diff --git a/.github/workflows/build_and_publish.yml b/.github/workflows/build_and_publish.yml index 3c84d8e..59d3f88 100644 --- a/.github/workflows/build_and_publish.yml +++ b/.github/workflows/build_and_publish.yml @@ -6,37 +6,19 @@ on: - created jobs: - build-n-publish: - name: Build and publish Python distribution to PyPI - runs-on: ubuntu-latest - permissions: - id-token: write - steps: - - name: Check out git repository - uses: actions/checkout@v4 - - - name: Set up Python 3.11 - uses: actions/setup-python@v5 - with: - python-version: 3.11 - - - name: Install build tools - run: >- - python -m - pip install - wheel - twine - --user - - - name: Build a binary wheel and a source tarball - run: >- - python - setup.py - sdist - bdist_wheel - - - name: Publish distribution 📦 to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + pypi: + name: Build and publish to PyPI + runs-on: ubuntu-latest + # Environment and permissions trusted publishing. + environment: + name: release + permissions: + id-token: write + steps: + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 + - run: uv build + - run: uv publish --trusted-publishing always docker-image-CI: name: Docker Image CI @@ -44,7 +26,7 @@ jobs: steps: - name: Check out git repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Publish main image (Dockerfile) to Registry uses: elgohr/Publish-Docker-Github-Action@v5 diff --git a/.github/workflows/tests_and_cov.yml b/.github/workflows/tests_and_cov.yml index 84020f7..78e3db7 100644 --- a/.github/workflows/tests_and_cov.yml +++ b/.github/workflows/tests_and_cov.yml @@ -12,23 +12,22 @@ jobs: setup: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - name: Check out git repository + uses: actions/checkout@v4 - - name: Set up Python 3.11 + - name: Set up Python uses: actions/setup-python@v5 with: - python-version: 3.11 + python-version-file: ".python-version" - # Cache package installation step to speed up the following step - - uses: actions/cache@v4 + - name: Install uv + uses: astral-sh/setup-uv@v3 with: - path: ${{ env.pythonLocation }} - key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }} }} + enable-cache: true + cache-dependency-glob: "uv.lock" - - name: Install deps - run: | - pip install --upgrade --upgrade-strategy eager -e . - pip check + - name: Install the project + run: uv sync --all-extras --dev test: needs: setup @@ -36,22 +35,19 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python 3.11 - uses: actions/setup-python@v5 + - name: Install uv + uses: astral-sh/setup-uv@v3 with: - python-version: 3.11 + enable-cache: true + cache-dependency-glob: "uv.lock" - # Cache package installation step to speed up the following step - - uses: actions/cache@v4 + - name: Set up Python + uses: actions/setup-python@v5 with: - path: ${{ env.pythonLocation }} - key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }} - - - name: Install pytest - run: pip install pytest pytest-cov + python-version-file: ".python-version" - name: Run pytest - run: pytest --cov --rootdir=/home/runner/work/stranger + run: uv run pytest tests --cov --rootdir=/home/runner/work/stranger - name: Upload coverage uses: actions/upload-artifact@v4 @@ -65,10 +61,10 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - name: Set up Python 3.11 + - name: Set up Python uses: actions/setup-python@v5 with: - python-version: 3.11 + python-version-file: ".python-version" - name: Install deps run: | python -m pip install --upgrade pip diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..24ee5b1 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.13 diff --git a/CHANGELOG.md b/CHANGELOG.md index 20934ae..e81ee65 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,10 @@ All notable changes to this project will be documented in this file. This project adheres to [Semantic Versioning](http://semver.org/). +## [unreleased] +### Fixed +- Switch build system to uv-hatchling + ## [0.9.2] ### Fixed - Use codecov badge and fix scout link on README page diff --git a/Dockerfile b/Dockerfile index 71aa057..8e5eb0b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,13 +5,14 @@ # docker run -v $PWD:$PWD clinical-genomics/stranger:v0.9.0 stranger --help # docker run -v $PWD:$PWD clinical-genomics/stranger:v0.9.0 stranger -f /bin/stranger/stranger/resources/variant_catalog_hg38.json $PWD/sample.joint.repeats.merged.vcf.gz > $PWD/sample.repeats.stranger.vcf ############################################### -FROM continuumio/miniconda3:23.3.1-0-alpine +FROM ghcr.io/astral-sh/uv:python3.13-alpine -# Install git -RUN conda install -c anaconda git && \ - cd /bin && \ - git clone --depth 1 https://github.com/Clinical-Genomics/stranger.git && \ - cd stranger && \ - pip install --editable . +# Copy the project into the image +ADD . /app -ENTRYPOINT ["stranger"] +# Sync the project into a new environment, using the frozen lockfile +WORKDIR /app +RUN uv sync --frozen + + +ENTRYPOINT ["uv", "run", "stranger"] diff --git a/README.md b/README.md index 9535ad0..5479f6a 100644 --- a/README.md +++ b/README.md @@ -11,15 +11,18 @@ Annotates output files from [ExpansionHunter][hunter] and [TRGT][trgt] with the ## Installation +Stranger uses the `uv` project manager. It is very quick and lightweight - see the [uv installation instructions](https://docs.astral.sh/uv/getting-started/installation/). + ``` git clone github.com/clinical-genomics/stranger cd stranger -pip install --editable . +uv pip install --editable . ``` ## Usage ``` +uv run stranger --help Usage: stranger [OPTIONS] VCF Annotate str variants with str status diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..b2b523a --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,67 @@ +[project] +name = "stranger" +version = "0.9.2" +description = "Annotate VCF files with STR variants with pathogenicity implications" +authors = [{name="Daniel Nilsson", email="daniel.nilsson@ki.se"}, {name="Mans Magnuson", email="mans.magnusson@scilifelab.se"}] +license = {text = "MIT License"} +readme = "README.md" +include = [ + "README.md", + "stranger/**/*", + "tests/**/*" +] +requires-python = ">=3.7" +keywords = ["vcf", "variants", "str"] +classifiers = [ + "License :: OSI Approved :: MIT License", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Development Status :: 5 - Production/Stable", + "Programming Language :: Python :: Implementation :: CPython", + "Operating System :: MacOS :: MacOS X", + "Operating System :: Unix", + "Intended Audience :: Science/Research", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Topic :: Scientific/Engineering :: Medical Science Apps.", +] +dependencies = [ + "click", + "coloredlogs", + "importlib-resources>=5.12.0", + "PyYAML", +] + +[project.urls] +Repository = "https://github.com/Clinical-Genomics/stranger" +Changelog = "https://github.com/Clinical-Genomics/stranger/blob/main/CHANGELOG.md" +"Bug Tracker" = "https://github.com/Clinical-Genomics/stranger/issues" + + +[project.scripts] +stranger = "stranger.cli:cli" + +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[tool.black] +line-length = 100 +target-version = ['py313'] + +[tool.ruff] +src = ["stranger", "tests", "scripts"] +line-length = 100 + +[tool.isort] +profile = "black" + +[dependency-groups] +dev = [ + "pytest-cov>=4.1.0", + "pytest>=7.4.4", +] +lint = [ + "black>=23.3.0", + "isort>=5.11.5", + "ruff>=0.8.0", +] diff --git a/setup.py b/setup.py deleted file mode 100755 index b50f001..0000000 --- a/setup.py +++ /dev/null @@ -1,156 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -# Note: To use the 'upload' functionality of this file, you must: -# $ pip install twine -"""Based on https://github.com/kennethreitz/setup.py""" - -import io -import os -import sys -from shutil import rmtree - -from setuptools import Command, find_packages, setup -from setuptools.command.test import test as TestCommand - -# Package meta-data. -NAME = "stranger" -DESCRIPTION = "Annotate VCF files with str variants" -URL = "https://github.com/moonso/stranger" -EMAIL = "mans.magnusson@scilifelab.com" -AUTHOR = "Måns Magnusson" -REQUIRES_PYTHON = ">=3.6.0" -VERSION = None - -# What packages are required for this module to be executed? -REQUIRED = [ - "click", - "coloredlogs", - "pyyaml", -] - -# What packages are optional? -EXTRAS = { - "tests": ["pytest", "pytest-cov"], -} - -# The rest you shouldn't have to touch too much :) -# ------------------------------------------------ -# Except, perhaps the License and Trove Classifiers! -# If you do change the License, remember to change the Trove Classifier for that! - -here = os.path.abspath(os.path.dirname(__file__)) - -# Import the README and use it as the long-description. -# Note: this will only work if 'README.md' is present in your MANIFEST.in file! -try: - with io.open(os.path.join(here, "README.md"), encoding="utf-8") as f: - long_description = "\n" + f.read() -except FileNotFoundError: - long_description = DESCRIPTION - -# Load the package's __version__.py module as a dictionary. -about = {} -if not VERSION: - with open(os.path.join(here, NAME, "__version__.py")) as f: - exec(f.read(), about) -else: - about["__version__"] = VERSION - - -class UploadCommand(Command): - """Support setup.py upload.""" - - description = "Build and publish the package." - user_options = [] - - @staticmethod - def status(s): - """Prints things in bold.""" - print("\033[1m{0}\033[0m".format(s)) - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - def run(self): - try: - self.status("Removing previous builds…") - rmtree(os.path.join(here, "dist")) - except OSError: - pass - - self.status("Building Source and Wheel (universal) distribution…") - os.system("{0} setup.py sdist bdist_wheel --universal".format(sys.executable)) - - self.status("Uploading the package to PyPI via Twine…") - os.system("twine upload dist/*") - - self.status("Pushing git tags…") - os.system("git tag v{0}".format(about["__version__"])) - os.system("git push --tags") - - sys.exit() - - -# This is a plug-in for setuptools that will invoke py.test -# when you run python setup.py test -class PyTest(TestCommand): - """Set up the py.test test runner.""" - - def finalize_options(self): - """Set options for the command line.""" - TestCommand.finalize_options(self) - self.test_args = ["--cov=stranger"] - self.test_suite = True - - def run_tests(self): - """Execute the test runner command.""" - # Import here, because outside the required eggs aren't loaded yet - import pytest - - sys.exit(pytest.main(self.test_args)) - - -# Where the magic happens: -setup( - name=NAME, - version=about["__version__"], - description=DESCRIPTION, - long_description=long_description, - long_description_content_type="text/markdown", - author=AUTHOR, - author_email=EMAIL, - python_requires=REQUIRES_PYTHON, - url=URL, - packages=find_packages(exclude=("tests",)), - entry_points={ - "console_scripts": ["stranger = stranger.__main__:base_command"], - }, - install_requires=REQUIRED, - extras_require=EXTRAS, - tests_require=EXTRAS["tests"], - include_package_data=True, - license="MIT", - keywords=["vcf", "variants", "str"], - classifiers=[ - # Trove classifiers - # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers - "License :: OSI Approved :: MIT License", - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.6", - "Programming Language :: Python :: Implementation :: CPython", - "Operating System :: MacOS :: MacOS X", - "Operating System :: Unix", - "Intended Audience :: Science/Research", - "Topic :: Scientific/Engineering :: Bio-Informatics", - ], - # $ setup.py publish support. - cmdclass={ - "upload": UploadCommand, - "test": PyTest, - }, -) diff --git a/stranger/__main__.py b/stranger/__main__.py index d5e644c..5e53468 100755 --- a/stranger/__main__.py +++ b/stranger/__main__.py @@ -9,6 +9,7 @@ Invoke as `stranger` (if installed) or ``python -m stranger`` (no install required). """ + import sys from stranger.cli import cli as base_command diff --git a/stranger/cli.py b/stranger/cli.py index 9a8c56e..71e0569 100644 --- a/stranger/cli.py +++ b/stranger/cli.py @@ -1,7 +1,6 @@ import gzip import logging from codecs import getreader, open -from pprint import pprint as pp import click import coloredlogs @@ -36,7 +35,10 @@ def print_version(ctx, param, value): @click.option( "-f", "--repeats-file", - type=click.Path(exists=True), + type=click.Path( + exists=True, + path_type=str, + ), help="Path to a file with repeat definitions. See README for explanation", default=repeats_json_path, show_default=True, diff --git a/stranger/resources/__init__.py b/stranger/resources/__init__.py index 42ff9a4..f8a20d5 100644 --- a/stranger/resources/__init__.py +++ b/stranger/resources/__init__.py @@ -1,4 +1,8 @@ -import pkg_resources +try: + from importlib.resources import files +except ImportError: + # Try backported to piPY<37 `importlib_resources`. + from importlib_resources import files ###### Files ###### @@ -11,5 +15,5 @@ # Backround data path -repeats_path = pkg_resources.resource_filename("stranger", repeats_file) -repeats_json_path = pkg_resources.resource_filename("stranger", repeats_json) +repeats_path = files("stranger").joinpath(repeats_file) +repeats_json_path = files("stranger").joinpath(repeats_json) diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..1ebd419 --- /dev/null +++ b/uv.lock @@ -0,0 +1,503 @@ +version = 1 +requires-python = ">=3.7" +resolution-markers = [ + "python_full_version < 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