Release 2.0.0 · NeurodataWithoutBorders/pynwb

SweepTable has been deprecated in favor of the new icephys metadata tables. Use of SweepTable
is still possible but no longer recommended. @oruebel (#1349
TimeSeries.__init__ now requires the data argument because the 'data' dataset is required by the schema.
If a TimeSeries is read without a value for data, it will be set to a default value. For most
TimeSeries, this is a 1-dimensional empty array with dtype uint8. For ImageSeries and
DecompositionSeries, this is a 3-dimensional empty array with dtype uint8. @rly (#1274)
TimeSeries.__init__ now requires the unit argument because the 'unit' attribute is required by the schema.
If a TimeSeries is read without a value for unit, it will be set to a default value. For most
TimeSeries, this is "unknown". For IndexSeries, this is "N/A" according to the NWB 2.4.0 schema. @rly (#1274)

Added new intracellular electrophysiology hierarchical table structure from ndx-icephys-meta to NWB core.
This includes the new types TimeSeriesReferenceVectorData, IntracellularRecordingsTable,
SimultaneousRecordingsTable, SequentialRecordingsTable, RepetitionsTable and
ExperimentalConditionsTable as well as corresponding updates to NWBFile to support interaction
with the new tables. @oruebel (#1349)
Added support for NWB 2.4.0. See Release Notes
for more details. @oruebel, @rly (#1349)
Dropped Python 3.6 support, added Python 3.9 support. @rly (#1377)
Updated requirements to allow compatibility with HDMF 3 and h5py 3. @rly (#1377)
- When using HDMF 3 and h5py 3, users can now stream NWB files from an S3 bucket.

Added new tutorial for intracellular electrophysiology to describe the use of the new metadata tables
and declared the previous tutoral using SweepTable as deprecated. @oruebel (#1349)
Added new tutorial for querying intracellular electrophysiology metadata
(docs/gallery/domain/plot_icephys_pandas.py). @oruebel (#1349, #1383)
Added thumbnails for tutorials to improve presentation of online docs. @oruebel (#1349)
Used sphinx.ext.extlinks extension in docs to simplify linking to common targets. @oruebel (#1349)
Created new section for advanced I/O tutorials and moved parallel I/O tutorial to its own file. @oruebel (#1349)
Overhauled documentation on extensions. @bendichter, @rly, @oruebel (#1350)
Updated the optical physiology / Calcium imaging tutorial. @bendichter, @weiglszonja (#1375)
Added a tutorial on streaming using the ROS3 driver. @rly (#1393)

Added RRID for citing PyNWB to the docs. @oruebel (#1372)
Updated CI and tests to handle deprecations in libraries. @rly (#1377)
Added test utilities for icephys (pynwb.testing.icephys_testutils) to ease creation of test data
for tests and tutorials. @oruebel (#1349, #1383)
Added on-push and nightly tests of streaming using the ROS3 driver. @rly (#1393)
- These tests make use of a new dandiset for testing the API: https://gui.dandiarchive.org/#/dandiset/000126
Improve documentation and test for CorrectedImageStack, MotionCorrection. @rly, @bendichter (#1306, #1374)

Updated behavior of make clean command for docs to ensure tutorial files are cleaned up. @oruebel (#1349)
Enforced electrode ID uniqueness during insertion into table. @CodyCBakerPhD (#1344)
Fixed integration tests with invalid test data that will be caught by future hdmf validator version.
@dsleiter, @rly (#1366, #1376)
Fixed build warnings in docs. @oruebel (#1380)
Fix intersphinx links in docs for numpy. @oruebel (#1386)
Previously, the data argument was required in OpticalSeries.__init__ even though external_file could
be provided in place of data. OpticalSeries.__init__ now makes data optional. However, this has the
side effect of moving the position of data to later in the argument list, which may break code that relies
on positional arguments for OpticalSeries.__init__. @rly (#1274)
Fixed setup.py not being able to import versioneer when installing in an embedded Python environment. @ikhramts
(#1395)
Removed broken option to validate against a given namespace file and updated associated documentation. @rly (#1397)

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