patch: clean main

[danielboloc]

Overview

Refactors click commands into separate files and completes CIs to run all commands

JIRA

Please add here as many related tasks this PR covers with its brief description, if more than one ticket

• https://lifebit.atlassian.net/browse/LP-101992

Changes

Refactors commands into separate files and imported only into main

• Each module now has a new file for example cloudos_cli/jobs/cli.py where all the commands and subcommands are held

CI/CD Improvements (.github/workflows/ci.yml)

• Removed hardcoded job IDs - All tests now use dynamic job dependencies
• Added job outputs - job_run_and_status, bash_job, bash_array_job now output job_ids
• New CI tests: job_run_and_abort, job_resume, configure_profile
• Improved job dependencies - delete_workdir now depends on both job_workdir and job_resume
• Self-contained CI - No external workspace dependencies needed

Acceptance Criteria

PROD

CIs are now adding more functionality and test all commands (except link which is tested in the IA section). Therefore, manual tests are not performed for this workspace.

DEV

This Environment is interchangable with PROD if the acceptance criteria can only be tested in DEV for example. If that is the case please name this section PROD (or any new environment)

Proof this feature/patch works in this environment

Running job

Cloning job

Resuming job

AZURE

Proof this feature/patch works in this environment

Running job

Cloning job

Resuming job

Interactive Analysis

Proof this feature/patch works in this environment

Linking

[danielboloc]

@l-mansouri thanks for the review

• Good catch about the --debug, I have updated it in all commands

@dapineyro thanks for the review

• I have removed empty lines and with f'string' and left pytests for python versions 3.9, 3.11 and 3.13, but other CIs to only 3.9

General observations:

• I have noticed that job list --filter-queue stopped working mainly because now api/v2/jobs is not returning batch field (at least in my quick investigation). Opened a new issue --filter-queue options gives errror #292 to keep track and possibly do an independent PR fix. I have 'disabled' this CI until the issue is solved

CI workspace

ADAPT workspace

main branch in ADAPT

[dapineyro]

LGTM! Huge improvement @danielboloc , thanks!