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fix failing cells in example notebooks #268

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Merged
atravitz merged 11 commits into from
Dec 4, 2025
Merged

fix failing cells in example notebooks #268

atravitz merged 11 commits into from
Dec 4, 2025

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@atravitz atravitz commented Dec 3, 2025

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github-actions bot commented Dec 3, 2025

Colab 👈 Launch a Colab session on branch fix/notebook_tests

@atravitz atravitz mentioned this pull request Dec 3, 2025
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@atravitz atravitz requested review from IAlibay, hannahbaumann and mikemhenry and removed request for hannahbaumann December 4, 2025 00:14
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atravitz commented Dec 4, 2025

I care about full_tests passing here. The container image and openfe doc build tests are something that @mikemhenry and I need to discuss separately.

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mikemhenry approved these changes Dec 4, 2025
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LGTM -- Just a question about the json file size

openmm_septop/results/rbfe_lig_ejm_31_lig_ejm_42.json Outdated
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Does it make sense to compress this json? it is 9.89 MB -- if we need it like this then we need it like this, its okay for the example notebooks to get bigger but it feels like a gzip on it would be worth it (also sorry if there are already a lot of these in the notebook)

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oh yikes, yeah this is larger than I realized and we really don't need it now that we have a whole septop analysis notebook. i'll comment it out like I did with the abfe notebook.

@atravitz atravitz enabled auto-merge December 4, 2025 19:54
@atravitz atravitz disabled auto-merge December 4, 2025 20:50
@atravitz atravitz merged commit cef0451 into main Dec 4, 2025
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@atravitz atravitz deleted the fix/notebook_tests branch December 4, 2025 20:50
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@mikemhenry mikemhenry mikemhenry approved these changes

@IAlibay IAlibay Awaiting requested review from IAlibay

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