v0.4.16

v0.4.16

Improvements

• Allow NCBI taxonomy references for Subject.species. PR #290
• Added PyNWB v2.1.0 specific file generation functions to the testing submodule, and altered the tests for ImageSeries to use these pre-existing files when available. Also included an automated workflow to push the generated files to a DANDI-staging server for public access. PR #288

Fixes

• Fixed relative path detection for cross-platform strings in check_image_series_external_file_relative PR #288

v0.4.14

v0.4.14

Fixes

• Fixed an error with attribute retrieval specific to the cell_id of the IntracellularElectrode neurodata type that occured with respect to older versions of PyNWB. PR #264

v0.4.13

v0.4.13

DANDI Configuration

• check_subject_sex, check_subject_species, check_subject_age, check_subject_proper_age_range are now elevated to CRITICAL importance when using the "DANDI" configuration. Therefore, these are now required for passing dandi validate.

Improvements

• Enhanced human-readability of the return message from check_experimenter_form. PR #254
• Extended check for Subject.age field with estimated age range using '/' separator. PR #247
• Allowed network-dependent tests to be skipped by specifying the NWBI_SKIP_NETWORK_TESTS environment variable. PR #261

New Checks

• Added check for existence of IntracellularElectrode.cell_id PR #256
• Added check that bounds of age range for Subject.age using the '/' separator are properly increasing. PR #247
• Added check for existence of IntracellularElectrode.cell_id PR #256
• Added check for shape consistency between reference_images and the x, y, (z) dimensions of the image_mask of PlaneSegmentationobjects. PR #257

Fixes

• Fixed the folder-wide identifier pre-check for inspect_all to read NWB files with extensions. PR #262

v0.4.12

v0.4.12

Re-release of v0.4.10 for the conda-forge feedstock.

v0.4.10

v0.4.10

Improvements

• Added a utillity function for retrieving the version of a package in a form that allows easy comparison.
• Added a utility function for robust S3 retrieval (retries with exponential backoff) and implemented it within the core inspection functions in an attempt to resolve the ongoing S3 curl request failures.
• Allowed importance threshold to be specified as a string rather than an instance of the enum class.
• Added negative job slicing to all n_jobs arguments.

New Checks

• For objects new in NWB 2.5 called 'Images' - for the field named "order_of_images", which specifies the order of the images within the Images object, we check that the "order_of_images" contains references to all of the images only once that are in the Images object
  "order_of_images" contains no other images (e.g., from another object).
• Ensure that the form of each experimenter in the NWBFile metadata is of the form DANDI expects (Last, First Middle).
• Special check for unique identifiers over a folder path given to inspect_all.

Bug Fixes

• Critical fix for the config feature which resulted in secondary fields of messages failing to be parsed.

v0.4.5

v0.4.5

Bug fix

check_compass_direction_unit now correctly applies to CompassDirection objects.

v0.4.4

v0.4.4

Improvements

• Makes DANDI tests lazy.

v0.4.3

v0.4.3

Improvements

• Makes DANDI a lazy import for the automated S3 resolution feature.

New Checks

• If a SpatialSeries inside a CompassDirection object have proper units (radians or degrees).

Bug Fixes

• When an NWBFile fails io.read(), preventing the report from being generated.

v0.4.0

v0.4.0

Improvements

• Introduces the automated streaming feature to the CLI and inspect_all whenever the path input is a DANDISet link or ID.
• Allows the CLI to save a report even when there are no messages.

New Checks

• If external_files for ImageSeries are relative paths, not absolute - it also allows the CLI to save a report even when there are no messages.
• If a serialized dictionary is within a string value of a DynamicTable.
• If spike times fall within observed intervals on the Units table.
• If spatial series have the correct dimensionality.
• If optical series have wavelengths set in nanometers, a requirement of the NWB Schema.
• If file exists or url is valid for all items in the external_file field of ImageSeries.

Check Changes

• Elevated the latin binomial species name check to BEST_PRACTICE_VIOLATION level.
• Excludes Units tables and the ElectrodeTable of an NWBFile from the default operation of checking for single row tables.

Bug Fixes

• For particular children of TimeSeries that may have resolution set to None.
• When reading byte strings for various checks that assert particular practices on the contents of the strings.

v0.3.9

v0.3.9

Attempting to setup a conda-forge feedstock for the NWBInspector.