bed-reader 1.0.5b4__tar.gz → 1.0.6__tar.gz

{bed_reader-1.0.5b4 → bed_reader-1.0.6}/.github/workflows/ci.yml

@@ -26,12 +26,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
-      - name: Set up Rust
-        uses: actions-rs/toolchain@v1
+        uses: actions/checkout@v4
+      - name: Set up Rust (Pinned Version)
+        uses: dtolnay/rust-toolchain@1.81.0
         with:
-          toolchain: stable
-          override: true
+          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
@@ -48,10 +55,10 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: |
-            3.9
             3.10
             3.11
             3.12
+            3.13
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
@@ -73,10 +80,10 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: |
-            3.9
             3.10
             3.11
             3.12
+            3.13
 
       - name: Install cross-compilation dependencies
         if: matrix.target == 'aarch64'
@@ -92,7 +99,7 @@ jobs:
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.target }}
-          args: --release --out dist -i python3.9 -i python3.10 -i python3.11 -i python3.12
+          args: --release --out dist -i python3.10 -i python3.11 -i python3.12 -i python3.13
           manylinux: auto
 
       - name: Build wheels for x86_64
@@ -100,7 +107,7 @@ jobs:
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.target }}
-          args: --release --out dist -i python3.9 -i python3.10 -i python3.11 -i python3.12
+          args: --release --out dist -i -i python3.10 -i python3.11 -i python3.12 -i python3.13
           manylinux: auto
 
       - name: Upload wheels
@@ -119,10 +126,10 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: |
-            3.9
             3.10
             3.11
             3.12
+            3.13
           architecture: ${{ matrix.target }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
@@ -150,64 +157,49 @@ jobs:
           name: wheels
           path: dist
 
-  test:
-    name: Test
+  test_python:
+    name: Test Python
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9, "3.10", "3.11", "3.12"]
+        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
-    - uses: actions/setup-python@v4
+    - name: Install Rust
+      uses: actions-rs/toolchain@v1
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install flake8, etc
-      run: |
-        cd bed_reader
-        pwd
-        python -m pip install --upgrade pip
-        pip install flake8 pytest black isort --upgrade
-    - name: Lint with flake8, etc
-      run: |
-        echo "flake8"
-        flake8 .
-        echo "black"
-        black --version
-        black --verbose --check .
-        echo "isort"
-        isort --check-only .
-    - name: Test Python - Non-Windows
-      if: runner.os != 'Windows'
+        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 ${{ matrix.python-version }}
+    - name: Pinned Ruff
+      run:  uvx ruff@0.6.9 check bed_reader
+    - name: Lastest Ruff (just to check for warnings)
+      run: uvx ruff@latest check bed_reader || echo "Ignoring warnings from the latest version of ruff"
+    - name: Install minimal dependencies
+      run: uv sync --extra min_dev
+    - name: Run min tests
+      shell: bash
       run: |
-        pip install virtualenv
-        virtualenv vEnv; source vEnv/bin/activate
-        python -m pip install --upgrade pip maturin
-        maturin develop
-        pip install -r requirements-min-dev.txt
-        pytest bed_reader/tests/test_opt_dep.py
-        echo "requirements"
-        pip install -r requirements.txt
-        echo "requirements-dev"
-        pip install -r requirements-dev.txt
-        pytest bed_reader
-    - name: Test Python - Windows
-      if: runner.os == 'Windows'
+        if [[ "$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: |
-        pip install virtualenv
-        virtualenv vEnv; vEnv\Scripts\activate.ps1
-        echo "pwd"
-        pwd
-        python -m pip install --upgrade pip maturin
-        pip install -r requirements-min-dev.txt
-        pytest bed_reader/tests/test_opt_dep.py
-        echo "requirements"
-        pip install -r requirements.txt
-        echo "requirements-dev"
-        pip install -r requirements-dev.txt
-        echo "maturin"
-        maturin develop
-        echo "pytest"
-        pytest bed_reader
+        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-1.0.5b4 → 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-1.0.5b4 → 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