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update citation in docs #993

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orbeckst opened this issue Sep 20, 2016 · 8 comments
Closed
2 tasks done

update citation in docs #993

orbeckst opened this issue Sep 20, 2016 · 8 comments
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@tylerjereddy
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0.16.0

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@orbeckst
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orbeckst commented Sep 20, 2016 •
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Discussion MDAnalysis/MDAnalysis.github.io#27 lead to the new citation blurb: ask for both papers to be cited in academic work: http://www.mdanalysis.org/pages/citations/

We need to update the MDAnalysis docs in a similar way:

  • sphinx docs
  • README, meta data, etc
@orbeckst orbeckst added this to the 0.16.0 milestone Sep 20, 2016
@orbeckst orbeckst mentioned this issue Sep 20, 2016
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@tylerjereddy tylerjereddy self-assigned this Sep 23, 2016
@tylerjereddy tylerjereddy mentioned this issue Sep 23, 2016
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@orbeckst orbeckst mentioned this issue Sep 23, 2016
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@kain88-de kain88-de mentioned this issue Nov 27, 2016
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@richardjgowers
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Not 100% sure that all sphinx documentation has been checked for this change

@kain88-de
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Nope Sphinx docs need to be checked separately

@tylerjereddy
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I thought I had dealt with the few cases in the sphinx source -- I vaguely remember there only being 2 locations to update, but maybe I'm confused.

@orbeckst
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orbeckst commented Nov 29, 2016 •
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Double check the docs but I think a while back we did most of the rejiggling, including consolidating all references in one place in references.

Pages with MDA citations that immediately come to mind

I think these are all (I git grep 'Michaud-Agrawal').

@kain88-de
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Those were updated in develop already before by someone else.

@orbeckst
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I think the sphinx docs are fine, the SUMMARY and README still need to be done.

@tylerjereddy
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For reference on the sphinx updates and README, but I guess those were superseded by @kain88-de : #1001 (comment)

@orbeckst
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@tylerjereddy it seems that your edits for README / SUMMARY fell by the wayside, sorry. Would you mind re-doing them manually? If you make a PR with a branch in MDAnalysis I can also do some quick editing when I have a few minutes.

@tylerjereddy tylerjereddy mentioned this issue Nov 29, 2016
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orbeckst added a commit that referenced this issue Nov 29, 2016
@orbeckst
cleanup of README/INSTALL/LICENSE
3c3eeae 
- removed all licensing with respect to KD-tree/Biopython: we do not ship any
  Biopython code anymore
- changed license description for Gromacs xdrlib: it is now BSD-2-clause (like);
  the LICENSE file is correct
- removed any mentioning of LGPL for libmdaxdr because it is GPL v2 like everything else
- changed wiki and doc links to use our redirects docs.mdanalysis.org and wiki.mdanalysis.org
- cleaned up INSTALL: added quick install at top, removed most of the crud, and just link
  to the wiki
- changed the copyright in README to be in line with #993
richardjgowers pushed a commit that referenced this issue Nov 30, 2016
@tylerjereddy @richardjgowers
DOC: Wrapping up updates to MDA citation requirements (#1096)
1185630 
* DOC: Updates to MDA citation requirements in SUMMARY and README.

* cleanup of README/INSTALL/LICENSE

- removed all licensing with respect to KD-tree/Biopython: we do not ship any
  Biopython code anymore
- changed license description for Gromacs xdrlib: it is now BSD-2-clause (like);
  the LICENSE file is correct
- removed any mentioning of LGPL for libmdaxdr because it is GPL v2 like everything else
- changed wiki and doc links to use our redirects docs.mdanalysis.org and wiki.mdanalysis.org
- cleaned up INSTALL: added quick install at top, removed most of the crud, and just link
  to the wiki
- changed the copyright in README to be in line with #993

* updated citation header in C files

* fixed size of test data files (~70 MB)
abiedermann pushed a commit to abiedermann/mdanalysis that referenced this issue Jan 5, 2017
@tylerjereddy @richardjgowers
DOC: Wrapping up updates to MDA citation requirements (MDAnalysis#1096)
438a650 
* DOC: Updates to MDA citation requirements in SUMMARY and README.

* cleanup of README/INSTALL/LICENSE

- removed all licensing with respect to KD-tree/Biopython: we do not ship any
  Biopython code anymore
- changed license description for Gromacs xdrlib: it is now BSD-2-clause (like);
  the LICENSE file is correct
- removed any mentioning of LGPL for libmdaxdr because it is GPL v2 like everything else
- changed wiki and doc links to use our redirects docs.mdanalysis.org and wiki.mdanalysis.org
- cleaned up INSTALL: added quick install at top, removed most of the crud, and just link
  to the wiki
- changed the copyright in README to be in line with MDAnalysis#993

* updated citation header in C files

* fixed size of test data files (~70 MB)
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