fixed up ci-cd

Author: tclose

.github/workflows/ci-cd.yml

@@ -0,0 +1,92 @@
+#This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+# For deployment, it will be necessary to create a PyPI API token and store it as a secret
+# https://docs.github.com/en/actions/reference/encrypted-secrets
+
+name: Python package
+
+# Set once
+env:
+  SUBPACKAGE: dcm2niix
+
+on:
+  push:
+    branches: [ main ]
+    tags: [ '*' ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11, 3.12, 3.13]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+    - name: Install task package
+      run: |
+        pip install ".[test]"
+        python -c "import pydra.tasks.$SUBPACKAGE as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+    - name: Install development Pydra
+      run: pip install --no-deps git+https://github.com/nipype/pydra.git@new-syntax
+    - name: Test with pytest
+      run: |
+        pytest -sv --doctest-modules pydra/tasks/$SUBPACKAGE \
+            --cov pydra.tasks.$SUBPACKAGE --cov-report xml
+    - uses: codecov/codecov-action@v1
+      if: ${{ always() }}
+
+
+  deploy:
+    needs: [test]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.9]
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: recursive
+        fetch-depth: 0
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install build tools
+      run: python -m pip install --upgrade pip setuptools wheel twine
+    - name: Build source and wheel distributions
+      run: python setup.py sdist bdist_wheel
+    - name: Check distributions
+      run: twine check dist/*
+    - uses: actions/upload-artifact@v2
+      with:
+        name: distributions
+        path: dist/
+    # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
+    # Secrets are not accessible in the if: condition [0], so set an output variable [1]
+    # [0] https://github.community/t/16928
+    # [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter
+    - name: Check for PyPI token on tag
+      id: deployable
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      env:
+        PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
+      run: if [ -n "$PYPI_API_TOKEN" ]; then echo ::set-output name=DEPLOY::true; fi
+    - name: Upload to PyPI
+      if: steps.deployable.outputs.DEPLOY
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29  # v1.4.2
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}