Repository: Clinical-Genomics/stranger (language: python)

Issue:
Fix setup tools compatibility issues
- possibly migrate to poetry/uv or other toml based setup when we are at it


Discussion / hints:

Fix patch:
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/.python-version b/.python-version
new file mode 100644
index 0000000..24ee5b1
--- /dev/null
+++ b/.python-version
@@ -0,0 +1,1 @@
+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 < '3.8' or sys_platform != 'win32'",
+    "python_full_version >= '3.8' and sys_platform == 'win32'",
+]
+
+[[package]]
+name = "black"
+version = "23.3.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "click" },
+    { name = "mypy-extensions" },
+    { name = "packaging" },
+    { name = "pathspec" },
+    { name = "platformdirs" },
+    { name = "tomli", marker = "python_full_version < '3.11'" },
+    { name = "typed-ast", marker = "python_full_version < '3.8' and implementation_name == 'cpython'" },
+    { name = "typing-extensions", marker = "python_full_version < '3.10'" },
+]
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+wheels = [
+    { url = "https://files.pythonhosted.org/packages/5b/fa/c9e82bbe1af6266adf08afb563905eb87cab83fde00a0a08963510621047/zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556", size = 6758 },
+]


Test patch:
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