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Install also hdmf from git in the dev-deps CI run #1320

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merged 1 commit into from
Nov 16, 2023
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Inspired by #1312 and ongoing work for Zarr based backend for NWB.

@yarikoptic yarikoptic added the tests Add or improve existing tests label Aug 11, 2023
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codecov bot commented Aug 11, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (e99ee62) 88.88% compared to head (ed2803c) 88.94%.

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1320      +/-   ##
==========================================
+ Coverage   88.88%   88.94%   +0.05%     
==========================================
  Files          76       76              
  Lines       10240    10240              
==========================================
+ Hits         9102     9108       +6     
+ Misses       1138     1132       -6     
Flag Coverage Δ
unittests 88.94% <ø> (+0.05%) ⬆️

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see 2 files with indirect coverage changes

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@yarikoptic
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-dev errorring out ATM with

Run python -m pytest -s -v --cov=dandi --cov-report=xml dandi
ImportError while loading conftest '/home/runner/work/dandi-cli/dandi-cli/dandi/conftest.py'.
dandi/conftest.py:7: in <module>
    from .tests.fixtures import *  # noqa: F401, F403  # lgtm [py/polluting-import]
dandi/tests/fixtures.py:20: in <module>
    import pynwb
/opt/hostedtoolcache/Python/3.8.[17](https://github.com/dandi/dandi-cli/actions/runs/5835056703/job/15825908399?pr=1320#step:7:18)/x64/lib/python3.8/site-packages/pynwb/__init__.py:353: in <module>
    from . import io as __io  # noqa: F401,E402
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/pynwb/io/__init__.py:1: in <module>
    from . import base as __base
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/pynwb/io/base.py:3: in <module>
    from .core import NWBContainerMapper
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/pynwb/io/core.py:9: in <module>
    from pynwb.file import NWBFile
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/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/3.8.17/x64/lib/python3.8/site-packages/hdmf/container.py)
Error: Process completed with exit code 4.

Inspired by #1312 and ongoing work for
Zarr based backend for NWB.
@yarikoptic
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rebased

@yarikoptic yarikoptic marked this pull request as ready for review November 16, 2023 20:08
@yarikoptic
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it was green, taking out of draft. @jwodder any concerns/objections here?

@yarikoptic yarikoptic merged commit d6edcb6 into master Nov 16, 2023
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@yarikoptic yarikoptic deleted the dev-hdmf branch November 16, 2023 20:16
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🚀 PR was released in 0.58.1 🚀

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