From 5fcdd96c2cae89b3f80d552a94dc4bd63131e0cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fl=C3=A1vio=20Code=C3=A7o=20Coelho?= Date: Wed, 18 Dec 2024 10:12:38 -0300 Subject: [PATCH] Migrated package management to uv as described in issue #6 --- .python-version | 1 + poetry.lock | 1581 ---------------------------------------------- pyproject.toml | 62 +- requirements.txt | 2 +- setup.cfg | 115 ---- setup.py | 21 - 6 files changed, 35 insertions(+), 1747 deletions(-) create mode 100644 .python-version delete mode 100644 poetry.lock delete mode 100644 setup.cfg delete mode 100644 setup.py diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..e4fba21 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.12 diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 8ee2dd7..0000000 --- a/poetry.lock +++ /dev/null @@ -1,1581 +0,0 @@ -[[package]] -name = "alabaster" -version = "0.7.12" -description = "A configurable sidebar-enabled Sphinx theme" -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "argcomplete" -version = "2.0.0" -description = "Bash tab completion for argparse" -category = "dev" -optional = false -python-versions = ">=3.6" - -[package.extras] -test = ["coverage", "flake8", "pexpect", "wheel"] - -[[package]] -name = "attrs" -version = "22.1.0" -description = "Classes Without Boilerplate" -category = "dev" -optional = false -python-versions = ">=3.5" - -[package.extras] -dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"] -docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] -tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"] -tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"] - -[[package]] -name = "autoflake8" -version = "0.4.0" -description = "Tool to automatically fix some issues reported by flake8 (forked from autoflake)." -category = "dev" -optional = false -python-versions = ">=3.7,<4.0" - -[package.dependencies] -pyflakes = ">=2.3.0" - -[[package]] -name = "babel" -version = "2.11.0" -description = "Internationalization utilities" -category = "main" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -pytz = ">=2015.7" - -[[package]] -name = "certifi" -version = "2022.9.24" -description = "Python package for providing Mozilla's CA Bundle." -category = "main" -optional = false -python-versions = ">=3.6" - -[[package]] -name = "charset-normalizer" -version = "2.1.1" -description = "The Real First Universal Charset Detector. 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"src" +[tool.uv] +dev-dependencies = [ + "pytest>=8.3.4", + "pytest-cov>=6.0.0", + "ruff>=0.8.3", ] diff --git a/requirements.txt b/requirements.txt index 4f30e4e..e7ee341 100644 --- a/requirements.txt +++ b/requirements.txt @@ -13,4 +13,4 @@ pytest-cov matplotlib mypy sphinx -pyitlib +latexify-py diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index c4cc6b4..0000000 --- a/setup.cfg +++ /dev/null @@ -1,115 +0,0 @@ -# This file is used to configure your project. -# Read more about the various options under: -# http://setuptools.readthedocs.io/en/latest/setuptools.html#configuring-setup-using-setup-cfg-files - -[metadata] -name = epimodels -description = Library of mathematical epidemic models for use in simulation studies and inference -author = Flávio Codeço Coelho -author-email = fccoelho@gmail.com -license = mit -url = https://github.com/fccoelho/epimodels -long-description = file: README.md -# Change if running only on Windows, Mac or Linux (comma-separated) -platforms = any -# Add here all kinds of additional classifiers as defined under -# https://pypi.python.org/pypi?%3Aaction=list_classifiers -classifiers = - Development Status :: 4 - Beta - Programming Language :: Python - -[options] -zip_safe = False -packages = find_namespace: -include_package_data = True -package_dir = - =src -# DON'T CHANGE THE FOLLOWING LINE! IT WILL BE UPDATED BY PYSCAFFOLD! -# Add here dependencies of your project (semicolon/line-separated), e.g. -install_requires = - importlib-metadata; python_version<"3.8" - numpy - scipy - cython -# The usage of test_requires is discouraged, see `Dependency Management` docs -# tests_require = pytest; pytest-cov -# Require a specific Python version, e.g. Python 2.7 or >= 3.4 -python_requires = >= 3.6 - -[options.packages.find] -where = src -exclude = - tests - -[options.extras_require] -# Add here additional requirements for extra features, to install with: -# `pip install epimodels[PDF]` like: -# PDF = ReportLab; RXP -# Add here test requirements (semicolon/line-separated) -testing = - pytest - pytest-cov - -[options.entry_points] -# Add here console scripts like: -# console_scripts = -# script_name = epimodels.module:function -# For example: -# console_scripts = -# fibonacci = epimodels.skeleton:run -# And any other entry points, for example: -# pyscaffold.cli = -# awesome = pyscaffoldext.awesome.extension:AwesomeExtension - -[test] -# py.test options when running `python setup.py test` -# addopts = --verbose -extras = True - -[tool:pytest] -# Options for py.test: -# Specify command line options as you would do when invoking py.test directly. -# e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml -# in order to write a coverage file that can be read by Jenkins. -#addopts = -# --cov epimodels --cov-report term-missing -# --verbose -norecursedirs = - dist - build - .tox -testpaths = tests - -[aliases] -release = sdist bdist_wheel upload - -[bdist_wheel] -# Use this option if your package is pure-python -universal = 1 - -[build_sphinx] -source_dir = docs -build_dir = docs/_build - -[devpi:upload] -# Options for the devpi: PyPI server and packaging tool -# VCS export must be deactivated since we are using setuptools-scm -no-vcs = 1 -formats = - sdist - bdist_wheel - -[flake8] -# Some sane defaults for the code style checker flake8 -exclude = - .tox - build - dist - .eggs - docs/conf.py - -[pyscaffold] -# PyScaffold's parameters when the project was created. -# This will be used when updating. Do not change! -version = 4.0 -package = epimodels diff --git a/setup.py b/setup.py deleted file mode 100644 index 9f5f864..0000000 --- a/setup.py +++ /dev/null @@ -1,21 +0,0 @@ -""" - Setup file for epimodels. - Use setup.cfg to configure your project. - - This file was generated with PyScaffold 4.0. - PyScaffold helps you to put up the scaffold of your new Python project. - Learn more under: https://pyscaffold.org/ -""" -from setuptools import setup - -if __name__ == "__main__": - try: - setup(use_scm_version={"version_scheme": "no-guess-dev"}) - except: # noqa - print( - "\n\nAn error occurred while building the project, " - "please ensure you have the most updated version of setuptools, " - "setuptools_scm and wheel with:\n" - " pip install -U setuptools setuptools_scm wheel\n\n" - ) - raise