Skip to content

Conversation

@kopardev
Copy link
Contributor

  • refactor: jobby only uses sacct now; removed depencies on dashboard_cli; HPC-agnostic
  • refactor: adding tabulate dependency for jobby

@kopardev kopardev requested a review from kelly-sovacool April 28, 2025 17:31
@kopardev
Copy link
Contributor Author

@kelly-sovacool .. can you update https://ccbr.github.io/Tools/reference/jobby.html#ccbr_tools.jobby for the new jobby?

@kelly-sovacool
Copy link
Member

@kelly-sovacool .. can you update https://ccbr.github.io/Tools/reference/jobby.html#ccbr_tools.jobby for the new jobby?

FYI that page is generated from the docstrings in src/ccbr_tools/jobby.py (https://github.com/CCBR/Tools/blob/4e265bbc3a8f0401e218b81bcb4cc982ddc30aaa/src/ccbr_tools/jobby.py)

Copy link
Member

@kelly-sovacool kelly-sovacool left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

  • I suggested improving how exceptions are captured and raised in several places.
  • The regex for nextflow will have to use something like 'TaskHandler[jobId: [0-9]*' to actually capture them.

@kopardev kopardev marked this pull request as ready for review April 30, 2025 17:20
@codecov
Copy link

codecov bot commented Apr 30, 2025

Codecov Report

Attention: Patch coverage is 47.74194% with 81 lines in your changes missing coverage. Please review.

Project coverage is 70.63%. Comparing base (2478be2) to head (941a3aa).

Files with missing lines Patch % Lines
src/ccbr_tools/jobby.py 47.74% 81 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #59      +/-   ##
==========================================
- Coverage   72.77%   70.63%   -2.15%     
==========================================
  Files          21       21              
  Lines        1561     1539      -22     
==========================================
- Hits         1136     1087      -49     
- Misses        425      452      +27     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@kopardev
Copy link
Contributor Author

@kelly-sovacool .. what are these
image

@kopardev kopardev marked this pull request as draft May 1, 2025 00:36
@kopardev kopardev marked this pull request as ready for review May 1, 2025 00:37
@kelly-sovacool
Copy link
Member

kelly-sovacool commented May 1, 2025

@kopardev

@kelly-sovacool .. what are these image

Code coverage reports. This PR will decrease the overall project coverage by 2%. We could break up the jobby code into more functions and write more unit tests if we wanted to improve that figure.

@kelly-sovacool kelly-sovacool changed the title jobby update vnk overhaul jobby to use sacct May 1, 2025
@kelly-sovacool
Copy link
Member

kelly-sovacool commented May 1, 2025

FYI @kopardev I am moving module_list to another branch. It is completely independent of the jobby changes here and it would be better to hash that out in a separate PR.
#63

@kelly-sovacool kelly-sovacool merged commit c88f04d into main May 1, 2025
15 of 17 checks passed
@kelly-sovacool kelly-sovacool deleted the jobby_update_vnk branch May 1, 2025 20:43
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants