Add support for NWB schema 2.6.0 and prepare PyNWB 2.3.0 #1611
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* add age__reference and adjust tests * add to CHANGELOG.md * add period * Update file.py * Update CHANGELOG.md * Update src/pynwb/file.py * add arg check for Subject. If age__reference is provided, age must also be provided * add regression test for subject age * remove raising ValueError when age is omitted * flake8 * Update CHANGELOG.md * Update CHANGELOG.md * Update src/pynwb/file.py * update to allow Subject.age__reference to be None * test for Subject.age__reference == None * Update CHANGELOG.md * Update CHANGELOG.md * use mapper to allow None * update schema * forbid passing age__reference=None to Subject.__init__ * Update comment * fix flake8 * Run backwards compat tests in coverage * Add tests for get_nwb_version * Fix flake8 * Run IO utils tests in test suite Co-authored-by: Ryan Ly <[email protected]>
Codecov Report
@@ Coverage Diff @@
## dev #1611 +/- ##
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+ Coverage 91.43% 91.97% +0.54%
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Files 25 26 +1
Lines 2535 2581 +46
Branches 481 494 +13
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+ Hits 2318 2374 +56
+ Misses 137 132 -5
+ Partials 80 75 -5
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oruebel
reviewed
Dec 15, 2022
Co-authored-by: Oliver Ruebel <[email protected]>
* Check nwb_version on read (#1612) * Added NWBHDF5IO.nwb_version property and check for version on NWBHDF5IO.read * Updated icephys tests to skip version check when writing non NWBFile container * Add tests for NWB version check on read * Add unit tests for NWBHDF5IO.nwb_version property * Updated changelog Co-authored-by: Ryan Ly <[email protected]> * Bump setuptools from 65.4.1 to 65.5.1 (#1614) Bumps [setuptools](https://github.com/pypa/setuptools) from 65.4.1 to 65.5.1. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/CHANGES.rst) - [Commits](pypa/setuptools@v65.4.1...v65.5.1) --- updated-dependencies: - dependency-name: setuptools dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * modify export.rst to have proper links to the NWBFile API docs (#1615) * Create project_action.yml (#1617) * Create project_action.yml * Update project_action.yml * Update project_action.yml * Update project_action.yml (#1620) * Update project_action.yml (#1623) * Project action (#1626) * Create project_action.yml * Update project_action.yml * Update project_action.yml * Update project_action.yml * Show recommended usaege for hdf5plugin in tutorial (#1630) * Show recommended usaege for hdf5plugin in tutorial * Update docs/gallery/advanced_io/h5dataio.py * Update docs/gallery/advanced_io/h5dataio.py Co-authored-by: Heberto Mayorquin <[email protected]> Co-authored-by: Ben Dichter <[email protected]> Co-authored-by: Heberto Mayorquin <[email protected]> * Update iterative write and parallel I/O tutorial (#1633) * Update iterative write tutorial * Update doc makefiles to clean up files created by the advanced io tutorial * Fix #1514 Update parallel I/O tutorial to use H5DataIO instead of DataChunkIterator to setup data for parallel write * Update changelog * Fix flake8 * Fix broken external links * Update make.bat * Update CHANGELOG.md * Update plot_iterative_write.py * Update docs/gallery/advanced_io/plot_iterative_write.py Co-authored-by: Ryan Ly <[email protected]> * Update project_action.yml (#1632) * nwb_schema_2.6.0 * Update CHANGELOG.md * remove Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Oliver Ruebel <[email protected]> Co-authored-by: Ryan Ly <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Dichter <[email protected]> Co-authored-by: Heberto Mayorquin <[email protected]>
rly
changed the title
|
Fix #1642 |
mavaylon1
approved these changes
Feb 22, 2023
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NWB schema 2.6.0 will be released around January 5, 2023.
Currently, it contains the following changes:
Subject.agehas a new optional attribute,reference, which can take a value of "birth" (default) or "gestational".Required PyNWB changes:
Subject.age__reference: add age__reference and adjust tests #1540OnePhotonSeries: Adding OnePhotonSeries class #1593When merging this branch into
dev, do NOT squash and merge, so that individual PR contributions are kept.This branch should be merged after the NWB schema 2.6.0 release. A PyNWB release (2.2.0) should be made shortly after.