Cli edit #50
Cli edit #50
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hrshdhgd
commented
May 24, 2021
hrshdhgd
commented
- Documentation for the click options.
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@matentzn , All I've done so far is changed docstrings. Any idea why the build would be failing with the error |
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Before we merge this I would like:
At least one, better two or three tests per method in here (make TESTDIR configurable):
https://github.com/mapping-commons/sssom-py/blob/cli_edit/tests/tests.sh
Make sure all CLI methods are tested here:
https://github.com/mapping-commons/sssom-py/blob/cli_edit/tests/test_cli.py
I made a bunch of change to the annotations, but we wont make this perfect now; the goal here is to have cli in an ok state that we can iterate over.
sssom/cli.py
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| df = collapse(df) | ||
| msdf = from_tsv(input) | ||
| # df = parse(input) | ||
| df = collapse(msdf.df) | ||
| # , priors=list(priors) | ||
| rows = dataframe_to_ptable(df) | ||
| for row in rows: | ||
| logging.info("\t".join(row)) |
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I guess I am responsible for this... what was I thinking. This isn't logging output, it's the primary output
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This is my mistake, not yours.. I want to generally be able to stream outputs from all commands in that way; what is the best way to do this then - using print() in conjunction with a stream (either a file output stream or stdout)?
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@hrshdhgd I will fix this
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for ptable we are now using print, but I want to ensure with the architecture so will review with @cmungall on Monday and merge.
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I have committed tests as well. Things that are pending:
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Alright this has become too massive, sorry about that @cmungall and I will review this on Monday together and merge it in. |
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go ahead and merge! |
