Expose similar options to downstream run_checks (#443)

* outer level tqdm over all files

* expose similar options to downstream run_checks

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix upper level

* expose JSON encoder

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Upcoming
 
+### Improvements
+
+* Exposed progress bar control to `inspect_all` and `run_checks` to allow compatibility with more generic visualizations of inspection progress related to the NWB GUIDED. [#443](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/443)
+
 # v0.4.34
 
 ### Fixes

src/nwbinspector/__init__.py

@@ -1,6 +1,13 @@
 from .version import __version__
 from .register_checks import available_checks, Importance
-from .nwbinspector import inspect_all, inspect_nwbfile, inspect_nwbfile_object, run_checks, load_config
+from .nwbinspector import (
+    InspectorOutputJSONEncoder,
+    inspect_all,
+    inspect_nwbfile,
+    inspect_nwbfile_object,
+    run_checks,
+    load_config,
+)
 from .nwbinspector import inspect_nwb  # TODO: remove after 7/1/2023
 from .checks.ecephys import *
 from .checks.general import *

src/nwbinspector/nwbinspector.py

@@ -581,9 +581,10 @@ def inspect_nwbfile(
                 )
 
         try:
-            nwbfile_object = robust_s3_read(command=io.read, max_retries=max_retries)
+            in_memory_nwbfile = robust_s3_read(command=io.read, max_retries=max_retries)
+
             for inspector_message in inspect_nwbfile_object(
-                nwbfile_object=nwbfile_object,
+                nwbfile_object=in_memory_nwbfile,
                 checks=checks,
                 config=config,
                 ignore=ignore,
@@ -686,16 +687,39 @@ def inspect_nwbfile_object(
         yield inspector_message
 
 
-def run_checks(nwbfile: pynwb.NWBFile, checks: list):
+def run_checks(
+    nwbfile: pynwb.NWBFile,
+    checks: list,
+    progress_bar_class: Optional[tqdm] = None,
+    progress_bar_options: Optional[dict] = None,
+) -> Iterable[InspectorMessage]:
     """
     Run checks on an open NWBFile object.
 
     Parameters
     ----------
-    nwbfile : NWBFile
-    checks : list
+    nwbfile : pynwb.NWBFile
+        The in-memory pynwb.NWBFile object to run the checks on.
+    checks : list of check functions
+        The list of check functions that will be run on the in-memory pynwb.NWBFile object.
+    progress_bar_class : type of tqdm.tqdm, optional
+        The specific child class of tqdm.tqdm to use to make progress bars.
+        Defaults to not displaying progress per set of checks over an invidiual file.
+    progress_bar_options : dict, optional
+        Dictionary of keyword arguments to pass directly to the `progress_bar_class`.
+
+    Yields
+    ------
+    results : a generator of InspectorMessage objects
+        A generator that returns a message on each iteration, if any are triggered by downstream conditions.
+        Otherwise, has length zero (if cast as `list`), or raises `StopIteration` (if explicitly calling `next`).
     """
-    for check_function in checks:
+    if progress_bar_class is not None:
+        check_progress = progress_bar_class(iterable=checks, total=len(checks), **progress_bar_options)
+    else:
+        check_progress = checks
+
+    for check_function in check_progress:
         for nwbfile_object in nwbfile.objects.values():
             if check_function.neurodata_type is None or issubclass(type(nwbfile_object), check_function.neurodata_type):
                 try: