[Bug]: File count in output includes directories

[rly]

What happened?

When the check_unique_identifiers issue is raised, the directory is counted as a "file" in the output line Found 21 issues over 3 files. This can be confusing to users (see comment dandi/dandi-cli#1266 (comment)). I'm not sure if there are other directory-level issues like this.

Suggestion: change Found 21 issues over 3 files to Found 21 issues over 2 files and 1 directory or Found 21 issues over 3 files and directories

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NWBInspector Report Summary

Timestamp: 2023-04-11 13:52:44.461154-07:00
Platform: macOS-13.2.1-arm64-i386-64bit
NWBInspector version: 0.4.27

Found 21 issues over 3 files:
       1 - CRITICAL
      10 - BEST_PRACTICE_VIOLATION
      10 - BEST_PRACTICE_SUGGESTION
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0  CRITICAL
===========

0.0  /Users/rly/Documents/NWB_Data/dandisets/000037/sub-408021: check_unique_identifiers - 'NWBFile' object at location '/'
       Message: The identifier '758519303_with_stim' is used across the .nwb files: ['sub-408021_ses-758519303_behavior+image+ophys.nwb', 'sub-408021_ses-758519303_behavior+image+ophys_new_IDs.nwb']. The identifier of any NWBFile should be a completely unique value - we recommend using uuid4 to achieve this.

Operating System

M1 macOS

Python Version

3.11

Were you streaming with ROS3?

No

Package Versions

Copy and paste your output here

Code of Conduct

• I agree to follow this project's Code of Conduct
• Have you ensured this bug was not already reported?
• To the best of your ability, have you ensured this is a bug within the code that checks the NWBFile, rather than a bug in the NWBFile reader (e.g., PyNWB or MatNWB)?

[CodyCBakerPhD]

Can you please attach a .txt. or .json of the full report? You may have to use the --detailed flag as well to prevent aggregation

I'm having trouble reproducing the issue - the number of files displayed in that header is simply the number of unique NWB files that had messages returned: https://github.com/NeurodataWithoutBorders/nwbinspector/blob/dev/src/nwbinspector/inspector_tools.py#L118

So what I'm looking for in the full report is all the messages from all the files to confirm they appear as expected

I could technically add some directory logic to the string (like evaluate the unique parents of each file) but TBH I don't think it's all that helpful; the inspector and reports have no notion of sub-directories (or even memory of the top-level directory), only files, and files are found by recursive globbing from the main CLI calls