Release 0.21.0

Merge pull request AMICI-dev#2266 from dweindl/release_0.21.0
dweindl · Jan 16, 2024 · 224e9be · 224e9be
2 parents ffcbf66 + a8cebe6
commit 224e9be
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diff --git a/.github/actions/install-macos-dependencies/action.yml b/.github/actions/install-macos-dependencies/action.yml
@@ -0,0 +1,31 @@
+name: Install AMICI dependencies for MacOS
+description: Install AMICI dependencies for MacOS
+
+runs:
+  using: "composite"
+  steps:
+    # use all available cores
+    - run: echo "AMICI_PARALLEL_COMPILE=" >> $GITHUB_ENV
+      shell: bash
+
+    # AMICI repository root
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+      shell: bash
+
+    # BioNetGen path
+    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
+      shell: bash
+
+    # CMake hints
+    # Ensure CMake is using the python version that we will use for the python tests later on
+    - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
+      shell: bash
+
+    # install amici dependencies
+    - name: homebrew
+      run: brew install hdf5 swig gcc libomp boost
+      shell: bash
diff --git a/.github/actions/setup-sonar-tools/action.yml b/.github/actions/setup-sonar-tools/action.yml
@@ -16,7 +16,8 @@ runs:
 
     - name: Install sonarcloud tools
       run: |
-        sudo apt-get install nodejs curl unzip \
+        sudo apt-get update \
+        && 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/ \

diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -1,5 +1,5 @@
 name: Deploy Branch
-on: [push, merge_group, workflow_dispatch]
+on: [push, pull_request, merge_group, workflow_dispatch]
 
 jobs:
   sdist:

diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
@@ -43,7 +43,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.10" ]
+        python-version: [ "3.11" ]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
@@ -67,10 +67,10 @@ jobs:
           sudo apt-get update \
             && sudo apt-get install -y \
               pandoc \
-              python3-venv
+            && pip install tox
 
       - name: Set up SWIG
         uses: ./.github/actions/setup-swig
 
       - name: Run sphinx
-        run: scripts/run-sphinx.sh
+        run: tox -e doc
diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
@@ -1,5 +1,5 @@
 name: Installation
-on: [push, merge_group, workflow_dispatch]
+on: [push, pull_request, merge_group, workflow_dispatch]
 
 jobs:
   archive:

diff --git a/.github/workflows/test_matlab.yml b/.github/workflows/test_matlab.yml
@@ -1,5 +1,12 @@
 name: Matlab
-on: [push, merge_group, workflow_dispatch]
+on:
+  push:
+  merge_group:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - master
+
 
 jobs:
   matlab:

diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
@@ -72,7 +72,7 @@ jobs:
         run: |
           source ./build/venv/bin/activate \
             && pytest --cov-report=xml:coverage.xml \
-              --cov=./ python/tests/test_*petab*.py
+              --cov=./ python/tests/test_*petab*.py python/tests/petab/
 
       # run test models
       - name: Run PEtab test suite
@@ -85,6 +85,7 @@ jobs:
             tests/petab_test_suite/
 
       - name: Codecov
+        if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
         uses: codecov/[email protected]
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

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"]
+        python-version: ["3.9", "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
@@ -6,6 +6,7 @@ on:
   pull_request:
     branches:
       - master
+      - develop
 
 jobs:
   ubuntu-cpp-python-tests:
@@ -65,6 +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/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -84,6 +86,7 @@ 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/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -92,6 +95,7 @@ jobs:
         fail_ci_if_error: true
 
     - name: Run sonar-scanner
+      if: ${{ env.SONAR_TOKEN != '' }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
@@ -137,6 +141,7 @@ 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/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -156,6 +161,7 @@ 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/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -164,6 +170,7 @@ jobs:
         fail_ci_if_error: true
 
     - name: Run sonar-scanner
+      if: ${{ env.SONAR_TOKEN != '' }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
@@ -211,8 +218,8 @@ jobs:
 
     # TODO: Include notebooks in coverage report
 
-  osx:
-    name: Tests OSX
+  macos_cpp_py:
+    name: Tests MacOS C++/Python
     runs-on: macos-latest
 
     steps:
@@ -224,16 +231,11 @@ jobs:
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
-    # Ensure CMake is using the python version that we will use for the python tests later on
-    - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
-    - run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
-    - run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
+    - name: Install dependencies
+      uses: ./.github/actions/install-macos-dependencies
 
-    # install amici dependencies
     - name: homebrew
-      run: brew install hdf5 swig gcc cppcheck libomp boost
+      run: brew install cppcheck
 
     - name: Build AMICI
       run: scripts/buildAll.sh
@@ -247,8 +249,47 @@ jobs:
     - name: cppcheck
       run: scripts/run-cppcheck.sh
 
-    - name: Python tests
-      run: scripts/run-python-tests.sh
-
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
+
+    - name: Python tests
+      run: |
+        scripts/run-python-tests.sh \
+          test_pregenerated_models.py \
+          test_splines_short.py \
+          test_misc.py
+
+
+  macos_python:
+    name: Tests MacOS Python
+    runs-on: macos-latest
+
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - uses: actions/checkout@v3
+    - run: git fetch --prune --unshallow
+
+    - name: Install dependencies
+      uses: ./.github/actions/install-macos-dependencies
+
+    - name: Install python package
+      run: |
+        pip show numpy > /dev/null || python3 -m pip install numpy
+        scripts/installAmiciSource.sh
+
+    - name: Check OpenMP support
+      run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+
+    - name: Get BioNetGen
+      run: scripts/buildBNGL.sh
+
+    - name: Python tests
+      run: |
+        scripts/run-python-tests.sh \
+          --ignore=test_pregenerated_models.py \
+          --ignore=test_splines_short.py \
+          --ignore=test_misc.py
diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml
@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
         experimental: [false]
 
     steps:
@@ -44,15 +44,27 @@ jobs:
     - name: Install apt dependencies
       uses: ./.github/actions/install-apt-dependencies
 
-    # install AMICI
     - name: Build BNGL
       run: scripts/buildBNGL.sh
+
     - name: Install python package
       run: scripts/installAmiciSource.sh
 
+    # until https://github.com/dateutil/dateutil >2.8.2 is released https://github.com/dateutil/dateutil/issues/1314
+    - run: source build/venv/bin/activate && pip3 install git+https://github.com/dateutil/dateutil.git@296d419fe6bf3b22897f8f210735ac9c4e1cb796
+      if: matrix.python-version == '3.12'
+
+    # install pysb before sympy to allow for sympy>=1.12 (https://github.com/pysb/pysb/commit/e83937cb8c74afc9b2fa96595b68464946745f33)
+    - run: source build/venv/bin/activate && pip3 install git+https://github.com/pysb/pysb
+
+    # until sympy>1.12 is released
+    - run: source build/venv/bin/activate && pip3 install git+https://github.com/sympy/sympy.git@master
+      if: matrix.python-version == '3.12'
+
     - name: Python tests
       run: |
         source build/venv/bin/activate \
-          && pip3 install git+https://github.com/pysb/pysb \
-          && python3 -m pytest --ignore-glob=*petab* \
+          && python3 -m pytest \
+            --durations=10 \
+            --ignore-glob=*petab* \
             --ignore-glob=*test_splines.py ${AMICI_DIR}/python/tests
diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -54,6 +54,7 @@ jobs:
         path: tests/amici-semantic-results
 
     - name: Codecov SBMLSuite
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
       uses: codecov/[email protected]
       with:
         token: ${{ secrets.CODECOV_TOKEN }}

diff --git a/.github/workflows/test_windows.yml b/.github/workflows/test_windows.yml
@@ -7,6 +7,7 @@ on:
     - cron:  '48 4 * * *'
   pull_request:
     branches:
+      - develop
       - master
 
 jobs:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,12 +1,6 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
-      name: isort (python)
-      args: ["--profile", "black", "--filter-files", "--line-length", "79"]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
@@ -16,15 +10,28 @@ repos:
     args: [--allow-multiple-documents]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/psf/black
-  rev: 23.7.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.11
   hooks:
-    - id: black-jupyter
-      # It is recommended to specify the latest version of Python
-      # supported by your project here, or alternatively use
-      # pre-commit's default_language_version, see
-      # https://pre-commit.com/#top_level-default_language_version
-      language_version: python3.11
-      args: ["--line-length", "79"]
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+        - --config
+        - python/sdist/pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - python/sdist/pyproject.toml
+
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+    -   id: pyupgrade
+        args: ["--py39-plus"]
+        additional_dependencies: [pyupgrade==3.15.0]
 
 exclude: '^(ThirdParty|models)/'
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -24,4 +24,4 @@ build:
     - libatlas-base-dev
     - swig
   tools:
-    python: "3.9"
+    python: "3.11"
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,6 +7,7 @@ on: @@
         - cron:  '48 4 * * *'
       pull_request:
         branches:
+          - develop
           - master
     jobs:
@@ Expand Down @@