Reorganize blech_process.log to group by status

[abuzarmahmood]

Summary

Restructures blech_process.log so the top-level keys are complete and attempted instead of electrode numbers. Also updates related log handling in other files.

Changes

• blech_process.py: Log entries are now grouped under their status (complete or attempted)
  • When processing starts, electrode is added to attempted
  • On successful completion, electrode is moved from attempted to complete
  • Re-processing an electrode removes it from complete before adding to attempted
• blech_run_process.sh: Updated to read incomplete electrodes from the new structure
• utils/blech_utils.py: Updated pipeline_graph_check.write_to_log to remove script from attempted when marking as completed

New log structure

{
  "complete": {
    "0": {"start_time": "...", "end_time": "..."},
    "1": {"start_time": "...", "end_time": "..."}
  },
  "attempted": {
    "16": {"start_time": "..."},
    "17": {"start_time": "..."}
  }
}

Fixes #729

[abuzarmahmood]

Solution Overview

The log file structure has been reorganized from a flat electrode-keyed format to a status-keyed format.

Before (flat structure)

{
  "0": {"start_time": "...", "status": "complete", "end_time": "..."},
  "16": {"start_time": "...", "status": "attempted"}
}

After (status-grouped structure)

{
  "complete": {
    "0": {"start_time": "...", "end_time": "..."}
  },
  "attempted": {
    "16": {"start_time": "..."}
  }
}

Implementation details

1. Initialization: Creates complete and attempted top-level keys if they don't exist
2. Processing start: Adds electrode to attempted (removes from complete if re-processing)
3. Processing complete: Moves electrode from attempted to complete with end_time

This makes it easier to see at a glance which electrodes completed successfully vs which are still in progress or failed.

[abuzarmahmood]

Added update to blech_run_process.sh to correctly read incomplete electrodes from the new log structure.

The completion check now reads from process_log.get('attempted', {}).keys() instead of iterating all entries and checking the status field.

[abuzarmahmood]

Added update to utils/blech_utils.py:

pipeline_graph_check.write_to_log now removes the script from attempted when marking it as completed, keeping the execution log structure consistent with the new pattern.