Drop Python3.7 support (#1635)

... following numpy. Supported Python versions are 3.8--3.10. All tests are run (at least) on Python 3.8, except for macos tests which uses the default system python (currently 3.9). Closes #1633 * Update valgrind suppressions * CMake: require py>=3.8 * Performance test: More time for sdist after change to 'build' * GHA: Use Python3.8 as default * Doc: Update Python requirement * Allow numpy >=1.22.0 * Fixup sdist
AMICI-dev · Jan 12, 2022 · dd12502 · dd12502
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commit dd12502
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Showing 25 changed files with 336 additions and 82 deletions.
diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -7,7 +7,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    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

diff --git a/.github/workflows/deploy_protected.yml b/.github/workflows/deploy_protected.yml
@@ -16,7 +16,15 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    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

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -10,7 +10,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    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

diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
@@ -19,7 +19,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    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

diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
@@ -18,7 +18,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    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
 
@@ -44,7 +53,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    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/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
@@ -7,7 +7,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    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
 
@@ -46,7 +55,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    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/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
@@ -21,7 +21,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    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 \

diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
@@ -21,7 +21,16 @@ jobs:
     env:
       ENABLE_GCOV_COVERAGE: TRUE
 
+    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

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: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9, '3.10']
         os: [ubuntu-20.04, macos-latest]
 
     runs-on: ${{ matrix.os }}

diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
@@ -12,7 +12,16 @@ jobs:
       ENABLE_GCOV_COVERAGE: "TRUE"
       CI_SONARCLOUD: "TRUE"
 
+    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/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml
@@ -22,12 +22,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10']
         experimental: [false]
-# Temporarily disabled because the respective jobs somehow runs infinitely
-#        include:
-#          - python-version:  3.10.0-alpha.5
-#            experimental: true
 
     steps:
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -27,8 +27,14 @@ jobs:
       matrix:
         cases: ["1 - 250", "251 - 500", "501 - 750", "751 - 1000",
                 "1000-1250", "1251-1780"]
+        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: 1

diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml
@@ -16,7 +16,16 @@ jobs:
     # TODO: prepare image with more deps preinstalled
     runs-on: ubuntu-20.04
 
+    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/documentation/README.md b/documentation/README.md
@@ -67,7 +67,7 @@ Graphics for documentation are kept in `documentation/gfx/`.
 
 ### When using Markdown
 
-* Note that there are some incompatibilities of Github Markdown and Doxygen
+* Note that there are some incompatibilities of GitHub Markdown and Doxygen
   Markdown. Ideally documentation should be written in a format compatible with
   both.
   This affects for example images links which currently cause trouble in

diff --git a/documentation/gfx/amici_workflow.png b/documentation/gfx/amici_workflow.png