Support NeuroConv 0.9.3 by bendichter · Pull Request #1056 · NeurodataWithoutBorders/nwb-guide

bendichter · 2026-02-13T04:53:26Z

Bumps neuroconv from 0.6.1 to 0.9.2 (latest) in a single PR.

Key Changes

Backend (manage_neuroconv.py)

ElectrodeColumns/UnitColumns sync: neuroconv 0.6.2+ populates default column definitions; frontend validator cross-references these → errors. Fixed by syncing columns metadata with all schema properties, including data_type inference.
temporally_align_data_interfaces: Added metadata=None, conversion_options=None kwargs (neuroconv 0.7.0 API change)
_ensure_dandi_staging_alias(): Registers dandi-staging as alias for dandi-sandbox in dandi >= 0.74.0
automatic_dandi_upload: staging= → sandbox= parameter (neuroconv 0.9.0 API change)

Frontend

Table.js bug fix: value == "" was true for 0 due to JS type coercion; fixed to value === "" || value == null

Environment / CI

Bump neuroconv to 0.9.2 across all platform environments
Pin h5py < 3.13 on macOS arm64 (HDF5 symbol mismatch with pytables in PyInstaller builds)
Loosen ndx-pose (>= 0.1.1) and nwbinspector (>= 0.6.2) pins
Remove neo and pandas pins (no longer needed with neuroconv >= 0.8.0)
Remove deprecated macos-13 CI runners from all workflows

E2E Tests

Update SpikeGLX source data: file_path → folder_path + stream_id (neuroconv 0.9.0 API change)

Supersedes #1043, #1049, #1053.

Key changes: - Bump neuroconv from 0.6.1 to 0.9.1 across all environments - Sync ElectrodeColumns/UnitColumns metadata with all schema properties (incl. data_type inference) - Fix Table.js: value == '' was true for 0 (JS coercion bug) - Add metadata/conversion_options kwargs to temporally_align_data_interfaces (0.7.0 API change) - Add _ensure_dandi_staging_alias() for dandi >= 0.74.0 compat - Update automatic_dandi_upload param: staging → sandbox (0.9.0 API change) - Pin h5py < 3.13 on macOS arm64 (HDF5 symbol mismatch with pytables) - Remove deprecated macos-13 CI runners from all workflows - Update E2E tests: SpikeGLX now uses folder_path + stream_id (0.9.0 API change) - Loosen ndx-pose (>= 0.1.1) and nwbinspector (>= 0.6.2) pins - Remove neo and pandas pins (no longer needed with neuroconv >= 0.8.0)

for more information, see https://pre-commit.ci

- Update scikit-learn 1.4.0 → 1.6.1 (numpy 2.x compatibility) - Pin tqdm_publisher, tzlocal, ndx-pose, nwbinspector, numcodecs to specific versions - Remove stale scipy < 1.12.0 constraint on MAC-intel - Remove _ensure_dandi_staging_alias (no longer needed with neuroconv 0.9.1) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

bendichter · 2026-02-13T21:03:03Z

The ExampleDataTests failures on Windows and macOS are caused by a regression in neuroconv's validate_conversion_options (introduced in catalystneuro/neuroconv#1139). It JSON-encodes conversion_options before schema validation, which fails on the progress_bar_class type object and callback functions that GUIDE passes in iterator_opts.

Fix PR: catalystneuro/neuroconv#1667

bendichter · 2026-02-18T14:26:40Z

As far as I can tell, catalystneuro/neuroconv#1667 was the only blocking issue. When that is released in NeuroConv 0.9.3, these tests should pass

bendichter · 2026-02-18T14:29:32Z

fyi @h-mayorquin

environments/environment-Linux.yml

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

The coerce_schema_compliance_recursive function used elif between patternProperties and properties checks, so schemas with both (like Ophys with Fluorescence/DfOverF pattern props alongside ImagingPlane regular props) would skip regular property coercion. This caused emission_lambda to remain as a string/None instead of being converted to float, breaking BrukerTiff conversions. Also fix resolve_references to recursively resolve nested $refs and handle patternProperties, and add str-to-float coercion as a safety net for number fields. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

for more information, see https://pre-commit.ci

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

BrukerTiffSinglePlaneConverter inherits from BaseDataInterface (not NWBConverter) and doesn't override get_metadata_schema(), so the converter's schema lacks Ophys properties. This caused the schema-based NaN coercion in replace_none_with_nan to miss emission_lambda, leaving it as the string "NaN" instead of float NaN. Add replace_nan_strings() as a schema-independent fallback that converts all string "NaN" values (JavaScript NaN artifacts) to float NaN. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Rename VideoInterface to ExternalVideoInterface, remove duplicate AlphaOmegaRecordingInterface, add WhiteMatterRecordingInterface schema, and regenerate all interface schemas with latest neuroconv. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

for more information, see https://pre-commit.ci

…-recording-interface Add WhiteMatterRecordingInterface

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

for more information, see https://pre-commit.ci

…ording-interface Add Plexon2RecordingInterface

Regenerate schemas to preserve pydantic's DirectoryPath and FilePath format types instead of resolving them all to generic "path". Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

for more information, see https://pre-commit.ci

These files are generated by `python generateInterfaceSchema.py` and don't need to be tracked. This eliminates noisy diffs across 40+ JSON files on every neuroconv version bump. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

…at-types Restore file-path and directory-path format types in schemas

bendichter · 2026-03-03T20:02:51Z

@rly 's comment from review: add back intel support, with runners, which look something like "macos15-intel"

.github/workflows/build_and_deploy_mac.yml

.github/workflows/example_data_cache.yml

src/pyflask/manageNeuroconv/manage_neuroconv.py

rly · 2026-03-03T23:16:58Z

The WhiteMatter Recording interface shows this error on the source data input page:

@bendichter Can you resolve this? I don't have test data and cannot find any in ephy_testing_data. If it can't be resolved, I suggest not adding it in this PR.

The Plexon2 interface works only on Windows. We should limit its availability in this PR or a separate one.

The tutorial will need to be updated because the new SpikeGLX interface requires a stream name (both single session and multi-session tutorials) but that can be a separate PR.

Otherwise looks good to me. Thanks @bendichter !

src/supported_interfaces.json

The trailing comma after CellExplorerRecordingInterface caused JSON parse failures, breaking all DevTests, LiveServices, ExampleDataTests, and E2ELiveServices CI jobs. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

The ephys-datasets-macos-15-intel cache has never been saved due to repeated race conditions between concurrent PR workflow runs. This empty commit triggers a clean run to populate the cache. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Deleted ~5GB of stale/duplicate caches to make room for the macos-15-intel ephys cache that has never been successfully saved. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

The ephys-datasets-macos-15-intel cache reservation got permanently stuck from a race condition between concurrent workflow runs. Bumping the key prefix forces a fresh cache entry. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

rly · 2026-03-04T16:01:33Z

Thanks @bendichter !

bendichter force-pushed the support-neuroconv-latest branch 2 times, most recently from 0f981f5 to 7b4c587 Compare February 13, 2026 05:20

bendichter force-pushed the support-neuroconv-latest branch from ef5d1bc to b070be2 Compare February 13, 2026 05:21

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bendichter enabled auto-merge February 13, 2026 17:38

This was referenced Feb 18, 2026

Support NeuroConv 0.9.0 #1053

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Support NeuroConv 0.8.0 #1049

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Support NeuroConv 0.7.0 #1043

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bendichter commented Feb 19, 2026

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bendichter changed the title ~~Support NeuroConv 0.9.1~~ Support NeuroConv 0.9.2 Feb 19, 2026

Support NeuroConv 0.9.3

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bendichter changed the title ~~Support NeuroConv 0.9.2~~ Support NeuroConv 0.9.3 Feb 20, 2026

bendichter and others added 5 commits February 20, 2026 11:47

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Simplify number coercion to a single float field

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Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Add WhiteMatterRecordingInterface to supported interfaces

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Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

bendichter mentioned this pull request Feb 20, 2026

Add WhiteMatterRecordingInterface #1060

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bendichter and others added 6 commits February 20, 2026 14:49

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Merge pull request #1060 from NeurodataWithoutBorders/add-whitematter…

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…-recording-interface Add WhiteMatterRecordingInterface

Add Plexon2RecordingInterface to supported interfaces

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Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

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Merge pull request #1061 from NeurodataWithoutBorders/add-plexon2-rec…

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…ording-interface Add Plexon2RecordingInterface

bendichter and others added 4 commits February 20, 2026 18:50

Restore file-path and directory-path format types in schemas

0590c10

Regenerate schemas to preserve pydantic's DirectoryPath and FilePath format types instead of resolving them all to generic "path". Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

[pre-commit.ci] auto fixes from pre-commit.com hooks

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Gitignore auto-generated storybook schema files

a02494b

These files are generated by `python generateInterfaceSchema.py` and don't need to be tracked. This eliminates noisy diffs across 40+ JSON files on every neuroconv version bump. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Merge pull request #1062 from NeurodataWithoutBorders/fix-schema-form…

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…at-types Restore file-path and directory-path format types in schemas

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Update workflows to use macos-15-intel

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Keep numcodecs env comment

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Fix trailing comma in supported_interfaces.json

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The trailing comma after CellExplorerRecordingInterface caused JSON parse failures, breaking all DevTests, LiveServices, ExampleDataTests, and E2ELiveServices CI jobs. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Retrigger CI after clearing cache space

ea7c00f

Deleted ~5GB of stale/duplicate caches to make room for the macos-15-intel ephys cache that has never been successfully saved. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

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bendichter merged commit b3fba6d into main Mar 4, 2026
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bendichter deleted the support-neuroconv-latest branch March 4, 2026 16:01

bendichter mentioned this pull request Mar 4, 2026

Make tutorial data generation faster #1063

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This was referenced Mar 6, 2026

KeyError: "dandi-staging" when publishing to staging directory #1039

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[Feature]: Support NeuroConv versions 0.6.0 through latest 0.6.7 #956

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Support NeuroConv 0.9.3#1056

Support NeuroConv 0.9.3#1056
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Key Changes

Backend (manage_neuroconv.py)

Frontend

Environment / CI

E2E Tests

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