Merge branch 'develop' into jax_export

AMICI-dev · Oct 19, 2024 · 781bb3b · 781bb3b
2 parents 8143cc2 + 8f0c8fb
commit 781bb3b
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1 @@
+f59fed72eb4d0cedf6abf2a96fe95087ce61478a
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,11 @@
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    ignore:
+      - dependency-name: "*"
+        update-types: ["version-update:semver-patch", "version-update:semver-minor"]
+    target-branch: "develop"
diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/deploy_protected.yml b/.github/workflows/deploy_protected.yml
@@ -29,14 +29,14 @@ jobs:
           fi
 
   dockerhub:
-    name: Deploy Dockerhub
+    name: Deploy Docker Hub
     needs: [check-secret]
     if: needs.check-secret.outputs.secrets-defined == 'true'
     runs-on: ubuntu-22.04
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -50,7 +50,7 @@ jobs:
     - name: Set up Docker Buildx
       uses: docker/setup-buildx-action@v3
     - name: Publish to Registry
-      uses: elgohr/Publish-Docker-Github-Action@v4
+      uses: elgohr/Publish-Docker-Github-Action@v5
       with:
         name: dweindl/amici
         username: ${{ secrets.DOCKER_USERNAME }}

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -12,7 +12,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     environment:
       name: pypi
@@ -36,11 +36,6 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
-    - name: Remove direct dependencies from setup.cfg
-      # Remove any "git+https"-based dependencies that are not supported
-      #  by PyPI and are only required for testing.
-      run: sed -i '/git+https/d' python/sdist/setup.cfg
-
     - name: sdist
       run: scripts/buildSdist.sh
 
@@ -74,3 +69,29 @@ jobs:
             -H "Accept: application/vnd.github.v3+json" \
               https://api.github.com/repos/${DOWNSTREAM_REPOSITORY}/actions/workflows/${WORKFLOW_FILE}/dispatches \
             -d "{\"ref\": \"dev\", \"inputs\": {\"simulatorVersion\": \"${PACKAGE_VERSION}\", \"simulatorVersionLatest\": \"true\"}}"
+
+  dockerhub:
+    name: Release to Docker Hub
+    runs-on: ubuntu-22.04
+
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+    - uses: actions/checkout@v4
+    - run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@v3
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+    - name: Publish to Registry
+      uses: elgohr/Publish-Docker-Github-Action@v5
+      with:
+        name: dweindl/amici
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        workdir: container/
+        dockerfile: Dockerfile
+        tag_semver: true
+        platforms: linux/amd64,linux/arm64
diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
         extract_subexpressions: ["true", "false"]
     env:
       AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }}
@@ -52,18 +52,23 @@ jobs:
         AMICI_PARALLEL_COMPILE="" pip3 install -v --user \
             $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis,jax]
 
+    - run: |
+        python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \
+        &&  python3 -m pip install -U sympy
+
     # retrieve test models
     - name: Download and test benchmark collection
       run: |
         git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
           && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+          && pip3 install -e $BENCHMARK_COLLECTION/../src/python \
           && AMICI_PARALLEL_COMPILE="" tests/benchmark-models/test_benchmark_collection.sh
 
     # run gradient checks
     - name: Run Gradient Checks
       run: |
         pip install git+https://github.com/ICB-DCM/fiddy.git \
-          && cd tests/benchmark-models && pytest ./test_petab_benchmark.py
+          && cd tests/benchmark-models && pytest --durations=10 ./test_petab_benchmark.py
 
     # upload results
     - uses: actions/upload-artifact@v4

diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
@@ -20,7 +20,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -50,7 +50,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -83,7 +83,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/test_matlab.yml b/.github/workflows/test_matlab.yml
@@ -21,8 +21,8 @@ jobs:
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
     - name: Install MATLAB
-      uses: matlab-actions/setup-matlab@v1
+      uses: matlab-actions/setup-matlab@v2
     - name: Run script
-      uses: matlab-actions/run-command@v1
+      uses: matlab-actions/run-command@v2
       with:
         command: cd matlab; installAMICI; addpath tests; testModels
diff --git a/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
@@ -23,7 +23,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
@@ -15,14 +15,14 @@ jobs:
   build:
     name: PEtab Testsuite
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
 
     env:
       ENABLE_GCOV_COVERAGE: TRUE
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
@@ -58,7 +58,7 @@ jobs:
       - name: Install petab
         run: |
           source ./venv/bin/activate \
-            && pip3 install wheel pytest shyaml pytest-cov pysb
+            && pip3 install wheel pytest shyaml pytest-cov pysb>=1.16
 
       # retrieve test models
       - name: Download and install PEtab test suite
@@ -68,11 +68,26 @@ jobs:
             && source ./venv/bin/activate \
             && cd petab_test_suite && pip3 install -e .
 
+      - name: Install PEtab benchmark collection
+        run: |
+          git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
+            && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+            && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python
+
+      - name: Install petab
+        run: |
+          source ./venv/bin/activate \
+            && python3 -m pip uninstall -y petab \
+            && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \
+            && python3 -m pip install git+https://github.com/pysb/pysb@master \
+            && python3 -m pip install sympy>=1.12.1
+
+
       - name: Run PEtab-related unit tests
         run: |
           source ./venv/bin/activate \
             && pytest --cov-report=xml:coverage.xml \
-              --cov=./ python/tests/test_*petab*.py python/tests/petab/
+              --cov=./ python/tests/test_*petab*.py python/tests/petab_/
 
       # run test models
       - name: Run PEtab test suite

diff --git a/.github/workflows/test_pypi.yml b/.github/workflows/test_pypi.yml
@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-22.04, macos-latest]
 
     runs-on: ${{ matrix.os }}

diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
@@ -15,11 +15,11 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     steps:
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pooch
@@ -38,6 +38,11 @@ jobs:
     - name: Set up AMICI C++ libraries
       uses: ./.github/actions/setup-amici-cpp
 
+    - name: Install libsuitesparse-dev
+      # We don't need libsuitesparse-dev, but let's have it installed,
+      # to ensure that its presence does not break the build
+      run: sudo apt-get install -y libsuitesparse-dev
+
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
 
@@ -117,14 +122,21 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.10" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Cache
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
@@ -193,14 +205,21 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Cache
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
@@ -233,7 +252,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.11"
 
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
@@ -259,6 +278,17 @@ jobs:
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
 
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Python tests
       run: |
         scripts/run-python-tests.sh \
@@ -273,7 +303,7 @@ jobs:
 
     steps:
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/Library/Caches/pooch
@@ -282,7 +312,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.11"
 
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
@@ -301,6 +331,24 @@ jobs:
     - name: Get BioNetGen
       run: scripts/buildBNGL.sh
 
+
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
+    - name: Install PEtab benchmark collection
+      run: |
+        git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
+          && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+          && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python
+
     - name: Python tests
       run: |
         scripts/run-python-tests.sh \