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Upgrade to Modern Tools (#3)
* 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
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‎.bumpversion.toml‎

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

‎.gitignore‎

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*.py,cover
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.hypothesis/
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.pytest_cache/
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.ruff_cache/
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# Translations
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*.mo
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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.python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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env.bak/
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venv.bak/
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# Mac
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.DS_Store
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# IDEs
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# Spyder project settings
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.spyderproject
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# behave
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pretty.output
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allure_report/
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‎.pre-commit-config.yaml‎

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

‎.python-version‎

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3.13

‎Dockerfile‎

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

‎HISTORY.rst‎

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‎Makefile‎

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

‎app.py‎

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

‎pyproject.toml‎

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

‎requirements-deploy.txt‎

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