Update package infrastructure

.github/workflows/python-package.yml

@@ -1,60 +1,26 @@
-name: Python package
+name: Package testing
 
 on:
   push:
-    branches: [ master ]
+    branches:
+      - master
+    tags:
+      - "[0-9]+.[0-9]+.[0-9]+*"
+
   pull_request:
-    branches: [ master ]
+    types: [opened, reopened, ready_for_review, synchronize]
+
+  workflow_dispatch:
 
 jobs:
-  tests:
-    runs-on: ubuntu-latest
+  test:
+    if: github.event.pull_request.draft == false
+    runs-on: arc-runner
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install Tox
-      run: pip install tox
-    - name: Run tox using the version of Python in `PATH`
-      run: tox -e py
-  docs:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-    - name: Install Tox
-      run: pip install tox
-    - name: Check that docs build successfully
-      run: tox -e docs
-  linters:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-    - name: Install Tox
-      run: pip install tox
-    - name: Check code is compliant with linters
-      run: tox -e linters
-  packaging:
-    runs-on: ubuntu-latest
+        tox-env: [py311, py312, py313, linters, docs, package]
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-    - name: Install Tox
-      run: pip install tox twine
-    - name: Check package structure
-      run: tox -e packaging
+      - uses: actions/checkout@v4
+      - name: Run Tests
+        run: |
+          tox -e ${{ matrix.tox-env }}

MANIFEST.in

@@ -1,13 +1,5 @@
-# Include setup.py.
-# NOTE: This is needed until setuptools is fixed to include setup.py file by
-# default for scenarios where the invoking script is not setup.py.
-# For more details, see: https://github.com/pypa/setuptools/issues/1506.
-include setup.py
-# Include meta data.
 include LICENSE
-# Include documentation and files needed by documentation.
 recursive-include docs *.py *.rst
-# Include tests and files needed by tests
 include tox.ini
 include pyproject.toml
-recursive-include tests *.py
+recursive-include tests *.py

docs/conf.py

@@ -1,75 +1,12 @@
-import os.path
+"""Configuration."""
 
-# Get package metadata from '__about__.py' file.
-about = {}
-base_dir = os.path.dirname(os.path.abspath(os.path.dirname(__file__)))
-with open(
-    os.path.join(base_dir, 'src', 'ngs_test_utils', '__about__.py'), 'r'
-) as fh:
-    exec(fh.read(), about)
-if '__version__' not in about:
-    raise AttributeError(
-        "Package's version is not defined. Please, install the package."
-    )
+from importlib.metadata import metadata
 
-# -- General configuration ------------------------------------------------
-
-# The extension modules to enable.
-extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.extlinks',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.coverage',
-    'sphinx.ext.viewcode',
-]
-
-# The suffix(es) of source filenames.
-source_suffix = '.rst'
-
-# The master toctree document.
-master_doc = 'index'
+meta = metadata("ngs-test-utils")
 
 # General information about the project.
-project = 'NGS test utils'
-version = about['__version__']
+project = "NGS test utils"
+version = meta["version"]
 release = version
-author = about['__author__']
-copyright = about['__copyright__']
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-exclude_patterns = ['_build']
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = False
-
-# Warn about all references where the target cannot be found.
-nitpicky = True
-# Except for the following:
-nitpick_ignore = [
-    # This is needed to prevent warnings for container types, e.g.:
-    # :type foo: tuple(bool, str).
-    ('py:obj', '')
-]
-
-# -- Options for HTML output ----------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.
-html_theme = 'sphinx_rtd_theme'
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'NgsTestUtilsdoc'
-
-# Configuration for intersphinx.
-intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}
+author = meta["author"]
+copyright = "2024, " + author

pyproject.toml

@@ -1,10 +1,106 @@
 [build-system]
 requires = [
-    "setuptools",
-    "wheel",
+    "setuptools >= 64.0.0",
+    "setuptools_scm >= 6.4.0",
 ]
 build-backend = "setuptools.build_meta"
 
-[tool.black]
-target-version = ["py36", "py37", "py38"]
-line-length = 119
+[project]
+name = "ngs_test_utils"
+description = "Utilities for generation of synthetic NGS files"
+authors = [
+    {name = "Genialis, Inc."},
+    {email = "[email protected]"},
+]
+dynamic = ["version"]
+readme = "README.rst"
+license = {text = "Apache 2.0"}
+requires-python = ">=3.11, <3.14"
+keywords = [
+    "ngs",
+    "test",
+    "bioinformatics",
+]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+dependencies = [
+    "numpy",
+    "pybedtools",
+    "pysam",
+]
+
+[project.optional-dependencies]
+docs = [
+    "sphinx",
+]
+package = [
+    "build>=0.8.0",
+    "check-manifest>=0.48",
+    "twine>=4.0.1",
+]
+test = [
+    "ruff",
+    "pytest>=7.2.0",
+    "pytest-cov>=4.0.0",
+    "pytest-mock>=3.10.0",
+    "toml>=0.10.2",
+]
+
+[project.urls]
+repository = "https://github.com/genialis/ngs-test-utils"
+
+[tool.setuptools_scm]
+
+[tool.ruff]
+line-length = 99
+target-version = "py312"
+# Necessary for isort
+src = ["src"]
+
+[tool.ruff.lint]
+select = [
+    # pydocstyle
+    "D",
+    # pycodestyle
+    "E", "W",
+    # pyflakes
+    "F",
+    # isort
+    "I",
+    # Pyupgrade - use a more modern / newer syntax if it exists
+    "UP",
+    # Mccabe - detect too complex code
+    "C901",
+    # flake8-2022 - Checks for misuse of sys.version or sys.version_info
+    "YTT",
+    # flake8 bugbear - find common bugs and design problems
+    "B",
+    # find unused `noqa` directive
+    "RUF100",
+]
+ignore = [
+    # `one-blank-line-before-class` (D203) and
+    # `no-blank-line-before-class` (D211) are incompatible.
+    "D203",
+    # `multi-line-summary-first-line` (D212) and
+    # `multi-line-summary-second-line` (D213) are incompatible.
+    "D213",
+    # Setting an explicit stacklevel in warnings.warn(...) is just a reccomendation
+    "B028",
+    # We need assert statemets in tests
+    "S101",
+]
+
+[tool.ruff.lint.per-file-ignores]
+# tests folder does not enforce pydocstyle
+"tests/*" = ["D"]