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Merge cinnabar tutorials into a single how-to guide - #357
hannahbaumann wants to merge 14 commits into
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Actually, maybe this is a good time to address this: |
hannahbaumann
changed the title
…mpleNotebooks into rename-cinnabar-howto
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What about bolding the relative free energies and absolute free energies in the list to make it stand out?
Maybe a warning or note box for the cinnabar version or we could have a cell that checks it and errors if its not over 0.6?
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Thanks, yes made them bold and moved the version mentioning into a box!
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The requirement for all values to have an experimental point is no longer true in cinnabar so we can remove this.
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Thanks, removed this!
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Should the gather-septop command not be included in the first item as it also runs MLE on the relative differences?
Also do we need to sync up the outputs of the rbfe and septop dg reports to have the same headings?
Should we say something about mixed networks here or the section above and point to the new tutorial as the CLI steps will be an issue?
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- True, I added the gather-septop to the first bullet point
- Yes, I raised an issue here:
gathergives different DG header thangather-septopandgather-abfefor the--report dgopenfe#2346 - Yes, I added something in the section abbove!
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Why does this use slightly different DG values, if this from a different network to the DDG example above?
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YEs, I'm not sure why this was different, I now recreated the file to match the other output.
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Perfect, I think showing it works the same is better for the guide.
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I moved part of the note to the relative section above, but left this here as a reminder, please let me know if you feel like it wouldn't be necessary here.
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Yeah I think this is needed in both.
…mpleNotebooks into rename-cinnabar-howto
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Deleted these!
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Unless there's a reason for it, I'd prefer we link to where these links are rendered in the docs, rather than the github url.
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This was since the PR is not merged yet, but I now changed it and we can wait with this merge for the mixed network expose PR in openfe to be merged first.
For moving the cinnabar tutorial into the how-to guide: OpenFreeEnergy/openfe#2343