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[Bug]: Dev branches import failure from daily CI #940

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3 tasks done
CodyCBakerPhD opened this issue Aug 14, 2023 · 3 comments
Closed
3 tasks done

[Bug]: Dev branches import failure from daily CI #940

CodyCBakerPhD opened this issue Aug 14, 2023 · 3 comments

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@CodyCBakerPhD
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What happened?

Latest NeuroConv daily CI caught an HDMF import issue, wanted to make sure you're all aware of it

Steps to Reproduce

https://github.com/catalystneuro/neuroconv/actions/runs/5858028094/job/15881154685

Traceback

ImportError while loading conftest '/home/runner/work/neuroconv/neuroconv/docs/conversion_examples_gallery/conftest.py'.
docs/conversion_examples_gallery/conftest.py:4: in <module>
    from tests.test_on_data.setup_paths import ECEPHY_DATA_PATH, BEHAVIOR_DATA_PATH, OPHYS_DATA_PATH, TEXT_DATA_PATH
tests/test_on_data/setup_paths.py:7: in <module>
    from neuroconv.utils import load_dict_from_file
src/neuroconv/__init__.py:1: in <module>
    from .basedatainterface import BaseDataInterface
src/neuroconv/basedatainterface.py:7: in <module>
    from pynwb import NWBFile
/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pynwb/__init__.py:353: in <module>
    from . import io as __io  # noqa: F401,E402
/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pynwb/io/__init__.py:1: in <module>
    from . import base as __base
/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pynwb/io/base.py:3: in <module>
    from .core import NWBContainerMapper
/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pynwb/io/core.py:9: in <module>
    from pynwb.file import NWBFile
/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pynwb/file.py:11: in <module>
    from hdmf.container import ExternalResourcesManager
E   ImportError: cannot import name 'ExternalResourcesManager' from 'hdmf.container' (/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/hdmf/container.py)

Operating System

Windows

Python Executable

Conda

Python Version

3.8

Package Versions

No response

Code of Conduct

@oruebel
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oruebel commented Aug 14, 2023

Thanks @CodyCBakerPhD for the issue. ExternalResourcesManager has been renamed in #933 @mavaylon1 is working on a corresponding PR for PyNWB .

@mavaylon1
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@CodyCBakerPhD The fix should be out this week. We are merging some PRs into HDMF this week before doing a release. After the release, I will create a PR on pynwb to update the name change.

@rly
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rly commented Aug 15, 2023

Can you update the dev branch of pynwb first?

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4 participants