Merge branch 'develop' into maint_replace_pthreads

ICB-DCM · Dec 5, 2023 · ef80255 · ef80255
2 parents 3858d82 + 540e2f4
commit ef80255
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diff --git a/.github/workflows/deploy_dockerhub.yml b/.github/workflows/deploy_dockerhub.yml
@@ -9,7 +9,7 @@ jobs:
     - uses: actions/checkout@master
     - run: git archive -v -o container/charliecloud/parpe_base/parpe.tar.gz --format=tar.gz HEAD
     - name: Publish to Registry
-      uses: elgohr/Publish-Docker-Github-Action@2.8
+      uses: elgohr/Publish-Docker-Github-Action@v5
       with:
         name: dweindl/parpe
         username: ${{ secrets.DOCKER_USERNAME }}

diff --git a/.github/workflows/parpe_tests.yml b/.github/workflows/parpe_tests.yml
@@ -1,7 +1,13 @@
 # https://help.github.com/en/actions/reference/workflow-syntax-for-github-actions
 # https://help.github.com/en/actions/configuring-and-managing-workflows/using-environment-variables
 name: parPE tests
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron:  '48 4 * * *'
+
 jobs:
   container:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/petab_testsuite.yml b/.github/workflows/petab_testsuite.yml
@@ -63,7 +63,7 @@ jobs:
         PETAB_TEST_URL: https://github.com/PEtab-dev/petab_test_suite.git
       run: |
         cd $PARPE_BASE/ \
-          && git clone --depth 1 --branch develop $PETAB_TEST_URL \
+          && git clone --depth 1 --branch main $PETAB_TEST_URL \
           && $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
             pip3 install -e petab_test_suite
 

diff --git a/container/charliecloud/parpe_base/Dockerfile b/container/charliecloud/parpe_base/Dockerfile
@@ -1,12 +1,16 @@
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
-COPY . /u18
+COPY . /container-files
 
-RUN /u18/install.sh && rm -rf /tmp && mkdir /tmp
+RUN /container-files/install.sh && rm -rf /tmp && mkdir /tmp
 
 ENV BASH_ENV "/etc/drydock/.env"
+ENV CC clang
+ENV CXX clang++
+ENV OMPI_CC clang
+ENV OMPI_CXX clang++
 
-RUN /u18/install_parpe.sh
+RUN /container-files/install_parpe.sh
 
 ENV PARPE_DIR "/parPE"
 

diff --git a/container/charliecloud/parpe_base/install.sh b/container/charliecloud/parpe_base/install.sh
@@ -13,11 +13,11 @@ locale-gen en_US en_US.UTF-8
 dpkg-reconfigure locales
 
 echo "HOME=$HOME"
-cd /u18
 
 echo "================= parPE requirements ============"
 # using openmpi coming with libboost-all-dev instead of libmpich-dev
 apt-get install -q -y \
+  clang \
   cmake \
   curl \
   coinor-libipopt-dev \
@@ -28,16 +28,17 @@ apt-get install -q -y \
   libboost-all-dev \
   libceres-dev \
   libhdf5-dev \
+  libomp-dev \
+  nano \
   python3-dev \
   python3-pip \
   python3-venv \
   libspdlog-dev \
-  swig3.0 \
+  swig \
   unzip \
   wget
 
 # for setuptools to find:
-ln -s /usr/bin/swig3.0 /usr/bin/swig
 python3 -m pip install --upgrade pip
 pip3 install -U setuptools pkgconfig wheel
 

diff --git a/container/charliecloud/parpe_base/install_parpe.sh b/container/charliecloud/parpe_base/install_parpe.sh
@@ -7,7 +7,7 @@ export PARPE_BASE="${PARPE_DIR:-/parPE}"
 
 # unpack git archive
 mkdir "$PARPE_BASE" && cd "$PARPE_BASE"
-tar -xzf /u18/parpe.tar.gz
+tar -xzf /container-files/parpe.tar.gz
 
 # Build dependencies
 
@@ -18,7 +18,7 @@ cd "${AMICI_PATH}" \
   && scripts/buildSundials.sh
 mkdir -p "${AMICI_PATH}/build" && cd "${AMICI_PATH}/build"
 cmake \
-  -DCMAKE_BUILD_TYPE=Debug \
+  -DCMAKE_BUILD_TYPE=RelWithDebInfo \
   -DENABLE_PYTHON=ON \
   -DBUILD_TESTS=OFF \
   .. && make -j12

diff --git a/deps/AMICI/.coveragerc b/deps/AMICI/.coveragerc
@@ -6,6 +6,7 @@ omit =
     */amici_without_hdf5.py
     */ThirdParty/*
     *.template.*
+    /tmp/*
 parallel = true
 
 [report]

diff --git a/deps/AMICI/.github/workflows/deploy_branch.yml b/deps/AMICI/.github/workflows/deploy_branch.yml
@@ -5,9 +5,18 @@ jobs:
   sdist:
     name: Deploy Python Source Distribution
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [3.8]
 
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
       with:
         fetch-depth: 20
@@ -24,7 +33,7 @@ jobs:
         scripts/buildSdist.sh
 
     - name: "Upload artifact: sdist"
-      uses: actions/upload-artifact@v1
+      uses: actions/upload-artifact@v3
       with:
         name: sdist
-        path: python/sdist/dist
+        path: python/sdist/dist/amici-*.gz
diff --git a/deps/AMICI/.github/workflows/deploy_protected.yml b/deps/AMICI/.github/workflows/deploy_protected.yml
@@ -14,13 +14,21 @@ jobs:
     # https://github.com/marketplace/actions/publish-docker
     name: Deploy Dockerhub
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [3.8]
 
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
     - uses: actions/checkout@master
     - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
     - name: Publish to Registry
-      uses: elgohr/Publish-Docker-Github-Action@2.8
+      uses: elgohr/Publish-Docker-Github-Action@v4
       with:
         name: dweindl/amici
         username: ${{ secrets.DOCKER_USERNAME }}

diff --git a/deps/AMICI/.github/workflows/deploy_release.yml b/deps/AMICI/.github/workflows/deploy_release.yml
@@ -8,9 +8,18 @@ jobs:
   pypi:
     name: Deploy PyPI
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [3.8]
 
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
       with:
         fetch-depth: 20
@@ -36,7 +45,7 @@ jobs:
   bioSimulatorsUpdateCliAndDockerImage:
     name: Release to BioSimulators
     needs: pypi
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     env:
       # Owner/repository-id for the GitHub repository for the downstream command-line interface and Docker image
       DOWNSTREAM_REPOSITORY: biosimulators/Biosimulators_AMICI

diff --git a/deps/AMICI/.github/workflows/test_benchmark_collection_models.yml b/deps/AMICI/.github/workflows/test_benchmark_collection_models.yml
@@ -17,9 +17,22 @@ jobs:
   build:
     name: Benchmark Collection
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.8" ]
+        extract_subexpressions: ["true", "false"]
+    env:
+      AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }}
 
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
       with:
         fetch-depth: 20
@@ -30,8 +43,6 @@ jobs:
         sudo apt-get update \
           && sudo apt-get install -y swig libatlas-base-dev
 
-    - run: pip3 install pytest shyaml
-
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
     - run: echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH
 
@@ -42,7 +53,7 @@ jobs:
     - name: Install AMICI sdist
       run: |
         AMICI_PARALLEL_COMPILE=2 pip3 install -v --user \
-            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab]
+            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test]
 
     # retrieve test models
     - name: Download and test benchmark collection

diff --git a/deps/AMICI/.github/workflows/test_doc.yml b/deps/AMICI/.github/workflows/test_doc.yml
@@ -16,9 +16,18 @@ jobs:
   doxygen:
     name: Test Doxygen
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [3.8]
 
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
     - run: git fetch --prune --unshallow
 
@@ -42,9 +51,18 @@ jobs:
   sphinx:
     name: Test Sphinx
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [ 3.8 ]
 
     steps:
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
       - uses: actions/checkout@master
       - run: git fetch --prune --unshallow
 
@@ -55,12 +73,6 @@ jobs:
         run: |
           sudo scripts/downloadAndBuildDoxygen.sh
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          # Semantic version range syntax or exact version of a Python version
-          python-version: '3.8'
-
       # install amici dependencies
       - name: apt
         run: |

diff --git a/deps/AMICI/.github/workflows/test_install.yml b/deps/AMICI/.github/workflows/test_install.yml
@@ -5,9 +5,18 @@ jobs:
   archive:
     name: Archive Install
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [3.8]
 
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
     - run: git fetch --prune --unshallow
 
@@ -44,9 +53,18 @@ jobs:
   sdist:
     name: sdist Install
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [3.8]
 
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
     - run: git fetch --prune --unshallow
 

diff --git a/deps/AMICI/.github/workflows/test_performance.yml b/deps/AMICI/.github/workflows/test_performance.yml
@@ -4,7 +4,7 @@ on:
     branches:
       - develop
       - master
-      - compile_without_optimization
+      - fix_perftest
 
   pull_request:
     branches:
@@ -19,9 +19,18 @@ jobs:
   build:
     name: Performance Test
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [3.8]
 
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
       with:
         fetch-depth: 20
@@ -31,7 +40,7 @@ jobs:
       run: |
         sudo apt-get update \
           && sudo apt-get install -y swig libatlas-base-dev
-    - run: pip3 install petab shyaml
+    - run: pip3 install petab shyaml build
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
     - run: echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH
@@ -40,7 +49,8 @@ jobs:
     - name: Create AMICI sdist
       run: |
         cd python/sdist \
-          && check_time.sh create_sdist /usr/bin/python3 setup.py sdist
+          && check_time.sh create_sdist python3 -m build --sdist
+
     - name: Install AMICI sdist
       run: |
         AMICI_PARALLEL_COMPILE=2 check_time.sh \
@@ -53,10 +63,10 @@ jobs:
     # import test model
     - name: Import test model
       run: |
-        check_time.sh petab_import python tests/performance/test.py import
+        AMICI_IMPORT_NPROCS=2 check_time.sh petab_import python tests/performance/test.py import
 
     - name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
-      uses: actions/upload-artifact@v1
+      uses: actions/upload-artifact@v3
       with:
         name: CS_Signalling_ERBB_RAS_AKT
         path: CS_Signalling_ERBB_RAS_AKT/CS_Signalling_ERBB_RAS_AKT_petab