rc/2.1.0 #1618
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rc/2.1.0 #1618
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Codecov Report
@@ Coverage Diff @@
## master #1618 +/- ##
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+ Coverage 35.58% 35.65% +0.07%
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Files 344 345 +1
Lines 33568 33612 +44
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+ Hits 11946 11986 +40
- Misses 21622 21626 +4
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Update rc 2 1 to be current with master
Updated from using OphysLimsApi constructor in parametrization, it was causing a failure while collecting tests.
On my windows machine these tests fail as a result of the Postgresquery mixin and being unable to grab env variables for databases. I added in a DbCredentials namedtuple object to the failing tests to give false credentials so that the constructor no longer fails and tests run as expected.
Failing tests in AllenSDK caused by no env variables set
This is a combination of 2 commits: 1) Add warning if loading outdated Visual Coding Neuropixels nwb files 2) Move check_nwbfile_version and make more generically usable
…ning Add warning if loading outdated Visual Coding Neuropixels nwb files
Scipy 1.5.0 fixed a ks_2samp bug that resulted in incorrect p-values being reported. This change was picked up by our brain observatory analysis regression tests. This commit updates the expected output file's Kolmogorov Smirnov test p-values so that they reflect the correct values returned by the most up to date ks_2samp implementation.
…ld-failure Update regression test affected by updated scipy ks_2samp function
This has been inserted as a place for Visual Behavior Scientists to add definitions that they think will benefit end user understanding.
Keys for the name of stimulus are different between eceephys and behavior ophys. This adds in a small function to get the key represented in each data type and raise an exception if one key is not found. This was added to allow ophys behavior experiments to write to nwb files.
I updated the function to be more generic and removed specific case verbaige. I also fixed the failing tests on Linux and Mac. The regex for the tests was returning an error on Linux and Mac.
Updated the Docstring to better capture the puprose of the function. This better aligns with the expectation of functional performance.
* Added function to set the stop_time for omitted stimuli for writing NWB This function had to be added as the omitted stimuli did not by design have an ending timestamp. These stimuli therfore could not be written to NWB files as the interval data object in PyNWB requires an ending time. This commit adds a function that adds a stop_time to a omitted row that is based off the known time that omitted stimuli are shown. This allows for omitted stimuli types to be written to NWB intervals. * Added doc strings to stimulus_presentations.py I added documentation for the functions in stimulus_presentations.py that I have touched during investigation. These functions are get_stimulus_presentations and get_visual_stimuli_df. I added doc strings to better explain what is happening in the code.
* Added column name exceptions from column creation Behavior Ophys NWB files were erroring because a column of name 'image_mask' already existed in the PlaneSegmentation NWB NWB object. These columns are initilized by the PlaneSegmentation object on creation and do not need to be added during writing. These column names were added to the list of column exceptions as they already exist. This allows NWB files to be written for Behavior Ophys experiments. Also added descriptions for the columns written to the NWB file in the cell specimen table.
…WB-failures Address behavior ophys nwb failures from unpinning PyNWB, these have already been reviewed by @njmei in the individual pull requests.
…tud_for_visual_behavior_definitions Create Stub for Visual Behavior Definitions
Contributor
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This is the release candidate for release 2.1.0, tentatively slated for release on July 16th 2020. All new features should target this branch (bugfixes ought to instead target master). Please see the confluence guide for more information on the release process. before merge
merge!
after merge
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Updated index.rst with release information for AllenSDK v2.1.0.
Updated changelog to reflect changes coming in AllenSDK 2.1.0
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This is the PR for version 2.1.0 which has a tentative release date of ~6/25/20.