0.0.12rc2

This release candidate includes a number of changes. We have added a new FocusCounter diagnostic tool for characterizing results of coordinate-based meta-analyses, and have added cluster-level correction to the MKDAChi2 Estimator's Monte Carlo FWE correction method. We have also made some changes to the documentation formatting that should hopefully make the NiMARE documentation more informative and easier to read.

What's Changed

🛠 Breaking Changes

• Replace multiprocessing with joblib for parallelization and change n_cores default to 1 by @tsalo in #597
• Incorporate joblib into ALESubtraction and fix SCALE docstring by @tsalo in #641

🎉 Exciting New Features

• Add FocusCounter diagnostic tool by @tsalo in #649
• Support cluster-level Monte Carlo FWE correction in the MKDAChi2 Estimator by @tsalo in #650

🐛 Bug Fixes

• Retain updated Estimator in Corrector-generated MetaResults by @tsalo in #633
• Do not inherit IBMAEstimator's aggressive_mask from previous Datasets by @tsalo in #652

Other Changes

• Reduce SCALE memory usage by @tsalo in #632
• Improve memory management in MKDAChi2 Estimator by @tsalo in #638
• Remove Peaks2Maps-related tests by @tsalo in #643
• Disable MA map pre-generation in CorrelationDecoder by @tsalo in #637
• Switch testing from CircleCI to GitHub Actions by @tsalo in #642
• Override unusable methods and improve documentation by @tsalo in #645

Full Changelog: 0.0.11...0.0.12rc2

0.0.12rc1

This release candidate continues to optimize certain elements of NiMARE processing for its NeuroLibre preprint.

What's Changed

🛠 Breaking Changes

• Replace multiprocessing with joblib for parallelization and change n_cores default to 1 by @tsalo in #597

🐛 Bug Fixes

• Retain updated Estimator in Corrector-generated MetaResults by @tsalo in #633

Other Changes

• Reduce SCALE memory usage by @tsalo in #632
• Improve memory management in MKDAChi2 Estimator by @tsalo in #638

Full Changelog: 0.0.11...0.0.12rc1

0.0.11

This release continues fixes and improvements we've made for the NiMARE manuscript. Additionally, we are starting to dramatically refactor how NiMARE stores meta-analytic data, with the end goals of (1) synchronizing NiMARE data storage with the NIMADS standard, (2) internally representing data and results in a manner that is compatible with NeuroStore, and (3) implementing a meta-analysis model specification that can be employed with both NiMARE and Neurosynth 2.0.

What's Changed

🛠 Breaking Changes

• Replace Nilearn templates with ones stored in resources folder and unset maximum Nilearn version by @tsalo in #621
• Implement cluster mass-based cluster-level Monte Carlo correction for CBMA algorithms by @tsalo in #609
• Use scikit-learn for LDAModel by @tsalo in #607

🎉 Exciting New Features

• New diagnostics module, with post-meta-analysis Jackknife method by @tsalo in #592

👎 Deprecations

• Flag peaks2maps for removal in 0.0.13/0.1.0 by @tsalo in #616

🐛 Bug Fixes

• Only download group maps when creating dataset and raise error if no images are found for a contrast by @jdkent in #580
• Force maskers to be array images instead of proxy images by @tsalo in #588

Other Changes

• Add test steps and explicit support for Python 3.9 by @JulioAPeraza in #578
• Add major classes/functions to parent namespaces by @tsalo in #600
• Make non-user-facing utility functions semi-private and improve docs by @tsalo in #604
• Move files used by examples from tests to resources by @tsalo in #605
• Improve documentation of CBMA and add methods pages by @tsalo in #610
• Use tmpdir for memmap files instead of the NiMARE data directory by @tsalo in #599

Full Changelog: 0.0.10...0.0.11

0.0.11rc1

Release Notes

This release candidate includes certain enhancements and fixes necessary for the NiMARE software paper (https://github.com/NBCLab/nimare-paper).

Changes

• [REF] Use new function to run LDA commands (#587) @tsalo
• [FIX] Force maskers to be array images instead of proxy images (#588) @tsalo
• [FIX] only download group maps when creating dataset and raise error if no images are found for a contrast (#580) @jdkent
• [ENH] Add test steps and explicit support for Python 3.9 (#578) @JulioAPeraza

0.0.10

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

0.0.10rc2

Release Notes

This second release candidate for 0.0.10 includes a major overhaul of the Neurosynth fetching and conversion functions. The Neurosynth database now follows a very different file format, in order to match NeuroQuery's convention. We also have a new function to fetch NeuroQuery, and the Neurosynth conversion functions will work with NeuroQuery data as well.

Changes

• [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

0.0.10rc1

Release Notes

This release prepares for NeuroHackademy. The most relevant changes are the new ROIAssociationDecoder and the custom __repr__ methods.

Changes

• [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

0.0.9

Release Notes

This release primarily improves testing and documentation, but there are a few new features as well.
The new features include (1) a new "merge" method for Datasets, to combine two Datasets into a new one, (2) a new ImageTransformer class for generating new images from existing ones of different types, (3) a new "inspect" method for Correctors, to make it easier for users to see what kinds of multiple comparisons correction methods are available for a Corrector type and a specific MetaResult.

Special thanks to @alexenge for the new ALE subtraction and conjunction analysis example and to @JulioAPeraza for enhancing NiMARE's docstrings with "versionadded" and "versionchanged" directives!

Changes

• [TST, REF] Address pandas SettingWithCopyWarnings (#534) @tsalo
• [ENH] Accept multiple annotations files in Neurosynth converter (#531) @tsalo
• [ENH] Add Corrector.inspect class method (#530) @tsalo
• [TST] Cover cases where some studies are missing coordinates (#527) @tsalo
• [ENH] Add drop_invalid option to Dataset.get() and Estimator.fit() (#526) @tsalo
• [ENH] Support lists of targets in ImageTransformer (#518) @tsalo
• [DOC] Add versionadded and versionchanged directives to docstrings (#501) @JulioAPeraza
• [DOC] Add example for ALE subtraction and conjunction analysis (#519) @alexenge
• [ENH] Add merge method to Dataset class (#517) @tsalo
• [ENH] Add ImageTransformer class (#513) @tsalo
• [ENH] Add overwrite option to transform_images (#509) @tsalo

0.0.9rc2

Release Notes

This release candidate adds the ImageTransformer class for the OHBM tutorial.

Changes

• [ENH] Add ImageTransformer class (#513) @tsalo

0.0.9rc1

Release Notes

This release candidate adds an overwrite option in preparation for the OHBM 2021 NiMARE tutorial.

Changes

• [ENH] Add overwrite option to transform_images (#509) @tsalo