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Re-structure the cookbooks - #2319
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| The typical way to use the Python API is to load a number of molecules you want to calculate free energies of, construct a :class:`LigandNetwork` connecting them in an efficient way, and then combine that with information for how each ligand should be simulated to construct an :class:`AlchemicalNetwork`, which specifies the entire simulation campaign. This provides a lot of flexibility in how molecules are specified, mapped, connected, and simulated, without exposing a great deal of complexity. OpenFE recommends this workflow for most users. | ||
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| .. container:: deflist-flowchart |
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I moved this to the introduction to the user guide instead, though the same chart is also in the under the hood, which we can revisit when we re-organize the user guide maybe?
| A network of ligand transformations. | ||
| loading_molecules | ||
| user_charges | ||
| bespoke_parameters |
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It is pulling the recap heading out of the bespokefit guide and making it an entry here, can we stop it here or do we need to use a smaller heading in that guide?
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I think we have to do that in the ExampleNotebooks repo. Maybe in a separate PR there we can also update some of the titles of the cookbooks since some of these are not great.
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@jthorton I updated the titles here: OpenFreeEnergy/ExampleNotebooks#351
I mostly tried to make them a bit shorter and better suited for display in a side bar, please let me know what you think!
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Can we build the docs against it here by changing
Line 198 in c9eeacd
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Targeting the rename branch for now.
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| Cookbook | ||
| ======== | ||
| How-to guides |
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Should we rename the file as well?
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I was thinking of doing that in a follow up PR as it would also mean renaming things in different links, but I could also already do that here!
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I'll leave it up to you happy for either.
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| .. admonition:: How-to guides | ||
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| * :doc:`/cookbook/dumping_transformation` |
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Should this one be in the execution/index.rst page?
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Yes, I think this could either be in the user guide or we could also have a notebook that looks at saving and inspecting json files and combines the two notebooks?
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Yeah I like the idea of a single notebook on working with the JSON files. In the meantime, we could just add this one to the how-to-guide links on the execution page its currently just a TODO?
| .. TODO make figure | ||
| .. .. figure:: ??? | ||
| :alt: Setup -> (AlchemicalNetwork) -> Execution -> (ProtocolResults) -> Gather | ||
| .. container:: deflist-flowchart |
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The formatting seems to have got messed up with this one.
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I changed this again! Not sure though yet if this is too much detail for the intro page.
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This is working now and does show a nice flow of the workflow so I think it would be okay to keep. I think the section names should match those in the list above so users can match them up.
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Changed the section names!
…ergy/openfe into restructure-cookbooks
…ergy/openfe into restructure-cookbooks
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Some minor optional points but this is looking much better thanks @hannahbaumann !
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this looks so much better! 
Nitpick: could we make the following changes so all the titles are consistent and fit the "How To ___" structure?
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| .. rst-class:: arrow-down | ||
| * | ||
| repairing_broken_networks |
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I don't feel super strongly about this, but it makes more sense to me to have "Working with Results" before "Repairing and extending", since it's likely a user would inspect results before deciding to repair or extend.
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I agree, moved this to after the results.
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
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LGTM! just a reminder to merge OpenFreeEnergy/ExampleNotebooks#351 first and change this back to point to main!
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pre-commit.ci autofix.newsentry, or the changes are not user-facing.Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).
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