feat(update): Migrate to Poetry

.github/workflows/main.yml → .github/workflows/Crunchy_CI.yml

@@ -1,8 +1,8 @@
-name: Build
+name: Crunchy CI
 on: [push, pull_request]
 
 jobs:
-  build:
+  test-coverage:
     name: Test Crunchy (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ubuntu-latest
     strategy:
@@ -15,6 +15,11 @@ jobs:
     - name: Git checkout
       uses: actions/[email protected]
 
+    - name: Install and configure Poetry
+      uses: snok/install-poetry@v1
+      with:
+        virtualenvs-create: false
+
     - name: Get Conda
       uses: conda-incubator/[email protected]
       with:
@@ -32,15 +37,16 @@ jobs:
       run: |
         conda install -c bioconda samtools
 
-    - name: Install dependencies
-      shell: bash -l {0}
-      run: |
-        python -m pip install --upgrade pip
-        python setup.py install
+    - name: Install Dependencies
+      run: poetry install
 
-    - name: Test with pytest
-      shell: bash -l {0}
+    - name: Unit tests and coverage
       run: |
-        pip install pytest
-        pip install pytest-mock
-        py.test -rxs tests/
+        poetry run pytest --cov=./ --cov-report xml --cov-report term
+
+    - name: Upload coverage to Codecov
+      uses: codecov/[email protected]
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
+        flags: unittests

.github/workflows/build_and_publish_pypi.yml

@@ -1,38 +1,34 @@
 name: Publish to PyPI
 
 on:
- release:
-  types:
-   - created
+  release:
+    types:
+      - created
 
 jobs:
- build-n-publish:
-  name: Build and publish Python distribution to PyPI
-  runs-on: ubuntu-18.04
-  steps:
-   - name: Check out git repository
-     uses: actions/checkout@v2.5.0
+  build-n-publish:
+    name: Build and publish Python distribution to PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out git repository
+        uses: actions/checkout@v4.1.1
 
-   - name: Set up Python
-     uses: actions/setup-python@v4.3.1
-     with:
-      python-version: "3.10"
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
 
-   - name: Install build tools
-     run: >-
-        python -m
-        pip install
-        wheel
-        twine
-        --user
-   - name: Build a binary wheel and a source tarball
-     run: >-
-        python
-        setup.py
-        sdist
-        bdist_wheel
-   - name: Publish distribution 📦 to PyPI
-     uses: pypa/[email protected]
-     with:
-       user: __token__
-       password: ${{ secrets.pypi_password }}
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: false
+
+      - name: Build and Publish Distribution to PyPI 📦
+        env:
+          PYPI_USERNAME: __token__
+          PYPI_PASSWORD: ${{ secrets.pypi_password }}
+          POETRY_REQUESTS_TIMEOUT: 60
+        run: |
+          poetry publish --no-interaction --build \
+            --username $PYPI_USERNAME \
+            --password $PYPI_PASSWORD