[Bug]: Dev tests for roiextractors failing

CodyCBakerPhD commented 9 months ago

What happened?

@pauladkisson the dev tests have been failing for a while due to some SI issues; when those got cleaned up we realized the recent ScanImage changes had also been triggering dev failures

Could you figure out the best path to resolve this? Perhaps updating the tests here on NeuroConv then cutting new release of ROI Extractors?

Steps to Reproduce

https://github.com/catalystneuro/neuroconv/actions/runs/7889445509/job/21529329343

Traceback

No response

Operating System

Windows

Python Executable

Conda

Python Version

3.7

Package Versions

No response

Code of Conduct

[X] I agree to follow this project's Code of Conduct
[X] Have you ensured this bug was not already reported?

pauladkisson commented 9 months ago

Thanks for the catch! Will check it out

pauladkisson commented 9 months ago

I have been unable to replicate this bug with a fresh environment on the latest commit in main

steps:

conda create --name "neuroconv_env" python=3.9
conda activate neuroconv_env
pip install --no-cache-dir -e .'[full,test]' 
pytest tests/test_on_data/test_imaging_interfaces.py -k TestScanImageImagingInterfaceRecent

output:

============================================================================= test session starts =============================================================================
platform darwin -- Python 3.9.18, pytest-8.0.0, pluggy-1.4.0
rootdir: /Users/pauladkisson/Documents/CatalystNeuro/NWB/neuroconv
configfile: pyproject.toml
plugins: cov-4.1.0
collected 33 items / 30 deselected / 3 selected                                                                                                                               

tests/test_on_data/test_imaging_interfaces.py ...                                                                                                                       [100%]

============================================================================== warnings summary ===============================================================================
../../../../../../opt/anaconda3/envs/neuroconv_env/lib/python3.9/site-packages/hdmf/container.py:11
  /opt/anaconda3/envs/neuroconv_env/lib/python3.9/site-packages/hdmf/container.py:11: DeprecationWarning: 
  Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),
  (to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)
  but was not found to be installed on your system.
  If this would cause problems for you,
  please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466

    import pandas as pd

src/neuroconv/tools/yaml_conversion_specification/_yaml_conversion_specification.py:7
src/neuroconv/tools/yaml_conversion_specification/_yaml_conversion_specification.py:7
  /Users/pauladkisson/Documents/CatalystNeuro/NWB/neuroconv/src/neuroconv/tools/yaml_conversion_specification/_yaml_conversion_specification.py:7: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need.
    from jsonschema import RefResolver, validate

tests/test_on_data/test_imaging_interfaces.py::TestScanImageImagingInterfaceRecent::test_conversion_as_lone_interface
tests/test_on_data/test_imaging_interfaces.py::TestScanImageImagingInterfaceRecent::test_interface_alignment
  /opt/anaconda3/envs/neuroconv_env/lib/python3.9/site-packages/roiextractors/extractors/tiffimagingextractors/scanimagetiffimagingextractor.py:381: FutureWarning: 
          This extractor is being deprecated on or after December 2023 in favor of
          ScanImageTiffMultiPlaneImagingExtractor or ScanImageTiffSinglePlaneImagingExtractor.  Please use one of these
          extractors instead.

    warn(deprecation_message, category=FutureWarning)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================================================================ 3 passed, 30 deselected, 5 warnings in 37.90s ================================================================

CodyCBakerPhD commented 9 months ago

@pauladkisson The dev tests that I linked to in the actions test against the current main branch of ROI Extractors; the main tests (using latest releases) work as you show

pauladkisson commented 9 months ago

Ah ok, thanks for the clarification, I can see the bug now.

catalystneuro / neuroconv