Created pyproject.toml and removed setup.py

Author: pbashyal-nmdp

.gitignore

@@ -110,6 +110,9 @@ ENV/
 env.bak/
 venv.bak/
 
+# Mac
+.DS_Store
+
 # IDEs
 # Spyder project settings
 .spyderproject

.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]

Makefile

@@ -54,21 +54,18 @@ clean-test: ## remove test and coverage artifacts
 	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
+	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
@@ -77,8 +74,7 @@ coverage: ## check code coverage quickly with the default Python
 	$(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
@@ -88,19 +84,11 @@ 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
+	uv sync --all-groups
 	pre-commit install
 
 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 "====================================================================="

pyproject.toml

@@ -0,0 +1,74 @@
+[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 = "Another 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==2.13.2",
+  "flake8==7.0.0",
+  "bump2version==1.0.1",
+  "coverage==7.4.1",
+]
+
+test = [
+  "pytest==8.0.0",
+  "behave==1.2.6",
+  "PyHamcrest==2.1.0",
+]
+
+deploy=[
+  "connexion[swagger-ui]==2.14.2",
+  "gunicorn==21.2.0"
+]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "-ra -q"
+testpaths = [
+    "tests",
+    "integration",
+]
+
+[tool.ruff]
+exclude = [".git", ".venv", "tests",]