Skip to content

Towards PEP621 #3528

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
IAlibay merged 22 commits into from
Dec 15, 2022
Merged

Towards PEP621 #3528

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
22 commits
Select commit Hold shift + click to select a range
82e0328
Initial attempt at PEP 621 for main MDA package
IAlibay Feb 13, 2022
6e4c9b0
version should be string
IAlibay Feb 13, 2022
40be8aa
toml tables not python
IAlibay Feb 13, 2022
90f5616
switch to project.urls, hope the whitespace works
IAlibay Feb 13, 2022
5b44eb9
quoted keys _should_ be fine?
IAlibay Feb 13, 2022
3f5b303
pyproject.toml for testsuite
IAlibay Feb 13, 2022
fe05f9f
uncomment test
IAlibay Feb 13, 2022
ad006fb
Merge branch 'develop' into issue-3526
IAlibay Mar 27, 2022
e118a12
Remove testsuite pyproject.toml for now, dynamic version
IAlibay Mar 27, 2022
fda7634
try to circumvent disutil issues with manifest
IAlibay Mar 27, 2022
b00d4c5
Add trove-classifiers for better testing of pyproject.toml classifiers
IAlibay Mar 27, 2022
3153109
temp disable readme from pyproject.toml
IAlibay Mar 27, 2022
755a65e
don't forget packaging
IAlibay Mar 27, 2022
fa6063a
move readme to dynamic section
IAlibay Mar 27, 2022
a7ed38b
revert manifest
IAlibay Mar 27, 2022
fd7ccda
remove readme completely for now
IAlibay Mar 27, 2022
81926ce
Merge branch 'develop' into issue-3526
IAlibay Dec 7, 2022
2977ddb
various pyproject.toml fixups
IAlibay Dec 7, 2022
6c1b3ab
Add changelog entry
IAlibay Dec 7, 2022
f638e1b
fix typo
IAlibay Dec 7, 2022
68d4735
Merge branch 'develop' into issue-3526
IAlibay Dec 7, 2022
aa643aa
Merge branch 'develop' into issue-3526
IAlibay Dec 15, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions .github/actions/setup-deps/action.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,8 @@ inputs:
default: 'pytest-cov'
pytest-xdist:
default: 'pytest-xdist'
trove-classifiers:
default: 'trove-classifiers'
# pip-install optional dependencies
duecredit:
default: 'duecredit'
Expand Down Expand Up @@ -145,6 +147,7 @@ runs:
${{ inputs.coverage }}
${{ inputs.pytest-cov }}
${{ inputs.pytest-xdist }}
${{ inputs.trove-classifiers }}
PIP_OPT_DEPS: |
${{ inputs.duecredit }}
${{ inputs.parmed }}
Expand Down
1 change: 1 addition & 0 deletions package/CHANGELOG
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@ Fixes
(e.g. bonds, angles) (PR #3779).

Enhancements
* MDAnalysis now follows PEP621 (PR #3528)
* Added a reader for GROMACS TNG files based on PyTNG (PR #3765,
Issue #3237, partially addressing Issue #865)
* Added ability for hbond analysis to use types when resnames are not
Expand Down
195 changes: 0 additions & 195 deletions package/pypi-description.rst
View file
Open in desktop

This file was deleted.

87 changes: 87 additions & 0 deletions package/pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,3 +25,90 @@ requires = [
"setuptools",
"wheel",
]

[project]
name = "MDAnalysis"
dynamic = ['version',]
license = {file = "LICENSE"}
readme = "README.rst"
description = "An object-oriented toolkit to analyze molecular dynamics trajectories."
authors = [
{name = 'MDAnalysis Development Team', email = 'mdanalysis@numfocus.org'}
]
maintainers = [
{name = 'MDAnalysis Core Developers', email = 'mdanalysis@numfocus.org'}
]
requires-python = ">=3.8"
dependencies = [
Copy link
Member Author

@IAlibay IAlibay Feb 13, 2022

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I wasn't too sure how to deal with the optional deps here.

Tests -> should I just add MDAnalysisTests as the dep? How do you dynamically set the version number in pyproject.toml?
Extra deps ->

  • Not sure what the keyword should be here (it's unclear if you can just say "extra").
  • How do we deal with conda only deps? Does it matter?

Copy link
Member

@tylerjereddy tylerjereddy Feb 14, 2022

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

conda only deps seems like a bad idea in general, not sure you can do much about them here..

As for dependencies, I think it should just be the mandatory runtime dependencies, and then [project.optional-dependencies] can contain sections for test, doc, and dev tools (I'd suggest just looking at i.e., the SciPy example pyproject.toml and adapting for our purposes, if you aren't already doing that).

Copy link
Member Author

@IAlibay IAlibay Mar 27, 2022

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Sounds good, for now let's just skip [project.optional-dependencies] since most are conda based, I'll raise an issue on merge of this PR with all the things that can be added at a later date to augment the pyproject.toml.

'numpy>=1.20.0',
'biopython>=1.71',
'networkx>=2.0',
'GridDataFormats>=0.4.0',
'mmtf-python>=1.0.0',
'joblib>=0.12',
'scipy>=1.5.0',
'matplotlib>=1.5.1',
'tqdm>=4.43.0',
'threadpoolctl',
'packaging',
'fasteners',
'gsd>=1.9.3',
]
keywords = [
"python", "science", "chemistry", "biophysics", "molecular-dynamics",
"computational-chemistry", "molecular-simulation", "analysis",
"trajectory-analysis",
]
classifiers = [
'Development Status :: 6 - Mature',
'Environment :: Console',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)',
'Operating System :: POSIX',
'Operating System :: MacOS :: MacOS X',
'Operating System :: Microsoft :: Windows',
'Programming Language :: Python',
'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
'Programming Language :: Python :: 3.10',
'Programming Language :: Python :: 3.11',
'Programming Language :: C',
'Topic :: Scientific/Engineering',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Chemistry',
'Topic :: Software Development :: Libraries :: Python Modules',
]

[project.optional-dependencies]
extra_formats = [
"netCDF4>=1.0",
"h5py>=2.10",
"chemfiles>=0.10",
"pyedr>=0.7.0",
]
analysis = [
"seaborn",
"scikit-learn",
"tidynamics>=1.0.0",
]
doc = [
Copy link
Member Author

@IAlibay IAlibay Dec 7, 2022

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

missing test entry because passing in a dynamic version for MDAnalysisTests doesn't really work...

"sphinx",
"sphinx-sitemap",
"sphinx_rtd_theme",
"msmb_theme==1.2.0",
"sphinxcontrib-bibtex",
"pybtex",
"pybtex-docutils",
]


[project.urls]
Documentation = 'https://docs.mdanalysis.org/'
"User Guide" = 'https://userguide.mdanalysis.org/'
"Issue Tracker" = 'https://github.com/mdanalysis/mdanalysis/issues'
"User Group" = 'https://groups.google.com/g/mdnalysis-discussion/'
Discord = 'https://discord.com/channels/807348386012987462/'
Blog = 'https://www.mdanalysis.org/blog/'
Twitter = 'https://twitter.com/mdanalysis'
Source = 'https://github.com/mdanalysis/mdanalysis'

7 changes: 3 additions & 4 deletions package/setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -573,7 +573,7 @@ def long_description(readme):
'Development Status :: 6 - Mature',
'Environment :: Console',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
'License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)',
'Operating System :: POSIX',
'Operating System :: MacOS :: MacOS X',
'Operating System :: Microsoft :: Windows ',
Expand Down Expand Up @@ -610,8 +610,7 @@ def long_description(readme):

setup(name='MDAnalysis',
version=RELEASE,
description=('An object-oriented toolkit to analyze molecular dynamics '
'trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber.'),
description='An object-oriented toolkit to analyze molecular dynamics trajectories.',
long_description=LONG_DESCRIPTION,
long_description_content_type='text/x-rst',
author='MDAnalysis Development Team',
Expand All @@ -629,7 +628,7 @@ def long_description(readme):
'Twitter': 'https://twitter.com/mdanalysis',
'Source': 'https://github.com/mdanalysis/mdanalysis',
},
license='GPL 2',
license='GPL-2.0-or-later',
classifiers=CLASSIFIERS,
provides=['MDAnalysis'],
packages=find_packages(),
Expand Down
4 changes: 2 additions & 2 deletions testsuite/setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@ def run(self):
'Development Status :: 6 - Mature',
'Environment :: Console',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
'License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)',
'Operating System :: POSIX',
'Operating System :: MacOS :: MacOS X',
'Operating System :: Microsoft :: Windows ',
Expand Down Expand Up @@ -129,7 +129,7 @@ def run(self):
'Issue Tracker': 'https://github.com/mdanalysis/mdanalysis/issues',
'Source': 'https://github.com/mdanalysis/mdanalysis',
},
license='GPL 2',
license='GPL-2.0-or-later',
classifiers=CLASSIFIERS,
packages=find_packages(),
package_dir={'MDAnalysisTests': 'MDAnalysisTests',
Expand Down