Fix import from deprecated inspector tools module

LorenFrankLab · Oct 8, 2024 · 6dc69f8 · 6dc69f8
1 parent f6399c8
commit 6dc69f8
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Showing 3 changed files with 6 additions and 8 deletions.
diff --git a/environment.yml b/environment.yml
@@ -8,7 +8,7 @@ dependencies:
 - scipy
 - pandas
 - pynwb
-- nwbinspector
+- nwbinspector>=5.0.0
 - dask
 - ipython
 - black

diff --git a/pyproject.toml b/pyproject.toml
@@ -25,7 +25,7 @@ dependencies = [
     "scipy",
     "pandas",
     "pynwb",
-    "nwbinspector",
+    "nwbinspector>=5.0.0",
     "ndx_franklab_novela",
     "pyyaml",
     "neo",

diff --git a/src/trodes_to_nwb/convert.py b/src/trodes_to_nwb/convert.py
@@ -341,11 +341,11 @@ def _inspect_nwb(nwbfile_path: Path, logger: logging.Logger):
     )
     logger.info("NWB Inspector output:")
     logger.info(messages)
-    formatted_messages = nwbinspector.inspector_tools.format_messages(messages=messages)
+    formatted_messages = nwbinspector.format_messages(messages=messages)
     report_file_path = (
         nwbfile_path.parent / f"{nwbfile_path.stem}_nwbinspector_report.txt"
     )
-    nwbinspector.inspector_tools.save_report(
+    nwbinspector.save_report(
         report_file_path=report_file_path,
         formatted_messages=formatted_messages,
         overwrite=True,
@@ -366,12 +366,10 @@ def _inspect_nwb(nwbfile_path: Path, logger: logging.Logger):
         print(
             f"NWB Inspector found the following {len(critical_errors)} critical errors:"
         )
-        formatted_critical_errors = nwbinspector.inspector_tools.format_messages(
+        formatted_critical_errors = nwbinspector.format_messages(
             messages=critical_errors
         )
-        nwbinspector.inspector_tools.print_to_console(
-            formatted_messages=formatted_critical_errors
-        )
+        nwbinspector.print_to_console(formatted_messages=formatted_critical_errors)
     else:
         print("NWB Inspector found 0 critical errors")