From f5d41f27f1e6cdaff47f5942a2c5a84aefdeabe0 Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Tue, 3 Dec 2024 16:08:01 -0800 Subject: [PATCH] build: move ORCID to metadata in pyproject.toml, fix pixi (#3416) Using ORCID in the authors/maintainers field was never really supported (see https://discuss.python.org/t/adding-extra-fields-in-the-pyproject-toml-authors-maintainers-list/16848/12 for discussion), and now is actively breaking `pixi`. Move it to `metadata` key instead. Also track extras ("test", "demo", "doc", "storage", "all") in the pixi default environment, which makes the pixi.lock more reproducible. --- pixi.lock | 2869 ++++++++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 121 +- 2 files changed, 2950 insertions(+), 40 deletions(-) diff --git a/pixi.lock b/pixi.lock index a8742ca2d9..c07f862a53 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3,6 +3,8 @@ environments: default: channels: - url: https://conda.anaconda.org/conda-forge/ + indexes: + - https://pypi.org/simple packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 @@ -209,6 +211,134 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-h4ab18f5_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda + - pypi: https://files.pythonhosted.org/packages/7e/b3/6b4067be973ae96ba0d615946e314c5ae35f9f993eca561b356540bb0c2b/alabaster-1.0.0-py3-none-any.whl + - 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Tessa Pierce-Ward" }, + { name="Mohamed Abuelanin" }, + { name="Harriet Alexander" }, + { name="Abhishek Anant" }, + { name="Keya Barve" }, + { name="Colton Baumler" }, + { name="Olga Botvinnik" }, + { name="Phillip Brooks" }, + { name="Luca Cappelletti" }, + { name="Peter Cock" }, + { name="Daniel Dsouza" }, + { name="Jade Gardner" }, + { name="Laurent Gautier" }, + { name="Tim Head" }, + { name="Mahmudur Rahman Hera" }, + { name="Hannah Eve Houts" }, + { name="Lisa K. Johnson" }, + { name="Fabian Klötzl" }, + { name="David Koslicki" }, + { name="Katrin Leinweber" }, + { name="Marisa Lim" }, + { name="Ricky Lim" }, + { name="Bradley Nelson" }, + { name="Ivan Ogasawara" }, + { name="Taylor Reiter" }, + { name="Camille Scott" }, + { name="Andreas Sjödin" }, + { name="Connor T. Skennerton" }, + { name="Jason Stajich" }, + { name="Daniel Standage" }, + { name="S. Joshua Swamidass" }, + { name="Connor Tiffany" }, + { name="Pranathi Vemuri" }, + { name="Erik Young" }, + { name="Nick H" }, + { name="C. Titus Brown" }, +] + +maintainers = [ + { name="Luiz C. Irber, Jr", email="luiz@sourmash.bio" }, + { name="C. Titus Brown", email="titus@idyll.org" }, + { name="N. Tessa Pierce-Ward", email="ntpierce@ucdavis.edu" }, +] + +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Environment :: Console", + "Environment :: MacOS X", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: BSD License", + "Natural Language :: English", + "Operating System :: POSIX :: Linux", + "Operating System :: MacOS :: MacOS X", + "Programming Language :: Rust", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.10", + "Topic :: Scientific/Engineering :: Bio-Informatics", +] + +dependencies = [ + "screed>=1.1.3,<2", + "cffi>=1.14.0", + "numpy", + "matplotlib", + "scipy", + "deprecation>=2.0.6", + "cachetools>=4,<6", + "bitstring>=3.1.9,<5", +] + +requires-python = ">=3.10" + +[metadata] +license = { text = "BSD 3-Clause License" } authors = [ { name="Luiz Irber", orcid="0000-0003-4371-9659" }, { name="N. Tessa Pierce-Ward", orcid="0000-0002-2942-5331" }, @@ -51,44 +128,6 @@ authors = [ { name="C. Titus Brown", orcid="0000-0001-6001-2677" }, ] -maintainers = [ - { name="Luiz C. Irber, Jr", email="luiz@sourmash.bio", orcid="0000-0003-4371-9659" }, - { name="C. Titus Brown", email="titus@idyll.org", orcid="0000-0001-6001-2677" }, - { name="N. Tessa Pierce-Ward", email="ntpierce@ucdavis.edu", orcid="0000-0002-2942-5331" }, -] - -classifiers = [ - "Development Status :: 5 - Production/Stable", - "Environment :: Console", - "Environment :: MacOS X", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: BSD License", - "Natural Language :: English", - "Operating System :: POSIX :: Linux", - "Operating System :: MacOS :: MacOS X", - "Programming Language :: Rust", - "Programming Language :: Python :: 3.12", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.10", - "Topic :: Scientific/Engineering :: Bio-Informatics", -] - -dependencies = [ - "screed>=1.1.3,<2", - "cffi>=1.14.0", - "numpy", - "matplotlib", - "scipy", - "deprecation>=2.0.6", - "cachetools>=4,<6", - "bitstring>=3.1.9,<5", -] - -requires-python = ">=3.10" - -[metadata] -license = { text = "BSD 3-Clause License" } - [project.urls] "Homepage" = "https://sourmash.bio/" "Documentation" = "https://sourmash.readthedocs.io" @@ -254,11 +293,10 @@ run.parallel = true run.plugins = ["covdefaults"] [tool.pixi.project] -name = "sourmash" channels = ["conda-forge"] platforms = ["linux-64", "linux-aarch64", "osx-64", "osx-arm64", "win-64"] -[tool.pixi.dependencies] +[tool.pixi.feature.dev.dependencies] clangdev = ">=16.0.6,<16.1" cxx-compiler = ">=1.7.0,<1.8" git = "2.41.0.*" @@ -277,5 +315,8 @@ deprecation = ">=2.0.6" cachetools = ">=4,<6" bitstring = ">=3.1.9,<5" +[tool.pixi.environments] +default = { features = ["dev", "test", "demo", "doc", "storage", "all"], solve-group = "default" } + [tool.pixi.system-requirements] macos = "11.0"