Entwicklung mathematisch-mechanischer Modelle zur Beschreibung des
+            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 = *.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
+    }
+  }
+}

.dockerignore

+# .git
+Tests/Data
+_out/images

.editorconfig

-root = true
-
 [*]
-indent_style = tab
-insert_final_newline = true
+indent_style = space
 charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
+indent_size = 4
 
-[*.md]
+[*.{md,pandoc}]
 trim_trailing_whitespace = false
-indent_style = spaces
-indent_size = 4
+
+[*.{json,yml,yaml,toml,html,css,js,scss,md}]
+indent_size = 2

.gitattributes

+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto
+
+# Gocad T Surface files should always be converted to native line endings.
+*.ts text
+
 # Enable style checks on source files
 *.h   hooks.style=uncrustify
 *.cpp hooks.style=uncrustify

.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

 *.bak*
-build*/
+/build*/
 *.sw[op]
 tags
 .ExternalData_*
+.DS_Store
 
 # CLion IDE project files
 *.iml
-.idea/workspace.xml
-.idea/tasks.xml
-.idea/dictionaries
-.idea/modules.xml
+.idea
+
+# Visual Studio Code project files
+.vscode
+
+*.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
+
+variables:
+  # Build config
+  BUILD_TYPE: Release
+  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 && $CI_PROJECT_PATH != "ogs/ogs"'
+      when: never
+    - if: "$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
+      variables:
+        PIPELINE_NAME: "master pipeline"
+
+include:
+  - 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/quickcheck"]
-	path = ThirdParty/quickcheck
-	url = git://github.com/ufz/quickcheck.git
-[submodule "ThirdParty/VtkFbxConverter"]
-	path = ThirdParty/VtkFbxConverter
-	url = git://github.com/ufz-vislab/VtkFbxConverter.git
-[submodule "ThirdParty/VtkOsgConverter"]
-	path = ThirdParty/VtkOsgConverter
-	url = git://github.com/ufz-vislab/VtkOsgConverter.git
-[submodule "ThirdParty/tetgen"]
-	path = ThirdParty/tetgen
-	url = https://github.com/ufz/tetgen.git
-[submodule "vtkdiff"]
-	path = ThirdParty/vtkdiff
-	url = https://github.com/ufz/vtkdiff.git
-[submodule "ThirdParty/tclap"]
-	path = ThirdParty/tclap
-	url = https://github.com/ufz/tclap.git

.hooks/pre-commit

+#!/usr/bin/env bash
+
+# Activate via the following setting in .git/config
+# [core]
+#    hooksPath = .hooks
+#
+# **Or** by copying this file to .git/hooks/pre-commit
+
+echo "Running pre-commit hook.."
+
+set -e
+
+RETURN_CODE=0
+
+### git-lfs check ###
+BINARY_FILES=""
+CHANGED_FILES=$(git diff --cached --name-only --diff-filter=ACM)
+LFS_FILES=$(echo $CHANGED_FILES | xargs git check-attr filter | grep 'filter: lfs$' | sed -e 's/: filter: lfs//')
+
+for FILE in $LFS_FILES; do
+    SOFT_SHA=$(git hash-object -w $FILE)
+    RAW_SHA=$(git hash-object -w --no-filters $FILE)
+
+    if [ $SOFT_SHA == $RAW_SHA ]; then
+        BINARY_FILES="$FILE\n$BINARY_FILES"
+    fi
+done
+
+if [[ -n "$BINARY_FILES" ]]; then
+    echo "Attention!"
+    echo "----------"
+    echo "You tried to commit files tracked by git-lfs as standard git objects:"
+    echo -e "\x1B[31m$BINARY_FILES\x1B[0m"
+    echo "Revert your changes and commit those files with git-lfs!"
+    echo "See https://docs.opengeosys.org/docs/devguide/getting-started/prerequisites"
+    echo "----------"
+    RETURN_CODE=1
+fi
+
+exit $RETURN_CODE

.idea/.name

-ogs
\ No newline at end of file

.idea/codeStyleSettings.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectCodeStyleSettingsManager">
-    <option name="PER_PROJECT_SETTINGS">
-      <value>
-        <option name="AUTODETECT_INDENTS" value="false" />
-        <option name="OTHER_INDENT_OPTIONS">
-          <value>
-            <option name="INDENT_SIZE" value="4" />
-            <option name="CONTINUATION_INDENT_SIZE" value="8" />
-            <option name="TAB_SIZE" value="4" />
-            <option name="USE_TAB_CHARACTER" value="true" />
-            <option name="SMART_TABS" value="false" />
-            <option name="LABEL_INDENT_SIZE" value="0" />
-            <option name="LABEL_INDENT_ABSOLUTE" value="false" />
-            <option name="USE_RELATIVE_INDENTS" value="false" />
-          </value>
-        </option>
-        <option name="RIGHT_MARGIN" value="100" />
-        <Objective-C>
-          <option name="INDENT_NAMESPACE_MEMBERS" value="0" />
-          <option name="NAMESPACE_BRACE_PLACEMENT" value="2" />
-          <option name="FUNCTION_BRACE_PLACEMENT" value="2" />
-        </Objective-C>
-        <Objective-C-extensions>
-          <option name="GENERATE_INSTANCE_VARIABLES_FOR_PROPERTIES" value="ASK" />
-          <option name="RELEASE_STYLE" value="IVAR" />
-          <option name="TYPE_QUALIFIERS_PLACEMENT" value="BEFORE" />
-          <file>
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="Import" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="Macro" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="Typedef" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="Struct" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="Enum" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="Constant" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="Global" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="FunctionPredecl" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="Function" />
-          </file>
-          <class>
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="Property" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="Synthesize" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="InitMethod" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="StaticMethod" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="InstanceMethod" />
-            <option name="com.jetbrains.cidr.lang.util.OCDeclarationKind" value="DeallocMethod" />
-          </class>
-        </Objective-C-extensions>
-        <XML>
-          <option name="XML_LEGACY_SETTINGS_IMPORTED" value="true" />
-        </XML>
-        <codeStyleSettings language="ObjectiveC">
-          <option name="CLASS_BRACE_STYLE" value="2" />
-          <indentOptions>
-            <option name="CONTINUATION_INDENT_SIZE" value="4" />
-            <option name="USE_TAB_CHARACTER" value="true" />
-          </indentOptions>
-        </codeStyleSettings>
-        <codeStyleSettings language="XML">
-          <indentOptions>
-            <option name="USE_TAB_CHARACTER" value="true" />
-          </indentOptions>
-        </codeStyleSettings>
-      </value>
-    </option>
-    <option name="USE_PER_PROJECT_SETTINGS" value="true" />
-  </component>
-</project>
\ No newline at end of file

.idea/misc.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="CMakeWorkspace" IGNORE_OUTSIDE_FILES="true" PROJECT_DIR="$PROJECT_DIR$" />
-  <component name="ProjectLevelVcsManager" settingsEditedManually="false">
-    <OptionsSetting value="true" id="Add" />
-    <OptionsSetting value="true" id="Remove" />
-    <OptionsSetting value="true" id="Checkout" />
-    <OptionsSetting value="true" id="Update" />
-    <OptionsSetting value="true" id="Status" />
-    <OptionsSetting value="true" id="Edit" />
-    <ConfirmationsSetting value="0" id="Add" />
-    <ConfirmationsSetting value="0" id="Remove" />
-  </component>
-  <component name="ProjectRootManager" version="2" />
-</project>
\ No newline at end of file