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Merged
singjc merged 8 commits into from
Jan 19, 2026
Merged

Update packaging #137

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6c09097
PEP 639 compliance
DimitriPapadopoulos Jan 16, 2026
2718ac4
Update pyproject.toml
DimitriPapadopoulos Jan 16, 2026
0cadce3
Update Python versions in Trove classifiers
DimitriPapadopoulos Jan 16, 2026
5298303
Ooops...
DimitriPapadopoulos Jan 16, 2026
0739358
Fix authors
DimitriPapadopoulos Jan 16, 2026
4dbf3ce
Python 3.13 not supported yet
DimitriPapadopoulos Jan 17, 2026
390de13
Merge branch 'main' into PEP639
singjc Jan 19, 2026
894a5e0
Keep the OpenMS team as the only author
DimitriPapadopoulos Jan 19, 2026
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21 changes: 12 additions & 9 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,30 +1,33 @@
[build-system]
requires = ["flit_core >=3.2,<4"]
requires = ["flit_core >=3.12,<4"]
build-backend = "flit_core.buildapi"

[project]
name = "pyopenms_viz"
module = "pyopenms_viz"
dist-name = "pyopenms_viz"
author = "OpenMS Team"
authors = [
{name = "OpenMS Team", email = "webmaster@openms.de"},
{name = "Joshua Charkow", email = "joshuacharkow@gmail.com"},
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@jcharkow jcharkow Jan 19, 2026

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We can likely remove my name/email and just keep the OpenMS team in this new format

]
version = "1.0.0"
author-email = "joshuacharkow@gmail.com"
home-page = "https://github.com/OpenMS/pyopenms_viz/"
description = "A package for visualizing mass spectrometry data using pandas dataframes"
readme = "README.md"
readme-content-type = "text/markdown"
classifiers = [
"Intended Audience :: Science/Research",
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Copilot AI Jan 16, 2026

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The 'License :: OSI Approved :: BSD License' classifier was removed but not replaced with a more specific classifier. Consider adding 'License :: OSI Approved :: BSD License' back to the classifiers list to maintain discoverability on PyPI, as classifiers serve a different purpose than the license field.

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"Intended Audience :: Science/Research",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",

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@DimitriPapadopoulos DimitriPapadopoulos Jan 16, 2026 •
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Your suggestion is not compliant with current Python packaging standards and PyPi is perfectly aware of the license field.

And where does "classifiers serve a different purpose than the license field" come from? Please provide links to authoritative documentation.

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@DimitriPapadopoulos DimitriPapadopoulos Jan 17, 2026

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PyPI moved to license in 2024:
pypi/warehouse#16620 (comment)

"License :: OSI Approved :: BSD License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Chemistry",
]
requires-python = ">=3.10, <=3.13"
license = "BSD-3-Clause"
license-files = ["LICENSE"]
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Copilot AI Jan 16, 2026

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The license-files field is redundant when using the SPDX license identifier format. When license is specified as a string (SPDX identifier), the license-files field is not needed according to PEP 621. Either use license = {text = \"BSD-3-Clause\"} with license-files, or use just license = \"BSD-3-Clause\" without license-files.

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license-files = ["LICENSE"]

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@DimitriPapadopoulos DimitriPapadopoulos Jan 16, 2026 •
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Where does this come from? It's a bad idea and it's not compliant with PEP 639.

See "Use a default value for license-files if not specified" in Appendix: Rejected Ideas of PEP 639.

requires-python = ">=3.10, <3.13"
dependencies = ["pandas>=0.17"]

[project.urls]
Homepage = "https://github.com/OpenMS/pyopenms_viz/"

[project.optional-dependencies]
testing = ["pytest", "syrupy"]
all = ["bokeh>=3.4.1", "plotly", "matplotlib"]
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