Use inspect_nwbfile() instead of inspect_nwb(); address bug in recent ruamel.yaml versions
#1285
Conversation
|
Huh, were they actual errors? I thought it was just a simple |
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #1285 +/- ##
==========================================
- Coverage 89.04% 88.93% -0.12%
==========================================
Files 76 76
Lines 9896 9896
==========================================
- Hits 8812 8801 -11
- Misses 1084 1095 +11
Flags with carried forward coverage won't be shown. Click here to find out more.
☔ View full report in Codecov by Sentry. |
|
@CodyCBakerPhD Our test suite is configured to turn any warning into an error, so it seems that the deprecation warning was raised as an error, which was caught by the validation method and turned into a validation failure. |
|
Gotcha, thanks for catching that so quickly then! |
| @@ -19,7 +19,7 @@ | |||
| from dandischema.models import Dandiset as DandisetMeta | |||
| from dandischema.models import get_schema_version | |||
| from etelemetry import get_project | |||
| from nwbinspector import Importance, inspect_nwb, load_config | |||
| from nwbinspector import Importance, inspect_nwbfile, load_config | |||
There was a problem hiding this comment.
Do we need to boost minimal version for nwbinspector ?
There was a problem hiding this comment.
I don't know what version inspect_nwbfile() was added in. CC @CodyCBakerPhD
There was a problem hiding this comment.
It was added in the latest version, so yes I would bump minimal.
There was a problem hiding this comment.
latest = 0.4.28
Keep in mind etelemetry complains (just a warning I think) if running validation when not using the latest release too, but upgrading the requirement is never a bad idea either
|
Thank you @jwodder for being proactive with this one! |
|
🚀 PR was released in |
The test suite has been failing for the past few days with the following causes:
Calls to
nwbinspector.inspect_nwb()(used to validate NWB files) were returning an error message reading:and this ended up in the set of validation errors. I have replaced
inspect_nwb()withinspect_nwbfile().A bug in recent versions of
ruamel.yamlwas causing a certain spot inorganize.pyto fail. I addressed this by removing theage.pop("units", None)line, which seems to be unnecessary (at least in ruamel.yaml 0.17.21, released 2022-02-12, the last release before this month).