bed-reader 1.0.5b3__tar.gz → 1.0.6__tar.gz

bed_reader-1.0.6/.github/workflows/ci.yml

@@ -0,0 +1,205 @@
+# This file was originally generated by maturin v0.14.17
+
+name: CI3
+
+on:
+  push:
+  schedule:
+    - cron: '0 0 1 * *'
+  pull_request:
+  workflow_dispatch:
+    
+env:
+  CARGO_TERM_COLOR: always
+
+permissions:
+  contents: read
+
+jobs:
+
+  test_rust:
+    name: Test Rust
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up Rust (Pinned Version)
+        uses: dtolnay/rust-toolchain@1.81.0
+        with:
+          components: clippy, rustfmt, rust-src
+      - name: Run Clippy (strict for this pinned version of Rust)
+        run: cargo clippy --all-targets --all-features -- -D warnings
+      - name: Set up Rust (Latest Stable)
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          components: clippy, rustfmt, rust-src
+      - name: Run Clippy (lenient for latest version)
+        run: cargo clippy --all-targets --all-features -- -A warnings || echo "Clippy warnings from the latest version"
+      - name: Test Rust no-default-features
+        run: cargo test --verbose --no-default-features
+      - name: Test Rust default features
+        run: cargo test --verbose
+  
+  
+  macos:
+    runs-on: macos-13
+    strategy:
+      matrix:
+        target: [x86_64, aarch64]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: |
+            3.10
+            3.11
+            3.12
+            3.13
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+          
+  linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        target: [x86_64, aarch64]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: |
+            3.10
+            3.11
+            3.12
+            3.13
+
+      - name: Install cross-compilation dependencies
+        if: matrix.target == 'aarch64'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gcc-aarch64-linux-gnu
+          
+      - name: Build wheels for aarch64
+        if: matrix.target == 'aarch64'
+        env:
+          CC: aarch64-linux-gnu-gcc
+          CFLAGS: -march=armv8-a -D__ARM_ARCH=8
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist -i python3.10 -i python3.11 -i python3.12 -i python3.13
+          manylinux: auto
+
+      - name: Build wheels for x86_64
+        if: matrix.target == 'x86_64'
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist -i -i python3.10 -i python3.11 -i python3.12 -i python3.13
+          manylinux: auto
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+          
+  windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        target: [x64]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: |
+            3.10
+            3.11
+            3.12
+            3.13
+          architecture: ${{ matrix.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+        
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+  test_python:
+    name: Test Python
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+    runs-on: ${{ matrix.os }}
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+    - name: Install Rust
+      uses: actions-rs/toolchain@v1
+      with:
+        toolchain: stable
+        override: true
+    - name: Install the latest version of uv
+      uses: astral-sh/setup-uv@v3
+    - name: Install Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
+    - name: Pinned Ruff
+      run:  uvx ruff@0.6.9 check bed_reader
+    - name: Lastest Ruff (just to check for warnings)
+      run: uvx ruff@latest check bed_reader || echo "Ignoring warnings from the latest version of ruff"
+    - name: Install minimal dependencies
+      run: uv sync --extra min_dev
+    - name: Run min tests
+      shell: bash
+      run: |
+        if [[ "$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 --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 .

bed_reader-1.0.6/.github/workflows/docs.yml

@@ -0,0 +1,45 @@
+name: Build and Deploy Documentation
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:  # This allows manual triggering of the workflow
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout the code
+        uses: actions/checkout@v3
+
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Install Python
+        run: uv python install
+
+      - name: Install Rust
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true        
+
+      - name: Setup, Lint, and Test Python
+        run: |
+          uv sync --extra dev --extra sparse --extra samples
+          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
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: doc/build/html

{bed_reader-1.0.5b3 → bed_reader-1.0.6}/.gitignore

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

{bed_reader-1.0.5b3 → bed_reader-1.0.6}/CHANGELOG.md

@@ -5,6 +5,10 @@ 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).
 
+## [1.06] - 2024-10-17
+
+- Add support for Python 3.13. Fix minor reported bug.
+
 ## [1.05] - 2024-7-1
 
 - Add support for Python's Numpy 2