Merge pull request #82 from Clinical-Genomics/depend_setuptools

Fix #81 - setuptools not explicit in all distros - switch to uv

.github/workflows/build_and_publish.yml

@@ -6,45 +6,27 @@ 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
    runs-on: ubuntu-latest
    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

.github/workflows/tests_and_cov.yml

@@ -12,46 +12,42 @@ 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
     runs-on: ubuntu-latest
     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

.python-version

@@ -0,0 +1 @@
+3.13

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

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"]

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

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="[email protected]"}, {name="Mans Magnuson", email="[email protected]"}]
+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",
+]