Merge pull request #11 from PennChopMicrobiomeProgram/10-update-ci-an…

…d-docs

Update CI workflows and docs

.github/workflows/pr.yml

@@ -0,0 +1,14 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main, master ]
+  pull_request:
+    branches: [ main, master ]
+
+  workflow_dispatch:
+
+jobs:
+  run-tests:
+    uses: ./.github/workflows/test.yml
+    secrets: inherit

.github/workflows/release.yml

@@ -0,0 +1,104 @@
+name: Release Package
+
+on:
+  release:
+    types: [published]
+
+  workflow_dispatch:
+
+jobs:
+  check-version:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install Library
+        run: |
+            python -m pip install .
+            python -m pip install setuptools
+
+      - id: get_version
+        uses: battila7/get-version-action@v2
+
+      - name: Check version
+        run: |
+          LIBRARY_VERSION=$(unassign --version)
+          GITHUB_VERSION=${{ steps.get_version.outputs.version-without-v }}
+          if [[ $LIBRARY_VERSION == $GITHUB_VERSION ]]; then
+            echo "Versions match, continuing..."
+          else
+            echo "Versions don't match, exiting..."
+            echo "Library version: $LIBRARY_VERSION"
+            echo "GitHub version: $GITHUB_VERSION"
+            exit 1
+          fi
+
+  run-tests:
+    uses: ./.github/workflows/test.yml
+    secrets: inherit
+
+  build-and-publish-to-pypi:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    needs: [run-tests, check-version]
+
+    permissions:
+        contents: read
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+
+    - name: Build package
+      run: python -m build
+
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
+
+  build-and-push-to-dockerhub:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    needs: [run-tests, check-version]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ctbushman/unassigner
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/test.yml

@@ -0,0 +1,90 @@
+name: Tests
+
+on:
+  workflow_call:
+
+  workflow_dispatch:
+
+jobs:
+  tests-with-coverage:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.x'
+
+      - name: setup-conda
+        uses: s-weigand/setup-conda@v1.1.0
+
+      - name: Install dependencies
+        run: |
+          conda install -c bioconda vsearch
+          python -m pip install --upgrade pip
+          python -m pip install pytest pytest-cov
+          python -m pip install .
+
+      - name: Run tests and collect coverage
+        run: pytest --cov tests
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+
+  tests:
+    name: Run Tests
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.12']
+        os: [ubuntu-latest] # setup-conda action currently doesn't work with latest macOS runners
+        include:
+          - python-version: '3.11'
+            os: ubuntu-latest
+          - python-version: '3.10'
+            os: ubuntu-latest
+          - python-version: '3.9'
+            os: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: setup-conda
+        uses: s-weigand/setup-conda@v1.1.0
+
+      - name: Install dependencies
+        run: |
+          conda install -c bioconda vsearch
+          python -m pip install --upgrade pip
+          python -m pip install pytest
+          python -m pip install .
+
+      - name: Run tests
+        run: pytest -s -vvvv -l --tb=long tests
+
+  lint:
+    name: Lint Code Base
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install Dependencies
+        run: pip install black
+
+      - name: Lint Code Base
+        run: |
+          black --check .

Dockerfile

@@ -0,0 +1,21 @@
+FROM condaforge/mambaforge:latest
+
+# Setup
+WORKDIR /home
+
+COPY . .
+
+# Install environment
+RUN mamba create --name primertrim -c conda-forge -c bioconda vsearch
+
+ENV PATH="/opt/conda/envs/primertrim/bin/:${PATH}"
+
+# "Activate" the environment
+SHELL ["conda", "run", "--no-capture-output", "-n", "primertrim", "/bin/bash", "-c"]
+
+RUN pip install /home/
+
+RUN echo "Python: $(python --version), Conda: $(conda --version), Vsearch: $(vsearch -v)" > installed_packages.txt
+
+# Run
+CMD "bash"