vdjmatch 0.0.1__tar.gz

vdjmatch-0.0.1/.github/workflows/docs.yml

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+name: docs
+
+on:
+  push:
+    branches: [dev, master]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Per-ref so a dev push never cancels an in-flight master Pages deploy.
+concurrency:
+  group: pages-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install docs toolchain
+        # autodoc imports vdjmatch with heavy deps (seqtree, polars) mocked in docs/conf.py,
+        # so the native seqtree toolchain is not needed to build docs.
+        run: pip install sphinx pydata-sphinx-theme nbsphinx ipython
+      - name: Build HTML (fail on warnings)
+        run: sphinx-build -W --keep-going -b html docs docs/_build/html
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  deploy:
+    needs: build
+    # The github-pages environment only allows deploys from the default branch; on dev we
+    # validate the build (above) but skip deployment so the workflow stays green.
+    if: github.ref == 'refs/heads/master'
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

vdjmatch-0.0.1/.github/workflows/publish.yml

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+name: Publish To PyPI
+
+on:
+  release:
+    types:
+      - published
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    # vdjmatch is pure Python (hatchling) -> one sdist + one universal wheel via `build`.
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install build tooling
+        run: python -m pip install --upgrade pip build twine
+      - name: Build sdist + wheel
+        run: python -m build
+      - name: Check distributions
+        run: python -m twine check dist/*
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-dist
+          path: dist/
+
+  smoke:
+    name: Smoke-test wheel (py${{ matrix.python-version }})
+    needs: build
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.12"]
+    steps:
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: actions/download-artifact@v4
+        with:
+          name: python-dist
+          path: dist/
+      - name: Install built wheel (deps incl. seqtree resolved from PyPI)
+        run: |
+          pip install --upgrade pip
+          pip install dist/*.whl
+      - name: Import vdjmatch
+        run: python -c "import vdjmatch; print('[OK] vdjmatch', vdjmatch.__version__)"
+
+  publish:
+    name: Publish To PyPI
+    needs: [build, smoke]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      contents: read
+      id-token: write  # required for OIDC trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
+        with:
+          name: python-dist
+          path: dist/
+      - name: Validate package version matches release tag
+        if: github.event_name == 'release'
+        run: |
+          python - <<'PY'
+          from pathlib import Path
+          import tomllib
+          version = tomllib.loads(Path("pyproject.toml").read_text())["project"]["version"]
+          tag = "${{ github.event.release.tag_name }}"
+          norm = tag[1:] if tag.startswith("v") else tag
+          if version != norm:
+              raise SystemExit(f"Version mismatch: pyproject.toml={version}, tag={tag}")
+          print(f"Version check passed: {version} == {tag}")
+          PY
+      - name: List distributions
+        run: ls -R dist/
+      - name: Publish distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

vdjmatch-0.0.1/.github/workflows/tests.yml

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+name: tests
+
+on:
+  push:
+    branches: [dev, master]
+  pull_request:
+    branches: [dev, master]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  unit:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+      - name: Install vdjmatch + test deps (seqtree resolved from PyPI)
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[test,bench]"
+      - name: Run unit tests
+        run: pytest -m "not slow" -ra

vdjmatch-0.0.1/.gitignore

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+# Python
+.venv/
+__pycache__/
+*.py[cod]
+*.egg-info/
+build/
+dist/
+.pytest_cache/
+.hypothesis/
+.ruff_cache/
+.cache/
+# vdjmatch caches / outputs
+*.annot.txt
+*.annot.summary.txt
+.vdjmatch_cache/
+# editors / OS
+.idea/
+*.iml
+.DS_Store
+
+# Sphinx build output
+docs/_build/