v1.2.0

What's Changed

• updates for empty by @stevevanhooser in #659
• Update prepare-release-modular.yml by @stevevanhooser in #667
• updates to EMPTY by @stevevanhooser in #658
• Update NDI Cloud API clients for soft delete and undelete by @google-labs-jules[bot] in #668
• Pass on new updates by @stevevanhooser in #669
• Update epochprobemap_daqsystem_vhlab for stimulus triggers log by @google-labs-jules[bot] in #670
• Add vhtaste_sync DAQ system by @google-labs-jules[bot] in #671
• Fix: Enable reading rising events in stimulator probe by @google-labs-jules[bot] in #672
• Haley nansen tutorial by @jesshaley in #675
• Tutorials updates by @jesshaley in #674
• Add EDAM ontology lookup for 'format' prefix by @jesshaley in #677
• Add NDI Cloud Developer Manual documentation by @stevevanhooser in #678
• Add ndi.fun.plot.stimulusTimeseries wrapper by @google-labs-jules[bot] in #679
• Add commonTriggersOverlappingEpochs syncrule by @google-labs-jules[bot] in #673
• Return stimulus data and time data from ndi.fun.plot.stimulusTimeseries by @google-labs-jules[bot] in #680
• Add guide for writing new stimulus reader classes by @google-labs-jules[bot] in #662
• Fix cloud test cleanup and pagination by @google-labs-jules[bot] in #682
• Increase test pauses to improve stability by @google-labs-jules[bot] in #681
• fixing case where one epoch maps to multiple epochs on another device by @stevewds in #683
• Update cloud sync documentation for SyncOptions defaults by @google-labs-jules[bot] in #684
• Support linked sessions in database_existbinarydoc and fix dataset_erase bug by @jesshaley in #685
• Add downloadGenericFiles function to ndi.cloud by @jesshaley in #676
• Fix ndi.ontology.EMPTY lookup and parsing by @jesshaley in #686
• Update README.md by @stevevanhooser in #687
• fix jules bug by @stevevanhooser in #688
• Add filter and pyraview NDI documents by @google-labs-jules[bot] in #689
• Enhancement/manual by @stevevanhooser in #691
• Update RRID lookup to return species by @jesshaley in #690
• Update syncgraph.m by @stevevanhooser in #692
• Ontology table row add dependency output by @jesshaley in #694
• docs: refactor neuron extracellular snippet to bypass table conversion by @google-labs-jules[bot] in #695
• Add epochNodeName function and tests by @google-labs-jules[bot] in #696
• Enhancement/pyraviewer by @stevevanhooser in #697
• Fix file skipping for large files in zipForUpload by @google-labs-jules[bot] in #700
• Bugs/intan ingestion by @stevevanhooser in #698
• feat(probe): add ndi.fun.probe.export_binary and tests by @google-labs-jules[bot] in #701
• feat: implement randomPulses sync rule and move syncRandomTriggers by @google-labs-jules[bot] in #702
• Feature/sync random triggers by @stevevanhooser in #703
• Add initial symmetry testing artifact generator and instructions by @google-labs-jules[bot] in #704
• Silence missing artifact warnings in NDI symmetry testing by @google-labs-jules[bot] in #705
• Add CI workflow for NDI symmetry tests by @stevevanhooser in #706
• Add dataset symmetry tests for MATLAB and Python artifact validation by @stevevanhooser in #707
• Add symmetry tests for blank sessions across lab configurations by @stevevanhooser in #708
• Export JSON documents for each session in dataset artifacts by @stevevanhooser in #709
• Make compareSessionSummary order-independent for cell arrays by @stevewds in #710
• Add symmetry test suite for session ingestion artifacts by @stevevanhooser in #711
• Add symmetry tests for downloadIngested dataset functionality by @stevevanhooser in #712
• Make session summary comparison order-independent for struct arrays by @stevevanhooser in #713
• Make dataset directory detection dynamic in artifact tests by @stevevanhooser in #714
• Remove macOS resource fork files from extracted artifacts by @stevevanhooser in #715
• Add dataset-level summary and comparison utilities by @stevevanhooser in #716
• Handle EDAM sub-ontology prefixes in OBO ID lookups by @stevevanhooser in #717
• Replace isequal with isequaln for NaN-aware comparisons by @stevevanhooser in #718
• added sync that allows for some missing pulses by @stevewds in #719
• Add logging for trigger count mismatches in sync rule by @stevevanhooser in #720
• Add find_calculator_subclasses static method to discover calculator implementations by @stevevanhooser in #721
• Fix calcbuild crash when documentation_structure.mat is missing by @stevevanhooser in #723
• Skip empty template placeholder dependencies in document resolution by @stevevanhooser in #725
• Updates to tableDocMaker, dependency_value_n, dateUpdated by @jesshaley in #724
• Errors with openbinarydoc and zipUpload for linked session by @jesshaley in #726
• Add testLogin function to validate NDI Cloud authentication by @stevevanhooser in #727
• Replace websave with ndi.cloud.api.files.getFile for cloud downloads by @stevevanhooser in #728
• Clarify file overwrite behavior in getFile documentation by @stevevanhooser in #729
• Add integration test for reading ingested cloud datasets by @stevevanhooser in #730
• Update requirements.txt by @stevewds in #732
• Add vhneuropixels DAQ system configuration by @stevevanhooser in #734
• Add analog event detection support to MFDAQ reader by @stevevanhooser in #735
• Add Neuropixels GLX stimulus reader for Nielsen visual stimulus by @stevevanhooser in #737
• Babu data import by @jesshaley in #733
• Refactor session copying and add linked-to-ingested conversion by @stevevanhooser in #736
• Kristina neuropixels by @stevevanhooser in #738
• Add vhlab Neuropixels GLX support with AJBPod stimulus reader by @stevevanhooser in #739
• Add comprehensive documentation to graphical_edit_calculator method by @stevevanhooser in #740
• Fix docfiletext argument in graphical_edit_calculator by @stevevanhooser in #741
• Docs: drop stale tutorial pointer; document specific_test_inds and typed I/O for generate_mock_docs by @stevevanhooser in #742
• Add document class counts API endpoint support by @stevevanhooser in #743
• Test /ndiquery scope-by-dataset-IDs form by @stevevanhooser in #744
• Add bulkFetch API for synchronous multi-document retrieval by @stevevanhooser in #745
• Replace websave with curl-based downloads to prevent corruption by @stevevanhooser in #746
• Default uploads to curl with pinned headers by @stevevanhooser in #747
• update babu-import to test by @stevevanhooser in #749
• Remove isRaw field from file listing API response by @stevevanhooser in #751
• Merge pull request #749 from VH-Lab/main by @stevevanhooser in #750
• Split test suite into cloud and non-cloud workflows by @stevevanhooser in #752
• Extract ontology system into separate ndi-ontology-matlab package by @stevevanhooser in #753
• Add retry logic and convergence delay to dataset deletion in tests by @stevevanhooser in #754
• Add bulk upload job polling and status tracking APIs by @stevevanhooser in #756
• Add polling functions for dataset publication status by @stevevanhooser in #757
• Improve device detection for epoch probe mapping by checking for .rhd files by @stevevanhooser in #760
• Add ndi.preferences singleton for managing user preferences by @stevevanhooser in #758
• Improve NDI Cloud authentication validation and organization handling by @stevevanhooser in #761
• Improve cloud login testing with token validation and UI login by @stevevanhooser in #762
• Improve documentation for ndi.session.dir constructor by @stevevanhooser in #765
• Update dir.m documentation by @jesshaley in #764
• Add MATLAB BYOL license management and hello-matlab pipeline support by @stevevanhooser in #766
• Add verbose logging to ndi.cloud.testLogin for debugging by @stevevanhooser in #763
• Refactor ComputeTest: separate pipeline completion from abort testing by @stevevanhooser in #769
• Make NDI_CLOUD_TEST_USER_HAS_MATLAB_LICENSE a required configuration by @stevevanhooser in #770
• Parallelize cloud API tests across multiple CI runners by @stevevanhooser in #771
• Add RHD series file navigators for prefix-grouped recordings by @stevevanhooser in #772
• Add cross-platform preferences and cloud profile persistence by @stevevanhooser in #773
• Improve API error handling with robust formatApiError utility by @stevevanhooser in #791
• Refactor stimulus on/off pairing to handle clipped events by @stevevanhooser in #790
• Fix sync index corruption when document or binary uploads fail by @stevevanhooser in #806
• Tolerate heterogeneous file entries in ListFiles.execute (#807) by @jesshaley in #808
• Skip all hidden files and directories in epoch navigator by @stevevanhooser in #810
• Don't treat HTTP 504 as success in bulkDeleteDocuments by @jesshaley in #811
• Improve NDI_CLOUD_RUN_HELLO_MATLAB environment variable handling by @stevevanhooser in #818
• Filter out macOS AppleDouble shadow files from epochprobemap matching by @stevevanhooser in #819
• Add Kilosort curated-output import pipeline for probes by @stevevanhooser in #814
• Add image-series (frame-based) DAQ system support to NDI by @stevevanhooser in #824
• Add vhPrairie2p file navigator (epochs from BASE/BASE-NNN directory pairs) by @stevevanhooser in #825
• Audit remediation (cloud/security/perf/symmetry) + review refinements by @stevevanhooser in #828
• Audit remediation: cloud API/sync, security, Java validator, perf, symmetry infra by @audriB in #827
• Authenticate GitHub API requests in CI workflows to avoid rate limiting by @stevevanhooser in #830
• Add ensemble document type and sparse array I/O utilities by @stevevanhooser in #833
• Add blech_clust HDF5 export function for ensemble spike data by @stevevanhooser in #832
• Add NDI Navigator GUI with collapsible pane architecture by @stevevanhooser in #837
• Expand pyraview probe support beyond n-trode probes by @stevevanhooser in #838
• Apply NDI Cloud design system to navigator UI by @stevevanhooser in #839
• Dock progress bars into navigator pane instead of standalone window by @stevevanhooser in #840
• Add KIASORT spike-sorting integration and electrode-geometry tools by @stevevanhooser in #834
• Add Katz Lab blech_clust HDF5 exporter GUI app by @stevevanhooser in #842
• cedspike2: read 64-bit son64/.smrx files via NDR (sonpipe dispatch) by @stevevanhooser in #843
• Add lab-specific sync rules to ndi.setup.lab by @stevevanhooser in #844
• Remove redundant MATLAB path restoration steps from CI workflows by @stevevanhooser in #845
• Add VHLab spike sorter wrapper app to NDI GUI by @stevevanhooser in #841
• Restrict badge commit workflow to pull requests only by @stevevanhooser in #846
• vhlab PrairieView imaging: DAQ system, image probe timeseries + sub-frame timing, SelectC/SelectZ by @stevevanhooser in #847
• Add UCLA and NeuroNexus probe geometry definitions and improve library by @stevevanhooser in #849
• Add session info window and ingestion status badges to navigator by @stevevanhooser in #848
• Add object-type marker system for quick session/dataset detection by @stevevanhooser in #852
• Replace DAQ tree view with table layout in session info panel by @stevevanhooser in #853
• Add NDI navigator shortcut and fix ingestion status handling by @stevevanhooser in #850
• Fix spike array dimension ordering for blech_clust HDF5 compatibility by @stevevanhooser in #856
• Add wide mean waveform recalculation from raw binary for Kilosort by @stevevanhooser in #857
• Add session management and filter improvements to GUI by @stevevanhooser in #854
• Add organization name and upload permission fields to user API by @stevevanhooser in #858
• Add NDI Cloud dataset synchronization UI to datasets pane by @stevevanhooser in #859
• Make dataset cloud status on-demand (Check Cloud status menu item) by @stevevanhooser in #860
• Add cache-clearing: session menu item, ndi.fun.clearAllCaches, and a broom button by @stevevanhooser in #861
• Fix vhajbpod_np epoch matching: one epoch per Epoch_Set, per-set NI-DAQ triggers by @stevevanhooser in #863
• Kilosort import: prompt for raw file and high-pass filter when recalculating spike shapes by @stevevanhooser in #864
• Add stimulus parameter analysis UI to stimulus decoder by @stevevanhooser in #865
• Add Pipeline Editor GUI app wrapper by @stevevanhooser in #866
• Add streaming mean waveform recalculation for Kilosort imports by @stevevanhooser in #867
• Fix curl library path issues on Linux/macOS after MATLAB upgrades by @stevevanhooser in #868
• Fix Windows SQLite-locked teardown: close all connections before rmdir (#870) by @stevevanhooser in #874
• Skip samplerate query for eventmarktext channels in mfdaq reader by @stevevanhooser in #875
• Fix RayoLab stimulus metadata ingestion (# wildcard in metadata regexp) by @stevevanhooser in #876
• Update GMC_Sorter export to support Version 4 multi-shank API by @stevevanhooser in #877
• Add forceUpdate option to lab and rayolab setup functions by @stevevanhooser in #880
• Make probe folder names platform-independent by sanitizing illegal characters by @stevevanhooser in #881
• Give calculator self-tests a way to verify their results by @stevevanhooser in #882
• Stop mock elements from colliding on a reused reference number by @stevevanhooser in #883
• Seed the mock trial-to-trial variability by @stevevanhooser in #884
• Draw the mock trial-to-trial noise fresh on every run by @stevevanhooser in #885
• Add a calculator document type by @stevevanhooser in #888
• Declare the calculator type on simple_calc and tuningcurve_calc, with versioned schemas by @stevevanhooser in #889
• Regenerate the stored expectations at class_version 2, and fix run()'s return value by @stevevanhooser in #890
• Validate document-supplied class names by lineage; stop cancelling the prod cloud suite mid-run by @stevevanhooser in #891
• Cloud security and correctness fixes, plus the MATLAB symmetry battery (supersedes #886) by @stevevanhooser in #892
• NDI-matlab — security/correctness proposals + symmetry counterparts (14 commits), JAR-free by @audriB in #886
• Read analyzer trialno as a list of stimulus sequence positions by @stevevanhooser in #893
• Supply the cloud file handler when adding documents, not just when opening them by @stevevanhooser in #894
• Fix duplicate document deletion and add required files to tests by @stevevanhooser in #895
• Fix three ndi_common JSON defects DID's validator now rejects by @stevevanhooser in #896
• Fail loudly when the DID database has branches but not 'a' by @stevevanhooser in #899
• Fix syncrule document resurrection in syncgraph updates by @stevevanhooser in #900
• Fail the whatVaries divergence audit, and retire the entry it caught by @stevevanhooser in #901
• Compare stimulus parameters with isequaln, so an all-NaN one is constant by @stevevanhooser in #902
• Document the blech_clust spike_array axis order for both readers by @stevevanhooser in #904
• Make a missing symmetry artifact an assumption failure, not a silent pass by @stevevanhooser in #903
• Accumulate the upper x-limit in plot_extracellular_spikeshapes, not the running minimum by @stevevanhooser in #905
• Add the ndi.fun.parseText symmetry battery by @stevevanhooser in #906
• Add the VHSB round-trip symmetry battery by @stevevanhooser in #908
• Add the shrinking-interval VHSB case, now that vhlab-toolbox-matlab#145 is fixed by @stevevanhooser in #909
• Fix regex syntax error in babu PT3602 parser rule by @stevevanhooser in #910
• Add the statusIcon badge cross-language battery (MATLAB side) by @stevevanhooser in #911
• Add the elementClass cross-language battery (tests only) by @stevevanhooser in #913
• Assign cloudDatasetId before uploadDataset's ingestion refusal returns by @stevevanhooser in #915
• Track failed document downloads and exclude from sync index by @stevevanhooser in #917
• writeSyncIndex: atomic write, checked fopen, no leaked handles by @stevevanhooser in #919
• +cloud/profile: move preferences to ~/.ndi/ and let findIndex accept nickname/email/UID by @stevevanhooser in #921
• +common/PathConstants + +session/sessiontable: land preferences in ~/.ndi/ by @stevevanhooser in #923
• OldDatasetTest: explain why the corpus is copied before opening (parity note for ndi-python#99) by @stevevanhooser in #924
• +ndi/dataset: route database_closebinarydoc through the session that opened the binarydoc (#509) by @stevevanhooser in #925
• simple_calc_v2_schema: use Infinity, not Inf (invalid JSON) by @stevevanhooser in #926
• Symmetry battery for ndi.fun.ensemble.filter by @stevevanhooser in #927
• ensembleFilterCases: add sparse activity coverage by @stevevanhooser in #928
• Add spatial gene expression and gene list document schemas by @stevevanhooser in #887
• Add GMC_Sorter exporter for raw voltage spike sorting by @stevevanhooser in #851
• Add JRCLUST spike sorting pipeline integration by @stevevanhooser in #879
• Add JRCLUST spike sorting pipeline to NDI (export, run, curate, import, GUI) by @stevevanhooser in #930
• Fix invalid bare Inf in two ndi_common schema JSON files by @stevevanhooser in #931
• Move the GEF reader out of ndi.fun.doc.gene into NDR by @stevevanhooser in #929
• Add ndi.gui.app.GeneIngest: list, ingest and delete spatial transcriptomics datasets by @stevevanhooser in #932
• Add signed URL set API endpoints for cloud file access by @stevevanhooser in #934
• compute: thread organizationId through startSession + tests (#936) by @stevevanhooser in #937
• Signed URL set client in ndi.cloud.api.documents by @stevevanhooser in #939
• ProgressBarWindow: add silent (headless) mode by @stevevanhooser in #942
• Push CI badges to a dedicated badges branch by @stevevanhooser in #943
• Make ndi.document a subclass of did.document by @stevevanhooser in #940
• Fix #946: extract_docs_files drops files.series_info into the dataset it writes by @stevevanhooser in #947
• Fix main: a dataset copy of a populated file series is refused, not stored by @stevevanhooser in #951
• Two silent-failure fixes in the cloud document path by @stevevanhooser in #949
• Fix #945: stop destroying files.series_info after download, and test the round trip that found it by @stevevanhooser in #944
• Fix #912: pass the blank's stimulus id to vlt's control_stimid by @stevevanhooser in #954
• Replace fatalAssert* with assert* in cloud test suite (#935) by @stevevanhooser in #953
• Batch presign in download_file_from_cloud (DID #173 step 3) by @stevevanhooser in #955
• extract_docs_files: copy the series members, not just the manifest by @stevevanhooser in #957
• Reconstruct series ingest_locations on cloud download by @stevevanhooser in #959
• Drop dead isfile(destPath) short-circuit in download_file_from_cloud by @stevevanhooser in #960
• Upload file series members, not just the series manifest by @stevevanhooser in #961
• Fix #964: retire uploadToNDICloud and scanForUpload; newDataset delegates to uploadDataset by @stevevanhooser in #965
• Route downloadGenericFiles through batchSignedUrlLookup by @stevevanhooser in #963
• Lift the .gef/.h5ad ingestion path out of the GUI, and remember where a tile landed by @stevevanhooser in #933
• Read a series member's bytes back out of the cloud (#966) by @stevevanhooser in #967
• Reach the bulk-download all-documents branch, and cover it (#948) by @stevevanhooser in #970
• Insist the batch presign path is used, and say so when it is not (#968) by @stevevanhooser in #969
• Correct two class headers that #969 falsified by @stevevanhooser in #972
• Pin openMINDS_MATLAB to v0.11.0, fix renamed base class by @ehennestad in #973
• GEF Manager, an HDF5 table of contents, and one-based tile files by @stevevanhooser in #977
• GEF Manager: raise the open window for a session instead of duplicating it by @stevevanhooser in #985
• Offline test for a cloud-only series manifest (SyncFiles=false shape) (#986) by @stevevanhooser in #987
• Cloud companion: SyncFiles=false round-trip in FileSeriesRoundTripTest (#986) by @stevevanhooser in #988
• Retry once when the batch signer returns a partial map by @stevevanhooser in #992
• Clamp the ingested mfdaq reader's window to what the epoch has by @stevevanhooser in #994
• feat(cloud.api): file-tier control wrappers by @stevevanhooser in #990
• perf(dataset): add ingested session without a 2x temp-copy stage by @stevevanhooser in #998
• Refactor file listing API to support pagination by @stevevanhooser in #1002
• Make listFiles/listFilesAll keyset (cursor) based by @stevevanhooser in #1004
• largeFileListingScenario: assert getDataset.fileCount and fix numRequests reference by @stevevanhooser in #1006
• Upgrade openminds-metadata-models-for-matlab to 0.12.0 by @stevevanhooser in #1009
• Add ndi.cloud.api.feedback commands and ndi.unittest.cloud.feedbackTest by @stevevanhooser in #1023
• Fix cloud login: decode JWT payload with matlab.net.base64decode by @stevevanhooser in #1024
• NDI Cloud file CRC-32: lookupFiles, checksummed uploads, crc32 in file listings by @stevevanhooser in #1025
• Add ndi.cloud.api.files.waitForFileUpload; wait for upload processing in uploadSingleFile and FilesTest by @stevevanhooser in #1027
• Lightsheet pyramids: ingest from OME-Zarr or SmartSPIM, chunk materialization, cloud round trip, and napari viewing by @stevevanhooser in #979
• ProgressBarWindow: the bar fills its row (R2026a draws it 2.7 px tall) by @jesshaley in #1020
• Fix tuningcurve calculator dealing over a single stimulus property by @stevevanhooser in #1029
• Wait up to 60 s for each bulk document download chunk by @stevevanhooser in #1030
• Add ndi.cloud.api.admin organization and user commands by @stevevanhooser in #1031
• Make cloud upload/download batch sizes configurable via preferences by @stevevanhooser in #1033
• Find external programs automatically: install/find NDI-python's tools, ffmpeg and Rscript (ndi.python.install, ndi.fun.findExecutable) by @stevevanhooser in #1032
• Keep other NDI versions' preferences when saving NDI_Preferences.json by @stevevanhooser in #1036
• Support users in multiple NDI Cloud organizations by @stevevanhooser in #1037
• Add update check/install for git and toolbox installs, with an Update button in the navigator by @stevevanhooser in #1038
• Updater: leave untracked files alone; stop only for ones in the way by @stevevanhooser in #1039
• ndi_install: put stashed changes back after updating by @stevevanhooser in #1042
• Cloud CI: upload coverage of the cloud package to Codecov by @stevevanhooser in #1043
• CI: tests badge sums the no-cloud run and the Cloud CI shards by @stevevanhooser in #1044
• Report actual and expected values when a calculator self-test fails by @stevevanhooser in #1046

New Contributors

• @audriB made their first contribution in #827

Full Changelog: v1.1.2...v1.2.0