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Fix/one photon series #1660

Merged
merged 4 commits into from
Mar 14, 2023
Merged

Fix/one photon series #1660

merged 4 commits into from
Mar 14, 2023

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bendichter
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Motivation

What was the reasoning behind this change? Please explain the changes briefly.

How to test the behavior?

Show how to reproduce the new behavior (can be a bug fix or a new feature)

Checklist

  • Did you update CHANGELOG.md with your changes?
  • Have you checked our Contributing document?
  • Have you ensured the PR clearly describes the problem and the solution?
  • Is your contribution compliant with our coding style? This can be checked running flake8 from the source directory.
  • Have you checked to ensure that there aren't other open Pull Requests for the same change?
  • Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

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codecov bot commented Mar 10, 2023

Codecov Report

Merging #1660 (76aa95b) into dev (60ec5db) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##              dev    #1660   +/-   ##
=======================================
  Coverage   91.99%   91.99%           
=======================================
  Files          26       26           
  Lines        2585     2585           
  Branches      496      496           
=======================================
  Hits         2378     2378           
  Misses        132      132           
  Partials       75       75           
Flag Coverage Δ
integration 71.52% <0.00%> (ø)
unit 83.67% <100.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/pynwb/ophys.py 96.05% <100.00%> (ø)

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

@bendichter
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bendichter commented Mar 10, 2023

This appears to be failing due to some sort of h5py issue in Python 3.8 on windows

Traceback (most recent call last):
  File "test.py", line 115, in __run_example_tests_helper
    _import_from_file(script)
  File "test.py", line 63, in _import_from_file
    return imp.load_source(os.path.basename(script), script)
  File "C:\hostedtoolcache\windows\Python\3.8.10\x64\lib\imp.py", line 171, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 702, in _load
  File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 848, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "docs\gallery\domain\brain_observatory.py", line 41, in <module>
    dataset = boc.get_ophys_experiment_data(ophys_experiment_id)
  File "D:\a\pynwb\pynwb\.tox\gallery-py38-upgraded\lib\site-packages\allensdk\core\brain_observatory_cache.py", line 554, in get_ophys_experiment_data
    return BrainObservatoryNwbDataSet(file_name)
  File "D:\a\pynwb\pynwb\.tox\gallery-py38-upgraded\lib\site-packages\allensdk\core\brain_observatory_nwb_data_set.py", line 145, in __init__
    meta = self.get_metadata()
  File "D:\a\pynwb\pynwb\.tox\gallery-py38-upgraded\lib\site-packages\allensdk\core\brain_observatory_nwb_data_set.py", line 739, in get_metadata
    with h5py.File(self.nwb_file, 'r') as f:
  File "D:\a\pynwb\pynwb\.tox\gallery-py38-upgraded\lib\site-packages\h5py\_hl\files.py", line 567, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
  File "D:\a\pynwb\pynwb\.tox\gallery-py38-upgraded\lib\site-packages\h5py\_hl\files.py", line 231, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
  File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py\h5f.pyx", line 106, in h5py.h5f.open
OSError: Unable to open file (file signature not found)

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3 participants