From 52028287836a44339c399dbe13a0d0af6cad2a2c Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Wed, 24 Dec 2025 11:36:43 -0500 Subject: [PATCH] docs: add CLI documentation for --ignore and --select flags Add new sections to the CLI user guide explaining how to: - Skip specific checks using the --ignore flag with single or comma-separated check names - Run only specific checks using the --select flag Include a note about heuristic-based checks that may produce false positives for edge cases like long-running experiments. --- .../using_the_command_line_interface.rst | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/docs/user_guide/using_the_command_line_interface.rst b/docs/user_guide/using_the_command_line_interface.rst index aa2a4b8c..27e74e62 100644 --- a/docs/user_guide/using_the_command_line_interface.rst +++ b/docs/user_guide/using_the_command_line_interface.rst @@ -151,6 +151,42 @@ For example, +Skipping Specific Checks +------------------------ + +The NWBInspector provides the ``--ignore`` flag to skip specific checks by name. This is useful when you have +legitimate data that triggers heuristic-based checks, or when certain checks are not applicable to your use case. + +To skip a single check: + +:: + + nwbinspector path/to/my/data.nwb --ignore check_time_intervals_duration + +To skip multiple checks, provide a comma-separated list (no spaces): + +:: + + nwbinspector path/to/my/data.nwb --ignore check_time_intervals_duration,check_units_table_duration + +.. note:: + + Some checks are heuristic-based and may produce false positives for edge cases. For example, + ``check_time_intervals_duration`` and ``check_units_table_duration`` flag sessions longer than one year, + which is typically an error but may be valid for certain long-running experiments. Use the ``--ignore`` + flag to skip these checks when you have verified the data is correct. + + +Selecting Specific Checks +------------------------- + +Conversely, if you only want to run specific checks, use the ``--select`` flag: + +:: + + nwbinspector path/to/my/data.nwb --select check_subject_exists,check_subject_species_exists + + External Modules ----------------