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JonnyTran / OpenOmics

A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.
https://openomics.readthedocs.io/en/latest/
MIT License
31 stars 13 forks source link

Review 2 - Documentations - Readthedocs documentations should be updated #119

Closed JonnyTran closed 3 years ago

JonnyTran commented 3 years ago

Description

@gawbul

Docstrings seem to be available throughout the codebase for all relevant functions, however, I found the documentation on Read the Docs to be lacking in comparison, particularly in providing detail of function parameters that are otherwise available in the docstrings.

There is no link to the contribution guidelines from the main README, which I feel would be beneficial, however contributing guidelines are available in https://github.com/BioMeCIS-Lab/OpenOmics/blob/master/CONTRIBUTING.rst and on Read the Docs.

Just being finicky, I personally would prefer a common format for the README and CONTRIBUTING documents etc. Either both in reStructuredText or both in Markdown. There seems to be an outdated README.rst that could probably be replaced with the current README.md?

JonnyTran commented 3 years ago

Revamped openomics.readthedocs.io !

gawbul commented 3 years ago

Looks awesome 🤩

gawbul commented 3 years ago

I did notice that this section of the docs https://openomics.readthedocs.io/en/latest/usage/getting-started.html#creating-a-multi-omics-dataset was missing the following:

from openomics import MultiOmics

Otherwise, the following statement fails:

luad_data = MultiOmics(cohort_name="LUAD", omics_data=[mRNA, mRNA, lncRNA, som, pro])

E.g.:

Traceback (most recent call last):
  File "/Users/stephenmoss/Dropbox/Code/openomics_test.py", line 39, in <module>
    luad_data = MultiOmics(cohort_name="LUAD", omics_data=[mRNA, mRNA, lncRNA, som, pro])
NameError: name 'MultiOmics' is not defined
JonnyTran commented 3 years ago

Thanks for pointing this out. I will fix that.