Update packaging metadata and config (#1).

Github actions, pre commit configurations, linting etc.

.github/workflows/pypi-publish.yml

@@ -0,0 +1,51 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Publish to PyPI
+
+on:
+  push:
+    tags: "*"
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest tox
+    # - name: Lint with flake8
+    #   run: |
+    #     # stop the build if there are Python syntax errors or undefined names
+    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with tox
+      run: |
+        tox
+    - name: Build docs
+      run: |
+        tox -e docs
+    - run: touch ./docs/_build/html/.nojekyll
+    - name: GH Pages Deployment
+      uses: JamesIves/[email protected]
+      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
+    - name: Build Project and Publish
+      run: |
+        python -m tox -e clean,build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/pypi-test.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Test the library
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ]
+
+    name: Python ${{ matrix.python-version }}
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest tox
+    # - name: Lint with flake8
+    #   run: |
+    #     # stop the build if there are Python syntax errors or undefined names
+    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with tox
+      run: |
+        tox

.pre-commit-config.yaml

@@ -0,0 +1,52 @@
+exclude: '^docs/conf.py'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+  - id: trailing-whitespace
+  - id: check-added-large-files
+  - id: check-ast
+  - id: check-json
+  - id: check-merge-conflict
+  - id: check-xml
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: requirements-txt-fixer
+  - id: mixed-line-ending
+    args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+- repo: https://github.com/PyCQA/docformatter
+  rev: v1.7.5
+  hooks:
+    - id: docformatter
+      additional_dependencies: [tomli]
+      args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+      # --config, ./pyproject.toml
+
+- repo: https://github.com/psf/black
+  rev: 23.10.1
+  hooks:
+  - id: black
+    language_version: python3
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.3
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+
+## If like to embrace black styles even in the docs:
+# - repo: https://github.com/asottile/blacken-docs
+#   rev: v1.13.0
+#   hooks:
+#   - id: blacken-docs
+#     additional_dependencies: [black]
+
+## Check for misspells in documentation files:
+# - repo: https://github.com/codespell-project/codespell
+#   rev: v2.2.5
+#   hooks:
+#   - id: codespell

AUTHORS.md

@@ -1,3 +1,4 @@
 # Contributors
 
 * LTLA [[email protected]](mailto:[email protected])
+* jkanche [[email protected]](mailto:[email protected])

docs/conf.py

@@ -72,6 +72,7 @@
     "sphinx.ext.ifconfig",
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -166,12 +167,23 @@
 # If this is True, todo emits a warning for each TODO entries. The default is False.
 todo_emit_warnings = True
 
+autodoc_default_options = {
+    # 'members': 'var1, var2',
+    # 'member-order': 'bysource',
+    'special-members': True,
+    'undoc-members': True,
+    'exclude-members': '__weakref__, __dict__, __str__, __module__, __init__'
+}
+
+autosummary_generate = True
+autosummary_imported_members = True
+
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = "alabaster"
+html_theme = "furo"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

docs/requirements.txt

@@ -1,6 +1,8 @@
+furo
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
 sphinx>=3.2.1
+sphinx-autodoc-typehints

pyproject.toml

@@ -7,3 +7,18 @@ build-backend = "setuptools.build_meta"
 # For smarter version schemes and other configuration options,
 # check out https://github.com/pypa/setuptools_scm
 version_scheme = "no-guess-dev"
+
+[tool.ruff]
+line-length = 120
+src = ["src"]
+exclude = ["tests"]
+extend-ignore = ["F821"]
+
+[tool.ruff.pydocstyle]
+convention = "google"
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
+
+[tool.black]
+force-exclude = "__init__.py"

setup.cfg

@@ -5,17 +5,17 @@
 
 [metadata]
 name = IRanges
-description = Add a short description here!
+description = Python implementation of the [**IRanges**](https://bioconductor.org/packages/IRanges) Bioconductor package.
 author = LTLA
 author_email = [email protected]
 license = MIT
 license_files = LICENSE.txt
 long_description = file: README.md
 long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
-url = https://github.com/pyscaffold/pyscaffold/
+url = https://github.com/biocpy/iranges
 # Add here related links, for example:
 project_urls =
-    Documentation = https://pyscaffold.org/
+    Documentation = https://github.com/biocpy/iranges
 #    Source = https://github.com/pyscaffold/pyscaffold/
 #    Changelog = https://pyscaffold.org/en/latest/changelog.html
 #    Tracker = https://github.com/pyscaffold/pyscaffold/issues
@@ -41,16 +41,16 @@ package_dir =
     =src
 
 # Require a min/specific Python version (comma-separated conditions)
-# python_requires = >=3.8
+python_requires = >=3.8
 
 # Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0.
 # Version specifiers like >=2.2,<3.0 avoid problems due to API changes in
 # new major versions. This works if the required packages follow Semantic Versioning.
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    biocutils
-    biocframe
+    biocutils>=0.0.6
+    biocframe>=0.4.0
 
 
 [options.packages.find]
@@ -62,12 +62,17 @@ exclude =
 # Add here additional requirements for extra features, to install with:
 # `pip install IRanges[PDF]` like:
 # PDF = ReportLab; RXP
+optional =
+    numpy
 
 # Add here test requirements (semicolon/line-separated)
 testing =
     setuptools
     pytest
     pytest-cov
+    biocframe
+    biocutils
+    numpy
 
 [options.entry_points]
 # Add here console scripts like:

setup.py

@@ -1,10 +1,8 @@
-"""
-    Setup file for IRanges.
-    Use setup.cfg to configure your project.
+"""Setup file for IRanges. Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.5.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.5.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
 from setuptools import setup