bed-reader 1.1.0__tar.gz → 1.2.0__tar.gz

bed_reader-1.2.0/.github/dependabot.yml

@@ -0,0 +1,16 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: monthly
+    open-pull-requests-limit: 1
+    # Version-specific refs hard-code a compiler and may not accept toolchain
+    # inputs. Review installer SHA changes manually to preserve MSRV/stable
+    # coverage. The `stable` compiler itself still updates on every CI run.
+    ignore:
+      - dependency-name: dtolnay/rust-toolchain
+    groups:
+      github-actions:
+        patterns:
+          - "*"

bed_reader-1.2.0/.github/workflows/ci.yml

@@ -0,0 +1,371 @@
+# This file was originally generated by maturin v0.14.17
+
+name: CI3
+
+# Full CI runs on pull requests, monthly, and for release tags (via
+# workflow_call). Pushes to main are not retested: branch protection requires
+# PRs to be up to date with main and to pass "CI result" before merging.
+# Documentation deployment on main is handled by docs.yml.
+on:
+  schedule:
+    - cron: '0 0 1 * *'
+  pull_request:
+  workflow_dispatch:
+  workflow_call:
+    
+env:
+  CARGO_TERM_COLOR: always
+  PYTHON_VERSIONS: |
+    3.11
+    3.12
+    3.13
+    3.14
+    3.15
+  PYTHON_VERSIONS_ARGS: "-i python3.11 -i python3.12 -i python3.13 -i python3.14 -i python3.15"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ci-${{ github.ref }}-${{ github.event_name }}
+  cancel-in-progress: true
+
+jobs:
+
+  test_rust:
+    name: Test Rust
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, windows-11-arm, macos-15, macos-15-intel]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - name: Set up Rust (Pinned Version)
+        uses: dtolnay/rust-toolchain@cfcaf53ba4c621917ec7f78a66bff7a8848ddad4 # 1.85.0
+        with:
+          components: clippy, rustfmt, rust-src
+      - name: Run Clippy (strict for this pinned version of Rust)
+        run: cargo clippy --locked --all-targets --all-features -- -D warnings
+      - name: Set up Rust (Latest Stable)
+        uses: dtolnay/rust-toolchain@b725eda525362e7cf34af9a7243cac1e3f01a7ec # generic installer
+        with:
+          toolchain: stable
+          components: clippy, rustfmt, rust-src
+      - name: Run Clippy (lenient for latest version)
+        run: cargo clippy --locked --all-targets --all-features
+      - name: Test Rust no-default-features
+        run: cargo test --locked --verbose --no-default-features
+      - name: Test Rust default features
+        run: cargo test --locked --verbose
+  
+  
+  macos:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - target: x86_64
+            os: macos-15-intel
+            deployment-target: "10.12"
+          - target: aarch64
+            os: macos-15
+            deployment-target: "11.0"
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
+        with:
+          python-version: ${{ env.PYTHON_VERSIONS }}
+      - name: Build wheels
+        env:
+          MACOSX_DEPLOYMENT_TARGET: ${{ matrix.deployment-target }}
+        uses: PyO3/maturin-action@e83996d129638aa358a18fbd1dfb82f0b0fb5d3b # v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --locked --out dist ${{ env.PYTHON_VERSIONS_ARGS }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        with:
+          name: wheels-macos-${{ matrix.target }}
+          path: dist
+          
+  linux:
+    # Native runners keep host build scripts and target C compilers aligned.
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - target: x86_64
+            os: ubuntu-latest
+          - target: aarch64
+            os: ubuntu-24.04-arm
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
+        with:
+          python-version: ${{ env.PYTHON_VERSIONS }}
+
+      - name: Build wheels
+        uses: PyO3/maturin-action@e83996d129638aa358a18fbd1dfb82f0b0fb5d3b # v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --locked --out dist ${{ env.PYTHON_VERSIONS_ARGS }}
+          manylinux: auto
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        with:
+          name: wheels-linux-${{ matrix.target }}
+          path: dist
+
+  windows:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: windows-latest
+            target: x64
+            architecture: x64
+          - os: windows-11-arm
+            target: aarch64-pc-windows-msvc
+            architecture: arm64
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
+        with:
+          python-version: ${{ env.PYTHON_VERSIONS }}
+          architecture: ${{ matrix.architecture }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@e83996d129638aa358a18fbd1dfb82f0b0fb5d3b # v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --locked --out dist ${{ env.PYTHON_VERSIONS_ARGS }}
+      - name: Upload wheels
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        with:
+          name: wheels-windows-${{ matrix.target }}
+          path: dist
+        
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - name: Build sdist
+        uses: PyO3/maturin-action@e83996d129638aa358a18fbd1dfb82f0b0fb5d3b # v1
+        with:
+          command: sdist
+          args: --out dist
+      - name: Upload sdist
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        with:
+          name: wheels-sdist
+          path: dist
+
+  merge_artifacts:
+    name: Merge Artifacts
+    needs: [macos, linux, windows, sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Create merged directory
+        run: mkdir -p merged_dist
+        
+      - name: Download all artifacts
+        uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
+        with:
+          path: artifacts
+          pattern: wheels-*
+          merge-multiple: true
+          
+      - name: List downloaded artifacts
+        run: find artifacts -type f | sort
+        
+      - name: Copy artifacts to merged directory
+        run: cp -r artifacts/* merged_dist/
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+        with:
+          version: "0.12.24"
+
+      - name: Checkout package validation requirements
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          path: source
+
+      - name: Validate distribution metadata
+        working-directory: source
+        run: |
+          uv sync --frozen --only-group dev --no-install-project --python 3.14
+          uv run --frozen --no-sync twine check --strict ../merged_dist/*
+        
+      - name: Upload merged artifacts
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        with:
+          name: wheels-all
+          path: merged_dist
+
+  test_python:
+    name: Test Python
+    env:
+      UV_PYTHON: ${{ matrix.python-version }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13", "3.14", "3.15"]
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, windows-11-arm, macos-15, macos-15-intel]
+    runs-on: ${{ matrix.os }}
+    steps:
+    - name: Checkout
+      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+    - name: Install Rust
+      uses: dtolnay/rust-toolchain@b725eda525362e7cf34af9a7243cac1e3f01a7ec # generic installer
+      with:
+        toolchain: stable
+        components: clippy, rustfmt, rust-src
+    - name: Install Python ${{ matrix.python-version }}
+      uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
+      with:
+        python-version: ${{ matrix.python-version }}
+        architecture: ${{ runner.arch == 'ARM64' && 'arm64' || 'x64' }}
+    - name: Install uv
+      uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+      with:
+        version: "0.12.24"
+    - name: Pinned Ruff
+      run:  uvx ruff@0.17.5 check bed_reader
+    - name: Install minimal dependencies
+      run: uv sync --frozen --extra min_dev
+    - name: Run min tests
+      shell: bash
+      run: |
+        if [[ "$RUNNER_OS" != "Windows" ]]; then
+          source .venv/bin/activate
+        else
+          source .venv/Scripts/activate
+        fi
+        pytest bed_reader/tests/test_opt_dep.py  
+    - name: Install all dependencies
+      run: uv sync --frozen --all-extras
+    - name: Run all tests
+      shell: bash
+      run: |
+        if [[ "$RUNNER_OS" != "Windows" ]]; then
+          source .venv/bin/activate
+        else
+          source .venv/Scripts/activate
+        fi
+        pytest .
+
+
+  artifact-test:
+    name: Installed wheel (${{ matrix.os }}, Python ${{ matrix.python-version }})
+    needs: merge_artifacts
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, windows-11-arm, macos-15, macos-15-intel]
+        python-version: ["3.11", "3.15"]
+    steps:
+      - name: Checkout test sources
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
+      - name: Install stable Python
+        uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: ${{ runner.arch == 'ARM64' && 'arm64' || 'x64' }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+        with:
+          version: "0.12.24"
+
+      - name: Download built distributions
+        uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
+        with:
+          name: wheels-all
+          path: artifact
+
+      - name: Install an exact compatible wheel
+        run: |
+          uv venv --python ${{ matrix.python-version }} .artifact-venv
+          uv pip install --python .artifact-venv --no-index --no-deps --only-binary :all: --find-links artifact bed-reader
+          uv pip install --python .artifact-venv "bed-reader[samples,sparse,dev]"
+
+      - name: Test outside the source checkout
+        shell: bash
+        working-directory: ${{ runner.temp }}
+        run: |
+          python -c "import pathlib, shutil, sys; shutil.copytree(pathlib.Path(sys.argv[1]) / 'bed_reader' / 'tests', pathlib.Path(sys.argv[2]) / 'bed_reader_artifact_tests')" "$GITHUB_WORKSPACE" "$RUNNER_TEMP"
+          uv run --no-project --python "$GITHUB_WORKSPACE/.artifact-venv" python -c "import bed_reader; assert '.artifact-venv' in bed_reader.__file__; print(bed_reader.__file__)"
+          uv run --no-project --python "$GITHUB_WORKSPACE/.artifact-venv" python -m pytest --import-mode=importlib --doctest-modules "$RUNNER_TEMP/bed_reader_artifact_tests"
+
+  sdist-test:
+    name: Source distribution (Python ${{ matrix.python-version }})
+    needs: sdist
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.15"]
+    steps:
+      - name: Checkout test sources
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
+      - name: Install stable Python
+        uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: ${{ runner.arch == 'ARM64' && 'arm64' || 'x64' }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+        with:
+          version: "0.12.24"
+
+      - name: Download source distribution
+        uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
+        with:
+          name: wheels-sdist
+          path: artifact
+
+      - name: Build and install from the source distribution
+        run: |
+          uv build --wheel --python ${{ matrix.python-version }} --no-sources --out-dir sdist-wheel artifact/*.tar.gz
+          uv venv --python ${{ matrix.python-version }} .artifact-venv
+          uv pip install --python .artifact-venv --no-index --no-deps --only-binary :all: --find-links sdist-wheel bed-reader
+          uv pip install --python .artifact-venv "bed-reader[samples,sparse,dev]"
+
+      - name: Compare complete direct and sdist-derived wheels
+        if: matrix.python-version == '3.11'
+        run: uv run --no-project --python 3.11 python scripts/verify_sdist_wheel.py artifact/*.tar.gz
+
+      - name: Test outside the source checkout
+        working-directory: ${{ runner.temp }}
+        run: |
+          python -c "import pathlib, shutil, sys; shutil.copytree(pathlib.Path(sys.argv[1]) / 'bed_reader' / 'tests', pathlib.Path(sys.argv[2]) / 'bed_reader_artifact_tests')" "$GITHUB_WORKSPACE" "$RUNNER_TEMP"
+          uv run --no-project --python "$GITHUB_WORKSPACE/.artifact-venv" python -c "import bed_reader; assert '.artifact-venv' in bed_reader.__file__; print(bed_reader.__file__)"
+          uv run --no-project --python "$GITHUB_WORKSPACE/.artifact-venv" python -m pytest --import-mode=importlib --doctest-modules "$RUNNER_TEMP/bed_reader_artifact_tests"
+
+  ci-result:
+    # The single required status check for branch protection. It runs even
+    # when other jobs fail, so a failure can never appear as a passing skip.
+    name: CI result
+    if: always()
+    needs: [test_rust, macos, linux, windows, sdist, merge_artifacts, test_python, artifact-test, sdist-test]
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    steps:
+      - name: Require every CI job to succeed
+        env:
+          RESULTS: ${{ toJSON(needs.*.result) }}
+        run: |
+          echo "$RESULTS"
+          jq -e 'all(.[]; . == "success")' <<< "$RESULTS"

bed_reader-1.2.0/.github/workflows/docs.yml

@@ -0,0 +1,55 @@
+name: Build and Deploy Documentation
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:  # This allows manual triggering of the workflow
+
+permissions:
+  contents: read
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    permissions:
+      contents: write
+
+    steps:
+      - name: Checkout the code
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
+      - name: Install stable Python
+        uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
+        with:
+          python-version: "3.14"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+        with:
+          version: "0.12.24"
+
+      - name: Install Rust
+        uses: dtolnay/rust-toolchain@b725eda525362e7cf34af9a7243cac1e3f01a7ec # generic installer
+        with:
+          toolchain: stable
+          components: rust-src
+
+      - name: Setup, Lint, and Test Python
+        run: |
+          uv sync --frozen --all-extras
+          source .venv/bin/activate
+          sphinx-build --version  # Verify Sphinx is installed
+
+      - name: Build the Sphinx documentation
+        working-directory: ./doc
+        run: |
+          source ../.venv/bin/activate
+          make html SPHINXOPTS="-W --keep-going -E -a"
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@84c30a85c19949d7eee79c4ff27748b70285e453 # v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: doc/build/html

bed_reader-1.2.0/.github/workflows/release.yml

@@ -0,0 +1,56 @@
+name: Release
+
+on:
+  push:
+    tags: ["v*"]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: release-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  validate-tag:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
+        with:
+          python-version: "3.14"
+      - name: Verify Python, Rust, and tag versions agree
+        env:
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: |
+          python - <<'PY'
+          import os
+          from pathlib import Path
+          import tomllib
+
+          python_version = tomllib.loads(Path("pyproject.toml").read_text())["project"]["version"]
+          rust_version = tomllib.loads(Path("Cargo.toml").read_text())["package"]["version"]
+          assert python_version == rust_version, (python_version, rust_version)
+          assert os.environ["RELEASE_TAG"] == f"v{python_version}", os.environ["RELEASE_TAG"]
+          PY
+
+  qualify:
+    needs: validate-tag
+    uses: ./.github/workflows/ci.yml
+
+  publish:
+    needs: qualify
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/bed-reader
+    permissions:
+      id-token: write
+    steps:
+      - name: Download the qualified distributions
+        uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
+        with:
+          name: wheels-all
+          path: dist
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@7245906fb61fa33a13554f9d5fb856fe61758086 # v1.14.3

{bed_reader-1.1.0 → bed_reader-1.2.0}/.gitignore

@@ -150,4 +150,3 @@ oldCargo.lock
 bed_reader/Untitled-1.ipynb
 del.rs
 src/orig.rs
-uv.lock

{bed_reader-1.1.0 → bed_reader-1.2.0}/CHANGELOG.md

@@ -5,6 +5,28 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.2.0] - 2026-11-13
+
+- Require Python 3.11 or later and prepare Python 3.15 wheels with PyO3 0.30.1,
+  Rust NumPy 0.30, and maturin 1.16.
+- Require Rust 1.85 or later. Upgrade cloud-file to 0.3.1 and use its u64 byte
+  ranges without narrowing file offsets. Rust callers supplying a CloudFile
+  must use cloud-file 0.3.
+- Refresh compatible dependencies and remove the vulnerable quick-xml chain.
+  Retain shared ndarray 0.16 and compiler-compatible psm/crc-fast versions in
+  the lockfile.
+- Track the uv lockfile, pin CI actions, and test installed wheels and source
+  distributions on boundary Python versions, including Linux and Windows ARM64.
+- Preserve caller arrays when replacing missing integer metadata, including
+  read-only arrays, and avoid NumPy's invalid NaN-to-integer conversion warning.
+- Prepare a tag-triggered PyPI release workflow that reuses the full CI suite,
+  validates metadata, and publishes the qualified artifacts with trusted publishing.
+  Compare complete direct and source-derived wheels without ignoring native code.
+
+## [1.1.1] - 2026-06-05
+
+- Fix Rust README CI badge.
+
 ## [1.1.0] - 2026-06-04
 
 - Add support for Python 3.14.