use poetry as a python package manager

.github/actions/setup-poetry-env/action.yml

@@ -0,0 +1,42 @@
+name: "setup-poetry-env"
+description: "Composite action to setup the Python and poetry environment."
+
+inputs:
+  python-version:
+    required: false
+    description: "The python version to use"
+    default: "3.11"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Set up python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install Poetry
+      env:
+        POETRY_VERSION: "1.7.1"
+      run: curl -sSL https://install.python-poetry.org | python - -y
+      shell: bash
+
+    - name: Add Poetry to Path
+      run: echo "$HOME/.local/bin" >> $GITHUB_PATH
+      shell: bash
+
+    - name: Configure Poetry virtual environment in project
+      run: poetry config virtualenvs.in-project true
+      shell: bash
+
+    - name: Load cached venv
+      id: cached-poetry-dependencies
+      uses: actions/cache@v4
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ inputs.python-version }}-${{ hashFiles('poetry.lock') }}
+
+    - name: Install dependencies
+      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      run: poetry install --no-interaction
+      shell: bash

.github/workflows/ci.yml

@@ -24,30 +24,19 @@ jobs:
     name: Lint, test, and compile documentation
     if: "!contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'"
     runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
+      fail-fast: false
+    defaults:
+      run:
+        shell: bash
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
 
-      - name: Install Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.9.9' # no particular microversion of 3.9 is required; 3.9.8 behaves oddly in GitHub actions
-
-      - name: Setup pip cache
-        uses: actions/cache@v2
-        with:
-          path: /opt/hostedtoolcache/Python
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Install pip and setuptools
-        run: |
-          python -m pip install --upgrade pip==23.0.1
-          python -m pip install --upgrade setuptools
-
       - name: Install Java # for pyNeuroML
         uses: actions/setup-java@v2
         with:
@@ -69,32 +58,21 @@ jobs:
           singularity-version: 3.7.1
 
       # install package
-      - name: Install the package
-        run: |
-          python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy
-          python -m pip install .[all]
-
-      # lint
-      - name: Install flake8
-        run: python -m pip install flake8
+      - name: Set up the environment
+        uses: ./.github/actions/setup-poetry-env
+        with:
+          python-version: ${{ matrix.python-version }}
 
       - name: Lint the package
         run: python -m flake8
 
-      # test and upload coverage report to Codecov
-      - name: Install pytest
-        run: python -m pip install pytest pytest-cov
-
-      - name: Install the requirements for the tests
-        run: python -m pip install .[tests]
-
       - name: Run the tests
         uses: GabrielBB/xvfb-action@v1
         env:
           MPLBACKEND: PDF
           # BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/  # uncomment to execute tests with the dev deployment
         with:
-          run: python -m pytest tests/ --cov=./biosimulators_utils --cov-report=xml
+          run: poetry run python -m pytest tests/ --cov=./biosimulators_utils --cov-report=xml
 
       - name: Upload the coverage report to Codecov
         uses: codecov/codecov-action@v2
@@ -104,22 +82,22 @@ jobs:
           file: ./coverage.xml
 
       # compile documentation
-      - name: Install the requirements for compiling the documentation
-        run: python -m pip install -r docs-src/requirements.txt
+      #- name: Install the requirements for compiling the documentation
+      #  run: python -m pip install -r docs-src/requirements.txt
 
-      - name: Compile the documentation
-        run: |
-          sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
-          mkdir -p docs-src/_static
-          sphinx-build docs-src docs
+      #- name: Compile the documentation
+      #  run: |
+      #    sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
+      #    mkdir -p docs-src/_static
+      #    sphinx-build docs-src docs
 
   release:
     name: Release a new version
     needs: [getVersionNumber, build]
     runs-on: ubuntu-22.04
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
           ref: dev
@@ -131,15 +109,15 @@ jobs:
           git config pull.rebase false
 
       - name: Install Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: '3.9'
 
       - name: Setup pip cache
         uses: actions/cache@v2
         with:
           path: /opt/hostedtoolcache/Python
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('poetry.lock') }}
           restore-keys: |
             ${{ runner.os }}-pip-
 

.gitignore

@@ -19,3 +19,5 @@ docs/.buildinfo
 docs/.doctrees/
 docs/_raw_sources/
 docs/_sources/
+
+.python-version