vcztools 0.0.1a3__tar.gz

vcztools-0.0.1a3/.clang-format

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+Language: Cpp
+BasedOnStyle: GNU
+SortIncludes:    false
+AllowShortIfStatementsOnASingleLine: false
+BreakBeforeBraces: Linux
+TabWidth:        4
+IndentWidth:     4
+ColumnLimit:     89
+SpaceBeforeParens:
+    ControlStatements
+SpacesInCStyleCastParentheses: false
+SpaceAfterCStyleCast: true
+IndentCaseLabels: true
+AlignAfterOpenBracket: DontAlign
+BinPackArguments: true
+BinPackParameters: true
+AlwaysBreakAfterReturnType: AllDefinitions
+
+# These are disabled for version 6 compatibility
+# StatementMacros: ["PyObject_HEAD"]
+# AlignConsecutiveMacros: true

vcztools-0.0.1a3/.github/workflows/cd.yml

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+name: CD
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  release:
+    types: [published]
+
+jobs:
+  packaging:
+    if: github.repository_owner == 'sgkit-dev'
+    name: Packaging
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip build validate-pyproject[all]
+          python -m build --sdist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist
+      - name: Build wheels
+        run: |
+          validate-pyproject pyproject.toml
+          docker run --rm -v `pwd`:/project -w /project quay.io/pypa/manylinux2014_x86_64 bash .github/workflows/docker/buildwheel.sh
+      - name: Check vcztools CLI
+        run: |
+          pip install numpy "zarr>=2.17,<3" click pyranges pyparsing
+          pip install vcztools --no-index --only-binary vcztools -f dist/wheelhouse
+          vcztools --help
+          # Make sure we don't have ``vcztools`` in the CWD
+          cd tests
+          python -m vcztools --help
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: linux-wheels
+          path: dist/wheelhouse
+
+  publish-to-pypi:
+    if: github.repository_owner == 'sgkit-dev' && github.event_name == 'release'
+    needs:
+      - packaging
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/vcztools
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all
+        uses: actions/download-artifact@v4.1.8
+      - name: Move to dist
+        run: |
+          mkdir dist
+          cp */*.{whl,gz} dist/.
+          ls dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+
+
+  publish-to-testpypi:
+    if: github.repository_owner == 'sgkit-dev' && github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+    needs:
+      - packaging
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/vcztools
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all
+        uses: actions/download-artifact@v4.1.8
+      - name: Move to dist
+        run: |
+          mkdir dist
+          cp */*.{whl,gz} dist/.
+          ls dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true
+          repository-url: https://test.pypi.org/legacy/

vcztools-0.0.1a3/.github/workflows/ci.yml

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+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  pre-commit:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - uses: pre-commit/action@v3.0.1
+  python_test:
+    name: Python tests
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    strategy:
+      matrix:
+        # Use macos-13 because pip binary packages for ARM aren't
+        # available for many dependencies
+        os: [macos-13, macos-14, ubuntu-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        exclude:
+          # Just run macos tests on one Python version
+          - os: macos-13
+            python-version: "3.10"
+          - os: macos-13
+            python-version: "3.11"
+          - os: macos-13
+            python-version: "3.12"
+          - os: macos-14
+            python-version: "3.9"
+          - os: macos-14
+            python-version: "3.10"
+          - os: macos-14
+            python-version: "3.12"
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Miniconda with Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge,bioconda
+      - name: Install dependencies
+        run: |
+          conda install bcftools
+          python -m pip install --upgrade pip
+          python -m pip install '.[dev]'
+          # Build the extension module in-place so pytest can find it
+          python3 setup.py build_ext --inplace
+      - name: Run tests
+        run: |
+          pytest
+
+  c_python_test:
+    name: CPython interface tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install system dependencies
+        run: |
+          sudo apt install -y gcovr
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install numpy pytest pytest_cov
+      - name: Build module with coverage
+        run: |
+          # Build the extension module in-place so pytest can find it
+          CFLAGS="--coverage" python3 setup.py build_ext --inplace
+      - name: Run tests
+        run: |
+          pytest -vs tests/test_cpython_interface.py
+      - name: Show coverage
+        run: |
+          gcovr --filter vcztools
+
+  c_test:
+    name: C tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt install -y ninja-build libcunit1-dev valgrind meson gcovr
+      - name: Build
+        working-directory: ./lib
+        run: |
+          meson setup -Db_coverage=true build
+      - name: Tests
+        working-directory: ./lib
+        run: |
+          ninja -C build test
+      - name: Show coverage
+        working-directory: ./lib
+        run: |
+          ninja -C build coverage-text
+          cat build/meson-logs/coverage.txt
+      - name: Valgrind
+        working-directory: ./lib
+        run: |
+          valgrind --leak-check=full --error-exitcode=1 ./build/tests
+
+  packaging:
+    name: Packaging
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build twine validate-pyproject[all]
+      - name: Check and install package
+        run: |
+          validate-pyproject pyproject.toml
+          python -m build
+          python -m twine check --strict dist/*
+          python -m pip install dist/*.whl
+      - name: Check vcztools CLI
+        run: |
+          vcztools --help
+          # Make sure we don't have ``vcztools`` in the CWD
+          cd tests
+          python -m vcztools --help
+
+  test-numpy-version:
+    name: Test numpy versions
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    strategy:
+      matrix:
+        numpy: ["==1.26", ">=2"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: '3.11'
+          channels: conda-forge,bioconda
+      - name: Install dependencies
+        run: |
+          conda install bcftools
+          python -m pip install --upgrade pip
+          python -m pip install '.[dev]'
+          # Build the extension module in-place so pytest can find it
+          python3 setup.py build_ext --inplace
+      - name: Install numpy${{ matrix.numpy }}
+        run: |
+          python -m pip install 'numpy${{ matrix.numpy }}'
+      - name: Run tests
+        run: |
+          pytest
+
+  test-zarr-version:
+    name: Test Zarr versions
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    strategy:
+      matrix:
+        zarr: ["==2.18.3", ">=3"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: '3.11'
+          channels: conda-forge,bioconda
+      - name: Install dependencies
+        run: |
+          conda install bcftools
+          python -m pip install --upgrade pip
+          python -m pip install '.[dev]'
+          # Build the extension module in-place so pytest can find it
+          python3 setup.py build_ext --inplace
+      - name: Install zarr${{ matrix.zarr }}
+        run: |
+          python -m pip install 'zarr${{ matrix.zarr }}'
+      - name: Run tests
+        run: |
+          pytest

vcztools-0.0.1a3/.github/workflows/docker/buildwheel.sh

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+#!/bin/bash
+DOCKER_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+source "$DOCKER_DIR/shared.env"
+
+set -e -x
+
+ARCH=`uname -p`
+echo "arch=$ARCH"
+
+# We're running as root in the docker container so git commands issued by
+# setuptools_scm will fail without this:
+git config --global --add safe.directory /project
+# Fetch the full history as we'll be missing tags otherwise.
+git fetch --unshallow
+for V in "${PYTHON_VERSIONS[@]}"; do
+    git reset --hard
+    git clean -fd
+    PYBIN=/opt/python/$V/bin
+    rm -rf build/       # Avoid lib build by one Python is used by another
+    $PYBIN/python -m venv env
+    source env/bin/activate
+    $PYBIN/python -m pip install --upgrade build
+    SETUPTOOLS_SCM_DEBUG=1 $PYBIN/python -m build
+done
+
+cd dist
+for whl in *.whl; do
+    auditwheel -v repair "$whl"
+    rm "$whl"
+done

vcztools-0.0.1a3/.github/workflows/docker/shared.env

@@ -0,0 +1,6 @@
+PYTHON_VERSIONS=(
+    cp39-cp39
+    cp310-cp310
+    cp311-cp311
+    cp312-cp312
+)

vcztools-0.0.1a3/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+.vscode
+vcz_test_cache/
+**/.DS_Store

vcztools-0.0.1a3/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-merge-conflict
+      - id: debug-statements
+      - id: mixed-line-ending
+      - id: check-case-conflict
+      - id: check-yaml
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.2
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format