Fix docs, add citation info, update repo infra #1362

rly · 2021-05-18T22:35:35Z

Motivation

Fix sphinx gallery issue - fix Fix sphinx gallery issue #1359
Flesh out changelog for upgrade of HDMF from 2.1.0 to 2.5.5.
Update requirements
Update GitHub templates
Update setup.cfg
Add due credit support - fix Add duecredit support #1322
Remove ColoredTestRunner for easier to debug verbose test output (see Revert use of ColoredTestRunner (#89) hdmf-dev/hdmf#588)

Checklist

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

codecov · 2021-05-18T22:36:16Z

Codecov Report

Merging #1362 (8ffda0d) into dev (13b6c4e) will increase coverage by 0.12%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##              dev    #1362      +/-   ##
==========================================
+ Coverage   73.41%   73.53%   +0.12%     
==========================================
  Files          37       37              
  Lines        2328     2331       +3     
  Branches      357      357              
==========================================
+ Hits         1709     1714       +5     
+ Misses        557      556       -1     
+ Partials       62       61       -1

Impacted Files	Coverage Δ
src/pynwb/icephys.py	`90.08% <ø> (ø)`
src/pynwb/misc.py	`87.31% <ø> (ø)`
src/pynwb/__init__.py	`73.72% <100.00%> (+0.58%)`	⬆️
src/pynwb/file.py	`82.75% <100.00%> (+0.62%)`	⬆️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 2934fb0...8ffda0d. Read the comment docs.

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

rly added 5 commits May 18, 2021 11:18

Fix sphinx gallery issue and update changelog

174deb1

Update requirements, GH templates, setup.cfg

b8ab773

Add due credit support

1dee610

Remove coloredtestrunner for easier to read verbose test output

44fa5a6

Add GH action badge, update citation

10b4188

rly mentioned this pull request May 18, 2021

Add NWB citation to README #1323

Closed

5 tasks

rly requested a review from oruebel May 18, 2021 22:36

rly added 3 commits May 18, 2021 15:41

Update sphinx config

0c8e940

Update sphinx config

23870a5

Fix flake8

8ffda0d

oruebel approved these changes May 19, 2021

View reviewed changes

rly merged commit 49ad17a into dev May 19, 2021

rly deleted the fix/sphinx_gallery branch May 19, 2021 17:53

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Fix docs, add citation info, update repo infra #1362

Fix docs, add citation info, update repo infra #1362

rly commented May 18, 2021

codecov bot commented May 18, 2021 •

edited

Loading

Fix docs, add citation info, update repo infra #1362

Fix docs, add citation info, update repo infra #1362

Conversation

rly commented May 18, 2021

Motivation

Checklist

codecov bot commented May 18, 2021 • edited Loading

Codecov Report

codecov bot commented May 18, 2021 •

edited

Loading