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@tsalo tsalo released this 06 Oct 19:51
· 262 commits to main since this release
0.0.10
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Release Notes

The 0.0.10 release includes a number of bug fixes and improvements. The two biggest changes are (1) support for fetching and using NeuroQuery's database, and (2) a reorganization of how Neurosynth's database is fetched and converted. Both databases now use a shared format, which separates coordinates, metadata, and features into different files with a semi-standardized naming structure. The fetching and conversion functions also now support accessing multiple vocabularies provided by these databases.

🔧 Breaking changes

  • The fetching functions for the Neurosynth and NeuroQuery databases now have a data_dir parameter, instead of a path parameter.
  • The Neurosynth and NeuroQuery databases are now in a very different format, so the fetching and conversion functions operate quite differently.
  • The low_memory parameter employed in many NiMARE classes and functions has been replaced with memory_limit.

✨ Enhancements

  • Add new methods to fetch and convert the NeuroQuery database.
  • Support the new format for the Neurosynth database.
  • A new decoding method for regions of interest taken from Neurosynth: ROIAssociationDecoder.
  • Custom __repr__ methods in many NiMARE classes, so now printing the object will show relevant information.
  • Reduce memory usage in CBMA Estimators.

🐛 Bug fixes

  • Extract relevant metadata in kernel transformers for Dataset-based transform calls.
  • Reference selected features instead of initial features in CorrelationDecoder.
  • Separate IJK calculation from coordinate space conversion.

Changes since last stable release

  • [TST] Test minimum versions of dependencies (#567) @tsalo
  • [FIX] Add pytest to docs dependencies (#572) @tsalo
  • [ENH, DOC] Document and use data directory approach in fetching functions (#570) @tsalo
  • [TST] Reorganize tests for speed (#571) @tsalo
  • [ENH] Add NeuroQuery 6308 vocab to resources (#568) @tsalo
  • [DOC] Improve documentation of decoders (#506) @JulioAPeraza
  • [DOC] Fill out CBMA docstrings (#564) @tsalo
  • [REF] Reduce memory in CBMA Estimators (#562) @tsalo
  • [FIX] Drop NQ tfidf features from manifest (#561) @tsalo
  • [FIX] Separate IJK calculation from coordinate space conversion (#556) @tsalo
  • [FIX] Reference selected features instead of initial features in CorrelationDecoder (#560) @tsalo
  • [DOC] Replace map and threshold for MACM example (#558) @tsalo
  • [FIX, DOC] Use appropriate structure in Neurosynth download example (#554) @tsalo
  • [DOC] Add admonition to about.rst linking to new site (#552) @tsalo
  • [DOC] Update docstrings (#551) @tsalo
  • [ENH] Support new format for Neurosynth and NeuroQuery data (#535) @tsalo
  • [DOC] Update citation for Enge et al. (2021) (#549) @alexenge
  • [FIX] Use resample=True in IBMA examples (#546) @tsalo
  • [FIX] Extract relevant metadata in kernel transformers for Dataset-based transform calls (#548) @tsalo
  • [DOC] Update ecosystem figure and documentation (#545) @tsalo
  • [ENH] Do not apply IBMA methods to voxels with zeros or NaNs (#544) @tsalo
  • [REF] Remove unused dependencies and unimplemented workflow (#541) @tsalo
  • [DOC] Change napoleon settings (#540) @tsalo
  • [ENH] Add ROI association decoder (#536) @tsalo
  • [ENH] Add custom __repr__ methods (#538) @tsalo
  • [FIX] Update CircleCI config to fix recent bug (#537) @tsalo
  • [ENH] Replace low_memory with memory_limit and reduce memory bottlenecks (#520) @tsalo

Contributors

tsalo, JulioAPeraza, and alexenge
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