Add/icephys meta #1349
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Add/icephys meta #1349
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@@ Coverage Diff @@
## rc/2.0.0 #1349 +/- ##
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+ Coverage 73.34% 77.04% +3.70%
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Files 37 37
Lines 2337 2692 +355
Branches 360 445 +85
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+ Hits 1714 2074 +360
+ Misses 562 541 -21
- Partials 61 77 +16
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@rly @ajtritt this PR is also ready for review. We should probably wait with the merge until NeurodataWithoutBorders/nwb-schema#470 and hdmf-dev/hdmf#551 have been merged so all the CI can be run. But other than that this PR should be complete. |
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…ence and TimeSeriesReferenceVectorData
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…or and improve rendering
Co-authored-by: Ryan Ly <rly@lbl.gov>
Co-authored-by: Ryan Ly <rly@lbl.gov>
Co-authored-by: Ryan Ly <rly@lbl.gov>
Co-authored-by: Ryan Ly <rly@lbl.gov>
Co-authored-by: Ryan Ly <rly@lbl.gov>
Co-authored-by: Ryan Ly <rly@lbl.gov>
…tBorders/pynwb into add/icephys_meta
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Jul 30, 2021
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This is good to merge into rc/2.0.0. Great work! |
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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 <rly@lbl.gov> Add ReadTheDocs badge to README (#1311) Co-authored-by: Ryan Ly <rly@lbl.gov> 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 <rly@lbl.gov> 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 <rly@lbl.gov> 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 <rly@lbl.gov> 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 <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/6_documenting_extension.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> * 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 <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/2_create_extension_spec_walkthrough.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/5_custom_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/4_auto_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/4_auto_api.rst * Update docs/source/extensions_tutorial/3_spec_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/5_custom_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update docs/source/extensions_tutorial/5_custom_api.rst Co-authored-by: Ryan Ly <rly@lbl.gov> * Update extensions_tutorial_home.rst * Minor text fixes * Minor text fixes * Minor text fixes Co-authored-by: Oliver Ruebel <oruebel@users.noreply.github.com> Co-authored-by: Ryan Ly <rly@lbl.gov> 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 <rly@lbl.gov> Add unique electrode id check (#1344) Co-authored-by: Ryan Ly <rly@lbl.gov> Fix integration tests with invalid test data that will be caught by future hdmf validator version (#1366) Co-authored-by: Ryan Ly <rly@lbl.gov> 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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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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Motivation
This PR is for integration of the ndx-icephys-meta structures with NWB core. Related PRs on the other repos are:
NeurodataWithoutBorders/nwb-schema#470
hdmf-dev/hdmf-common-schema#57
hdmf-dev/hdmf#551
oruebel/ndx-icephys-meta#82
Changes on this PR include
Current status update on the integration of the ndx-icephys-meta with the NWB core:
AlignedDynamicTableAdd/aligned dynamic table hdmf-dev/hdmf#551AlignedDynamciTableAdd aligned table tutorial hdmf-dev/hdmf#571DynamicTableRegionRework DynamicTable/DynamicTableRegion.get when the table contains a DTR hdmf-dev/hdmf#579DyanmicTable(e.g, addto_hierarchical_dataframefunction) Add functionality for linked DynamicTables hdmf-dev/hdmf#645. This PR has already undergone review and is ready to be merged once approved.Checklist
flake8from the source directory.#XXXnotation whereXXXis the issue number?