From 3c386fa11d4399d9126f2f979f4e02eea5cc4902 Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Fri, 22 Mar 2024 09:23:00 -0400 Subject: [PATCH 1/3] build: reorganize build metadata (#549) --- pyproject.toml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8022269a..8bf197ac 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,6 +20,7 @@ classifiers = [ "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", ] requires-python = ">=3.8" description = "VICC normalization routine for variations" @@ -49,7 +50,7 @@ Source = "https://github.com/cancervariants/variation-normalization" "Bug Tracker" = "https://github.com/cancervariants/variation-normalization/issues" [build-system] -requires = ["setuptools>=61.0"] +requires = ["setuptools>=64"] build-backend = "setuptools.build_meta" [tool.setuptools.dynamic] @@ -72,7 +73,8 @@ branch = true [tool.ruff] src = ["src"] -lint.select = [ +[tool.ruff.lint] +select = [ "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f "E", "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w "I", # https://docs.astral.sh/ruff/rules/#isort-i @@ -100,8 +102,7 @@ lint.select = [ "PGH", # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh "RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf ] - -lint.fixable = [ +fixable = [ "I", "F401", "D", @@ -132,7 +133,7 @@ lint.fixable = [ # W191 - tab-indentation* # PGH003 - blanket-type-ignore # *ignored for compatibility with formatter -lint.ignore = [ +ignore = [ "ANN101", "ANN003", "D203", "D205", "D206", "D213", "D300", "D400", "D415", "E111", "E114", "E117", "E501", From 65428ebe545ecaba7dd4784ad80396a4a6d04bbb Mon Sep 17 00:00:00 2001 From: Kori Kuzma Date: Tue, 23 Jul 2024 13:09:17 -0400 Subject: [PATCH 2/3] docs: update vrs versioning (#573) --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 2d4e7425..6d4d2c32 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ The variation-normalization repo depends on VRS models, and therefore each varia | variation-normalization branch | variation-normalizer version | gene-normalizer version | VRS version | | ---- | --- | ---- | --- | | [main](https://github.com/cancervariants/variation-normalization/tree/main) | 0.6.X | 0.1.X | [1.X.X](https://github.com/ga4gh/vrs) | -| [staging](https://github.com/cancervariants/variation-normalization/tree/staging) | 0.8.X | 0.3.X | [2.0-alpha](https://github.com/ga4gh/vrs/tree/2.0-alpha) | +| [staging](https://github.com/cancervariants/variation-normalization/tree/staging) | >=0.8.X | >=0.3.X | [2.0-alpha](https://github.com/ga4gh/vrs/tree/2.0-alpha) | ## About From e43d21ee7f24c2b26097cac2619f402732c74f73 Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Wed, 13 Nov 2024 14:36:20 -0500 Subject: [PATCH 3/3] chore: use base gitignore (#577) I think this file was leftover from when we took over the repo from WUSTL. This replaces it with the standard GitHub-provided Python ignore, plus our own configurations. --- .gitignore | 166 ++++++++++++++++++++++++++++++++++++++++++++++------- 1 file changed, 145 insertions(+), 21 deletions(-) diff --git a/.gitignore b/.gitignore index 12c84e4f..10526d42 100644 --- a/.gitignore +++ b/.gitignore @@ -1,39 +1,163 @@ -*.pyc +# Byte-compiled / optimized / DLL files __pycache__/ +*.py[cod] +*$py.class -instance/ +# C extensions +*.so -.pytest_cache/ +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ .coverage .coverage.* -htmlcov/ -.vim/ +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ -dist/ -*.egg-info/ +# Translations +*.mo +*.pot -.DS_Store +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal -.mypy_cache/ +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy -src/variation/data +# Sphinx documentation +docs/_build/ +docs/build/ -Pipfile.lock +# PyBuilder +.pybuilder/ +target/ +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: .python-version -pyproject.toml +# 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 -# Jupyter Notebook -.ipynb_checkpoints/ +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock -# Logs -*.log +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/latest/usage/project/#working-with-version-control +.pdm.toml +.pdm-python +.pdm-build/ -# Zip -*.zip +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ -build/ -dynamodb_local_latest/ +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ -*.http +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/