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Tracking issue: annotations CLI config

See original GitHub issue

For discussion. cc @liaprins-czi

Disable annotations flag

Swap logic of the --annotations flag
Current behavior:
--experimental-annotations Enable user annotation of data. [default: False] Desired behavior:
--disable-annotations Disable in-app annotation of data. [default: False]

Naming

Rename --annotations-file to --annotations-input-file
Remove experimental from all args

Defaults

If no input file is specified, prompt the user for a name on startup (including their unique hash)
If no output dir is specified, default to (1) h5ad directory if local and available; (2) cwd if not

Misc

Make sure the docs are updated
Update tests!

Issue Analytics

State:
Created 4 years ago
Reactions:1
Comments:14 (12 by maintainers)

Top GitHub Comments

1reaction

sidneymbellcommented, Mar 3, 2020

That’s possible, although in this case I personally think it’s higher value to keep the h5ad and the annotations csv together whenever possible. I’ll defer to @liaprins-czi on this one 😃

0reactions

bkmartinjrcommented, Mar 3, 2020

In the meantime, would you mind updating the output-dir default @bkmartinjr? TY!

sure, drop me an issue and flag it for 0.15. I probably won’t get to it until later this week

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