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- collected references in references.rst; removedt the full MDAnalysis references from the index page and just link to the citations in references.rst - use reST citation syntax so that one can refer to the citations from *anywhere* in the docs; in this way we only need to maintain them in a single place - added ENCORE reference - added MDAnalysis SciPy reference - reformatted all references to a common style; note that I needed to manually break some lines to avoid starting lines with character followed by period (such as 'O. Beckstein') because reST/sphinx interpretes 'O.' as a enumerated list and messes up the format.
- created top level encore.rst that reproduces some text from encore.similarity - added stubs for complete automodule loading when possible or wrote small rst files with header and automodule/member loading - combined Clustering submodules and Dimensionality Reduction submodules each into one file
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@mtiberti / @wouterboomsma please have a look at the encore docs. I only made sure that all files are referenced somewhere and show up with a header. Please feel free to change as you see fit. In On this branch docs are not built and published so you have to do it yourself. The following works for me (I use a virtualenv): pip install -e package/
cd package/doc/sphinx
make htmlthen browse |
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@orbeckst Thanks for the comments. I'll try to fix this in the coming week. |
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@wouterboomsma if you look through what I have done and only have minor corrections then add them as comments/reviews. If this is basically ok then we just need someone like @kain88-de to say ok and merge and then you can still add more doc changes later. If something is fundamentally wrong with what I wrote then we obviously don't want to merge this. Ultimately you or one of the other ENCORE devs are the ones who can make this call. |
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@orbeckst Thanks for putting in this work. I've found a bunch of small things with weird whitespace in the code etc. Are you sure it wouldn't be easier if I make the changes locally and then make a PR to this branch? |
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@wouterboomsma feel free make a PR against this branch. About the MemoryReader docs. I think they need to be added here |
- fixes #1056 (comment) - added entry to reST sphinx docs - added/changed docs in coordinates/memory.py: - included AnalysisFromFunction example from MDAnalysis/MDAnalysis.github.io#30 (comment) - included transfer_to_memory() example - included example for how to make a in-memory trajectory of a sub-system with Merge() and Universe.load_new() from #915 (comment) - minor reST fixes in the MemoryReader docs (e.g., renamed the Examples section because the numpy format napoleon parser treats this heading special and does not recognize it as a standard section)
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I added the MemoryReader docs in 5a24204, including the examples discussed in
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@orbeckst, Hehe, I just made almost exactly the same changes locally yesterday. I'll just merge them and finalise our edits. I'll submit a PR later today. |
* Fixes in Encore and MemoryReader documentation to make it render with sphinx. * Edits in Encore and MemoryReader documentation. * Renamed PrincipleComponentAnalysis to PrincipalComponentAnalysis. Minor edits in documentation. * Changed spacing issues
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@orbeckst & @wouterboomsma are you happy with the current state now? |
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I'm happy. |
…import error message [ci skip]
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added minor fix to one of the encore citation reST and fixed an error message in analysis.density, just because I couldn't be bothered to put it into a separate commit/PR.... I am happy. Once we decide on the order of the MemoryReader (afc vs fac) #1063 we just have to adapt those parts of the docs but at least they are correct as of now. @kain88-de are you going to merge? |
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…docs Issue 1047 encore docs
3 participants
Fixes #1047
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