add NumFOCUS sponsorship (issue #2460) #2467

richardjgowers · 2020-01-23T11:57:01Z

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Tests?
Docs?
CHANGELOG updated?
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richardjgowers · 2020-01-23T11:58:35Z

So on the template for numfocus attribution there's a little thing that they use for automatic audits. This is in markdown, whereas our readme is rst, so it look like a quick rejig into markdown is required... unless anyone objects?

IAlibay · 2020-01-23T12:39:40Z

Not that it adds much to the discussion, it is interesting that a thrawl through github doesn't seem to indicate any cases of this auditing tag being used anywhere (I was having a look through to see if anyone came up with an alternative for .rst files).

Considering this template is new as of last September, I assume this isn't something they have fully implemented yet?

codecov · 2020-01-23T14:09:49Z

Codecov Report

Merging #2467 into develop will increase coverage by 0.13%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           develop    #2467      +/-   ##
===========================================
+ Coverage    90.21%   90.34%   +0.13%     
===========================================
  Files          177      179       +2     
  Lines        22642    23813    +1171     
  Branches      2933     3010      +77     
===========================================
+ Hits         20427    21515    +1088     
- Misses        1616     1691      +75     
- Partials       599      607       +8

Impacted Files	Coverage Δ
package/MDAnalysis/core/_get_readers.py	`96.29% <0%> (-3.71%)`	⬇️
package/MDAnalysis/core/topologyattrs.py	`97.4% <0%> (-0.72%)`	⬇️
package/MDAnalysis/core/topologyobjects.py	`97.87% <0%> (-0.64%)`	⬇️
coordinates/base.py	`94.74% <0%> (-0.4%)`	⬇️
package/MDAnalysis/topology/__init__.py	`100% <0%> (ø)`	⬆️
package/MDAnalysis/topology/tables.py	`100% <0%> (ø)`	⬆️
package/MDAnalysis/coordinates/__init__.py	`100% <0%> (ø)`	⬆️
topology/__init__.py	`100% <0%> (ø)`	⬆️
coordinates/__init__.py	`100% <0%> (ø)`	⬆️
package/MDAnalysis/coordinates/ParmEd.py	`82.84% <0%> (ø)`
... and 8 more

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jbarnoud · 2020-01-24T13:49:26Z

So on the template for numfocus attribution there's a little thing that they use for automatic audits. This is in markdown, whereas our readme is rst, so it look like a quick rejig into markdown is required... unless anyone objects?

Could rst comments be of any help? https://docutils.sourceforge.io/docs/user/rst/quickref.html#comments

If NumFOCUS just search for the string, then it may be enough to have it appear in the readme somehow.

orbeckstASU

Testing if I can fully review even if I am not a dev.

orbeckst · 2020-01-24T18:31:57Z

So on the template for numfocus attribution there's a little thing that they use for automatic audits. This is in markdown, whereas our readme is rst, so it look like a quick rejig into markdown is required... unless anyone objects?

Raise an issue at https://github.com/numfocus/templates/issues and ask for how to use in rst ?

we are still missing some affiliation links

orbeckst

LGTM. Not sure if they want to see it on the site and then give use the sponsorship link or if we should wait.

README.rst

orbeckst

wait with merge until we have the sponsorship link

orbeckst · 2020-02-05T22:54:30Z

I'll add the link from #2506

- moved NumFOCUS to top (as in template https://github.com/numfocus/templates/blob/master/fiscal-sponsor-readme-attribution.md) - add link to Code of Conduct (as in template) - fixed link to governance (use website Governance section instead of repo file) - add NF donation link from #2506 - close #2506 - updated high level description

orbeckst · 2020-02-05T23:36:20Z

I added the links and did some general editing. However, two things are still bothering me

I am not sure that the resizing of the numfocus image actually works, at least not in the preview. According to the template it should be a height of 60px.
I don't know what to do with the magic markdown audit code [//]: # (numfocus-fiscal-sponsor-attribution) from the template.

jbarnoud · 2020-02-05T23:40:26Z

I don't know what to do with the magic markdown audit code [//]: # (numfocus-fiscal-sponsor-attribution) from the template.

Maybe we should just ask numfocus?

@jbarnoud

- added the audit anchor as a reST link target as suggested by @jbarnoud - added alt tag for NumFOCUS image

orbeckst · 2020-02-05T23:42:26Z

Yes, will do. (EDIT) after merging this one. We can fix it up once we know how. I just don't want to wait around.

orbeckst · 2020-02-05T23:47:51Z

Hm, apparently we ought to have a GOVERNANCE.md in the repo, even if it's only a stub, so will add one...

If your project has no GOVERNANCE.md at the root, then create a stub GOVERNANCE.md and include a link to your governance documentation or the appropriate parties to contact for more information.

This file is required as a NumFOCUS sponsored project.

) Fixes #2647, towards #2553 ## Work done in this PR Elements are now read from PDB files and added to the elements attribute of the universe. This is currently only done in cases where all elements in the PDB file are valid (i.e. match IUPAC naming). In all other cases a user warning is thrown and the elements are not assigned. ## Files changed - MDAnalysis/topology/PDBParser.py - MDAnalysisTests/topology/test_pdb.py - CHANGELOG and AUTHORS (new contributor)

WIP: issue #2460

4408590

orbeckstASU suggested changes Jan 24, 2020

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MDAnalysis deleted a comment from orbeckstASU Jan 27, 2020

kain88-de added 2 commits January 28, 2020 16:49

Add NumFOCUS sponsorship text

b74a05f

we are still missing some affiliation links

use rst syntax

1027ac4

orbeckst approved these changes Jan 28, 2020

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orbeckst requested changes Jan 31, 2020

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orbeckst changed the title ~~WIP: issue #2460~~ add NumFOCUS sponsorship (issue #2460) Feb 5, 2020

README: NumFOCUS audit anchor

5731ae2

- added the audit anchor as a reST link target as suggested by @jbarnoud - added alt tag for NumFOCUS image

orbeckst approved these changes Feb 5, 2020

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create GOVERNANCE.md

27e48a7

This file is required as a NumFOCUS sponsored project.

orbeckst merged commit 009ec22 into develop Feb 5, 2020

orbeckst deleted the richardjgowers-patch-1 branch February 5, 2020 23:58

orbeckst mentioned this pull request Feb 6, 2020

How to add the audit code in template.md to a reST file? numfocus/templates#2

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IAlibay added the Component-Docs label Sep 26, 2023

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add NumFOCUS sponsorship (issue #2460) #2467

add NumFOCUS sponsorship (issue #2460) #2467

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add NumFOCUS sponsorship (issue #2460) #2467

add NumFOCUS sponsorship (issue #2460) #2467

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richardjgowers commented Jan 23, 2020

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