Define dependencies in submission script

[jan-janssen]

Summary by CodeRabbit

• New Features

  • Enhanced job submission functionality to support job dependencies.

• Bug Fixes

  • Improved handling of job dependency lists in submission templates.

• Tests

  • Updated test scripts to validate job dependency settings in flux and slurm.

These updates improve the accuracy and efficiency of job scheduling by enabling users to define dependencies between jobs.

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Commits

Files that changed from the base of the PR and between 1611cab1e32f75a5a368735134404e1708f75bc1 and 90941d437ce5a814adf1b23502cbef2d3b63e6c3.

Walkthrough

The recent changes enhance the job submission functionality in pysqa by introducing dependency handling. The submit_job function now includes a dependency_list parameter, and related utility functions have been updated accordingly. Additionally, shell scripts for flux and slurm have been modified to handle job dependencies, ensuring that jobs are executed in the correct order based on specified dependencies.

Changes

File(s)	Change Summary
pysqa/ext/modular.py	Updated submit_job to include dependency_list and modified _list_command_to_be_executed signature.
pysqa/utils/basic.py	Added dependency_list parameter to several functions and adjusted _list_command_to_be_executed.
tests/config/flux/flux.sh	Added a conditional block to set job dependencies using the flux command.
tests/config/slurm/slurm.sh	Included conditional #SBATCH --dependency=afterok line based on the dependency variable.

In the world of code, dependencies align,
Jobs wait their turn, in a sequence so fine.
Scripts now whisper to flux and slurm,
"Patience, dear jobs, it's not yet your turn."
With harmony in code, the system's at ease,
Thanks to these changes, jobs flow like the breeze. 🌬️

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