new topology docs #1078
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1 task
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So this definitely needs doing. I wouldn't want to put it in a |
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If you prefer in the py then that's totally fine with me – as long as it is somewhere ;-). |
orbeckst
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Nov 19, 2016
- added missing docs for new topology system (#363) - removed some of the obviously old outdated topology discussions (but still need proper discussion of #363 changes – see issue #1078 ) - added rst sphinx stubs for new modules in core - updated rst docs (added links, reformatted, fixed, found out that Napoleon REQUIRES two lines before .. versionchanged/versionadded) - removed AtomGroup.rst - restructured core_modules - fixed Universe and AtomGroup reST references (core changes in #363) find . -name '*.rst' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Universe (MDAnalysis.core.universe.Universe)g' find . -name '*.py' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Universe)(MDAnalysis.core.universe.Universe)g' find . -name '*.rst' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.AtomGroup)(MDAnalysis.core.groups.AtomGroup)g' find . -name '*.py' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.AtomGroup)(MDAnalysis.core.groups.AtomGroup)g' - fixed reST links for other changes in core (#363) - AtomGroup.Atom --> groups.Atom - AtomGroup.Merge --> universe.Merge - AtomGroup.ResidueGroup --> groups.ResidueGroup (no SegmentGroup needed to be fixed, no Residue or Segment found) - core.Selection --> core.selection find . \( -name '*.py' -o -name '*.rst' \) -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Atom)(MDAnalysis.core.groups.Atom)g' find . \( -name '*.py' -o -name '*.rst' \) -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Merge)(MDAnalysis.core.universe.Merge)g' find . \( -name '*.py' -o -name '*.rst' \) -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.ResidueGroup)(MDAnalysis.core.universe.ResidueGroup)g' - many more doc fixes everywhere - broken reST links - added more cross references and SeeAlso
6 tasks
4 tasks
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Related #1108 to explain what we mean with a unique segment/residue |
abiedermann
pushed a commit
to abiedermann/mdanalysis
that referenced
this issue
Jan 5, 2017
- added missing docs for new topology system (MDAnalysis#363) - removed some of the obviously old outdated topology discussions (but still need proper discussion of MDAnalysis#363 changes – see issue MDAnalysis#1078 ) - added rst sphinx stubs for new modules in core - updated rst docs (added links, reformatted, fixed, found out that Napoleon REQUIRES two lines before .. versionchanged/versionadded) - removed AtomGroup.rst - restructured core_modules - fixed Universe and AtomGroup reST references (core changes in MDAnalysis#363) find . -name '*.rst' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Universe (MDAnalysis.core.universe.Universe)g' find . -name '*.py' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Universe)(MDAnalysis.core.universe.Universe)g' find . -name '*.rst' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.AtomGroup)(MDAnalysis.core.groups.AtomGroup)g' find . -name '*.py' -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.AtomGroup)(MDAnalysis.core.groups.AtomGroup)g' - fixed reST links for other changes in core (MDAnalysis#363) - AtomGroup.Atom --> groups.Atom - AtomGroup.Merge --> universe.Merge - AtomGroup.ResidueGroup --> groups.ResidueGroup (no SegmentGroup needed to be fixed, no Residue or Segment found) - core.Selection --> core.selection find . \( -name '*.py' -o -name '*.rst' \) -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Atom)(MDAnalysis.core.groups.Atom)g' find . \( -name '*.py' -o -name '*.rst' \) -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.Merge)(MDAnalysis.core.universe.Merge)g' find . \( -name '*.py' -o -name '*.rst' \) -print0 | xargs -0 perl -wpi~ -e 's(MDAnalysis\.core\.AtomGroup\.ResidueGroup)(MDAnalysis.core.universe.ResidueGroup)g' - many more doc fixes everywhere - broken reST links - added more cross references and SeeAlso
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Working on this this week. PR incoming soon. |
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@dotsdl if you want to put up a skeleton of topics it'll make it easier for me to chip in. Or use a project board or something? |
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@richardjgowers I can do that. I'll make a project board. |
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Expected behaviour
The philosophy behind the new topology system #363 should be outlined.
Actual behaviour
At the moment, PR #1077 only removed obviously outdated comments in the docs in
topology/__init__.py.See also TODO in
core/topology.pyand the structuredoc/sphinx/documentation_pages/core_module.rst.Perhaps it would be worthwhile making this a proper rst file underdoc/sphinxinstead of cramming all the docs into a__init__.pyetc (?).The text was updated successfully, but these errors were encountered: