[Zarr-Support] Refactor nwbRead around HDF5 backend reader#796
Merged
ehennestad merged 78 commits intomainfrom Apr 13, 2026
Merged
[Zarr-Support] Refactor nwbRead around HDF5 backend reader#796ehennestad merged 78 commits intomainfrom
nwbRead around HDF5 backend reader#796ehennestad merged 78 commits intomainfrom
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Extend the test helper to treat types.untyped.DataPipe like DataStub by calling load() on actualValue before comparing.
…ject-checks-in-tutorialtests
Replace the old SKIP_PYNWB_COMPATIBILITY_TEST_FOR_TUTORIALS env var with SKIP_PYNWB_TESTS across tests and nwbtest.m, and update +tests/nwbtest.default.env.
Update CI workflow matrix keys and usage in prepare_release.yml, run_tests.yml, and configurations/matlab_release_matrix_strategy.yml to use the new key (matrix.skip-pynwb-tests) and wire the MATLAB setenv accordingly.
Move conditional installation of pynwb into the workflows (install pynwb only when skip-pynwb-tests == '0') and remove the direct git+ dependency from +tests/requirements.txt (update comment to reflect conditional installs).
Also add TestTags = {'UsesPython'} to PyNWBIOTest.
These changes centralize the CI control of pynwb installation and standardize the skip variable name.
…nore-nwbinspector-subject-checks-in-tutorialtests
checking if this class attribute trips up docs build
Move TestTags to methods blocks. Check if that fixes issue with sphinx build of docs
…nore-nwbinspector-subject-checks-in-tutorialtests
Install pynwb and nwbinspector from PyPI stable releases in the main test workflow so CI only fails due to matnwb regressions. Add a separate weekly workflow that tests against the dev branches to catch upstream incompatibilities early without blocking PRs. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Added more details in comments Removed unused vars NWB_TEST_DEBUG, GITHUB_TOKEN Added PYNWB_REPO_DIR
Replace custom venv/download/GitHub API infrastructure with a simple
approach: read tutorial files from PYNWB_REPO_DIR env var pointing to
a pre-cloned pynwb repo, and run them against the system Python. The
CI workflows are now responsible for cloning the repo and setting the
env var. TestTags = {'UsesPython'} added so the tag selector in the
dev workflow picks up these tests, and SKIP_PYNWB_TESTS correctly
excludes them on older MATLAB releases.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Covers prerequisites, running tests via nwbtest() and the MATLAB unit testing framework, Python dependency setup, environment variable configuration, and test authoring conventions. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
actions/checkout requires path to be within the workspace directory. Use path: pynwb-repo (inside workspace) instead of ../pynwb-repo. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Suppress output
Suppress warning that happens due to wrong values in the file's version attribute in the source schemas for v 2.2.0 and 2.6.0
Added section about setting up dynamically loaded filters
Move test tags to methods block, as testtags in classdef breaks the sphinx/docs build
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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…taset Codex removed some relevant comments Carry over some changes from refactored io.parseDataset
Keep comments in readAttributeValue
ehennestad
changed the title
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #796 +/- ##
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+ Coverage 95.49% 95.51% +0.02%
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Files 192 195 +3
Lines 7097 7151 +54
==========================================
+ Hits 6777 6830 +53
- Misses 320 321 +1 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Add note on implementation detail of not using abstract class explicitly
ehennestad
changed the title
nwbRead around HDF5 backend reader
bendichter
approved these changes
Apr 13, 2026
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Summary
In order to support reading Zarr NWB files, this PR adds a backend reader abstraction and concrete HDF5 class to read HDF5 backed files, by extracting direct h5-library calls from
nwbReadand parse helpers into the reader class.Details
Included:
io.backend.base.Readerio.backend.BackendFactoryio.backend.hdf5.HDF5ReadernwbRead,parseGroup,parseDataset, andparseAttributes