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Update tutorials - #79
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dilpath
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Thanks! Some comments apply to all notebooks, e.g. naming of inputs/outputs in the mapping table.
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## main #79 +/- ##
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+ Coverage 95.13% 95.20% +0.06%
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Thanks for the feedback! I have now implemented it. Lets now wait for AMICI to update, then we can update the code, and finally merge this PR. |
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Co-authored-by: BSnelling <branwen.snelling@crick.ac.uk> Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
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dilpath
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dilpath
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Looks good! Thanks. No need to resolve all comments in this PR -- can instead create issues and I can then resolve some of them too.
| experiment_ids = measurements["experimentId"].unique() | ||
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| # experiments | ||
| # Each experiment consists of a single simulation period starting at t=0. | ||
| # No conditions are applied, so the `conditionId` column is left empty. | ||
| experiments = { | ||
| "experimentId": experiment_ids, | ||
| "time": [0] * len(experiment_ids), | ||
| "conditionId": [None] * len(experiment_ids), | ||
| } | ||
| pd.DataFrame(experiments).to_csv( | ||
| save_directory / "experiments.tsv", sep="\t", index=False | ||
| ) |
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Experiments/conditions table is optional in PEtab v2
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In general we could delete all outputs of the cells in all notebooks, and only render them on readthedocs
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Opened an issue for this one: #94
At the moment the outputs from some cells are included in order to make the docs read nicely, while others are deleted because their outputs are long/don't render nicely/include warnings. It'll be a bit of work to update them so they all execute cleanly (and prettily) so I'll make that a separate PR.
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Ah OK. Fine for me if those "ugly" cells just have their output disabled if possible in the notebook, if it's some effort to make it pretty.
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This PR updates the PEtab-SciML tutorials to:
data.
The tutorial text is ready for review. The code snippets and accompanying PEtab files are
currently outdated and will be updated once the linter is in place. This can be done at a
later stage, and the PR should not be merged until then.
This PR is related to completing #23