Release 0.21.2

Merge pull request #2287 from dweindl/release_0.21.2
AMICI-dev · Feb 6, 2024 · fa7c0bd · fa7c0bd
2 parents ec4ee25 + 5e64ed4
commit fa7c0bd
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Showing 63 changed files with 648 additions and 573 deletions.
diff --git a/.github/actions/setup-swig/action.yml b/.github/actions/setup-swig/action.yml
@@ -7,7 +7,7 @@ inputs:
   swig_version:
     description: 'Swig version to build'
     required: false
-    default: '4.1.1'
+    default: '4.2.0'
 
 runs:
   using: "composite"

diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -13,11 +13,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
@@ -31,7 +31,7 @@ jobs:
         scripts/buildSdist.sh
 
     - name: "Upload artifact: sdist"
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: sdist
         path: python/sdist/dist/amici-*.gz
diff --git a/.github/workflows/deploy_protected.yml b/.github/workflows/deploy_protected.yml
@@ -25,10 +25,10 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/checkout@v3
+    - 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@v2

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -14,13 +14,20 @@ jobs:
       matrix:
         python-version: [3.9]
 
+    environment:
+      name: pypi
+      url: https://pypi.org/p/amici
+
+    permissions:
+      id-token: write
+
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
@@ -40,8 +47,6 @@ jobs:
     - name: Publish a Python distribution to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        user: __token__
-        password: ${{ secrets.pypi_password }}
         packages-dir: python/sdist/dist
 
   bioSimulatorsUpdateCliAndDockerImage:

diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
@@ -29,11 +29,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
@@ -49,15 +49,15 @@ jobs:
     - name: Install AMICI sdist
       run: |
         pip3 install --user petab[vis] && \
-        AMICI_PARALLEL_COMPILE=2 pip3 install -v --user \
+        AMICI_PARALLEL_COMPILE="" pip3 install -v --user \
             $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis]
 
     # 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/" \
-          && AMICI_PARALLEL_COMPILE=2 tests/benchmark-models/test_benchmark_collection.sh
+          && AMICI_PARALLEL_COMPILE="" tests/benchmark-models/test_benchmark_collection.sh
 
     # run gradient checks
     - name: Run Gradient Checks
@@ -66,9 +66,9 @@ jobs:
           && cd tests/benchmark-models && pytest ./test_petab_benchmark.py
 
     # upload results
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
-        name: computation times
+        name: computation-times-${{ matrix.python-version }}-${{ matrix.extract_subexpressions }}
         path: |
           tests/benchmark-models/computation_times.csv
           tests/benchmark-models/computation_times.png
diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
@@ -24,11 +24,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - name: Set up doxygen
@@ -47,11 +47,11 @@ jobs:
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - run: git fetch --prune --unshallow
 
       - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
@@ -13,11 +13,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -54,11 +54,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -87,11 +87,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

diff --git a/.github/workflows/test_matlab.yml b/.github/workflows/test_matlab.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

diff --git a/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
@@ -27,11 +27,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20
 
@@ -51,7 +51,7 @@ jobs:
 
     - name: Install AMICI sdist
       run: |
-        AMICI_PARALLEL_COMPILE=2 check_time.sh \
+        AMICI_PARALLEL_COMPILE="" check_time.sh \
             install_sdist pip3 install -v --user \
             $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
 
@@ -64,7 +64,7 @@ jobs:
         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@v3
+      uses: actions/upload-artifact@v4
       with:
         name: model_performance_test
         path: model_performance_test

diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
@@ -26,11 +26,11 @@ jobs:
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 20
 
@@ -78,15 +78,14 @@ jobs:
       - name: Run PEtab test suite
         run: |
           source ./build/venv/bin/activate \
-          && AMICI_PARALLEL_COMPILE=2 pytest -v \
+          && AMICI_PARALLEL_COMPILE="" pytest -v \
             --cov-report=xml:coverage.xml \
             --cov-append \
             --cov=amici \
             tests/petab_test_suite/
 
       - name: Codecov
-        if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-        uses: codecov/codecov-action@v3.1.0
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: coverage.xml

diff --git a/.github/workflows/test_pypi.yml b/.github/workflows/test_pypi.yml
@@ -36,7 +36,7 @@ jobs:
           fi
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
@@ -19,11 +19,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -66,8 +66,7 @@ jobs:
           ${AMICI_DIR}/python/tests/test_splines.py
 
     - name: Codecov Python
-      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v3.1.0
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: build/coverage_py.xml
@@ -86,8 +85,7 @@ jobs:
         && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
 
     - name: Codecov CPP
-      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v3.1.0
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.info
@@ -114,11 +112,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -141,8 +139,7 @@ jobs:
           ${AMICI_DIR}/python/tests/test_splines_short.py
 
     - name: Codecov Python
-      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v3.1.0
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: build/coverage_py.xml
@@ -161,8 +158,7 @@ jobs:
         && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
 
     - name: Codecov CPP
-      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v3.1.0
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.info
@@ -190,11 +186,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -224,11 +220,11 @@ jobs:
 
     steps:
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - name: Install dependencies
@@ -266,11 +262,11 @@ jobs:
 
     steps:
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
     - name: Install dependencies

diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml
@@ -33,11 +33,11 @@ jobs:
     - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 20