Upgrade to Modern Tools

.bumpversion.toml

@@ -0,0 +1,37 @@
+[tool.bumpversion]
+current_version = "0.0.1"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = false
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = false
+message = "Bump version: {current_version} → {new_version}"
+moveable_tags = []
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = []
+post_commit_hooks = []
+
+
+[[tool.bumpversion.files]]
+filename = "my_project_template/__init__.py"
+search =  "__version__ = \"{current_version}\""
+replace = "__version__ = \"{new_version}\""
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search =  "version = \"{current_version}\""
+replace = "version = \"{new_version}\""
+
+[[tool.bumpversion.files]]
+filename = "api-spec.yaml"
+search =  "version: {current_version}"
+replace = "version: {new_version}"

.gitignore

@@ -50,6 +50,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+.ruff_cache/
 
 # Translations
 *.mo
@@ -65,39 +66,16 @@ db.sqlite3-journal
 instance/
 .webassets-cache
 
-# Scrapy stuff:
-.scrapy
-
 # Sphinx documentation
 docs/_build/
 
-# PyBuilder
-target/
-
 # Jupyter Notebook
 .ipynb_checkpoints
 
 # IPython
 profile_default/
 ipython_config.py
 
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
 # SageMath parsed files
 *.sage.py
 
@@ -110,6 +88,9 @@ ENV/
 env.bak/
 venv.bak/
 
+# Mac
+.DS_Store
+
 # IDEs
 # Spyder project settings
 .spyderproject
@@ -134,3 +115,4 @@ dmypy.json
 # behave
 pretty.output
 allure_report/
+

.pre-commit-config.yaml

@@ -1,13 +1,12 @@
 repos:
-    -   repo: https://github.com/pre-commit/pre-commit-hooks
-        rev: v4.2.0
-        hooks:
-            -   id: trailing-whitespace
-            -   id: end-of-file-fixer
-            -   id: check-yaml
-            -   id: check-added-large-files
-    -   repo: https://github.com/psf/black
-        rev: 22.3.0
-        hooks:
-            -   id: black
-                language_version: python3
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.12.12
+    hooks:
+      # Run the linter.
+      - id: ruff-check
+        types_or: [python, pyi]
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [python, pyi]

.python-version

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

Dockerfile

@@ -1,19 +1,19 @@
-FROM python:3.11-slim-buster
+FROM python:3.13-slim-trixie
 
 LABEL MAINTAINER="Pradeep Bashyal"
 
-WORKDIR /app
-
-COPY requirements.txt /app
-RUN pip install --no-cache-dir --upgrade pip && \
-    pip install --no-cache-dir -r requirements.txt
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
-COPY requirements-deploy.txt /app
-RUN pip install --no-cache-dir -r requirements-deploy.txt
+WORKDIR /app
 
 COPY app.py /app/
 COPY api.py /app/
 COPY api-spec.yaml /app/
 COPY my_project_template /app/my_project_template
 
-CMD ["gunicorn"  , "--bind", "0.0.0.0:8080", "--worker-tmp-dir", "/dev/shm", "app:app"]
+# Sync the project into a new environment, asserting the lockfile is up to date
+COPY pyproject.toml /app/
+COPY uv.lock /app/
+RUN /bin/uv sync --locked --group deploy
+
+CMD [".venv/bin/gunicorn"  , "--bind", "0.0.0.0:8080", "--worker-tmp-dir", "/dev/shm", "app:app"]

Makefile

@@ -1,5 +1,6 @@
 PROJECT_NAME := $(shell basename `pwd`)
 PACKAGE_NAME := my_project_template
+VERSION := 0.0.1
 
 .PHONY: clean clean-test clean-pyc clean-build docs help test test-all
 .DEFAULT_GOAL := help
@@ -53,56 +54,48 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 	rm -fr allure_report
 
-lint: ## check style with flake8
-    # stop the build if there are Python syntax errors or undefined names \
-	  exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-	flake8 $(PACKAGE_NAME) tests --count --select=E9,F63,F7,F82 --show-source --statistics
-	flake8 $(PACKAGE_NAME) --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+lint: ## check style with ruff
+	uv tool run ruff check
 
 behave: clean-test ## run the behave tests, generate and serve report
-	- 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
-	PYTHONPATH=. pytest
+	uv run pytest
 
 test: clean-test ## run all(BDD and unit) tests
-	PYTHONPATH=. pytest
-	behave
+	uv run pytest
+	uv run behave
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source my_project_template -m pytest
+	coverage run --source $(PACKAGE_NAME) -m pytest
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
 dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
+	uv build
 	ls -l dist
 
 docker-build: ## build a docker image for the service
-	docker build -t my-project-template-service:0.0.1 .
+	docker build -t $(PACKAGE_NAME):$(VERSION) .
 
 docker: docker-build ## build a docker image and run the service
-	docker run --name my-project-template -p 8080:8080 my-project-template-service:0.0.1
-
-install: clean ## install the package to the active Python's site-packages
-	pip install --upgrade pip setuptools
-	python setup.py install
-	pip install -r requirements.txt
-	pip install -r requirements-tests.txt
-	pip install -r requirements-dev.txt
-	pip install -r requirements-deploy.txt
+	docker run --name $(PACKAGE_NAME) -p 8080:8080 $(PACKAGE_NAME):$(VERSION)
+
+sync: clean ## install the package to the active Python's site-packages
+	uv sync --all-groups
+	pre-commit install
+
+install: sync ## Sync pyproject.toml to .venv as well as install tools
 	pre-commit install
+	uv tool install bump-my-version
 
 venv: ## creates a Python3 virtualenv environment in venv
-	python3 -m venv venv --prompt $(PROJECT_NAME)-venv
-	@echo "====================================================================="
-	@echo "To activate the new virtual environment, execute the following from your shell"
-	@echo "source venv/bin/activate"
+	uv venv --prompt $(PROJECT_NAME)-venv
 
 activate: ## activate a virtual environment. Run `make venv` before activating.
 	@echo "====================================================================="
 	@echo "To activate the new virtual environment, execute the following from your shell"
-	@echo "source venv/bin/activate"
+	@echo "source .venv/bin/activate"

app.py

@@ -5,13 +5,13 @@
 
 app = connexion.App(__name__)
 application = app.app
-api = app.add_api("api-spec.yaml")
+app.add_api("api-spec.yaml")
 
 
 @app.route("/")
 def index():
-    return redirect(api.base_path + "/ui")
+    return redirect("/ui")
 
 
 if __name__ == "__main__":
-    app.run(port=8080, debug=True)
+    app.run(port=8080)

pyproject.toml

@@ -0,0 +1,72 @@
+[project]
+name = "nmdp-python-project-template"
+version = "0.0.1"
+description="Python Project Template. Standardized Python project structure for NMDP projects"
+requires-python = ">=3.13"
+dependencies = [
+]
+authors = [
+  {name = "Pradeep Bashyal", email = "[email protected]"},
+  {name = "NMDP Person"},
+  {email = "[email protected]"},
+]
+maintainers = [
+  {name = "Pradeep Bashyal", email = "[email protected]"},
+]
+readme = "README.md"
+license = "LGPL-3.0-only"
+keywords = ["HLA", "matching"]
+classifiers = [
+  # Prevent a package from being uploaded to PyPI
+  # "Private :: Do Not Upload"
+
+  # How mature is this project? Common values are
+  #   3 - Alpha
+  #   4 - Beta
+  #   5 - Production/Stable
+  "Development Status :: 2 - Pre-Alpha",
+
+  # Indicate who your project is intended for
+  "Intended Audience :: Developers",
+  "Topic :: Software Development :: Build Tools",
+
+  # Specify the Python versions you support here.
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
+]
+
+[project.urls]
+Homepage = "https://nmdp-bioinformatics.org/"
+Documentation = "https://github.com/nmdp-bioinformatics/nmdp-python-project-template/README.md"
+Repository = "https://github.com/nmdp-bioinformatics/nmdp-python-project-template"
+Issues = "https://github.com/nmdp-bioinformatics/nmdp-python-project-template/issues"
+Changelog = "https://github.com/nmdp-bioinformatics/nmdp-python-project-template/blob/master/CHANGELOG.md"
+
+[dependency-groups]
+dev = [
+  "pre-commit>=4.2.0",
+  "ruff>=0.11.11",
+  "allure-behave==2.15.0",
+  "coverage==7.10.6",
+]
+
+test = [
+  "pytest==8.4.2",
+  "behave==1.3.3",
+  "pyhamcrest==2.1.0",
+]
+
+deploy=[
+  "connexion[swagger-ui,flask,uvicorn]==3.2.0",
+  "gunicorn==23.0.0"
+]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "-ra -q"
+testpaths = [
+    "tests",
+]
+
+[tool.ruff]
+exclude = [".git", ".venv", "tests",]