Add some preliminary guesser docs #409
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Thanks @lilyminium for adding this documentation. I left some comments, but generally LGTM and it's very informative.
Do I understand correctly that there are currently no guessers other than the default?
Apologies if I din't provide some suggested changes for formatting, but I reviewed on mobile and back quotes are not an easy thing to add.
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| The default guesser has been created to reproduce pre-v2.8.0 MDAnalysis guessing behaviour as much as possible. **Default behaviours will change in MDAnalysis version 3**, as detailed in deprecation warnings. |
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Do we have/want to include more details about what "as close as possible" means (i.e. are there small differences and corner cases)?
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As far as I recall the only real change is the ITPParser now has an extra Elements attribute, which is a bit specific to mention -- I've added a link to the 2.8.0 changelog for interested readers.
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
- address @RMeli comments - minor grammar fixes - moved note on radii guessing to explicit rst note
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@RMeli @lilyminium I made some edits, hopefully addressing most of @RMeli 's comments. Are we ok with merging so that we can make progress on the User Guide? |
fix whitespace to make pre-hook check happy
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Thanks. Ping me if you need me to press the merge button. ;) |
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Huzzah it renders -- merging now! |
* add some preliminary guesser docs * fix ipython blocks * Apply suggestions from code review Co-authored-by: Rocco Meli <r.meli@bluemail.ch> * link to Guesser API * Update guessing.rst - address @RMeli comments - minor grammar fixes - moved note on radii guessing to explicit rst note * Apply suggestions from code review fix whitespace to make pre-hook check happy * fix ipython block * add changes from review * add link to changelog --------- Co-authored-by: Oliver Beckstein <orbeckst@gmail.com> Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
Supersedes #213, just a preliminary first attempt at jotting down what I think people would want to know and some possible gotchas with the new guessing interface. I've mostly tried to avoid duplicating the API docs where possible, except for the attribute guessing where there is some additional info in the user guide (which we can move over to core API docs if it belongs better there).
If there are any other items that should really be added, please suggest them here!
📚 Documentation preview 📚: https://mdanalysisuserguide--409.org.readthedocs.build/en/409/