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kain88-de
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Nov 18, 2016
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kain88-de
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kain88-de
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Looks good besides the TODO issue
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| :class:`Topology` is the core object that holds all topology information. | ||
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| TODO: Add in-depth discussion. |
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Can you make an issue for that. So we are sure to remove all TODO:s in the docs before the release
richardjgowers
approved these changes
Nov 18, 2016
- added rst stubs for sphinx - updated rst docs (added links, reformatted, fixed, found out that Napoleon REQUIRES two lines before .. versionchanged/versionadded) - removed AtomGroup.rst TODO: - explain topology system and clean up core_modules.rst (work for @richardjgowers and @dotsdl)
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'
- 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'
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rebased against develop and force-pushed |
- broken reST links - removed some of the obviously old outdated topology discussions (but still need proper discussion of #363 changes) - added more cross references and SeeAlso - even more fixes everywhere
abiedermann
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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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There were no docs for the #363 changes and many reST links were broken.
Changes made in this Pull Request:
MDAnalysis.core.AtomGroup.AtomGroup-->MDAnalysis.core.groups.AtomGroupPR Checklist