Add NotificationSummary class for structured, version-stamped inspection reports

[Copilot]

Notifications were written as a raw JSON array with no version-stamping, no human-readable format, and no aggregation of repeated notification types.

New: NotificationSummary

Introduced nwb2bids.NotificationSummary — a lightweight wrapper around a list of notifications that produces structured, version-stamped reports.

import nwb2bids

dataset_converter = nwb2bids.convert_nwb_dataset(nwb_paths=[...], run_config=run_config)
summary = nwb2bids.NotificationSummary(
    notifications=dataset_converter.notifications,
    run_id=run_config.run_id,
)

print(summary)          # aggregated human-readable report
summary.to_json()       # full non-aggregated JSON string (all individual entries)
summary.to_file(path)   # write .json or .txt based on suffix; aggregate=True by default

Key behaviors

• __str__ — aggregated by identifier, with occurrence count and merged file paths per type; suitable for notebooks and IPython
• to_json() — full, non-aggregated dump; wraps the notifications array in {"nwb2bids_version": ..., "run_id": ..., "notifications": [...]}
• to_file(path, aggregate=True) — format inferred from suffix (.json vs text); aggregated by default (one entry per notification type with count field and merged paths), aggregate=False writes every individual notification

Updated: DatasetConverter.convert_to_bids_dataset()

Now uses NotificationSummary and writes both the .txt (human-readable) and .json (structured) report files on every run. Previously only the JSON file was written and it lacked version metadata.

Breaking change to .json report format

The {run_id}_notifications.json file is now a JSON object rather than a bare array:

{
  "nwb2bids_version": "0.1.0",
  "run_id": "datetime-20240101120000",
  "notifications": [
    { "identifier": "InvalidSpecies", "count": 2, "severity": "ERROR", ... }
  ]
}

Original prompt

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This section details on the original issue you should resolve

<issue_title>Generate nice 'report' of inspections</issue_title>
<issue_description>Right now I just form and dump a list of messages through .model_dump on each message of a DatasetConverter

Would be nice to create (and version-stamp) official report structure in both human readable text and JSON, similar to BIDs and NWB Inspector</issue_description>

Comments on the Issue (you are @copilot in this section)

@CodyCBakerPhD Plan:

• introduce a new class, the NotificationSummary which takes a list of notifications as input
• this class should have a nice-looking __str__ override for printing out in places like notebooks and ipython consoles
• it should have to_json (dumps all information in full) and to_file (with a flag determining whether to aggregate over similar types of notifications or show all information; default is to aggregate methods)
• this should be used in place of the other method which dumps notifications to the .nwb2bids directory and should dump a copy of both files by default</comment_new>

• Fixes Generate nice 'report' of inspections #104

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