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Fix build warnings in docs #1380

Merged
merged 6 commits into from
Jul 8, 2021
Merged

Fix build warnings in docs #1380

merged 6 commits into from
Jul 8, 2021

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oruebel
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@oruebel oruebel commented Jul 8, 2021 •
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Motivation

Fix build warnings in docs.

Fix #1379
Fix #1378

How to test the behavior?

cd docs
make html

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 Jul 8, 2021 •
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Codecov Report

Merging #1380 (b9945ec) into dev (10823a7) will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##              dev    #1380   +/-   ##
=======================================
  Coverage   73.53%   73.53%           
=======================================
  Files          37       37           
  Lines        2331     2331           
  Branches      357      357           
=======================================
  Hits         1714     1714           
  Misses        556      556           
  Partials       61       61

Continue to review full report at Codecov.

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@oruebel
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oruebel commented Jul 8, 2021

The following warning currently remains

src/pynwb/validate.py:docstring of pynwb.validate:1: WARNING: duplicate object description of pynwb.validate, other instance in pynwb, use :noindex: for one of them

It appears this is due a collision between the validate function defined in pynwb.__init__.py and the module pynwb/validate.py. Any suggestions how to best fix this warning?

@oruebel oruebel requested review from rly and ajtritt July 8, 2021 17:40
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rly commented Jul 8, 2021

Should we also remove the notebooks in docs/notebooks that are referenced by docs/source/tutorial_source/convert.py?

@oruebel oruebel merged commit 441c64f into dev Jul 8, 2021
@oruebel oruebel deleted the fix/doc_build_warns branch July 8, 2021 18:49
rly pushed a commit that referenced this pull request Aug 10, 2021
@oruebel @rly
Add icephys meta pt 2 (#1349)
edf8565 
Use  extension in docs to simplify linking to common targets

Move advanced data I/O tutorials to their own section and move parallel I/O tutorial

Update Changelog for tutorials

Updated deprecation warning in SweepTable tutorial

Fix minor spelling error in make_test_files

Several corrections and enhancments for the icephys tutorial

Moved functions to create icephys test file from tests to pynwb

Moved functions to create icephys test file from tests to pynwb

Start for new tutorial to show conversion of icephys tables to pandas dataframes

Test to_hierarchical_dataframe and to_denormalized_dataframe functions

Updated tutorial to convert icephys tabels to pandas

Fix minor spelling error in NWBFile docstring

Add TimeseriesReferenceVectorData.get method to mask missing values on load

Update IntracellularRecordingsTable. Update add_recording defaults for startindex and count to None and update to_dataframe method to handle missing values in TimeSeriesReferenceVectorData

Update create_icephys_testfile to create testdata with missing stimuli

Update existing tests to match the new behavior

Update icephys tutorial for match new behavior

Update icephys pandas tutorial to demonstrate new behavior

Remove debug print statements

Add table augmentation and queries to the icephys_pandas tutorial

Fix flake8

Update to use keyword args

Clarify text in icephys tutorial

Fix flake8 on tutorial

Fix flake8

Update to use dev branch of nwb-schema

Set default name and default description for TimeSeriesReferenceVectorData

added icephys_testutils to pynwb.testing.__init__

Added test for IntracellularRecordingsTable.to_dataframe with options

Always use MaskedArrya in TimeSeriesReferenceVectorData instead of MaskedConstant

Add tests for TimeSeriesReferenceVectorData.get

Updated change log

Fix minor docstring issue in TimeSeriesReferenceData.get

Clarify docstring for TimeSeriesReferenceData.get

Fix build warnings in docs (#1380)

* Remove unused and outdated convert.rst from the docs  Fix #1378
* Fix extra numbered footnote reference in ophys tutorial
* Change code block highlighting from c to bash to avoid build warning
* Fix duplicate target here warning in 3_spec_api.rst
* Fix missing section label for crossreferencing between the extension tutorial and gallery
* Updated Changelog

Update CHANGELOG.md

Update icephys.py

Update docs/gallery/domain/plot_icephys.py

Update plot_icephys.py

Minor text fixes

Update plot_icephys_pandas.py

Minor text edits

Update icephys_testutils.py

Minor docstring edits

Update file.py

Fix typos

Update docs/gallery/domain/plot_icephys.py Replace master with main

Mention use of create_icephys_testfile function

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

Remove old comment in TimeSeriesReferenceVectorData

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

Fix typo in changelog

Fix broken link target

Fix flake8 in docs/gallery

Minor text fixes

Minor text and formatting fixes

Update tests/unit/test_icephys_metadata_tables.py

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

Use namedtuple instead of numpy masked structed array to represent values of TimeSeriesReferenceVectorData

Update tests/unit/test_icephys_metadata_tables.py

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

Update tests/unit/test_icephys_metadata_tables.py

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

Update tests/unit/test_icephys_metadata_tables.py

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

Update tests/unit/test_icephys_metadata_tables.py

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

Update tests/unit/test_icephys_metadata_tables.py

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

Update tests/unit/test_icephys_metadata_tables.py

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

Update tests/unit/test_icephys_metadata_tables.py

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

Update tests/unit/test_icephys_metadata_tables.py

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

Fix bad indent in test

Update base.py - minor text edits

Use hdmf 3.1.1

Enhance introspection, slicing, and data addition for TimeSeriesReference and TimeSeriesReferenceVectorData

Updated icephys query tutorial to use latest get_linked_tables behavior and improve rendering

Fix flake8 in gallery

Fix spelling in error message

Update src/pynwb/base.py

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

Update src/pynwb/base.py

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

Update src/pynwb/base.py

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

Update src/pynwb/base.py

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

Update src/pynwb/base.py

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

Update src/pynwb/base.py

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

Fix bug in TimeSeriesReference.timestamps and add comments

Fix gallery tests to handle allensdk pinning pynwb/hdmf

Fix rebase
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@rly rly rly approved these changes

@ajtritt ajtritt Awaiting requested review from ajtritt

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Docs build warnings Update or remove tutorial_source/convert.rst
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@oruebel @rly