Merge branch 'develop' into maint_replace_pthreads

.github/workflows/benchmark_models.yml

@@ -9,6 +9,9 @@ jobs:
     name: benchmark models
     steps:
     - uses: actions/checkout@master
+    - name: chown checkout directory
+      # https://github.com/actions/runner/issues/2033
+      run: chown -R $(id -u):$(id -g) $PWD
 
     - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV
     - run: echo "PARPE_BUILD=${PARPE_BASE}/build" >> $GITHUB_ENV
@@ -68,6 +71,6 @@ jobs:
     - name: Benchmark models --- tests
       run: |
         cd $PARPE_BASE/benchmark_collection \
-          && AMICI_PARALLEL_COMPILE=4 \
+          && AMICI_PARALLEL_COMPILE="" \
              BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
              $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv ./all.sh

.github/workflows/parpe_tests.yml

@@ -21,14 +21,17 @@ jobs:
 
     steps:
     - uses: actions/checkout@master
+    - name: chown checkout directory
+      # https://github.com/actions/runner/issues/2033
+      run: chown -R $(id -u):$(id -g) $PWD
     - run: git fetch --prune --unshallow
 
     - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV
     - run: echo "PARPE_BUILD=${PARPE_BASE}/build" >> $GITHUB_ENV
     - run: echo "AMICI_PATH=${PARPE_BASE}/deps/AMICI/" >> $GITHUB_ENV
 
     # sonar cloud
-    - run: echo "SONAR_SCANNER_VERSION=4.6.1.2450" >> $GITHUB_ENV
+    - run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
     - run: echo "SONAR_SCANNER_HOME=/root/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
     - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
     - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
@@ -57,7 +60,8 @@ jobs:
 
     - name: Install parPE Python deps
       run: |
-        pip install -r ${PARPE_BASE}/python/requirements.txt
+        pip install -r ${PARPE_BASE}/python/requirements.txt \
+          && sudo apt install lcov
 
     - name: "Install parPE deps: fides"
       run: |
@@ -103,22 +107,26 @@ jobs:
 
     - name: Cache sonar files
       id: cache-sonar
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: sonar_cache
         key: ${{ runner.os }}-sonar_cache
 
     - name: Run sonar-scanner
+      if: ${{ env.SONAR_TOKEN != '' }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
       run: |
         sonar-scanner \
          -Dsonar.cfamily.build-wrapper-output=bw-output \
          -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')"
 
     - name: Run example notebooks
       run: |
-        misc/run_notebook.sh examples/parpeamici/steadystate/parpeExampleSteadystateBasic.ipynb examples/parpeamici/steadystate/parpeExampleSteadystateHierarchical.ipynb
+        misc/run_notebook.sh \
+          examples/parpeamici/steadystate/parpeExampleSteadystateBasic.ipynb \
+          examples/parpeamici/steadystate/parpeExampleSteadystateHierarchical.ipynb
 
     - name: Run valgrind
       run: |

.github/workflows/petab_testsuite.yml

@@ -10,6 +10,9 @@ jobs:
     name: PEtab test suite
     steps:
     - uses: actions/checkout@master
+    - name: chown checkout directory
+      # https://github.com/actions/runner/issues/2033
+      run: chown -R $(id -u):$(id -g) $PWD
 
     - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV
     - run: echo "PARPE_BUILD=${PARPE_BASE}/build" >> $GITHUB_ENV

.readthedocs.yml

@@ -19,9 +19,12 @@ sphinx:
 #  - pdf
 
 python:
-  version: 3.8
   install:
     - requirements: doc/requirements_doc.txt
-
 build:
-  image: latest
+  os: "ubuntu-22.04"
+#  apt_packages:
+#    - libatlas-base-dev
+#    - swig
+  tools:
+    python: "3.11"

CMakeLists.txt

@@ -1,5 +1,5 @@
-cmake_minimum_required(VERSION 3.13) # pkg_search_module GLOBAL
-cmake_policy(VERSION 3.13)
+cmake_minimum_required(VERSION 3.15) # pkg_search_module GLOBAL
+cmake_policy(VERSION 3.15...3.28)
 
 if(POLICY CMP0074)
   # Use package_ROOT environment variables

container/charliecloud/parpe_base/install.sh

@@ -31,6 +31,7 @@ apt-get install -q -y \
   libomp-dev \
   nano \
   python3-dev \
+  python3-numpy \
   python3-pip \
   python3-venv \
   libspdlog-dev \

container/charliecloud/parpe_base/install_parpe.sh

@@ -21,7 +21,7 @@ cmake \
   -DCMAKE_BUILD_TYPE=RelWithDebInfo \
   -DENABLE_PYTHON=ON \
   -DBUILD_TESTS=OFF \
-  .. && make -j12
+  .. && make -j
 
 # install fides optimizer
 cd "$PARPE_BASE/ThirdParty" && ./installFides.sh
@@ -55,7 +55,7 @@ CC=mpicc CXX=mpiCC cmake \
       -DTESTS_MPIEXEC_COMMAND="$mpi_cmd" \
       ..
 
-make -j12 VERBOSE=1
+make -j VERBOSE=1
 
 # MPI settings for python tests
 export PARPE_TESTS_MPIEXEC="mpiexec -n 5 --oversubscribe --allow-run-as-root --mca btl_vader_single_copy_mechanism none --mca btl ^openib --mca oob_tcp_if_include lo --mca btl_tcp_if_include lo --mca orte_base_help_aggregate 0"

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

deps/AMICI/.coveragerc

@@ -16,4 +16,3 @@ exclude_lines =
     raise
     except:
     import
-

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

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

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"

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

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

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