Overhaul the package (#49)

This is a major rewrite of the package for better consistency with the IRanges R/Bioconductor package.

- Using pybind11, reimplement inter-range methods to a cpp implementation using code derived from the R package.
- Better Start/End/Width resolver that is similar to the R implementation.
- Overhaul of many of the find overlaps and search methods to better align with R's expectations of how they work.
- Update docstrings, more tests.

.github/workflows/build-docs.yml

@@ -0,0 +1,40 @@
+name: Build documentation
+
+on:
+  push:
+    tags:
+      - "*"
+
+jobs:
+  test:
+    name: Build docs
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+          cache: 'pip'
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install cmake pybind11 numpy tox
+
+      - name: Build docs
+        run: |
+          python setup.py build_ext --inplace
+          cp build/lib*/iranges/lib_iranges* src/iranges/
+          tox -e docs
+          touch ./docs/_build/html/.nojekyll
+
+      - name: GH Pages Deployment
+        if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/')
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: gh-pages # The branch the action should deploy to.
+          folder: ./docs/_build/html
+          clean: true # Automatically remove deleted files from the deploy branch

.github/workflows/publish-pypi.yml

@@ -0,0 +1,62 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "*"
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # macos-13 is an intel runner, higher macos's are apple silicon
+        # At some point, maybe get this to work on windows-latest
+        os: [ubuntu-latest, macos-13, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.22.0
+        env:
+          CIBW_ARCHS_LINUX: x86_64 # remove this later so we build for all linux archs
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
+          CIBW_SKIP: pp*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@v1.12.2
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/run-tests.yml

@@ -0,0 +1,32 @@
+name: Test the library
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    name: Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Get latest CMake
+        uses: lukka/get-cmake@latest
+
+      - name: Test with tox
+        run: |
+          pip install tox
+          tox

CHANGELOG.md

@@ -1,5 +1,14 @@
 # Changelog
 
+## Version 0.4.0
+
+This is a major rewrite of the package partly driven by performance and for better consistency with the IRanges R/Bioconductor package.
+
+- Using pybind11, reimplement inter-range methods to a cpp implementation using code derived from the R package.
+- Better Start/End/Width resolver that is similar to the R implementation.
+- Overhaul of many of the find overlaps and search methods to better align with R's expectations of how these methods work.
+- Update docstrings, more tests.
+
 ## Version 0.3.0
 
 - chore: Remove Python 3.8 (EOL)

README.md

@@ -12,7 +12,7 @@
 
 [![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
 [![PyPI-Server](https://img.shields.io/pypi/v/IRanges.svg)](https://pypi.org/project/IRanges/)
-![Unit tests](https://github.com/BiocPy/IRanges/actions/workflows/pypi-test.yml/badge.svg)
+![Unit tests](https://github.com/BiocPy/IRanges/actions/workflows/run-tests.yml/badge.svg)
 
 # Integer ranges in Python
 

lib/CMakeLists.txt

@@ -0,0 +1,24 @@
+cmake_minimum_required(VERSION 3.24)
+
+project(iranges
+    VERSION 1.0.0
+    DESCRIPTION "Building the rds shared library"
+    LANGUAGES CXX)
+
+find_package(pybind11 CONFIG)
+
+# pybind11 method:
+pybind11_add_module(iranges
+    src/coverage.cpp
+    src/interranges.cpp
+    src/init.cpp
+)
+
+set_property(TARGET iranges PROPERTY CXX_STANDARD 17)
+
+target_link_libraries(iranges PRIVATE pybind11::pybind11)
+
+set_target_properties(iranges PROPERTIES
+    OUTPUT_NAME lib_iranges
+    PREFIX ""
+)