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Add detailed docstrings and usage examples to Ersilia'a publish module and few update on the test module #1443

Merged
merged 14 commits into from
Dec 16, 2024
Merged

Add detailed docstrings and usage examples to Ersilia'a publish module and few update on the test module #1443

merged 14 commits into from
Dec 16, 2024

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Abellegese
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Thank you for taking your time to contribute to Ersilia, just a few checks before we proceed

  • Have you followed the guidelines in our Contribution Guide
  • Have you written new tests for your core changes, as applicable?
  • Have you successfully ran tests with your changes locally?

Description

  • This PR improves the documentation of several publish module files by adding detailed docstrings, summaries, and usage examples to public functions.

Specifically on the test.py file

  • Update the function that checks single input now to check output file produced by the run command.
  • Update the function that checks sample generated examples now to check the content on the test module.
  • Add a feature to warn user to install dependencies needed to run the test command.

Related to #1423

Abellegese and others added 14 commits December 13, 2024 15:23
@Abellegese
Merge sample command with the example command (ersilia-os#1422)
5546a7c 
* Merge sample command with the example command

* Fix example command usage
@DhanshreeA @Abellegese
Generalize Standard Run (ersilia-os#1411)
50f14a6 
* Modify header calculation to choose from predefined example output file or standard example output file

* Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function

* Remove unused method

* Make csv serialization work for any kind of model api response

* Remove the standard flag from the CLI since it is now the default run

* Update tests
@Abellegese
Unnecessary files removed
6e34915
@Abellegese
Unnecessary files removed
a9ae405
@Abellegese
Unnecessary files removed
8620ccf
@Abellegese
Unnecessary files removed
45eed7e
@Abellegese
Unnecessary files removed
bae8994
@Abellegese
Some import cleanup
54444a3
@Abellegese
Few code fixes
85cc376
@Abellegese
Few code fixes
12f7b2c
@Abellegese
Add detailed docstrings and usage examples to Ersilia'a publish modul…
d24564a 
…e and few update on the ModelTester
@Abellegese
Merge branch 'master' into refactor/docstring-module-publish
64c2fb9
@DhanshreeA
Merge branch 'master' into refactor/docstring-module-publish
50b328d
@DhanshreeA
Merge branch 'master' into refactor/docstring-module-publish
382ee68
@DhanshreeA
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@Abellegese can you look into the failing workflows?

@Abellegese
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Yep I am taking a look. Will fix it @DhanshreeA

@Abellegese
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Nothing appears failing so far.

@Abellegese Abellegese changed the title Refactor/docstring module publishAdd detailed docstrings and usage examples to Ersilia'a publish module and few update on the test module Add detailed docstrings and usage examples to Ersilia'a publish module and few update on the test module Dec 16, 2024
@DhanshreeA DhanshreeA merged commit ef369d6 into ersilia-os:master Dec 16, 2024
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2 participants
@Abellegese @DhanshreeA