consolidate package info files by orbeckst · Pull Request #2808 · MDAnalysis/mdanalysis

orbeckst · 2020-06-30T23:50:22Z

Changes made in this Pull Request:

generate LONG_DESCRIPTION from README.rst (remove SUMMARY.txt (out of date) and
add code to setup.py to extract reST suitable for PyPi)
updated README.rst (links to User Guide, add sections similar to https://www.mdanalysis.org/) and
removed raw html by including a down-scaled version of the NF logo
update links to website throughout
added Travis job to check that we can build a pypi source distribution package (sdist)
cleaned up MANIFEST.in

PR Checklist

Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

orbeckst · 2020-06-30T23:52:06Z

More could be done here, e.g., the README and INSTALL file duplicate content. Instead of being fancy and generating them somehow, perhaps we just reduce them to the minimum necessary and make sure that they contain helpful links?

Please contribute to the PR, not sure if I have much more time to work on it.

codecov · 2020-07-01T03:03:48Z

Codecov Report

Merging #2808 into develop will increase coverage by 0.02%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop    #2808      +/-   ##
===========================================
+ Coverage    92.20%   92.22%   +0.02%     
===========================================
  Files          184      184              
  Lines        24103    24170      +67     
  Branches      3134     3134              
===========================================
+ Hits         22224    22291      +67     
  Misses        1814     1814              
  Partials        65       65

Impacted Files	Coverage Δ
package/MDAnalysis/__init__.py	`92.50% <ø> (ø)`
package/MDAnalysis/core/_get_readers.py	`96.05% <ø> (ø)`
package/MDAnalysis/core/universe.py	`96.95% <100.00%> (ø)`
util.py	`88.10% <0.00%> (+0.08%)`	⬆️
coordinates/base.py	`94.82% <0.00%> (+0.28%)`	⬆️
auxiliary/base.py	`91.31% <0.00%> (+0.56%)`	⬆️

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IAlibay

Just a couple of questions, main one being that the logo doesn't seem to be centered in: https://github.com/MDAnalysis/mdanalysis/tree/update-pypi-SUMMARY

README.rst

package/doc/sphinx/source/conf.py

pep8speaks · 2020-07-07T23:31:05Z

Hello @orbeckst! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2020-07-13 23:27:30 UTC

orbeckst · 2020-07-07T23:51:58Z

Btw, thanks for reviewing @IAlibay ... I had removed you from the initial list as I didn't want to pile even more on you. So thank you for doing it nevertheless.

orbeckst · 2020-07-12T05:47:28Z

@IAlibay do you think that anything else needs changing here?

IAlibay

lgtm, just a few minor comments to possibly consider.

IAlibay · 2020-07-13T12:09:45Z

README.rst

 .. _`MDAnalysis.analysis`: https://docs.mdanalysis.org/documentation_pages/analysis_modules.html
-.. _`tutorials`: https://www.mdanalysis.org/pages/learning_MDAnalysis/
-.. _`guide`: https://github.com/MDAnalysis/mdanalysis/wiki/Guide-for-Developers
+.. _`tutorials`: https://www.mdanalysis.org/UserGuide/examples/README.html


I realise it points in the same place, but for consistency should this be: https://userguide.mdanalysis.org/1.0.0/examples/README.html instead?

Yes, thanks, or rather https://userguide.mdanalysis.org/examples/README.html (so that we don't have to update the version info)

IAlibay · 2020-07-13T12:15:38Z

package/setup.py

+                  flags=re.DOTALL)
+    assert m, "README.rst does not contain a level-1 heading"
+    return buffer[m.end():]
+


Shouldn't there be two blank lines here? I would have expected pep8speaks to pick this one up, so maybe there's a PEP8 special case for empty lines between functions and if __name__ == '__main__' that I'm not aware of.

fixed (together with other PEP8 complaints)

- generate LONG_DESCRIPTION from README.rst - remove SUMMARY.txt (out of date) - read top-level repository README.rst for LONG_DESCRIPTION - changed README.rst - add installation instruction (link) - add links to Quickstart Guide, User Guide, and API docs - add links to issue tracker and mailing list in text (Contributing) - replaced links to wiki with links to User Guide - remove raw html from README (raw html not allowed on PyPi) - replace NumFOCUS logo image with reduced size version (200 x 61 px) and standard reST image syntax (logo added to web site in commit MDAnalysis/MDAnalysis.github.io@ec4fe2c ) - fix broken link - tutorials direct to Examples in User Guide - add link to video section of "Learning MDAnalysis" - passes `twine check` - cleaned up MANIFEST.in (for pypi packages) - fixed links in Py files - Make sure that we always use the SSL url of the home page git grep -l 'http://www\.mdanalysis\.org' | xargs perl -wpi~ -e 's(https://www\.mdanalysis\.org)(https://www.mdanalysis.org)' - fixed link to issue tracker in files git grep -l 'issues.mdanalysis.org' | xargs perl -wpi~ -e 's(https?://issues\.mdanalysis\.org)(https://github.com/MDAnalysis/mdanalysis/issues) - fixed PEP8 issues in files - various updates in testsuite/README (link to userguide, update badges) - use User Guide as style reference Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com>

- explicit PYPI_CHECK in script section - switch travis to beta for config validation - https://docs.travis-ci.com/user/build-config-validation - get feedback on problems with the config yml file Note: Use ci-helper's algorithm for installing numpy and don't pin a numpy version, not even for the simple PYPI_CHECK section

orbeckst · 2020-07-13T23:28:22Z

I rewrote the history to cleanly separate the meta data updates and the addition of a the package build check in Travis CI. (EDIT) so that this can be merged.

orbeckst force-pushed the update-pypi-SUMMARY branch 3 times, most recently from 93ef8cf to cf27760 Compare July 3, 2020 19:47

orbeckst requested review from IAlibay, RMeli, lilyminium and richardjgowers and removed request for IAlibay July 6, 2020 23:41

IAlibay requested changes Jul 7, 2020

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IAlibay approved these changes Jul 13, 2020

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orbeckst and others added 2 commits July 13, 2020 16:20

orbeckst force-pushed the update-pypi-SUMMARY branch from 0b0d4c2 to bbc3dcb Compare July 13, 2020 23:27

orbeckst merged commit 75706b4 into develop Jul 14, 2020

orbeckst deleted the update-pypi-SUMMARY branch July 14, 2020 06:30

This was referenced Jul 14, 2020

Backport 1.0.1 #2798

Merged

Have dependencies files #2769

Open

fiona-naughton added the maintainability label Sep 25, 2023

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Comment last updated at 2020-07-13 23:27:30 UTC

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orbeckst commented Jun 30, 2020 •

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