Closed d33bs closed 3 months ago
In chatting with @jenna-tomkinson, we discussed that getting a file-based output would potentially be more useful than text-based output. The filename could use the input filename as the basis for output filename, for example example.csv
would become example.identify_outliers.parquet
Thinking on file-based output a little more made me feel that that work might be best served after merging #32 and this PR. Generally, I'm worried that there may be complex scenarios where one would want a file vs not. It also might be possible to control the export of files through a similar mechanism to pd.DataFrame
, i.e. pd.DataFrame.to_parquet(...)
, etc. which could avoid us having to maintain additional code. Created #37 as a result.
Decided to implement this within the same PR.
Thanks @jenna-tomkinson for the review! I've addressed your comments and will now merge this in.
Description
This PR adds a CLI for
coSMicQC
through the use offire
. This work depends on changes from #32 . Along the journey towards these changes I discovered there were challenges in displayingpd.DataFrame
's (or relatedSCDataFrame
's) throughfire
CLI's. As a result, I added a patch inspired from work in https://github.com/google/python-fire/pull/446 by reassigning the_PrintResult
function to match the contents of the fix. Once the fix is merged infire
we should remove the patch and rely onfire
for these changes. When/if these changes are merged, I'll create an issue to track this so we don't forget to take action here.Along with these changes some docs were fixed.
This should be reviewed and merged after #32
Closes #14 Closes #37
What kind of change(s) are included?
Checklist
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