🚀 Enhancement

• Added HEDVersion to dataset description #232 (@CodyCBakerPhD)
• Replaced pytest/doctest with Sybil to add hidden assertions verifying tutorial outputs #227 (@asmacdo @CodyCBakerPhD)
• Updated writing of channels TSV file #225 (@CodyCBakerPhD)
• Updated writing of probes TSV file #220 (@CodyCBakerPhD)

🐛 Bug Fix

• Fixed confusing labels in assert_subdirectory_structure error messages #228 (@asmacdo @CodyCBakerPhD)
• Updated writing of electrode TSV file #221 (@CodyCBakerPhD)
• [pre-commit.ci] pre-commit autoupdate #223 (@pre-commit-ci[bot])
• Fixed some test markers and imports based on latest conda-forge tests #219 (@CodyCBakerPhD)

⚠️ Pushed to main

• Fix typo in CHANGELOG.md (@CodyCBakerPhD)

🏠 Internal

• Restored intel runners #233 (@CodyCBakerPhD)
• Config mypy #229 (@candleindark @CodyCBakerPhD)

📝 Documentation

• Updated DOI badge link in README #230 (@CodyCBakerPhD)
• Added CITATION.cff to repository (to be used for all formal citations) #224 (@asmacdo)

Authors: 4

• @pre-commit-ci[bot]
• Austin Macdonald (@asmacdo)
• Cody Baker (@CodyCBakerPhD)
• Isaac To (@candleindark)

Release Notes

Added and integrated a configuration model (#164)

This release incudes big changes to how arguments are passed in the nwb2bids API: the RunConfig object.

This class is a Pydantic model which encapsulates all previous configuration settings, such as the output BIDS directory and the additional metadata file path. This class is also now passed at time of initialization for all Converter classes and prior to calling the convert_nwb_dataset helper function. This reduces any confusion about which steps of the workflow take which arguments, and allows all internal actions to refer to the common location instead of having to manage passing values back-and-forth. It also has the added benefit of simplifying any future additions to configuration options, such as sanitization parameters.

CLI users are unaffected by these changes, aside from gaining a few new arguments - check them out with

nwb2bids convert --help

🚀 Enhancement

• Enhance error notifications #193 (@CodyCBakerPhD @pre-commit-ci[bot] [email protected])
• Added and integrated a configuration model #164 (@CodyCBakerPhD @candleindark @pre-commit-ci[bot])

🐛 Bug Fix

• Added automatic notification dump #216 ([email protected] @CodyCBakerPhD)
• Aggregated unique values across participant rows #206 (@CodyCBakerPhD @pre-commit-ci[bot])
• Skipped indexed columns; simplified skipping of timeseries #205 (@CodyCBakerPhD)
• Added column metadata to sidecar files #203 (@CodyCBakerPhD)
• Added tutorials to documentation #173 (@CodyCBakerPhD @pre-commit-ci[bot] [email protected] @asmacdo)
• Fixed broken symlinking of source NWB file #207 (@asmacdo @CodyCBakerPhD)
• Restrict sphinx version to below 9.0.0 #201 (@CodyCBakerPhD)
• Fixed regression when bids_directory does not exist, automatically create it #183 (@asmacdo @CodyCBakerPhD)
• [pre-commit.ci] pre-commit autoupdate #200 (@pre-commit-ci[bot])
• Fix notification targets and add manual dispatch to daily tests #196 (@CodyCBakerPhD)
• Corrected the labeling notification to proper BIDS #176 (@CodyCBakerPhD @pre-commit-ci[bot] [email protected])
• Added GeneratedBy to dataset_description.json #170 (@asmacdo @CodyCBakerPhD)
• [pre-commit.ci] pre-commit autoupdate #184 (@pre-commit-ci[bot])
• Added support for operating on DataLad datasets #165 (@CodyCBakerPhD @pre-commit-ci[bot] [email protected] @github-actions[bot])
• Revise config model #175 (@candleindark)
• Automatic release #157 (@github-actions[bot] @CodyCBakerPhD)
• Testing auto release (again) #156 (@CodyCBakerPhD)

🏠 Internal

• Completely remove macOS-13 from all workflows and split daily workflows into remote vs. non-remote #194 (@CodyCBakerPhD)
• Reduced CodeCov spam #161 (@CodyCBakerPhD)
• Automatic release #155 (@github-actions[bot] @CodyCBakerPhD)

📝 Documentation

• Added container usage instructions #209 (@asmacdo @CodyCBakerPhD)
• Improve README badge names #195 (@CodyCBakerPhD)
• Add documentation link/badge to README #186 (@asmacdo)
• doc: clarify NWB_PATHS are space separated #182 (@asmacdo)
• Small CHANGELOG fixes #166 (@CodyCBakerPhD)

🧪 Tests

• Skip two DataLad tests in Windows CI #197 (@CodyCBakerPhD @yarikoptic)

🔩 Dependency Updates

• [pre-commit.ci] pre-commit autoupdate #204 (@pre-commit-ci[bot])
• [pre-commit.ci] pre-commit autoupdate #192 (@pre-commit-ci[bot] @CodyCBakerPhD)
• [pre-commit.ci] pre-commit autoupdate #174 (@pre-commit-ci[bot])
• [pre-commit.ci] pre-commit autoupdate #169 (@pre-commit-ci[bot])

Authors: 7

• @github-actions[bot]
• @pre-commit-ci[bot]
• Austin Macdonald (@asmacdo)
• Cody Baker (@CodyCBakerPhD)
• CodyCBakerPhD ([email protected])
• Isaac To (@candleindark)
• Yaroslav Halchenko (@yarikoptic)

🚀 Enhancement

• Always include session entity, even with only one subject #148 (@asmacdo)

🐛 Bug Fix

• Remove list of required status checks #159 (@candleindark)
• Provide list of required status checks to auto #158 (@candleindark @CodyCBakerPhD)
• Testing auto release #152 (@CodyCBakerPhD)
• Resolved protected branch problem in execution of the "Release with Auto" GH workflow #151 (@candleindark)
• Add ability to read from raw dandiset metadata when invalid #107 (@CodyCBakerPhD)
• Upgraded to rich-click backend for CLI #121 (@CodyCBakerPhD)

⚠️ Pushed to main

• fix: hotfix failure point (@CodyCBakerPhD)

🏠 Internal

• Use two GitHub tokens in Release with Auto workflow #154 (@candleindark @CodyCBakerPhD)
• Improved and consolidated release and deploy workflow #138 (@candleindark)
• Provided fix for Setup Release Labels workflow #137 (@candleindark)
• Automated release and versioning with AUTO and hatch-vcs #114 (@candleindark @CodyCBakerPhD)
• Updated email notification conditions and body URL #135 (@CodyCBakerPhD)
• Set the default python version in a Hatch-managed environment to the project's lowest support Python version #117 (@candleindark @CodyCBakerPhD)

📝 Documentation

• Document how to install and run tests locally #144 (@asmacdo @CodyCBakerPhD)
• Moved repo files under .github #143 (@CodyCBakerPhD)
• Added contributing file #142 (@asmacdo @pre-commit-ci[bot] @CodyCBakerPhD)
• Filled in docs #139 (@CodyCBakerPhD)
• Fixed RTD build #131 (@asmacdo @pre-commit-ci[bot] @CodyCBakerPhD)
• Added logo for dark theme #127 (@asmacdo @pre-commit-ci[bot])
• Removed project title from README #125 (@CodyCBakerPhD)
• Updated logo image source in README.md #120 (@CodyCBakerPhD)

🧪 Tests

• Add daily tests and notifications #110 (@CodyCBakerPhD)

🔩 Dependency Updates

• [pre-commit.ci] pre-commit autoupdate #146 (@pre-commit-ci[bot])
• Added macos-15-intel runner; deprecate macos-13; removed temporary pin on h5py #145 (@CodyCBakerPhD)
• [pre-commit.ci] pre-commit autoupdate #134 (@pre-commit-ci[bot] @CodyCBakerPhD)
• Blacklisted h5py version dependency for macOS platform #136 (@CodyCBakerPhD)
• [pre-commit.ci] pre-commit autoupdate #122 (@pre-commit-ci[bot])

Authors: 4

• @pre-commit-ci[bot]
• Austin Macdonald (@asmacdo)
• Cody Baker (@CodyCBakerPhD)
• Isaac To (@candleindark)

v0.5.0

Features

Added a notification system via the return of nwb2bids.convert_nwb_dataset and attached as the .messages attribute to all converter objects.

Improvements

Began filtering benign PyNWB warnings during read operations.

Documentation

Preliminary documentation is now available at nwb2bids.readthedocs.io.

v0.4.0

Added a .from_remote_dandiset instantiation method for the DatasetConverter class. This requires installing the pip install nwb2bids[dandi] extra dependencies.

v0.3.0

Deprecations

The CLI call nwb2bids reposit and API function nwb2bids.reposit have been removed - please use nwb2bids convert and nwb2bids.convert_nwb_dataset instead.

The API instantiation method .from_nwb_directory has been standardized as .from_nwb_paths and now takes an iterable of either file or directory paths.

Features

The CLI now accepts a list of space-separated NWB file paths as input, enabling more robust wildcard syntax or xargs usage.
For example:

• nwb2bids convert file1.nwb file2.nwb
• nwb2bids convert file*.nwb
• find -iname "file*.nwb" | xargs nwb2bids convert

Added an API argument nwb_paths: list[str | pathlib.Path] to all relevant conversion functions.

Improvements

The BIDS directory arguments to the CLI (--bids-directory/-o) and API (bids_directory) are now optional, with the default case being the current working directory (which must be either empty or BIDS-compatible).

The default of all file_mode arguments is now the string "auto" instead of None.

Fixes

Ensured removal of any temporary directory created by BaseConverter._handle_file_mode(). @candleindark PR #44

Documentation

Updated README to accurately reflect CLI call syntax.

v0.2.0

Deprecations

The function nwb2bids.reposit has been soft deprecated - please use nwb2bids.convert_nwb_dataset instead.

Features

Added events table support.

Added ability to specify additional metadata to write into the BIDS dataset.

Added new object-oriented API, complete with Pydantic model validation, has been added in the form of nwb2bids.DatasetConverter, nwb2bids.SessionConverter, and the nwb2bids.bids_models submodule.

Improvements

Refactored source code to modern Python packaging standards.

Fixes

Debugged ecephys structure against BEP032 BIDS schema current to 6/26/2025.