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Update or remove tutorial_source/convert.rst #1378

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5 tasks done
oruebel opened this issue Jul 7, 2021 · 2 comments · Fixed by #1380
Closed
5 tasks done

Update or remove tutorial_source/convert.rst #1378

oruebel opened this issue Jul 7, 2021 · 2 comments · Fixed by #1380
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@oruebel
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priority: medium non-critical problem and/or affecting only a small set of NWB users topic: docs issues related to documentation

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@oruebel
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oruebel commented Jul 7, 2021 •
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Description

The page https://pynwb.readthedocs.io/en/stable/tutorial_source/convert.html should be removed or updated. The information is outdated and it looks like the page may also not be linked in the page index, at least according to Sphinx:

...pynwb/docs/source/tutorial_source/convert.rst: WARNING: document isn't included in any toctree

Checklist

  • Have you ensured the bug was not already reported?
  • Have you included a brief and descriptive title?
  • Have you included a clear description of the problem you are trying to solve?
  • Have you included a minimal code snippet that reproduces the issue you are encountering?
  • Have you checked our Contributing document?
@oruebel oruebel added help wanted topic: docs issues related to documentation labels Jul 7, 2021
@rly
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rly commented Jul 7, 2021

Yeah, it looks like that page and the linked notebooks use functionality that has been removed or changed in PyNWB, e.g.,

from pynwb.misc import UnitTimes, SpikeUnit
from pynwb.epoch import EpochTimeSeries
from pynwb.core import set_parents

@bendichter
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I say we remove it

@oruebel oruebel added the priority: medium non-critical problem and/or affecting only a small set of NWB users label Jul 7, 2021
@oruebel oruebel self-assigned this Jul 8, 2021
oruebel added a commit that referenced this issue Jul 8, 2021
@oruebel
Remove unused and outdated convert.rst from the docs Fix #1378
2d30e17
@oruebel oruebel mentioned this issue Jul 8, 2021
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oruebel added a commit that referenced this issue Jul 8, 2021
@oruebel
Fix build warnings in docs (#1380)
441c64f 
* 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
rly pushed a commit that referenced this issue 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 <rly@lbl.gov>

Remove old comment in TimeSeriesReferenceVectorData

Co-authored-by: Ryan Ly <rly@lbl.gov>

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 <rly@lbl.gov>

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 <rly@lbl.gov>

Update tests/unit/test_icephys_metadata_tables.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

Update tests/unit/test_icephys_metadata_tables.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

Update tests/unit/test_icephys_metadata_tables.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

Update tests/unit/test_icephys_metadata_tables.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

Update tests/unit/test_icephys_metadata_tables.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

Update tests/unit/test_icephys_metadata_tables.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

Update tests/unit/test_icephys_metadata_tables.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

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 <rly@lbl.gov>

Update src/pynwb/base.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

Update src/pynwb/base.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

Update src/pynwb/base.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

Update src/pynwb/base.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

Update src/pynwb/base.py

Co-authored-by: Ryan Ly <rly@lbl.gov>

Fix bug in TimeSeriesReference.timestamps and add comments

Fix gallery tests to handle allensdk pinning pynwb/hdmf

Fix rebase
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priority: medium non-critical problem and/or affecting only a small set of NWB users topic: docs issues related to documentation
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Fix build warnings in docs NeurodataWithoutBorders/pynwb
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@rly @bendichter @oruebel