improve extensions documentation #1350
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## dev #1350 +/- ##
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Coverage 73.53% 73.53%
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Branches 357 357
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oruebel
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May 13, 2021
docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst
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…rough.rst Co-authored-by: Oliver Ruebel <[email protected]>
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docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst
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docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst
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…rough.rst Co-authored-by: Oliver Ruebel <[email protected]>
…rough.rst Co-authored-by: Oliver Ruebel <[email protected]>
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docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst
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Co-authored-by: Ryan Ly <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>
bendichter
commented
May 25, 2021
Co-authored-by: Ryan Ly <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>
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@rly @bendichter is this one good to merge? |
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It is from my end
…On Wed, Jun 9, 2021, 9:35 PM Oliver Ruebel ***@***.***> wrote:
@rly <https://github.com/rly> @bendichter <https://github.com/bendichter>
is this one good to merge?
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oruebel
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Jun 10, 2021
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Looks good to me. @rly can you review and approve if there are no issues. On a separate note, there is still substantial overlap between these extensions docs and the tutorial sphinx gallery. Since these docs focus on creating extensions and looking at: https://pynwb.readthedocs.io/en/stable/tutorials/general/extensions.html#sphx-glr-tutorials-general-extensions-py I think a reasonable approach would be to update the tutorial to just focus on using extensions for reading/writing data. |
rly
approved these changes
Jun 17, 2021
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@bendichter This is good to go. Feel free to merge. |
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@bendichter And thanks for all the effort on this! It is very comprehensive. |
Dido. Really nice work! Thanks for all the effort. |
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Aug 10, 2021
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 and @oruebel I'd like to consolidate the extensions documentation into a multi-part series. This is still WIP, but can you take a look at it and let me know what you think?