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Use HDMF 2.5.2 #1360

Merged
merged 4 commits into from
May 11, 2021
Merged

Use HDMF 2.5.2 #1360

merged 4 commits into from
May 11, 2021

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rly
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@rly rly commented May 11, 2021

Use just released HDMF 2.5.2, and also add setuptools as a requirement (see hdmf-dev/hdmf#596)

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  • Have you checked our Contributing document?
  • Have you ensured the PR description clearly describes problem and the solution?
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  • 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 #XXX notation where XXX is the issue number?

@rly rly requested a review from oruebel May 11, 2021 20:24
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Codecov Report

Merging #1360 (d29ca63) into dev (66ef3ab) will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##              dev    #1360   +/-   ##
=======================================
  Coverage   73.41%   73.41%           
=======================================
  Files          37       37           
  Lines        2310     2310           
  Branches      354      354           
=======================================
  Hits         1696     1696           
  Misses        553      553           
  Partials       61       61

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@rly rly merged commit 4ad902c into dev May 11, 2021
@rly rly deleted the pin_hdmf branch May 11, 2021 20:31
rly pushed a commit that referenced this pull request Aug 10, 2021
@oruebel @rly
Add icephys meta (#1349)
e905aa2 
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 <[email protected]>

Add ReadTheDocs badge to README (#1311)

Co-authored-by: Ryan Ly <[email protected]>

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 <[email protected]>

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 <[email protected]>

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 <[email protected]>

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 <[email protected]>

* Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst

Co-authored-by: Oliver Ruebel <[email protected]>

* Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst

Co-authored-by: Oliver Ruebel <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Oliver Ruebel <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Oliver Ruebel <[email protected]>

* Update docs/source/extensions_tutorial/6_documenting_extension.rst

Co-authored-by: Oliver Ruebel <[email protected]>

* Update docs/source/extensions_tutorial/4_auto_api.rst

Co-authored-by: Oliver Ruebel <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Oliver Ruebel <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Oliver Ruebel <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Oliver Ruebel <[email protected]>

* 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 <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/4_auto_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/5_custom_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/4_auto_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/4_auto_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/4_auto_api.rst

* Update docs/source/extensions_tutorial/3_spec_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/5_custom_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update docs/source/extensions_tutorial/5_custom_api.rst

Co-authored-by: Ryan Ly <[email protected]>

* Update extensions_tutorial_home.rst

* Minor text fixes

* Minor text fixes

* Minor text fixes

Co-authored-by: Oliver Ruebel <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>

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 <[email protected]>

Add unique electrode id check (#1344)

Co-authored-by: Ryan Ly <[email protected]>

Fix integration tests with invalid test data that will be caught by future hdmf validator version (#1366)

Co-authored-by: Ryan Ly <[email protected]>

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
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@rly @oruebel