Upgrade to Modern Python (#4)

* Created pyproject.toml and removed setup.py

* Remove requirement*.txt files

* Add 'Bump My Version' config

* Update all the versions to the latest

* Make flask work with api-spec

* Docker support

- Use Python 3.13
- Update Dockerfile to use uv
- Update docker targets in Makefile

* Removed HISTORY file

* package in src/ and Docker build

 - Moved package under src/
 - Dockerfile builds image

* Update dockerfile and project

* Update all the versions to the latest
Fix Conflicts

* Make flask work with api-spec

* Use uv in GitHub Action

* Use ruff instead of black in CI

Author: pbashyal-nmdp

.bumpversion.toml

@@ -20,9 +20,8 @@ setup_hooks = []
 pre_commit_hooks = []
 post_commit_hooks = []
 
-
 [[tool.bumpversion.files]]
-filename = "my_project_template/__init__.py"
+filename = "src/my_project_template/__init__.py"
 search =  "__version__ = \"{current_version}\""
 replace = "__version__ = \"{new_version}\""
 
@@ -35,3 +34,8 @@ replace = "version = \"{new_version}\""
 filename = "api-spec.yaml"
 search =  "version: {current_version}"
 replace = "version: {new_version}"
+
+[[tool.bumpversion.files]]
+filename = "Makefile"
+search =  "VERSION := {current_version}"
+replace = "VERSION := {new_version}"

.dockerignore

@@ -1,3 +1,4 @@
+.git
 .github
 .eggs/
 build
@@ -6,9 +7,9 @@ dist
 *.egg-info
 tests
 venv
+.venv
 
 __pycache__
-*.pyc
 *.pyo
 *.pyd
 *.output

.github/workflows/black.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

.github/workflows/python-tests.yml

@@ -0,0 +1,20 @@
+name: CI
+on: push
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
+      # Update output format to enable automatic inline annotations.
+      - name: Run Ruff
+        run: ruff check --output-format=github .

.github/workflows/ruff.yml

@@ -1,15 +1,45 @@
-FROM python:3.13-slim-trixie
-
+FROM python:3.13-slim-trixie AS builder
 LABEL MAINTAINER="Pradeep Bashyal"
 
 COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
+ENV UV_COMPILE_BYTECODE=1
+ENV UV_LINK_MODE=copy
+ENV UV_PYTHON_PREFERENCE=only-managed
+
+WORKDIR /app
+# Install everything except the package
+RUN --mount=type=cache,target=/root/.cache/uv \
+    --mount=type=bind,source=uv.lock,target=uv.lock \
+    --mount=type=bind,source=pyproject.toml,target=pyproject.toml \
+    uv sync --locked --no-install-project --group deploy
+
+# Sync so that Python version is installed
+COPY . /app
+RUN --mount=type=cache,target=/root/.cache/uv \
+    uv sync --locked --group deploy && uv build
+
+
+# Final Docker Image
+FROM python:3.13-slim-trixie
+
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+
 WORKDIR /app
 
+# Copy the Python packages
+COPY --from=builder /app/.venv /app/.venv
+
+COPY --from=builder /app/dist/my_project_template-0.0.1-py3-none-any.whl /tmp/
+RUN python3 -m pip install /tmp/my_project_template-0.0.1-py3-none-any.whl
+
 COPY app.py /app/
 COPY api.py /app/
 COPY api-spec.yaml /app/
-COPY my_project_template /app/my_project_template
+COPY run-app.sh /app/
+
+# Put the uv built Python packages in the PATH
+ENV PYTHONPATH="/app/.venv/lib/python3.13/site-packages/:"
 
 # Sync the project into a new environment, asserting the lockfile is up to date
 COPY pyproject.toml /app/

Dockerfile

@@ -58,7 +58,7 @@ lint: ## check style with ruff
 	uv tool run ruff check
 
 behave: clean-test ## run the behave tests, generate and serve report
-	- uv run behave -f allure_behave.formatter:AllureFormatter -o allure_report
+	uv run behave -f allure_behave.formatter:AllureFormatter -o allure_report
 	allure serve allure_report
 
 pytest: clean-test ## run tests quickly with the default Python

Makefile

@@ -1,5 +1,9 @@
+[build-system]
+requires = ["uv_build>=0.8.15,<0.9.0"]
+build-backend = "uv_build"
+
 [project]
-name = "nmdp-python-project-template"
+name = "my_project_template"
 version = "0.0.1"
 description="Python Project Template. Standardized Python project structure for NMDP projects"
 requires-python = ">=3.13"

pyproject.toml

@@ -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