Change 'salish' submit job command to 'bash' #80
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Updated the submit job command for 'salish' from 'qsub' to 'bash'. Adjusted multiple test cases to reflect this change.
3 tasks
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #80 +/- ##
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Coverage 95.36% 95.37%
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Files 10 10
Lines 1316 1362 +46
Branches 73 77 +4
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+ Hits 1255 1299 +44
- Misses 57 58 +1
- Partials 4 5 +1
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This reverts commit a9631a4.
`salish` no longer uses a scheduler. So, its run execution script no longer needs either `#SBATCH` or `#PBS` directives sections. Also refactored `test_salish` to use `monkeypatch.setattr` instead of `patch`.
Replaced `with patch` context managers with `monkeypatch.setattr` in all TestModules test cases to improve code readability and consistency. Added new test for "salish" system to ensure future-proofing and full coverage of available systems.
This commit adds redirection of stdout and stderr to files within
`${RESULTS_DIR}` for the `salish` system, ensuring logging of output and error
streams. New tests were added to verify the functionality for both the
`--deflate` and non-deflate cases. Necessary changes were made in the
`_execute()` function and corresponding test cases to support this redirection.
Moved the _execute() call out of the script string construction for compatibility with Python 3.11. This change assigns the _execute call result to a variable before joining it into the final script.
Updated the job submission command for the 'salish' system from 'qsub' to 'bash'. Added logic to handle job submissions specifically for 'bash' and adjusted unit tests accordingly to ensure compatibility and functionality.
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re: issue #78
qsubtobashechoandmpiruncommands in the run script because their output is no longer automatically captured