migec 2.0.0a1__tar.gz

migec-2.0.0a1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  cpp:
+    name: C++ (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure
+        run: cmake -S . -B build -DMIGEC_TESTS=ON -DCMAKE_BUILD_TYPE=Release
+      - name: Build
+        run: cmake --build build --parallel
+      - name: Test
+        run: ctest --test-dir build --output-on-failure
+
+  python:
+    name: Python ${{ matrix.python-version }} (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.10", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v5
+      - name: Install
+        run: |
+          uv pip install --system scikit-build-core "pybind11>=3.0.2,<4" ninja cmake
+          uv pip install --system -e ".[test]" --no-build-isolation
+      - name: Show environment
+        # Prints all three versions, so the "kept in sync by hand" trio is visible on every run
+        # rather than at release time.
+        run: |
+          python -c "import migec, migec._core as c; print(migec.__version__, c.__version__, c.MIG_FORMAT_VERSION)"
+      - name: Test
+        run: python -m pytest tests/unit tests/synthetic -q
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      # Pinned: ruff's default rule set widens between releases, which turns a green local run
+      # into a red CI on an unrelated change.
+      - run: pip install ruff==0.15.9
+      - run: ruff check python/ tests/

migec-2.0.0a1/.github/workflows/docs.yml

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+name: Docs
+
+on:
+  push:
+    branches: [master]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install sphinx pydata-sphinx-theme
+      # -W: a warning is a broken cross-reference or a malformed table, and both render as
+      # silently wrong docs. Zero warnings, no exceptions.
+      - 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
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

migec-2.0.0a1/.github/workflows/publish.yml

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+name: Publish To PyPI
+
+# The PyPI trusted publisher for `migec` is configured against THIS filename and the `pypi`
+# environment below. Renaming either breaks publishing with an opaque OIDC error.
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  build-sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install build twine
+      - run: python -m build --sdist
+      - run: twine check dist/*
+      - uses: actions/upload-artifact@v4
+        with:
+          name: python-sdist
+          path: dist/*.tar.gz
+
+  build-wheels:
+    name: Wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # No Windows: this is a pipeline tool, and a Windows wheel would need a zlib we do not
+        # otherwise depend on. Source builds still configure there.
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pypa/cibuildwheel@v2.23.3
+        env:
+          CIBW_BUILD: "cp310-* cp311-* cp312-* cp313-*"
+          CIBW_SKIP: "*-musllinux_* *-manylinux_i686"
+          CIBW_TEST_COMMAND: "python -c \"import migec; print(migec.__version__)\""
+      - uses: actions/upload-artifact@v4
+        with:
+          name: python-wheels-${{ matrix.os }}
+          path: wheelhouse/*.whl
+
+  publish:
+    name: Publish To PyPI
+    needs: [build-sdist, build-wheels]
+    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:
+          path: dist
+          merge-multiple: true
+      - name: Validate package version matches release tag
+        run: |
+          python - <<'PY'
+          import os, re, sys, tomllib
+          with open("pyproject.toml", "rb") as fh:
+              version = tomllib.load(fh)["project"]["version"]
+          tag = os.environ["GITHUB_REF_NAME"].lstrip("v")
+          if version != tag:
+              sys.exit(f"pyproject version {version} != release tag {tag}")
+          print(f"version {version} matches tag")
+          PY
+      - run: ls -la dist
+      - uses: pypa/gh-action-pypi-publish@release/v1

migec-2.0.0a1/.github/workflows/testpypi.yml

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+name: Publish To TestPyPI
+
+# Manual dry run of publish.yml. Same build, different index.
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pypa/cibuildwheel@v2.23.3
+        env:
+          CIBW_BUILD: "cp312-*"
+          CIBW_SKIP: "*-musllinux_* *-manylinux_i686"
+          CIBW_TEST_COMMAND: "python -c \"import migec\""
+      - uses: actions/upload-artifact@v4
+        with:
+          name: testpypi-wheels-${{ matrix.os }}
+          path: wheelhouse/*.whl
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      contents: read
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

migec-2.0.0a1/.gitignore

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+# --- migec-specific ---
+# NB: .gitignore has no trailing comments -- the whole line is the pattern, so a comment after a
+# pattern silently makes it match nothing. Comments go on their own line.
+
+# cmake out-of-tree build, and scikit-build-core's build/{wheel_tag}
+build/
+# setup.sh creates this
+.venv/
+# intermediate record files; regenerate with `migec checkout`
+*.mig
+*.pumi
+# local experiments, never committed
+scratch/
+
+# --- python ---
+__pycache__/
+*.py[cod]
+*.egg-info/
+dist/
+.pytest_cache/
+.ruff_cache/
+.coverage
+htmlcov/
+
+# --- docs ---
+docs/_build/
+
+# --- os ---
+.DS_Store
+
+# Alignment indices pulled down by scripts/read_start_dispersion.py (X1). pysam writes the .bai
+# next to wherever it is pointed, which for an HTTP URL is the working directory -- 4.6 MB of it
+# reached a published sdist before this line existed.
+*.bam
+*.bai
+*.crai