Use HDMF 2.5.0 #1354

rly · 2021-04-13T21:04:46Z

Motivation

This PR updates PyNWB to use HDMF 2.5.0 (to be released) including updating some tests and minor behavior changes.

Checklist

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Is your contribution compliant with our coding style? This can be checked running flake8 from the source directory.
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codecov · 2021-04-22T22:38:23Z

Codecov Report

Merging #1354 (e062dab) into dev (695c562) will increase coverage by 0.03%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##              dev    #1354      +/-   ##
==========================================
+ Coverage   73.89%   73.92%   +0.03%     
==========================================
  Files          37       37              
  Lines        2283     2282       -1     
  Branches      346      346              
==========================================
  Hits         1687     1687              
  Misses        539      539              
+ Partials       57       56       -1

Impacted Files	Coverage Δ
src/pynwb/__init__.py	`73.13% <100.00%> (-0.20%)`	⬇️
src/pynwb/file.py	`84.53% <0.00%> (+0.32%)`	⬆️

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Declare SweepTable as deprecated on init Add TimeSeriesReferenceVectorData Container class Add simple test for TimeSeriesReferenceVectorData Update nwb-schema branch Add icephys metadata container classes Update NWBFile to support icephys metadata tables Add unit tests for icephys metadata tables Update imports and fix SweepTable integration tests Fix test available namespaces testcase Update SweepTable tutorial and declare as deprecated Add new icephys tutorial using the new hierarchical metadata tables Add IntracellularRecordingsTable illustration Fix flake8 issues Remove use of HierarchiclaDynamicTableMixin use for now Add source PowerPoint file for icephys docs add doc for TimeIntervals (#1352) * add doc for TimeIntervals * add allensdk back Fix make clean command for docs to also clean sphinx-gallery files Updated CHANGELOG to describe changes from this PR Add thumbnails for domain-specfic tutorials Add thumbnaisl for general tutorials Update changelog Remove ic_filtering/icephys_filtering duplicate and fix test Fix description of ExperimentalConditionsTable Use HDMF 2.5.0 (#1354) DOC: make template less puzzling in how to fill out ;-) (#1336) Co-authored-by: Ryan Ly <rly@lbl.gov> Add ReadTheDocs badge to README (#1311) Co-authored-by: Ryan Ly <rly@lbl.gov> Update to use upcoming HDMF 2.5.1 (#1355) Revert breaking changes to scratch API (#1356) Use HDMF 2.5.2 (#1360) Add `DfOverF` to docs (#1351) Co-authored-by: Ryan Ly <rly@lbl.gov> docs/gallery/general/file.py: Fix argument count in documentation add strain optional arg to Subject (#1241) * remove validate_core_schema. You can check the core schema with e.g. * Update Subject unit test * Fix Subject unit test, add check for date_of_birth Co-authored-by: Ryan Ly <rly@lbl.gov> add source channels to DecompSeries add option to include source_channels for DecompositionSeries (#1258) * add option to include source_channels for DecompositionSeries and include round trip test * Use latest schema * Add unit test Add optional link to Device in ImageSeries (#1265) * Add optional link to Device in ImageSeries * Add support for device in ImageSeries subclasses * Update ImageMaskSeries docstring * Update schema add continuity optional arg to TimeSeries.__init__ (#1226) * add continuity optional arg to TimeSeries.__init__ * use new enum feature of hdmf to check against controlled vocabulary * Fix flake8 * Add integration test * Fix flake8 * Add correct mapping for data.continuity Co-authored-by: Ryan Ly <rly@lbl.gov> Add support for ElectricalSeries.filtering dataset (#1270) Set fixed value for IZeroClampSeries stimulus description Fix test Update changelog Add note about allensdk py3.8 incompatibility Add workaround for validation against cached hdmf-experimental Update CI to avoid click8 incompatibility Use HDMF 2.5.5 Address comments, improve doc Fix docs, add citation info, update repo infra (#1362) Use latest HDMF, raise min pandas, dissociate req-min and setup reqs (#1363) Use nwb schema branch for icephys meta Ensure start_index and count are set to -1 if TimeSeries is None Add test for conversion of start_index and index_count vals Fix flake8 in __compute_index docstring Fix icephys metadata roundtrip NWBFile test base on update DynamicTableRegion behavior Update schema (updated version to 1.4.0-alpha) improve extensions documentation (#1350) * improve extensions documentation * adjustments to extensions.rst * add tips to extension docs * create multi-part extensions tutorial * move API building docs to chapter 5 of extensions guide * restructure and fix up some spots * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/6_documenting_extension.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * remove detailed GroupSpec API instructions from tutorial * remove instructions for generated the directory structure, and instead focus on generating the HTML and filling in the missing pieces. * add link to ndx catalog * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/5_custom_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/4_auto_api.rst * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/5_custom_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/5_custom_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update extensions_tutorial_home.rst * Minor text fixes * Minor text fixes * Minor text fixes Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> Co-authored-by: Ryan Ly <rly@lbl.gov> Set language for code block to fix readthedocs Add RRID for PyNWB Add RRID to README Update changelog make MotionCorrection test (#1374) * attempt to make MotionCorrection test. I don't understand why it's failing * Fix CorrectedImageStack nwbfields * Fix tests * Fix test * Fix flake8 * Fix test Co-authored-by: Ryan Ly <rly@lbl.gov> Add unique electrode id check (#1344) Co-authored-by: Ryan Ly <rly@lbl.gov> Fix integration tests with invalid test data that will be caught by future hdmf validator version (#1366) Co-authored-by: Ryan Ly <rly@lbl.gov> Improve documentation and test for CorrectedImageStack (#1306) Fix test for validator update (#1376) Update changelog Allow h5py 3 so that this can work with hdmf rc/3.0.0 Move SweepTable DeprectationWarning to the constructor of SweepTable to clean up code Suppress SweepTable Deprecation warning in icephys integration test Ignore and assert deprecation warning for SweepTable during SweepTable roundtrip tests Merge branch 'rc/2.0.0' into add/icephys_meta Fix falke8 on icephys tutorial galleries

rly added 8 commits March 24, 2021 12:58

Update test to account for new namespace in hdmf 2.5.0

1747826

Update get_class call

5111de1

Remove redundant merge

dbcaa55

Update get_class call

91d0a61

Move TestCatchDuplicateSpec test to HDMF

36ab7ed

Merge branch 'dev' into hdmf_2.5.0

de88fe3

Replace print validation errors with assert

1161a16

Update legal

267b150

rly mentioned this pull request Apr 22, 2021

Prepare for version 2.5.0 release hdmf-dev/hdmf#550

Merged

rly closed this Apr 22, 2021

rly reopened this Apr 22, 2021

rly marked this pull request as ready for review April 22, 2021 22:28

rly added 3 commits April 22, 2021 15:32

Update hdmf requirements

919a9cd

Delete test file

716b0ef

Update tox settings

e062dab

oruebel approved these changes Apr 22, 2021

View reviewed changes

rly merged commit b3ffdc7 into dev Apr 22, 2021

rly deleted the hdmf_2.5.0 branch April 22, 2021 22:51

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Use HDMF 2.5.0 #1354

Use HDMF 2.5.0 #1354

rly commented Apr 13, 2021

codecov bot commented Apr 22, 2021 •

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Use HDMF 2.5.0 #1354

Use HDMF 2.5.0 #1354

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rly commented Apr 13, 2021

Motivation

Checklist

codecov bot commented Apr 22, 2021 • edited Loading

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