0.0.7rc1

Release Notes

This release involves two changes worth mentioning. First, we have fixed a bug in how permutation-based p-values are calculated (thanks to @alexenge for identifying and reporting). Second, we have changed how the "empirical" null method is performed. The "empirical" method is now much slower, but more accurate, than the "analytic" approach.

Changes

• [FIX] Permutation p-values (#447) @tyarkoni
• [FIX,REF] start changing how to handle resampling (#439) @jdkent
• [FIX] transform_images extra dimension (#445) @jdkent
• [DOC] Add decoding description page (#443) @tsalo
• [MAINT] Switch to GitHub Actions for PyPi deployment (#441) @tsalo
• [ENH] Implement full coordinate-set empirical null method (#424) @tsalo
• [DOC] Fix NeuroStars link (#434) @tsalo
• [DOC] Add specialized issue templates (#433) @tsalo
• [MAINT] Add indexed_gzip as a dependency (#431) @tsalo

0.0.6

Release Notes

WARNING: This release was not deployed to PyPi. However, 0.0.7 is the same as 0.0.6, so just use that one.

This release involves two changes worth mentioning. First, we have fixed a bug in how permutation-based p-values are calculated (thanks to @alexenge for identifying and reporting). Second, we have changed how the "empirical" null method is performed. The "empirical" method is now much slower, but more accurate, than the "analytic" approach.

Changes

• [FIX] Permutation p-values (#447) @tyarkoni
• [FIX,REF] start changing how to handle resampling (#439) @jdkent
• [FIX] transform_images extra dimension (#445) @jdkent
• [DOC] Add decoding description page (#443) @tsalo
• [MAINT] Switch to GitHub Actions for PyPi deployment (#441) @tsalo
• [ENH] Implement full coordinate-set empirical null method (#424) @tsalo
• [DOC] Fix NeuroStars link (#434) @tsalo
• [DOC] Add specialized issue templates (#433) @tsalo
• [MAINT] Add indexed_gzip as a dependency (#431) @tsalo

0.0.5

Release Notes

This release is focused on fixing two bugs in v0.0.4. One bug affected which files were packaged with the library, such that some templates were missing. The other bug was introduced in v0.0.4 and invalidates cluster-level Monte Carlo-based FWE-correction in coordinate-based meta-analyses.

Changes

• [FIX] Convert histogram weights to null distribution in p-to-stat conversion (#430) @tsalo
• [FIX] Fix packaging of resources (#428) @tsalo
• [FIX] Include resources in library data files (#427) @tsalo

0.0.4

Release Notes

This release includes a number of substantial changes to NiMARE.

Major changes

1. We've added PyMARE as a dependency! PyMARE is a general-purpose meta-analysis library in Python that we now use to perform our image-based meta-analyses.
2. For image-based meta-analyses, we also now have a transforms module to calculate new image types from available data.
3. Datasets now have a number of attributes retained as properties, which will break compatibility with Datasets from older versions of NiMARE.
4. We now have multiple methods for converting summary statistics (e.g., ALE, OF) to p-values in all of our major CBMA algorithms, thanks to @tyarkoni! The two current methods for each algorithm are a fast, but slightly less accurate, "analytic" method and a slower, but more accurate, "empirical" method. For ALE, We generally recommend the "analytic" method for maximum compatibility with GingerALE. The implementations of these algorithms have also been streamlined and sped up somewhat.
5. We have a new generate module for simulating coordinate-based datasets, thanks to @jdkent!
6. A number of modules, classes, and functions that were not yet implemented have been pruned from the API to make it easier to work with. Don't worry, we're still planning to get around to them at some point.

Changes

• [FIX] Fix the warnings about mismatched kernels and estimators (#425) @tsalo
• [FIX] Add nullhist_to_p and crop invalid p-values (#409) @tsalo
• [TST] Do not download test peaks2maps to tmpdir (#419) @tsalo
• [FIX] Restructure Peaks2MapsKernel to operate like other kernels (#410) @tsalo
• [ENH] Improve convergence between ALE null methods (#411) @tsalo
• [DOC] Add warnings for CBMA kernel/estimator mismatch (#416) @tsalo
• [FIX] Remove rows with empty abstract before running LDAModel (#414) @JulioAPeraza
• [FIX] Sort all arrays and DataFrames in Dataset by ID (#402) @tsalo
• [FIX] Allow no coordinates in a dataset (#407) @jdkent
• [ENH] Add analytic null method to KDA estimator (#397) @tsalo
• [FIX] Use unzipped mask as temporary fix (#401) @tsalo
• [DOC] Update API and examples (#395) @tsalo
• [REF] CBMA re-organization and improvement (#393) @tyarkoni
• [MAINT] Pin to PyMARE 0.0.2 (#391) @tsalo
• [TST] Test both analytic and empirical methods in ALE and MKDA (#380) @jdkent
• [FIX] Change default seed to None (#392) @jdkent
• [PERF] Various performance improvements (#386) @tyarkoni
• Add performance tweaks to ALE analytical null generation (#390) @tyarkoni
• fix tests (#387) @tyarkoni
• [FIX] respect n_noise_foci value (#382) @jdkent
• [ENH] Add analytic null method to MKDADensity (#375) @tsalo
• [ENH] Add empirical null method to density-based CBMA Estimators (#372) @tsalo
• [REF] Refactor KernelTransformer hierarchy (#369) @tyarkoni
• [ENH] Add generate module (#343) @jdkent
• [FIX] enforce correct lowest p-value (#365) @jdkent
• [FIX] Treat vfwe as an array of floats for KDA (#362) @jdkent
• [DOC] Update roadmap.rst (#359) @tsalo
• [DOC] Add example of combining kernels and CBMA estimators (#346) @koudyk
• [MAINT] Add Dorota Jarecka to Zenodo file (#358) @djarecka
• [MAINT] Add Enrico Glerean's affiliation and ORCID (#357) @eglerean
• [ENH] Clip p-values based on number of permutations (#353) @tsalo
• [REF] Remove unused alpha argument in statsmodels call (#354) @tsalo
• [ENH] Replace TTest with PermutedOLS (#304) @tsalo
• [REF] Reduce dependencies (#345) @tsalo
• [ENH] Add Neurosynth data fetcher (#342) @tsalo
• [INFRA] Add json describing filename convention (#338) @tsalo
• [DOC] Enable CBMA example (#337) @tsalo
• [FIX] Add private setter method for Dataset.ids (#336) @tsalo
• [REF] More low-memory work (#334) @tsalo
• [FIX, DOC] Change natural log to base-ten and document output naming convention (#333) @tsalo
• [FIX] Pin setuptools again (#331) @tsalo
• [FIX] Update setuptools version (#330) @tsalo
• [FIX] Add setuptools to requirements (#329) @tsalo
• [TST] Add test for peaks2maps (#328) @tsalo
• [FIX, TST] Fix and test CorrelationDistributionDecoder (#327) @tsalo
• [TST] Use temporary directories with automatic teardown (#326) @tsalo
• [REF] Speed up CorrelationDecoder (#324) @tsalo
• [ENH] Support Dataset transformations in kernel transformers (#320) @tsalo
• [ENH] Add PairwiseCBMAEstimator class and add low_memory option to ALESubtraction (#319) @tsalo
• [TST] Improve meta-analysis tests (#318) @tsalo
• [DOC] Fix Lancaster xform and Sleuth conversion docstrings (#317) @tsalo
• [TST] Improve nimare.io test coverage (#314) @tsalo
• [REF] Reduce duplication by calling _check_ncores (#313) @tsalo
• [REF] Remove generate_cooccurrence (#312) @tsalo
• [REF] Operate on arrays in ALESubtraction (#311) @tsalo
• [TST] Add flake8-black to test requirements (#300) @akimbler
• [FIX] Support multiple header lines in Sleuth text files (#310) @tsalo
• [FIX] Operate on copy of df in extract_cogat() (#306) @tsalo
• [MAINT] Update setup configuration (#303) @tsalo
• [REF] Sort imports alphabetically (#299) @tsalo
• [REF] Run automated code formatting with black (#296) @tsalo
• [DOC] Remove whitespace from README (#295) @tsalo
• [MAINT, TST] Drop 3.5 support. Add tests for Python 3.7 and 3.8. (#293) @tsalo
• [MAINT] Delete unused files (#291) @tsalo
• [MAINT] Increase minimum tensorflow to 2.0.0 (#290) @tsalo
• [FIX] Update peaks2maps w.r.t. recent changes in the API (#287) @tsalo
• [FIX] Raise an error in Decoders if no features remain (#284) @tsalo
• [REF] Move CBMA methods up a level (#283) @tsalo
• [REF] Rename RandomEffectsGLM to TTest (#282) @tsalo
• [ENH] Split DerSimonianLaird and Hedges IBMA estimators (#281) @tsalo
• [DOC] Expand IBMA example (#280) @tsalo
• [ENH] Use PyMARE for image-based meta-analyses (#273) @tsalo
• [FIX] Replace NaNs in Datasets with Nones (#276) @tsalo
• [ENH] Support initialized and uninitialized kernels for CBMA (#275) @tsalo
• [ENH] Add functions to convert image types (#272) @tsalo
• [REF] Convert Dataset attributes to properties (#270) @tsalo
• [REF] Drop unimplemented annotators (#269) @tsalo
• [REF] Drop unimplemented parcellate module and meta-ICA workflow (#264) @tsalo
• [ENH] Use nearest-neighbor interpolation for masks (#258) @tsalo

0.0.3

Release Notes

This release consolidates changes prior to PyMARE integration. In addition to a number of bug fixes, this release also includes substantial changes to ALESubtraction, annotation storage, and Dataset size.

Changes

• [FIX] Preallocate ALE cFWE p-value array with ones instead of zeros (#254) @tsalo
• [ENH] Convert decoders to classes (#252) @tsalo
• [ENH] Add prefix to annotations to delineate sources (#250) @tsalo
• [REF] Drop Dataset.data attribute (#249) @tsalo
• [ENH] Remove voxel selection in ALESubtraction (#245) @tsalo
• [REF] Eliminate duplication in ALESubtraction (#244) @tsalo
• [FIX] Add minimum nibabel version (#237) @tsalo
• [TST] Fix CodeCov config file (#240) @tsalo
• [ENH] Add transforms module (#239) @tsalo
• [TST] Add workflow tests (#235) @tsalo
• [REF, ENH] Add CBMAEstimator base class (#232) @tsalo
• [MAINT] Add @nicholst's info to Zenodo file (#228) @tsalo
• [MAINT] Consolidate requirements files (#230) @tsalo
• [ENH] Dataset.get_X methods return available types when type is not provided (#205) @tsalo
• [FIX] Update workflows given recent changes (#226) @tsalo
• [REF] Reorganize submodules (#225) @tsalo
• [REF, DOC] Update meta-analysis output map names (#224) @tsalo
• [REF] Rename "permutation" to "montecarlo" (#223) @tsalo
• [DOC] Fix annotate API docs (#222) @tsalo
• [DOC] Improve API rendering and run some examples (#219) @tsalo
• [REF, DOC] Remove unused base classes and improve docs (#216) @tsalo
• [REF] Rename kernel_estimator attribute to kernel_transformer (#197) @tsalo
• [ENH] Make convert_sleuth_to_dataset more flexible (#166) @62442katieb

0.0.2

Changes

• [FIX] Mimic PyMARE's config more completely (#214)
• [FIX] Retain ALESubtraction results (#213)
• [TST] Add CI step for building docs (#212)
• [MAINT] Add workflow to autodeploy to PyPi (#210)
• [FIX] Fix bugs in LDAModel and paths to MALLET (#202)
• [DOC] Fix examples and add gallery back in (#201)
• [REF] Consolidate Dataset loading methods and refactor nimare.extract (#200)
• [ENH] Add extract submodule (again) (#199)
• [ENH] Improve Corrector transparency (#192)
• [TST] Expand test coverage and refactor LDA/CogAt (#193)
• [DOC] Update API documentation (#191)
• [FIX] Fix IO bug (#190)
• [FIX] Fix Neurosynth conversion. (#188)
• [MAINT] Add badges to README and RTD (#187)
• [MAINT] Add PyPi badges
• [MAINT] Add Zenodo DOI badge

Initial release

Release Notes

This is NiMARE's initial release. NiMARE is still alpha software, so the package may change dramatically from release to release and there may be bugs in the code. In this first release, NiMARE supports a range of coordinate- and image-based meta-analytic algorithms, ingestion of coordinate-based datasets from Sleuth and Neurosynth, dataset searching, a set of command-line workflows, and some miscellaneous tools like functional decoding.

Changes

• [MAINT] Add release drafter (#186) @tsalo
• [FIX] Update examples to prepare for release (#185) @tsalo
• [TST] Add test for FDRCorrector (#184) @tsalo
• [FIX] Fix missing parameter q of FDRCorrector (#182) @AlexPrz
• [REF] Distribute base classes into their associated modules (#177) @tsalo
• [FIX] Remove click from conf.py (#178) @tsalo
• [REF] Switch CLI from click to argparse (#169) @tsalo
• [FIX, STY] Fix flake8 issues (#176) @tsalo
• [REF] changes to IBMAEstimator hierarchy and masking functionality (#173) @tyarkoni
• [REF] Save pain test dataset to local directory (#174) @tyarkoni
• [FIX, DOC] Add m2r to docs-specific requirements file (#168) @tsalo
• [FIX, DOC] Add m2r to doc requirements (#167) @tsalo
• [DOC, REF] Reorganize docs and setup configuration (#165) @tsalo
• [DOC, REF] Add references submodule (#164) @tsalo
• [FIX, DOC] Improve docstrings and update Peaks2Maps (#162) @tsalo
• [REF] Separate multiple comparisons correction from estimators (#157) @tsalo
• [ENH] Initialize Estimators with hyperparameters, fit to Datasets (#155) @tsalo
• [FIX] Fix MetaResult (#154) @tsalo
• [REF, DOC] Update docs and remove dataset.extract (#153) @tsalo
• [REF] Update MetaResult and move general IBMA functions into new module (#152) @tsalo
• [REF] Remove unused base classes (#151) @tsalo
• [TST] Improve CircleCI configuration (#150) @tsalo
• [FIX] Don't run gallery examples (#147) @tsalo
• [DOC] Update Manifest to work with examples. (#149) @tsalo
• [FIX, TST] Fix CircleCI (#148) @tsalo
• [FIX] Support multiline experiment names in Sleuth converter (#146) @tsalo
• [DOC] Add examples gallery (#144) @tsalo
• [DOC] Further update docstrings (#143) @tsalo
• [DOC] Update docstrings (#142) @tsalo
• [ENH] Use log-P values for FWE maps in CBMA estimators (#136) @tsalo
• [MAINT] Add Julio to Zenodo file (#141) @tsalo
• [ENH] Support additional space descriptors (#140) @tsalo
• [ENH] Add FWHM argument to ALE CLI workflow. (#138) @tsalo
• [MAINT] Remove download_test_data.py (#139) @tsalo
• [REF] Refactor GCLDA model (#137) @tsalo
• [FIX] Clean up examples after changes to API (#135) @tsalo
• [DOC] Change outdated Slack link to Mattermost (#127) @tsalo
• [FIX] Fix up GCLDA and text extraction methods (#126) @tsalo
• [DOC] Add ecosystem info to documentation (#125) @tsalo
• [ENH] Add texts field to Dataset (#124) @tsalo
• [FIX] Remove absolute paths in dataset (#122) @tsalo
• [ENH] Add slice method for Datasets (#121) @tsalo
• [FIX, ENH] Fix discrete decoding and speed up Dataset initialization (#120) @tsalo
• [FIX] Loop through requested IDs in kernel transformers (#118) @tsalo
• [FIX] Remove deprecated sklearn dependency (#119) @tsalo
• [DOC] Add favicon for website (#116) @tsalo
• [DOC] Add badges (#114) @tsalo
• [DOC] Update documentation and website (#112) @tsalo
• [ENH] Add MACM and Neurosynth/Sleuth conversion workflows (#111) @tsalo
• [STY, FIX] Fix style problems (#110) @tsalo
• [REF] Reorganize package to incorporate Transformers and Estimators (#107) @tsalo
• [TST] Add CodeCov and linting to CI (#100) @tsalo
• [ENH] Add ALE subtraction analysis to CLI (#106) @tsalo
• [DOC] Minor fixes to documentation. (#105) @tsalo
• [FIX] Assign transform to ALE MNI template (#104) @tsalo
• [FIX] Fix ALE subtraction analysis (#103) @tsalo
• [DOC] Draft boilerplates for ALE and SCALE workflows (#98) @tsalo
• [REF] Replace printing with logging (#99) @tsalo
• [MAINT] Add Dylan to zenodo (#102) @Shotgunosine
• [DOC] Add Puck Reeders to zenodo.json (#101) @puckr
• Update (#1) @puckr
• [WIP, DOC] populate contributors.rst with maintainer information (#54) @jdkent
• [ENH] Use maximum number of cores in ALE/MKDA by default (#93) @tsalo
• [DOC] Add ImportWarnings to untested modules (#90) @tsalo
• [ENH] Add CI (circleci) (#62) @jdkent
• [FIX] Fix docs API and conf.py (#94) @tsalo
• Fix a typo (#91) @chrisgorgo
• Update, test scale cli. (#89) @62442katieb
• Adding workflows for metacluster and scale (#84) @62442katieb
• skeleton of MC correction hierarchy (#87) @tyarkoni
• ale CLI cleanup (#86) @chrisgorgo
• Updating the documentation of the website and logo? (#88) @JesseyWright
• Small speedups in kernel transforms (#85) @Shotgunosine
• adding the peaks2maps CLI command (#83) @chrisgorgo
• adding the conperm CLI command (#80) @chrisgorgo
• [ENH] Speed up ALE MA generation (#81) @tsalo
• ADD when ALE is called with 1 core, don't use a pool (#79) @Shotgunosine
• fix: suppress all warnings for now (#75) @satra
• [HOTFIX] Feed IBMA MetaResults function names instead of estimators (#76) @tsalo
• updating Dockerfile and create_dockerfiles (#69) @djarecka
• store originating estimator in MetaResult (#67) @tyarkoni
• Website Template Updates (#68) @JesseyWright
• Update .zenodo.json (#71) @bilgelm
• fix dep (#65) @chrisgorgo
• Adding command line interface (#63) @chrisgorgo
• changes in setup and requirements (#61) @djarecka
• Adding progress bars for permutations (#60) @chrisgorgo
• lazy load tensorflow, improve error reporting (#55) @chrisgorgo
• convert_sleuth_to_database (#56) @chrisgorgo
• [FIX] save_nidm_to_dset.ipynb (#51) @jdkent
• [FIX] Delete extra base class for parcellators (#52) @tsalo
• Added Peaks2MapsKernel (#42) @chrisgorgo
• [FIX] generate_ma_maps.ipynb (#50) @jdkent
• Add Angie to Zenodo file (#48) @tsalo
• Fix license ID (#47) @chrisgorgo
• [ENH] populate notebook with good images (#46) @jdkent
• [FIX] attempt to get nidm_pain_meta-analyses.ipynb working (#35) @jdkent
• quick fix for sphinx docs generation (#39) @bilgelm
• [ENH] Add Zenodo file and instructions to contributing guidelines (#38) @tsalo
• Small typo under example notebooks. (#29) @eglerean
• [FIX] remove abc as dependency (#32) @jdkent
• [FIX] Fix tests (#33) @tsalo
• [ENH] Add ability to convert Sleuth text files to NiMARE-compatible json files (#28) @tsalo
• [ENH] Add automated annotation tools (#18) @tsalo
• [ENH] Add decoders (#17) @tsalo
• [DOC, TST] Add tests and docs (#15) @tsalo
• [FIX] Correct subpeaks in pain dataset and use nilearn for templates/masks (#26) @tsalo
• Decoding (#4) @tsalo
• Annotation (#3) @tsalo
• Add ni18 poster (#2) @tsalo
• Add contributing guidelines and code of conduct (#14) @tsalo
• Add tail argument to IBMAs and use FSL for FFX GLM (#12) @tsalo
• Add image- and coordinate-based meta-analyses. (#11) @tsalo