Comments (2)
A thought before I forget - since we're likely going to use the https://openfree.energy/ domain here, are we interested in using subdomains for the api and userguide (something like docs.openfree.energy and userguide.openfree.energy)?
Just thinking - assuming all notebooks are userguide related, we probably wouldn't need to try to move things between repos on CI or release right? We can just keep a repository_dispatch to trigger both release workflows at the same time.
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Notebooks will be (mostly? I think?) user guide, but that doesn't mean that all user guide is 100% notebooks. Installation, for example, is a likely choice for standard RST. We might have other things (like theoretical background) that are easier to manage in RST than Jupyter.
It would be possible to maintain two sphinx repos, one for coding docs and one for user guide, but I'm not sure I see the advantage of that over just using one repo and copying in the notebooks. Moving notebooks isn't that hard; I mean, the core of getting a list of files from one github repo into a desired location is less than 10 lines of code.
Also, I think it's nice to have API in the sidebar when you're looking at user guide, and it's easier to add Sphinx links to API docs from the notebooks (and vice versa!) if they're in one repo. Sure, there's intersphinx, but....
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Related Issues (20)
- Add a warning/note in the setup that protein inputs may need to be equilibrated before running RBFE? HOT 1
- Get macos-12+, including osx-arm64 (i.e. macos-latest) runners working in CI HOT 1
- [docs] Showcase notebook failing to render HOT 2
- Unpin rdkit on mypy HOT 3
- Run through tutorial using 1.0 release HOT 3
- mark gaff tests as xfail HOT 1
- [docs] find new home for `OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb` example
- Using customized force field for small molecules HOT 8
- raise a warning if a user supplies an unsupported key in a settings yaml
- CalledProcessError: 9 HOT 2
- Fix OpenFE tests to match main on Lomap
- Validate OpenFE working on latest of our key tools
- Add rever instructions to release instructions in the wiki
- Add install instructions for the conda lock files
- Issue with PyMBAR4
- Using OPC water models for RBFE calculations HOT 3
- Using other versions of small ligand ff (GAFF) instead of the default one HOT 1
- [CLI] inspect command for json output files
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