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CHANGELOG.md

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Upcoming

New Checks

  • Added check_rate_is_not_zero for ensuring non-zero rate value of TimeSeries that has more than one frame. #389

Fixes

  • Use cached extension namespaces when calling pynwb validate instead of just the core namespace. #425

v0.4.30

Fixes

  • Fixed issue in check_empty_string_for_optional_attribute where it would not skip optional non-str fields. #400

v0.4.29

  • Support for Python 3.7 has officially been dropped by the NWB Inspector. Please use Python 3.8 and above. #380

Fixes

  • check_time_interval_time_columns now only checks for start_time with is_ascending_series. #382

  • is_acending_series no longer asserts series to be strictly monotonic. #374

v0.4.28

Pending Deprecation (API)

  • To reduce ambiguity of the new intermediate workflow calls in the API, inspect_nwb will be deprecated in the next major release. It is replaced by either inspect_nwbfile (applied to a written file on disk) or inspect_nwbfile_object (an open object in memory). #364

New Checks

  • Added support for new options to subject.sex (XX or XO) conditional on the subject.species being either "C. elegens" or "Caenorhabditis elegens". #353

Improvements

  • Added an intermediate workflow to the main nwbinspector call pattern, named inspect_nwbfile_object. #364

v0.4.27

Fixes

  • Added a false positive skip condition to check_binary_columns when applied to special tables with pre-defined columns, such as the electrodes of Units. #349

v0.4.26

Fixes

  • Added a false positive skip condition to check_timestamps_match_first_dimension when applied to an ImageSeries that is using an external_file and therefore has an empty array set to data, but could have non-empty irregular timestamps for the video. PR #335

  • Fixed the skip condition for images checks that were incorrectly run when using PyNWB v2.0.0. PR #341

v0.4.25

Improvements

  • The version of the NWB Inspector can now be returned directly from the CLI via the --version flag. PR # 333

v0.4.24

Dependencies

  • Loosened upper bound of numpy version. PR # 330

v0.4.23

New Checks

  • Added check check_index_series_points_to_image to additionally about future deprecation of indexed_timeseries linked in IndexSeries. # 322

v0.4.22

Fixes

  • Add a special skip condition to check_timestamps_match_first_dimension when an IndexSeries uses an ImageSeries as a target. PR #321

v0.4.21

New Checks

  • Added check for unique ids for DynamicTables. PR #316

Fixes

  • Fix check_subject_proper_age_range to parse years. PR #314

  • Write a custom get_data_shape method that does not return maxshape, which fixes errors in parsing shape. PR #315

v0.4.20

Improvements

  • Added compression size consideration to check_image_series_size. PR #311

  • Added false positive skip condition for check_image_series_size for TwoPhotonSeries neurodata types. PR #301

Testing

  • Added downstream testing of DANDI to the per-PR suite as a requirement for merging. PR #306

Fixes

  • Fixed issue in run_checks following PR #303 that prevented iteration over certain check output types. PR #306

v0.4.19

Fixes

  • Fixed an issue with table checks that attempted to retrieve data from on-disk NWB files in a non-lazy manner. Also improved check_timestamps_match_first_dimension for TimeSeries objects, which similarly attempted to load unnecessary data into memory. PR #296 PR #307

v0.4.18

Hotfix

  • Fix to the assigned importance output of configured checks, which was reverting to pre-configuration values. PR #303

v0.4.17

Hotfix

  • Fix to skip certain tests if optional testing config path was not specified (mostly for conda-forge).

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 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

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

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