From 0db9490592b4fe855d5fcc7d002204e264948952 Mon Sep 17 00:00:00 2001 From: Pradeep Bashyal Date: Fri, 5 Sep 2025 15:18:19 -0500 Subject: [PATCH 01/14] Created pyproject.toml and removed setup.py --- .gitignore | 3 + .pre-commit-config.yaml | 23 +- Makefile | 28 +- pyproject.toml | 74 +++++ setup.py | 70 ---- uv.lock | 709 ++++++++++++++++++++++++++++++++++++++++ 6 files changed, 805 insertions(+), 102 deletions(-) create mode 100644 pyproject.toml delete mode 100644 setup.py create mode 100644 uv.lock diff --git a/.gitignore b/.gitignore index b33e2e9..c5ac6f5 100644 --- a/.gitignore +++ b/.gitignore @@ -110,6 +110,9 @@ ENV/ env.bak/ venv.bak/ +# Mac +.DS_Store + # IDEs # Spyder project settings .spyderproject diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0565c0e..3ca846e 100644 --- a/.pre-commit-config.yaml +++ b/.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] diff --git a/Makefile b/Makefile index 16ba077..53e051a 100644 --- a/Makefile +++ b/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 "=====================================================================" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..ba1f8bc --- /dev/null +++ b/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 = "pbashyal@nmdp.org"}, + {name = "Another person"}, + {email = "different.person@example.com"}, +] +maintainers = [ + {name = "Pradeep Bashyal", email = "pbashyal@nmdp.org"}, +] +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",] diff --git a/setup.py b/setup.py deleted file mode 100644 index a55ab2c..0000000 --- a/setup.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -# -# my_project_template My Project Template. -# Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved. -# -# This library is free software; you can redistribute it and/or modify it -# under the terms of the GNU Lesser General Public License as published -# by the Free Software Foundation; either version 3 of the License, or (at -# your option) any later version. -# -# This library is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or -# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public -# License for more details. -# -# You should have received a copy of the GNU Lesser General Public License -# along with this library; if not, write to the Free Software Foundation, -# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. -# -# > http://www.fsf.org/licensing/licenses/lgpl.html -# > http://www.opensource.org/licenses/lgpl-license.php -# - - -"""The setup script.""" - -from setuptools import setup, find_packages - -with open("README.md") as readme_file: - readme = readme_file.read() - -with open("HISTORY.rst") as history_file: - history = history_file.read() - -with open("requirements.txt") as requirements_file: - requirements = requirements_file.read().split("\n") - -with open("requirements-tests.txt") as requirements_file: - test_requirements = requirements_file.read().split("\n") - -setup( - name="my_project_template", - version="0.0.1", - author="Pradeep Bashyal", - author_email="pbashyal@nmdp.org", - python_requires=">=3.8", 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{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}\"" diff --git a/pyproject.toml b/pyproject.toml index 99415e0..a0284c7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -65,7 +65,6 @@ minversion = "6.0" addopts = "-ra -q" testpaths = [ "tests", - "integration", ] [tool.ruff] diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 1a349c0..0000000 --- a/setup.cfg +++ /dev/null @@ -1,22 +0,0 @@ -[bumpversion] -current_version = 0.0.1 -commit = True -tag = True - -[bumpversion:file:setup.py] -search = 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+++++++++++------ 4 files changed, 22 insertions(+), 38 deletions(-) create mode 100644 .python-version diff --git a/.gitignore b/.gitignore index 8112450..99b6943 100644 --- a/.gitignore +++ b/.gitignore @@ -50,6 +50,7 @@ coverage.xml *.py,cover .hypothesis/ .pytest_cache/ +.ruff_cache/ # Translations *.mo @@ -65,15 +66,9 @@ db.sqlite3-journal instance/ .webassets-cache -# Scrapy stuff: -.scrapy - # Sphinx documentation docs/_build/ -# PyBuilder -target/ - # Jupyter Notebook .ipynb_checkpoints @@ -81,23 +76,6 @@ target/ 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 diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..24ee5b1 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.13 diff --git a/Dockerfile b/Dockerfile index 3685756..735b1f1 100644 --- a/Dockerfile +++ b/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"] diff --git a/Makefile b/Makefile index 53e051a..78e2023 100644 --- a/Makefile +++ b/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 @@ -53,7 +54,7 @@ clean-test: ## remove test and coverage artifacts rm -fr .pytest_cache rm -fr allure_report -lint: ## check style with flake8 +lint: ## check style with ruff uv tool run ruff check behave: clean-test ## run the behave tests, generate and serve report @@ -68,7 +69,7 @@ test: clean-test ## run all(BDD and unit) tests 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 @@ -78,19 +79,23 @@ dist: clean ## builds source and wheel package 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 + docker run --name $(PACKAGE_NAME) -p 8080:8080 $(PACKAGE_NAME):$(VERSION) -install: clean ## install the package to the active Python's site-packages +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 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" From a81724af829f2f00621e4495cefb3e9c4185e4a1 Mon Sep 17 00:00:00 2001 From: Pradeep Bashyal Date: Fri, 5 Sep 2025 18:29:43 -0500 Subject: [PATCH 07/14] Removed HISTORY file --- HISTORY.rst | 8 -------- 1 file changed, 8 deletions(-) delete mode 100644 HISTORY.rst diff --git a/HISTORY.rst b/HISTORY.rst deleted file mode 100644 index 93c23ae..0000000 --- a/HISTORY.rst +++ /dev/null @@ -1,8 +0,0 @@ -======= -History -======= - -0.0.1 (2021-08-25) ------------------- - -* First release on PyPI. From 3685b502aca08d6775f7a4d7b619b5cb72f3e449 Mon Sep 17 00:00:00 2001 From: Pradeep Bashyal Date: Tue, 9 Sep 2025 10:02:05 -0500 Subject: [PATCH 08/14] package in src/ and Docker build - Moved package under src/ - Dockerfile builds image --- {my_project_template => src/my_project_template}/__init__.py | 0 .../my_project_template}/algorithm/match.py | 0 {my_project_template => src/my_project_template}/model/allele.py | 0 {my_project_template => src/my_project_template}/model/slug.py | 0 .../my_project_template}/my_project_template.py | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename {my_project_template => src/my_project_template}/__init__.py (100%) rename {my_project_template => src/my_project_template}/algorithm/match.py (100%) rename {my_project_template => src/my_project_template}/model/allele.py (100%) rename {my_project_template => src/my_project_template}/model/slug.py (100%) rename {my_project_template => src/my_project_template}/my_project_template.py (100%) diff --git a/my_project_template/__init__.py b/src/my_project_template/__init__.py similarity index 100% rename from my_project_template/__init__.py rename to src/my_project_template/__init__.py diff --git a/my_project_template/algorithm/match.py b/src/my_project_template/algorithm/match.py similarity index 100% rename from my_project_template/algorithm/match.py rename to src/my_project_template/algorithm/match.py diff --git a/my_project_template/model/allele.py b/src/my_project_template/model/allele.py similarity index 100% rename from my_project_template/model/allele.py rename to src/my_project_template/model/allele.py diff --git a/my_project_template/model/slug.py b/src/my_project_template/model/slug.py similarity index 100% rename from my_project_template/model/slug.py rename to src/my_project_template/model/slug.py diff --git a/my_project_template/my_project_template.py b/src/my_project_template/my_project_template.py similarity index 100% rename from my_project_template/my_project_template.py rename to src/my_project_template/my_project_template.py From 6fccefb7c1ca9f12b243a1e4965d16b65df58385 Mon Sep 17 00:00:00 2001 From: Pradeep Bashyal Date: Tue, 9 Sep 2025 13:25:38 -0500 Subject: [PATCH 09/14] Update dockerfile and project --- .bumpversion.toml | 8 ++++++-- .dockerignore | 3 ++- Dockerfile | 41 +++++++++++++++++++++++++++++++++-------- Makefile | 2 +- pyproject.toml | 6 +++++- uv.lock | 4 ++-- 6 files changed, 49 insertions(+), 15 deletions(-) diff --git a/.bumpversion.toml b/.bumpversion.toml index 51d6fde..e658893 100644 --- a/.bumpversion.toml +++ b/.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}" diff --git a/.dockerignore b/.dockerignore index 06f2cff..073ea4d 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,3 +1,4 @@ +.git .github .eggs/ build @@ -6,9 +7,9 @@ dist *.egg-info tests venv +.venv __pycache__ -*.pyc *.pyo *.pyd *.output diff --git a/Dockerfile b/Dockerfile index 735b1f1..d35d3f7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,19 +1,44 @@ -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/ -# 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 +# Put the uv built Python packages in the PATH +ENV PYTHONPATH="/app/.venv/lib/python3.13/site-packages/:" -CMD [".venv/bin/gunicorn" , "--bind", "0.0.0.0:8080", "--worker-tmp-dir", "/dev/shm", "app:app"] +CMD ["/app/run-app.sh"] diff --git a/Makefile b/Makefile index 78e2023..dff3f21 100644 --- a/Makefile +++ b/Makefile @@ -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 diff --git a/pyproject.toml b/pyproject.toml index 8ca4686..ad7543b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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" diff --git a/uv.lock b/uv.lock index 403e2b3..6bb4d88 100644 --- a/uv.lock +++ b/uv.lock @@ -486,9 +486,9 @@ wheels = [ ] [[package]] -name = "nmdp-python-project-template" +name = "my-project-template" version = "0.0.1" -source = { virtual = "." } +source = { editable = "." } [package.dev-dependencies] deploy = [ From 3055a0d513b191019f6ab0d6196d6d6c3c6f0944 Mon Sep 17 00:00:00 2001 From: Pradeep Bashyal Date: Fri, 5 Sep 2025 16:18:06 -0500 Subject: [PATCH 10/14] Update all the versions to the latest Fix Conflicts --- pyproject.toml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ad7543b..b22b1a3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,8 +7,7 @@ name = "my_project_template" version = "0.0.1" description="Python Project Template. Standardized Python project structure for NMDP projects" requires-python = ">=3.13" -dependencies = [ -] +dependencies = [] authors = [ {name = "Pradeep Bashyal", email = "pbashyal@nmdp.org"}, {name = "NMDP Person"}, @@ -61,7 +60,7 @@ test = [ ] deploy=[ - "connexion[swagger-ui,flask,uvicorn]==3.2.0", + "connexion[swagger-ui]==3.2.0", "gunicorn==23.0.0" ] From 523fb54c4f7eb83f425be6988734f943442fdce4 Mon Sep 17 00:00:00 2001 From: Pradeep Bashyal Date: Fri, 5 Sep 2025 16:44:11 -0500 Subject: [PATCH 11/14] Make flask work with api-spec --- pyproject.toml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index b22b1a3..ad7543b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,8 @@ name = "my_project_template" version = "0.0.1" description="Python Project Template. Standardized Python project structure for NMDP projects" requires-python = ">=3.13" -dependencies = [] +dependencies = [ +] authors = [ {name = "Pradeep Bashyal", email = "pbashyal@nmdp.org"}, {name = "NMDP Person"}, @@ -60,7 +61,7 @@ test = [ ] deploy=[ - "connexion[swagger-ui]==3.2.0", + "connexion[swagger-ui,flask,uvicorn]==3.2.0", "gunicorn==23.0.0" ] From 77b0e71e6a5a85565aa629da71b4e5d7d0de5c27 Mon Sep 17 00:00:00 2001 From: Pradeep Bashyal Date: Wed, 10 Sep 2025 17:51:49 -0500 Subject: [PATCH 12/14] Use uv in GitHub Action --- .github/workflows/python-tests.yml | 44 ++++++++++++++------------ tests/unit/test_my_project_template.py | 25 +++++++++++++++ 2 files changed, 48 insertions(+), 21 deletions(-) diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml index 6bfdc01..729d563 100644 --- a/.github/workflows/python-tests.yml +++ b/.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 diff --git a/tests/unit/test_my_project_template.py b/tests/unit/test_my_project_template.py index 8386e38..6806218 100644 --- a/tests/unit/test_my_project_template.py +++ b/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 From 0b1fe58a9f02bb88fced462c42fda0ef1d28ba6a Mon Sep 17 00:00:00 2001 From: Pradeep Bashyal Date: Wed, 10 Sep 2025 18:05:37 -0500 Subject: [PATCH 13/14] Use ruff instead of black in CI --- .github/workflows/black.yml | 10 ---------- .github/workflows/ruff.yml | 20 ++++++++++++++++++++ 2 files changed, 20 insertions(+), 10 deletions(-) delete mode 100644 .github/workflows/black.yml create mode 100644 .github/workflows/ruff.yml diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml deleted file mode 100644 index 3078c19..0000000 --- a/.github/workflows/black.yml +++ /dev/null @@ -1,10 +0,0 @@ -name: Format Check - -on: [push, pull_request] - -jobs: - lint: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - uses: psf/black@stable diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml new file mode 100644 index 0000000..91cd797 --- /dev/null +++ b/.github/workflows/ruff.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 . From 15e6eb4878ccffea2c7899a7fb68c6e0b636cb3c Mon Sep 17 00:00:00 2001 From: Pradeep Bashyal Date: Thu, 11 Sep 2025 15:17:55 -0500 Subject: [PATCH 14/14] Update bug_report template --- .github/ISSUE_TEMPLATE/bug_report.md | 16 +--------------- Makefile | 1 - 2 files changed, 1 insertion(+), 16 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index 81c7b58..ffafac7 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -12,10 +12,7 @@ A clear and concise description of what the bug is. **To Reproduce** Steps to reproduce the behavior: -1. Go to '...' -2. Click on '....' -3. Scroll down to '....' -4. See error + **Expected behavior** A clear and concise description of what you expected to happen. @@ -23,16 +20,5 @@ A clear and concise description of what you expected to happen. **Screenshots** If applicable, add screenshots to help explain your problem. -**Desktop (please complete the following information):** - - OS: [e.g. iOS] - - Browser [e.g. chrome, safari] - - Version [e.g. 22] - -**Smartphone (please complete the following information):** - - Device: [e.g. iPhone6] - - OS: [e.g. iOS8.1] - - Browser [e.g. stock browser, safari] - - Version [e.g. 22] - **Additional context** Add any other context about the problem here. diff --git a/Makefile b/Makefile index dff3f21..4d950c9 100644 --- a/Makefile +++ b/Makefile @@ -86,7 +86,6 @@ docker: docker-build ## build a docker image and run the service 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