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CHANGELOG.md

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Upcoming

Fixes

  • Fixed the suggested rate in check_regular_timestamps to be in Hz #467

v0.4.35

Fixes

  • Extended check_session_start_time_future_date and check_session_start_time_old_date to be timezone optional as allowed by PyNWB > 2.6.0 versions. #452

Improvements

  • Exposed progress bar control to inspect_all and run_checks to allow compatibility with more generic visualizations of inspection progress related to the NWB GUIDED. #443
  • Added Python 3.12 support. #457

Testing

  • Pinned action runners to MacOS x64 architecture; removed other deprecated steps of setup and continuous integration testing. #450

v0.4.34

Fixes

  • Fixed --modules flag in nwbinspector command line interface to allow for import of additional modules in the command line. This was necessary to be able to register new customized checks to the NWB Inspector. #446

v0.4.33

Fixes

  • Add safer retrieval of subject_id for in vitro protein filtering. #433

v0.4.32

Fixes

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

Improvements

  • Added automatic suppression of certain subject related checks when inspecting files using the "dandi" configuration that have a subject_id that starts with the keyphrase "protein"; e.g., "proteinCaMPARI3" to indicate the in vitro subject of the experiment is a purified CaMPARI3 protein.

v0.4.31

New Checks

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

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 occurred 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