0.0.13

What's Changed

This release was motivated because there were updates to underlying packages that broke the installation of NiMARE.
In addition, there are multiple breaking changes as well as new features outlined below.

🛠 Breaking Changes

• Remove Peaks2Maps from NiMARE by @tsalo in #644
• Remove duecredit in favor of BibTeX references by @tsalo in #736
• Switch from face+edge connectivity to face-only by @tsalo in #733
• Remove conperm and scale CLI workflows by @tsalo in #740

🎉 Exciting New Features

• Add tables attribute to MetaResult class by @tsalo in #734
• Add FocusFilter class for removing coordinates outside of a mask by @tsalo in #732
• Add parallelization option to CorrelationDecoder and CorrelationDistributionDecoder by @JulioAPeraza in #738
• Append the top 3 words to LDA topic names by @JulioAPeraza in #741
• Enhance LDA annotator by @JulioAPeraza in #742

🐛 Bug Fixes

• Shift centers of mass into clusters in Jackknife/FocusCounter by @tsalo in #735
• fix a bug in conversion from z statistics to p values by @yifan0330 in #749
• Remove "dataset" return_type option from kernel transformers by @JulioAPeraza in #752

Other Changes

• Fix import in download_neurosynth example by @PTDZ in #743
• Optimize compute_kda_ma by @liuzhenqi77 in #745
• Optimize dataset.get by @liuzhenqi77 in #746
• Fix MACM analysis example by @JulioAPeraza in #750
• Remove upper bound for matplotlib version by @ghisvail in #751
• Fix neurosyth download_abstracts example; inc biopython by @WillForan in #753
• Raise deprecation warnings with Python 3.6 and 3.7 by @JulioAPeraza in #754
• [MAINT] Fix various errors due to major version changes in dependencies by @jdkent in #757

New Contributors

• @PTDZ made their first contribution in #743
• @liuzhenqi77 made their first contribution in #745
• @yifan0330 made their first contribution in #749
• @ghisvail made their first contribution in #751
• @WillForan made their first contribution in #753

Full Changelog: 0.0.12...0.0.13

0.0.13rc1

What's Changed

Testing release code

🛠 Breaking Changes

• Remove Peaks2Maps from NiMARE by @tsalo in #644
• Remove duecredit in favor of BibTeX references by @tsalo in #736
• Switch from face+edge connectivity to face-only by @tsalo in #733
• Remove conperm and scale CLI workflows by @tsalo in #740

🎉 Exciting New Features

• Add tables attribute to MetaResult class by @tsalo in #734
• Add FocusFilter class for removing coordinates outside of a mask by @tsalo in #732
• Add parallelization option to CorrelationDecoder and CorrelationDistributionDecoder by @JulioAPeraza in #738
• Append the top 3 words to LDA topic names by @JulioAPeraza in #741
• Enhance LDA annotator by @JulioAPeraza in #742

🐛 Bug Fixes

• Shift centers of mass into clusters in Jackknife/FocusCounter by @tsalo in #735
• fix a bug in conversion from z statistics to p values by @yifan0330 in #749
• Remove "dataset" return_type option from kernel transformers by @JulioAPeraza in #752

Other Changes

• Fix import in download_neurosynth example by @PTDZ in #743
• Optimize compute_kda_ma by @liuzhenqi77 in #745
• Optimize dataset.get by @liuzhenqi77 in #746
• Fix MACM analysis example by @JulioAPeraza in #750
• Remove upper bound for matplotlib version by @ghisvail in #751
• Fix neurosyth download_abstracts example; inc biopython by @WillForan in #753
• Raise deprecation warnings with Python 3.6 and 3.7 by @JulioAPeraza in #754
• [MAINT] Fix various errors due to major version changes in dependencies by @jdkent in #757

New Contributors

• @PTDZ made their first contribution in #743
• @liuzhenqi77 made their first contribution in #745
• @yifan0330 made their first contribution in #749
• @ghisvail made their first contribution in #751
• @WillForan made their first contribution in #753

Full Changelog: 0.0.12...0.0.13rc1

0.0.12

This release continues ongoing work on improving memory usage. We have eliminated the memory_limit option in our Estimators in favor of using sparse arrays. We expect to see a corresponding increase in fit times, especially for Monte Carlo FWE correction- however, we plan to address this in future releases.

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
• Stop storing MetaResults as attributes of fitted Estimators by @tsalo in #657
• Refactor Correctors and remove statsmodels requirement by @tsalo in #679

🎉 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
• Support vfwe_only in CBMAEstimator even when null_method isn't montecarlo by @tsalo in #678
• Add warning when coordinates dataset contains both positive and negative z_stats by @JulioAPeraza in #699
• Add parameter estimate standard error to IBMA results by @tsalo in #691
• Use sparse array in ALE, ALESubtraction, SCALE, KDA, and MKDADensity by @JulioAPeraza in #725

🐛 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
• Use beta maps in PermutedOLS instead of z maps by @tsalo in #715

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
• Document other meta-analysis tools outside our ecosystem by @tsalo in #654
• Reorganize and streamline examples by @tsalo in #656
• Convert CBMAEstimator method to function by @tsalo in #658
• Add explicit support for Python 3.10 by @tsalo in #648
• Use BibTeX citations in documentation by @tsalo in #670
• Replace relative imports with absolute ones by @tsalo in #674
• Simplify organization of base classes by @tsalo in #675
• Note why we don't implement TFCE in NiMARE (currently) by @tsalo in #680
• Dropping the memory-mapping option for Estimators and kernel transformers by @JulioAPeraza in #681
• Optimize locating coordinates in convert_neurosynth_to_dataset by @ryanhammonds in #682
• Reduce memory usage of KernelTransformer.transform and meta.utils.compute_kda_ma by @JulioAPeraza in #676
• Generate automatic CHANGELOG from release note and add it to docs by @JulioAPeraza in #684
• Add manual changelog to documentation by @tsalo in #635
• Automatically update CHANGELOG.md for prereleases as well by @JulioAPeraza in #688
• Fix tag-name issue in update-changelog workflow by @JulioAPeraza in #689
• Optimize numpy operations in MKDADensity Estimator and (M)KDAKernel by @adelavega in #685
• Add PAT to automatically commit release notes to CHANGELOG.md by @JulioAPeraza in #695
• Fix CHANGELOG formatting issues by @JulioAPeraza in #701
• Add citation information to documentation by @tsalo in #712
• Add a glossary page to the documentation by @tsalo in #706
• Remove extraneous copy() statements by @jdkent in #662
• Add information about maintaining NiMARE to developer's guide by @tsalo in #703
• Pin minimum version of pandas by @jdkent in #722

New Contributors

• @ryanhammonds made their first contribution in #682
• @adelavega made their first contribution in #685

Full Changelog: 0.0.11...0.0.12

0.0.12rc7

Another release candidate to test a GitHub Action.

What's Changed

🎉 Exciting New Features

• Add warning when coordinates dataset contains both positive and negative z_stats by @JulioAPeraza in #699
• Add parameter estimate standard error to IBMA results by @tsalo in #691

Other Changes

• Fix CHANGELOG formatting issues by @JulioAPeraza in #701

Full Changelog: 0.0.12rc6...0.0.12rc7

0.0.12rc6

A release candidate to test our new Action.

What's Changed

Other Changes

• Optimize numpy operations in MKDADensity Estimator and (M)KDAKernel by @adelavega in #685
• Add PAT to automatically commit release notes to CHANGELOG.md by @JulioAPeraza in #695

New Contributors

• @adelavega made their first contribution in #685

Full Changelog: 0.0.12rc5...0.0.12rc6

0.0.12rc5

A release candidate to test our new Action.

What's Changed

Other Changes

• Fix tag-name issue in update-changelog workflow by @JulioAPeraza in #689

Full Changelog: 0.0.12rc4...0.0.12rc5

0.0.12rc4

A release candidate to test our new Action.

What's Changed

Other Changes

• Automatically update CHANGELOG.md for prereleases as well by @JulioAPeraza in #688

Full Changelog: 0.0.12rc3...0.0.12rc4

0.0.12rc3

Just a quick release for debugging.

What's Changed

🛠 Breaking Changes

• Stop storing MetaResults as attributes of fitted Estimators by @tsalo in #657
• Refactor Correctors and remove statsmodels requirement by @tsalo in #679

🎉 Exciting New Features

• Support vfwe_only in CBMAEstimator even when null_method isn't montecarlo by @tsalo in #678

Other Changes

• Document other meta-analysis tools outside our ecosystem by @tsalo in #654
• Reorganize and streamline examples by @tsalo in #656
• Convert CBMAEstimator method to function by @tsalo in #658
• Add explicit support for Python 3.10 by @tsalo in #648
• Use BibTeX citations in documentation by @tsalo in #670
• Replace relative imports with absolute ones by @tsalo in #674
• Simplify organization of base classes by @tsalo in #675
• Note why we don't implement TFCE in NiMARE (currently) by @tsalo in #680
• Dropping the memory-mapping option for Estimators and kernel transformers by @JulioAPeraza in #681
• Optimize locating coordinates in convert_neurosynth_to_dataset by @ryanhammonds in #682
• Reduce memory usage of KernelTransformer.transform and meta.utils.compute_kda_ma by @JulioAPeraza in #676
• Generate automatic CHANGELOG from release note and add it to docs by @JulioAPeraza in #684
• Add manual changelog to documentation by @tsalo in #635

New Contributors

• @ryanhammonds made their first contribution in #682

Full Changelog: 0.0.12rc2...0.0.12rc3

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