Use uv in GitHub Action

Author: pbashyal-nmdp

.github/workflows/python-tests.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: BDD and Unit Tests
 
 on:
@@ -10,24 +7,29 @@ on:
     branches: [ master ]
 
 jobs:
-  build:
-
+  run-tests:
+    name: python
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        if [ -f requirements-tests.txt ]; then pip install -r requirements-tests.txt; fi
-    - name: Test with pytest
-      run: |
-        pytest
-    - name: Run BDD Tests
-      run: |
-        behave
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          # Install a specific version of uv.
+          version: "0.8.15"
+
+      - name: Install the project
+        run: uv sync --locked  --group=test
+
+      - name: Run pytests
+        run: uv run pytest
+
+      - name: Run BDD Tests
+        run: uv run behave

tests/unit/test_my_project_template.py

@@ -26,6 +26,9 @@
 """Tests for `my_project_template` package."""
 
 import pytest
+from my_project_template.algorithm.match import slug_match
+from my_project_template.model.slug import SLUG
+from my_project_template.model.allele import Allele
 
 
 @pytest.fixture
@@ -40,3 +43,25 @@ def supported_genes():
 def test_content(supported_genes):
     """Sample pytest test function with the pytest fixture as an argument."""
     assert "HLA-A" in supported_genes
+
+
+def test_slug_match_identical_slugs():
+    """Test that identical SLUGs match."""
+    allele1 = Allele("HLA-A", "HLA-A*01:01")
+    allele2 = Allele("HLA-A", "HLA-A*02:01")
+    slug1 = SLUG(allele1, allele2)
+    slug2 = SLUG(allele1, allele2)
+    
+    assert slug_match(slug1, slug2) is True
+
+
+def test_slug_match_different_slugs():
+    """Test that different SLUGs do not match."""
+    allele1 = Allele("HLA-A", "HLA-A*01:01")
+    allele2 = Allele("HLA-A", "HLA-A*02:01")
+    allele3 = Allele("HLA-A", "HLA-A*03:01")
+    
+    slug1 = SLUG(allele1, allele2)
+    slug2 = SLUG(allele1, allele3)
+    
+    assert slug_match(slug1, slug2) is False