docs and automation

.github/workflows/build_and_publish.yml

@@ -15,12 +15,23 @@ jobs:
    - name: Check out git repository
      uses: actions/checkout@v4
 
-   - name: Set up Python 3.12
+   - name: Set up Python
      uses: actions/setup-python@v5
      with:
-      python-version: 3.12
+      python-version-file: ".python_version"
+
    - name: Install uv
      uses: astral-sh/setup-uv@v3
+     with:
+       enable-cache: true
+       cache-dependency-glob: "uv.lock"
+
+    - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run tests
+        # For example, using `pytest`
+        run: uv run pytest tests
 
    - name: Install build tools
      run: >-

.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
@@ -38,24 +37,17 @@ jobs:
 
       - name: Install uv
         uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version-file: ".python-version"
 
-        # Cache package installation step to speed up the following step
-      - uses: actions/cache@v4
-        with:
-          path: ${{ env.pythonLocation }}
-          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}
-
-
-      - name: Install pytest
-        run: pip install pytest pytest-cov
-
       - 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
@@ -69,10 +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

README.md

@@ -11,10 +11,12 @@ 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

pyproject.toml

@@ -3,7 +3,7 @@ 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 = "MIT"
+license = {text = "MIT License"}
 readme = "README.md"
 include = [
   "README.md",

stranger/resources/__init__.py

@@ -1,4 +1,8 @@
-from importlib_resources import files
+try:
+    from importlib.resources import files
+except ImportError:
+    # Try backported to piPY<37 `importlib_resources`.
+    from importlib_resources import files
 
 ###### Files ######