Update AMICI to v0.20.0

git subrepo clone (merge) --branch=v0.20.0 --force git@github.com:AMICI-dev/AMICI.git deps/AMICI subrepo: subdir: "deps/AMICI" merged: "ffcbf665" upstream: origin: "git@github.com:AMICI-dev/AMICI.git" branch: "v0.20.0" commit: "ffcbf665" git-subrepo: version: "0.4.6" origin: "https://github.com/ingydotnet/git-subrepo" commit: "110b9eb"
ICB-DCM · Dec 5, 2023 · 9d36c99 · 9d36c99
1 parent 540e2f4
commit 9d36c99
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diff --git a/deps/AMICI/.clang-format b/deps/AMICI/.clang-format
@@ -1,96 +1,13 @@
 ---
+BasedOnStyle: LLVM
+IndentWidth: 4
+---
 Language:        Cpp
-# BasedOnStyle:  LLVM
-AccessModifierOffset: -2
-AlignAfterOpenBracket: Align
-AlignConsecutiveAssignments: false
-AlignConsecutiveDeclarations: false
-AlignEscapedNewlinesLeft: false
-AlignOperands:   true
-AlignTrailingComments: true
-AllowAllParametersOfDeclarationOnNextLine: true
-AllowShortBlocksOnASingleLine: false
-AllowShortCaseLabelsOnASingleLine: false
-AllowShortFunctionsOnASingleLine: All
-AllowShortIfStatementsOnASingleLine: false
-AllowShortLoopsOnASingleLine: false
-AlwaysBreakAfterDefinitionReturnType: None
-AlwaysBreakAfterReturnType: None
-AlwaysBreakBeforeMultilineStrings: false
-AlwaysBreakTemplateDeclarations: false
-BinPackArguments: true
-BinPackParameters: true
-BraceWrapping:   
-  AfterClass:      false
-  AfterControlStatement: false
-  AfterEnum:       false
-  AfterFunction:   false
-  AfterNamespace:  false
-  AfterObjCDeclaration: false
-  AfterStruct:     false
-  AfterUnion:      false
-  BeforeCatch:     false
-  BeforeElse:      false
-  IndentBraces:    false
-BreakBeforeBinaryOperators: None
-BreakBeforeBraces: Attach
-BreakBeforeTernaryOperators: true
-BreakConstructorInitializersBeforeComma: false
-BreakAfterJavaFieldAnnotations: false
-BreakStringLiterals: true
-ColumnLimit:     80
-CommentPragmas:  '^ IWYU pragma:'
-ConstructorInitializerAllOnOneLineOrOnePerLine: false
-ConstructorInitializerIndentWidth: 4
-ContinuationIndentWidth: 4
-Cpp11BracedListStyle: true
-DerivePointerAlignment: false
-DisableFormat:   false
-ExperimentalAutoDetectBinPacking: false
-ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
-IncludeCategories: 
-  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
-    Priority:        2
-  - Regex:           '^(<|"(gtest|isl|json)/)'
-    Priority:        3
-  - Regex:           '.*'
-    Priority:        1
-IncludeIsMainRegex: '$'
-IndentCaseLabels: false
-IndentWidth:     4
-IndentWrappedFunctionNames: false
-JavaScriptQuotes: Leave
-JavaScriptWrapImports: true
-KeepEmptyLinesAtTheStartOfBlocks: true
-MacroBlockBegin: ''
-MacroBlockEnd:   ''
-MaxEmptyLinesToKeep: 1
-NamespaceIndentation: None
-ObjCBlockIndentWidth: 2
-ObjCSpaceAfterProperty: false
-ObjCSpaceBeforeProtocolList: true
-PenaltyBreakBeforeFirstCallParameter: 19
-PenaltyBreakComment: 300
-PenaltyBreakFirstLessLess: 120
-PenaltyBreakString: 1000
-PenaltyExcessCharacter: 1000000
-PenaltyReturnTypeOnItsOwnLine: 60
-PointerAlignment: Right
-ReflowComments:  true
-SortIncludes:    true
-SpaceAfterCStyleCast: false
-SpaceAfterTemplateKeyword: true
-SpaceBeforeAssignmentOperators: true
-SpaceBeforeParens: ControlStatements
-SpaceInEmptyParentheses: false
-SpacesBeforeTrailingComments: 1
-SpacesInAngles:  false
-SpacesInContainerLiterals: true
-SpacesInCStyleCastParentheses: false
-SpacesInParentheses: false
-SpacesInSquareBrackets: false
-Standard:        Cpp11
-TabWidth:        8
-UseTab:          Never
-...
-
+AlignAfterOpenBracket: BlockIndent
+BreakBeforeBinaryOperators: All
+BreakConstructorInitializers: BeforeComma
+ColumnLimit: 80
+PointerAlignment: Left
+QualifierAlignment: Custom
+QualifierOrder: ['inline', 'static', 'type', 'const']
+ReferenceAlignment: Left
diff --git a/deps/AMICI/.coveragerc b/deps/AMICI/.coveragerc
@@ -16,4 +16,3 @@ exclude_lines =
     raise
     except:
     import
-
diff --git a/deps/AMICI/.github/CODEOWNERS b/deps/AMICI/.github/CODEOWNERS
@@ -0,0 +1,4 @@
+# see https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
+
+# default owners
+* @AMICI-dev/amici-maintainers
diff --git a/deps/AMICI/.github/actions/install-apt-dependencies/action.yml b/deps/AMICI/.github/actions/install-apt-dependencies/action.yml
@@ -0,0 +1,16 @@
+name: Install apt dependencies
+description: Install apt dependencies for the AMICI Python package
+runs:
+  using: "composite"
+  steps:
+    - run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+              g++ \
+              libatlas-base-dev \
+              libboost-chrono-dev \
+              libboost-math-dev \
+              libboost-serialization-dev \
+              libhdf5-serial-dev \
+              swig
+      shell: bash
diff --git a/deps/AMICI/.github/actions/setup-amici-cpp/action.yml b/deps/AMICI/.github/actions/setup-amici-cpp/action.yml
@@ -0,0 +1,44 @@
+name: Set up AMICI C++
+description: |
+  Build the AMICI C++ interface and set things for for coverage analysis.
+  (Currently ubuntu-only).
+
+runs:
+  using: "composite"
+  steps:
+    # BioNetGen Path
+    - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
+      shell: bash
+
+    # use all available cores
+    - run: echo "AMICI_PARALLEL_COMPILE=" >> $GITHUB_ENV
+      shell: bash
+
+    # enable coverage
+    - run: echo "ENABLE_GCOV_COVERAGE=TRUE" >> $GITHUB_ENV
+      shell: bash
+
+    - name: Set up Sonar tools
+      uses: ./.github/actions/setup-sonar-tools
+
+    - name: Install apt dependencies
+      uses: ./.github/actions/install-apt-dependencies
+
+    - name: Install additional apt dependencies
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+            cmake \
+            python3-venv \
+            lcov
+      shell: bash
+
+    - name: Build AMICI dependencies
+      run: scripts/buildDependencies.sh
+      shell: bash
+
+    - name: Build AMICI
+      run: scripts/buildAmici.sh
+      shell: bash
+      env:
+        CI_SONARCLOUD: "TRUE"
diff --git a/deps/AMICI/.github/actions/setup-doxygen/action.yml b/deps/AMICI/.github/actions/setup-doxygen/action.yml
@@ -0,0 +1,20 @@
+name: Set up doxygen
+description: |
+  Download, build, and install doxygen.
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install apt dependencies for doxygen
+      run: |
+        sudo apt-get update \
+          && sudo apt-get install -y \
+              bison \
+              ragel \
+              graphviz \
+              texlive-latex-extra
+      shell: bash
+
+    - name: Download and build doxygen
+      run: sudo scripts/downloadAndBuildDoxygen.sh
+      shell: bash
diff --git a/deps/AMICI/.github/actions/setup-sonar-tools/action.yml b/deps/AMICI/.github/actions/setup-sonar-tools/action.yml
@@ -0,0 +1,26 @@
+name: Set up Sonar tools
+description: Download and install sonar-scanner and build-wrapper
+runs:
+  using: "composite"
+  steps:
+    - run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "SONAR_SCANNER_HOME=${HOME}/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
+      shell: bash
+    - run: echo "${HOME}/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
+      shell: bash
+
+    - name: Install sonarcloud tools
+      run: |
+        sudo apt-get install nodejs curl unzip \
+        && curl --create-dirs -sSLo $HOME/.sonar/sonar-scanner.zip \
+          https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-scanner-cli-$SONAR_SCANNER_VERSION-linux.zip \
+        && unzip -o $HOME/.sonar/sonar-scanner.zip -d $HOME/.sonar/ \
+        && curl --create-dirs -sSLo $HOME/.sonar/build-wrapper-linux-x86.zip \
+          https://sonarcloud.io/static/cpp/build-wrapper-linux-x86.zip \
+        && unzip -o $HOME/.sonar/build-wrapper-linux-x86.zip -d $HOME/.sonar/ \
+      shell: bash
diff --git a/deps/AMICI/.github/actions/setup-swig/action.yml b/deps/AMICI/.github/actions/setup-swig/action.yml
@@ -0,0 +1,20 @@
+name: Set up SWIG
+description: |
+  Download and build SWIG and set the SWIG environment variable to the path of
+  the SWIG executable.
+
+inputs:
+  swig_version:
+    description: 'Swig version to build'
+    required: false
+    default: '4.1.1'
+
+runs:
+  using: "composite"
+  steps:
+    - name: Download and build SWIG
+      run: scripts/downloadAndBuildSwig.sh
+      shell: bash
+
+    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-${{ inputs.swig_version }}/install/bin/swig" >> $GITHUB_ENV
+      shell: bash
diff --git a/deps/AMICI/.github/workflows/deploy_branch.yml b/deps/AMICI/.github/workflows/deploy_branch.yml
@@ -1,5 +1,5 @@
 name: Deploy Branch
-on: [push, pull_request, workflow_dispatch]
+on: [push, merge_group, workflow_dispatch]
 
 jobs:
   sdist:
@@ -9,24 +9,22 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 20
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
+    - name: Set up SWIG
+      uses: ./.github/actions/setup-swig
 
-    - name: Build swig4
-      run: |
-        sudo scripts/downloadAndBuildSwig.sh
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
     - name: Create AMICI sdist
       run: |

diff --git a/deps/AMICI/.github/workflows/deploy_protected.yml b/deps/AMICI/.github/workflows/deploy_protected.yml
@@ -4,9 +4,12 @@ on:
     branches:
       - master
       - develop
+      - release**
   pull_request:
-    branches:
-      - master
+    paths:
+      - container/Dockerfile
+      # ensure all relevant files are still included in sdist
+      - python/sdist/MANIFEST.in
   workflow_dispatch:
 
 jobs:
@@ -18,21 +21,26 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/checkout@master
-    - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
+    - uses: actions/checkout@v3
+    - run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@v2
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2
     - name: Publish to Registry
       uses: elgohr/Publish-Docker-Github-Action@v4
       with:
         name: dweindl/amici
         username: ${{ secrets.DOCKER_USERNAME }}
         password: ${{ secrets.DOCKER_PASSWORD }}
-        workdir: docker/
+        workdir: container/
         dockerfile: Dockerfile
         tag_names: true
+        platforms: linux/amd64,linux/arm64
diff --git a/deps/AMICI/.github/workflows/deploy_release.yml b/deps/AMICI/.github/workflows/deploy_release.yml
@@ -12,35 +12,32 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 20
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig" >> $GITHUB_ENV
+    - name: Set up SWIG
+      uses: ./.github/actions/setup-swig
 
-    - name: Build swig4
-      run: |
-        sudo scripts/downloadAndBuildSwig.sh
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
     - name: sdist
-      run: |
-        scripts/buildSdist.sh
+      run: scripts/buildSdist.sh
 
     - name: Publish a Python distribution to PyPI
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.pypi_password }}
-        packages_dir: python/sdist/dist
+        packages-dir: python/sdist/dist
 
   bioSimulatorsUpdateCliAndDockerImage:
     name: Release to BioSimulators