Add NotificationSummary class for structured, version-stamped inspection reports

[Copilot]

• Explore codebase and understand notification system
• Create NotificationSummary class in src/nwb2bids/notifications/_notification_summary.py
  • Takes list[Notification] and optional run_id as input
  • __str__ override with nice human-readable report (aggregates by identifier)
  • to_json() returns full JSON string (all individual notifications, no aggregation)
  • to_file(path, aggregate=True) writes to file (.json or .txt based on suffix)
• Export NotificationSummary from notifications/__init__.py and top-level __init__.py
• Update DatasetConverter.convert_to_bids_dataset() to use NotificationSummary and write both .txt and .json files
• Add unit tests in tests/unit/test_notification_summary.py (15 tests)
• Update integration test test_notifications.py to match new JSON file structure and verify .txt report
• Fix tests/integration/test_convert_nwb_dataset.py::test_minimal_convert_nwb_dataset_from_directory for new JSON format
• Resolve merge conflicts from origin/main (dataset_converter.py and test_convert_nwb_dataset.py)
• All tests pass

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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[CodyCBakerPhD]

@copilot resolve the merge conflicts in this pull request to match your design

[Copilot]

@copilot resolve the merge conflicts in this pull request to match your design

Resolved in afa2aa1. The merge conflict itself was already resolved in a prior merge commit, but the rebase onto main introduced a new test (test_minimal_convert_nwb_dataset_from_directory) that was still asserting the old bare-list JSON format for the notifications file. Updated it to match the new dict structure with nwb2bids_version, run_id, and notifications keys.

[CodyCBakerPhD]

@copilot resolve the merge conflicts in this pull request

[Copilot]

@copilot resolve the merge conflicts in this pull request

Resolved in bb2e601. Merged the latest origin/main into the branch; conflicts in _dataset_converter.py (kept NotificationSummary usage) and test_convert_nwb_dataset.py (kept the new JSON structure assertions) were resolved in favour of this PR's design.

[codecov]

Codecov Report

❌ Patch coverage is 93.98496% with 8 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.08%. Comparing base (e9682af) to head (d10a60d).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...rc/nwb2bids/notifications/_notification_summary.py	93.70%	8 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #353      +/-   ##
==========================================
+ Coverage   85.42%   86.08%   +0.65%     
==========================================
  Files          41       42       +1     
  Lines        1818     1947     +129     
==========================================
+ Hits         1553     1676     +123     
- Misses        265      271       +6     

Flag	Coverage Δ
unittests	86.08% <93.98%> (+0.65%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
src/nwb2bids/__init__.py	100.00% <100.00%> (ø)
src/nwb2bids/_converters/_dataset_converter.py	86.87% <100.00%> (+0.05%)	⬆️
src/nwb2bids/notifications/__init__.py	100.00% <100.00%> (ø)
...rc/nwb2bids/notifications/_notification_summary.py	93.70% <93.70%> (ø)

... and 1 file with indirect coverage changes

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