diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 5606878c3..98375174a 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1,4 +1,4 @@ contact_links: - name: Usage question - url: https://neurostars.org/tag/nimare + url: https://neurostars.org/tags/c/software-support/234/nimare about: Please ask questions about using NiMARE on NeuroStars. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index ccb0050b1..a915c7136 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -36,7 +36,7 @@ jobs: fail-fast: false matrix: os: ["ubuntu-latest"] - python-version: ["3.7"] + python-version: ["3.8"] name: Style check defaults: run: diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index 88d6b3450..bee4ac83d 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -17,7 +17,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v2 with: - python-version: '3.7' + python-version: '3.8' - name: Install dependencies run: | python -m pip install --upgrade pip diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index b87f82b56..a293b88f4 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -38,7 +38,8 @@ jobs: fail-fast: false matrix: os: ["ubuntu-latest", "macos-latest"] - python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"] + python-version: ["3.8", "3.9", "3.10", "3.11"] + defaults: run: shell: bash @@ -50,7 +51,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: 'Install NiMARE' shell: bash {0} - run: pip install -e .[tests,peaks2maps-cpu] + run: pip install -e .[tests,cbmr] - name: 'Run tests' shell: bash {0} run: make unittest @@ -70,7 +71,7 @@ jobs: fail-fast: false matrix: os: ["ubuntu-latest"] - python-version: ["3.6"] + python-version: ["3.8"] defaults: run: shell: bash @@ -79,10 +80,10 @@ jobs: - name: 'Set up python' uses: actions/setup-python@v2 with: - python-version: 3.6 + python-version: 3.8 - name: 'Install NiMARE' shell: bash {0} - run: pip install -e .[minimum,tests,peaks2maps-cpu] + run: pip install -e .[minimum,tests,cbmr] - name: 'Run tests' shell: bash {0} run: make unittest @@ -102,7 +103,7 @@ jobs: fail-fast: false matrix: os: ["ubuntu-latest"] - python-version: ["3.7"] + python-version: ["3.8"] defaults: run: shell: bash @@ -114,7 +115,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: 'Install NiMARE' shell: bash {0} - run: pip install -e .[tests,peaks2maps-cpu] + run: pip install -e .[tests,cbmr] - name: 'Run tests' shell: bash {0} run: make test_performance_estimators @@ -134,7 +135,7 @@ jobs: fail-fast: false matrix: os: ["ubuntu-latest"] - python-version: ["3.7"] + python-version: ["3.8"] defaults: run: shell: bash @@ -146,7 +147,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: 'Install NiMARE' shell: bash {0} - run: pip install -e .[tests,peaks2maps-cpu] + run: pip install -e .[tests,cbmr] - name: 'Run tests' shell: bash {0} run: make test_performance_correctors @@ -166,7 +167,7 @@ jobs: fail-fast: false matrix: os: ["ubuntu-latest"] - python-version: ["3.7"] + python-version: ["3.8"] defaults: run: shell: bash @@ -178,7 +179,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: 'Install NiMARE' shell: bash {0} - run: pip install -e .[tests,peaks2maps-cpu] + run: pip install -e .[tests,cbmr] - name: 'Run tests' shell: bash {0} run: make test_performance_smoke @@ -189,9 +190,41 @@ jobs: path: coverage.xml if: success() + test_cbmr_importerror: + name: CBMR ImportError tests + needs: check_skip + if: ${{ needs.check_skip.outputs.skip == 'false' }} + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + os: ["ubuntu-latest"] + python-version: ["3.8"] + defaults: + run: + shell: bash + steps: + - uses: actions/checkout@v2 + - name: 'Set up python' + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - name: 'Install NiMARE' + shell: bash {0} + run: pip install -e .[tests] + - name: 'Run tests' + shell: bash {0} + run: make test_cbmr_importerror + - name: Upload artifacts + uses: actions/upload-artifact@v2 + with: + name: cbmr_importerror + path: coverage.xml + if: success() + upload_to_codecov: name: Upload coverage - needs: [run_unit_tests,run_unit_tests_with_minimum_dependencies,test_performance_estimators,test_performance_correctors,test_performance_smoke] + needs: [run_unit_tests,run_unit_tests_with_minimum_dependencies,test_performance_estimators,test_performance_correctors,test_performance_smoke,test_cbmr_importerror] runs-on: "ubuntu-latest" steps: - name: Checkout diff --git a/.github/workflows/update-changelog.yml b/.github/workflows/update-changelog.yml index 003b3585a..03825cd34 100644 --- a/.github/workflows/update-changelog.yml +++ b/.github/workflows/update-changelog.yml @@ -2,7 +2,7 @@ name: "Update Changelog" on: release: - types: [published] + types: [released] jobs: update: diff --git a/.gitignore b/.gitignore index e6b10c564..6ed6cb2b9 100644 --- a/.gitignore +++ b/.gitignore @@ -8,6 +8,7 @@ docs/auto_examples/ nimare/resources/data/neurovault-data/ nimare/tests/data/downloaded/ nimare/tests/resources/data/neurovault-data/ +_readthedocs/ .pytest_cache # diff --git a/.readthedocs.yml b/.readthedocs.yaml similarity index 82% rename from .readthedocs.yml rename to .readthedocs.yaml index f994a7eb1..f22c97350 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yaml @@ -5,15 +5,19 @@ # Required version: 2 +build: + os: "ubuntu-22.04" + tools: + python: "3.8" + # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py python: - version: 3.7 install: - method: pip path: . extra_requirements: - doc - system_packages: true + - cbmr diff --git a/CHANGELOG.md b/CHANGELOG.md index d7f7a7188..bf1345663 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,133 +2,242 @@ All notable changes to NiMARE releases are documented in this page. -## [Unreleased](https://github.com/neurostuff/NiMARE/compare/0.0.12rc7...HEAD) +## [Unreleased](https://github.com/neurostuff/NiMARE/compare/0.2.0...HEAD) - -## [0.0.12rc7](https://github.com/neurostuff/NiMARE/compare/0.0.12rc6...0.0.12rc7) - 2022-06-14 - -Another release candidate to test a GitHub Action. +## [0.2.0](https://github.com/neurostuff/NiMARE/compare/0.1.1...0.2.0) - 2023-11-02 ### What's Changed #### ๐ŸŽ‰ Exciting New Features -- Add warning when coordinates dataset contains both positive and negative z_stats by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/699 -- Add parameter estimate standard error to IBMA results by @tsalo in https://github.com/neurostuff/NiMARE/pull/691 +- Add Workflow and CBMAWorkflow classes. Support pairwise CBMA workflows by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/809 +- Remove `resample` argument from IBMA estimators by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/823 +- Add IBMAWorkflow by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/817 +- Make `torch` optional by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/836 +- Add Conjunction Analysis Workflow by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/841 + +#### ๐Ÿ› Bug Fixes + +- Fix the aspect ratio and size of the heatmap in Reports by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/815 +- Addresses new RTD configuration file requirements by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/829 +- Fix compatibility of ImageTransformer with Pandas 2.1.2 by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/843 +- [FIX] handle index errors by @jdkent in https://github.com/neurostuff/NiMARE/pull/839 +- [FIX] regular expression for no moderators by @jdkent in https://github.com/neurostuff/NiMARE/pull/821 +- Fix the NeuroLibre badge by @tsalo in https://github.com/neurostuff/NiMARE/pull/824 +- [FIX] handle null values in metadata by @jdkent in https://github.com/neurostuff/NiMARE/pull/831 #### Other Changes -- Fix CHANGELOG formatting issues by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/701 +- Add badges and citations for Aperture Neuro article by @tsalo in https://github.com/neurostuff/NiMARE/pull/834 +- Remove pytorch warning message by @yifan0330 in https://github.com/neurostuff/NiMARE/pull/828 -**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.12rc6...0.0.12rc7 +**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.1.1...0.2.0 -## [0.0.12rc6](https://github.com/neurostuff/NiMARE/compare/0.0.12rc3...0.0.12rc6) - 2022-06-08 +## [0.1.1](https://github.com/neurostuff/NiMARE/compare/0.1.0...0.1.1) - 2023-06-12 -A release candidate to test our new Action. + +Main change is to include `default.yml` and `default.tpl` in the python package distribution ### What's Changed +#### ๐ŸŽ‰ Exciting New Features + +- Combine analyses in Studyset by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/810 + #### Other Changes -- Optimize numpy operations in MKDADensity Estimator and (M)KDAKernel by @adelavega in https://github.com/neurostuff/NiMARE/pull/685 -- Add PAT to automatically commit release notes to `CHANGELOG.md` by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/695 +- [FIX] include default.yml as part of nimare package by @jdkent in https://github.com/neurostuff/NiMARE/pull/812 -### New Contributors +**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.1.0...0.1.1 -- @adelavega made their first contribution in https://github.com/neurostuff/NiMARE/pull/685 +## [0.1.0](https://github.com/neurostuff/NiMARE/compare/0.0.14...0.1.0) - 2023-06-02 -**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.12rc3...0.0.12rc6 + +### What's Changed -## [0.0.12rc3](https://github.com/neurostuff/NiMARE/compare/0.0.12rc2...0.0.12rc3) - 2022-03-21 +This is a big release, there are several large items we added: -Just a quick release for debugging. +- Coordinate Based Meta Regression! This is a great alternative to the kernel-based methods to detect convergence with more sensitivity and more flexibly compare between groups. +- Reports Module: now you can generate an html report for the simple kernel based methods, more estimators will be supported in upcoming releases -## What's Changed +#### ๐ŸŽ‰ Exciting New Features -### ๐Ÿ›  Breaking Changes +- [ENH] Support pre-generated maps in `CorrelationDecoder` by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/782 +- [ENH] add Coordinate Based Meta Regression by @yifan0330 in https://github.com/neurostuff/NiMARE/pull/721 +- [ENH] Add Corrector and Diagnostics attributes to MetaResult object by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/804 +- [ENH] Add NiMAREBase features to the Corrector base class by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/807 +- [ENH] Add `reports` module by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/802 -- Stop storing MetaResults as attributes of fitted Estimators by @tsalo in https://github.com/neurostuff/NiMARE/pull/657 -- Refactor Correctors and remove statsmodels requirement by @tsalo in https://github.com/neurostuff/NiMARE/pull/679 +#### ๐Ÿ› Bug Fixes -### ๐ŸŽ‰ Exciting New Features +- [FIX] Set `n_iters` defaults only for estimators with `null_method="montecarlo"` by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/803 +- [FIX] handle case of no sample size being reported by @jdkent in https://github.com/neurostuff/NiMARE/pull/792 +- [FIX] math display by @yifan0330 in https://github.com/neurostuff/NiMARE/pull/805 +- [FIX] allow analysis to have null points when converting from nimads to dataset by @jdkent in https://github.com/neurostuff/NiMARE/pull/808 -- Support `vfwe_only` in CBMAEstimator even when `null_method` isn't `montecarlo` by @tsalo in https://github.com/neurostuff/NiMARE/pull/678 +#### Other Changes -### Other Changes +- [MAINT] Drop support for Python 3.6 and 3.7 by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/780 +- [MAINT] remove codecov by @jdkent in https://github.com/neurostuff/NiMARE/pull/788 +- [DOC] change readthedocs badge from latest to stable by @jdkent in https://github.com/neurostuff/NiMARE/pull/786 +- [DOC] Add neurolibre link by @jdkent in https://github.com/neurostuff/NiMARE/pull/789 +- [MAINT] make indexed_gzip install optional by @jdkent in https://github.com/neurostuff/NiMARE/pull/791 +- [MAINT] Remove RC versions from Changelog by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/790 +- [MAINT] Unpin numpy version by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/794 +- [REF] Replace `_get_clusters_table` with nilearn's `get_clusters_table` by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/793 +- [MAINT] Support Python 3.11 by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/796 +- [MAINT] fix readthedocs by @jdkent in https://github.com/neurostuff/NiMARE/pull/797 -- Document other meta-analysis tools outside our ecosystem by @tsalo in https://github.com/neurostuff/NiMARE/pull/654 -- Reorganize and streamline examples by @tsalo in https://github.com/neurostuff/NiMARE/pull/656 -- Convert CBMAEstimator method to function by @tsalo in https://github.com/neurostuff/NiMARE/pull/658 -- Add explicit support for Python 3.10 by @tsalo in https://github.com/neurostuff/NiMARE/pull/648 -- Use BibTeX citations in documentation by @tsalo in https://github.com/neurostuff/NiMARE/pull/670 -- Replace relative imports with absolute ones by @tsalo in https://github.com/neurostuff/NiMARE/pull/674 -- Simplify organization of base classes by @tsalo in https://github.com/neurostuff/NiMARE/pull/675 -- Note why we don't implement TFCE in NiMARE (currently) by @tsalo in https://github.com/neurostuff/NiMARE/pull/680 -- Dropping the memory-mapping option for Estimators and kernel transformers by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/681 -- Optimize locating coordinates in convert_neurosynth_to_dataset by @ryanhammonds in https://github.com/neurostuff/NiMARE/pull/682 -- Reduce memory usage of `KernelTransformer.transform` and `meta.utils.compute_kda_ma` by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/676 -- Generate automatic CHANGELOG from release note and add it to docs by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/684 -- Add manual changelog to documentation by @tsalo in https://github.com/neurostuff/NiMARE/pull/635 +**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.14...0.1.0 -## New Contributors +## [0.0.14](https://github.com/neurostuff/NiMARE/compare/0.0.13...0.0.14) - 2023-03-31 -- @ryanhammonds made their first contribution in https://github.com/neurostuff/NiMARE/pull/682 +### What's Changed + +#### ๐Ÿ›  Breaking Changes + +- Support clusters table in Diagnostics by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/765 + +#### ๐ŸŽ‰ Exciting New Features + +- Add `save()` and `load()` methods to `MetaResult` objects by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/771 +- Incorporate Estimator and Corrector descriptions into MetaResult objects by @tsalo in https://github.com/neurostuff/NiMARE/pull/724 +- Add `cluster_threshold` option to Diagnostics by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/777 +- Add CBMA workflow by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/761 + +#### ๐Ÿ› Bug Fixes + +- Do not zero out one-tailed z-statistics for p-values > 0.5 by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/693 -**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.12rc2...0.0.12rc3 +#### Other Changes -## [0.0.12rc2](https://github.com/neurostuff/NiMARE/compare/0.0.12rc1...0.0.12rc2) - 2022-03-04 +- Support nibabel 5.0.0 by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/762 +- Link to NeuroStars software support category instead of neuro questions by @tsalo in https://github.com/neurostuff/NiMARE/pull/768 +- Revert "Do not zero out one-tailed z-statistics for p-values > 0.5" by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/769 +- [DOC] add note about SDM by @jdkent in https://github.com/neurostuff/NiMARE/pull/764 +- Replace `pandas.DataFrame.append` with `pandas.concat` by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/774 +- [ENH] rudimentary support for nimads by @jdkent in https://github.com/neurostuff/NiMARE/pull/763 +- Major refactoring of Diagnostics module by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/776 +- [DOC] add proper documentation to nimads module by @jdkent in https://github.com/neurostuff/NiMARE/pull/778 -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. +**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.13...0.0.14 + +## [0.0.13](https://github.com/neurostuff/NiMARE/compare/0.0.12...0.0.13) - 2023-01-17 ### 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. + #### ๐Ÿ›  Breaking Changes -- Replace multiprocessing with joblib for parallelization and change n_cores default to 1 by @tsalo in https://github.com/neurostuff/NiMARE/pull/597 -- Incorporate joblib into ALESubtraction and fix SCALE docstring by @tsalo in https://github.com/neurostuff/NiMARE/pull/641 +- Remove Peaks2Maps from NiMARE by @tsalo in https://github.com/neurostuff/NiMARE/pull/644 +- Remove duecredit in favor of BibTeX references by @tsalo in https://github.com/neurostuff/NiMARE/pull/736 +- Switch from face+edge connectivity to face-only by @tsalo in https://github.com/neurostuff/NiMARE/pull/733 +- Remove conperm and scale CLI workflows by @tsalo in https://github.com/neurostuff/NiMARE/pull/740 #### ๐ŸŽ‰ Exciting New Features -- Add FocusCounter diagnostic tool by @tsalo in https://github.com/neurostuff/NiMARE/pull/649 -- Support cluster-level Monte Carlo FWE correction in the MKDAChi2 Estimator by @tsalo in https://github.com/neurostuff/NiMARE/pull/650 +- Add `tables` attribute to MetaResult class by @tsalo in https://github.com/neurostuff/NiMARE/pull/734 +- Add FocusFilter class for removing coordinates outside of a mask by @tsalo in https://github.com/neurostuff/NiMARE/pull/732 +- Add parallelization option to `CorrelationDecoder` and `CorrelationDistributionDecoder` by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/738 +- Append the top 3 words to LDA topic names by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/741 +- Enhance LDA annotator by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/742 #### ๐Ÿ› Bug Fixes -- Retain updated Estimator in Corrector-generated MetaResults by @tsalo in https://github.com/neurostuff/NiMARE/pull/633 -- Do not inherit IBMAEstimator's aggressive_mask from previous Datasets by @tsalo in https://github.com/neurostuff/NiMARE/pull/652 +- Shift centers of mass into clusters in Jackknife/FocusCounter by @tsalo in https://github.com/neurostuff/NiMARE/pull/735 +- fix a bug in conversion from z statistics to p values by @yifan0330 in https://github.com/neurostuff/NiMARE/pull/749 +- Remove "dataset" `return_type` option from kernel transformers by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/752 #### Other Changes -- Reduce SCALE memory usage by @tsalo in https://github.com/neurostuff/NiMARE/pull/632 -- Improve memory management in MKDAChi2 Estimator by @tsalo in https://github.com/neurostuff/NiMARE/pull/638 -- Remove Peaks2Maps-related tests by @tsalo in https://github.com/neurostuff/NiMARE/pull/643 -- Disable MA map pre-generation in CorrelationDecoder by @tsalo in https://github.com/neurostuff/NiMARE/pull/637 -- Switch testing from CircleCI to GitHub Actions by @tsalo in https://github.com/neurostuff/NiMARE/pull/642 -- Override unusable methods and improve documentation by @tsalo in https://github.com/neurostuff/NiMARE/pull/645 +- Fix import in download_neurosynth example by @PTDZ in https://github.com/neurostuff/NiMARE/pull/743 +- Optimize compute_kda_ma by @liuzhenqi77 in https://github.com/neurostuff/NiMARE/pull/745 +- Optimize dataset.get by @liuzhenqi77 in https://github.com/neurostuff/NiMARE/pull/746 +- Fix MACM analysis example by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/750 +- Remove upper bound for matplotlib version by @ghisvail in https://github.com/neurostuff/NiMARE/pull/751 +- Fix neurosyth download_abstracts example; inc biopython by @WillForan in https://github.com/neurostuff/NiMARE/pull/753 +- Raise deprecation warnings with Python 3.6 and 3.7 by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/754 +- [MAINT] Fix various errors due to major version changes in dependencies by @jdkent in https://github.com/neurostuff/NiMARE/pull/757 + +### New Contributors -**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.11...0.0.12rc2 +- @PTDZ made their first contribution in https://github.com/neurostuff/NiMARE/pull/743 +- @liuzhenqi77 made their first contribution in https://github.com/neurostuff/NiMARE/pull/745 +- @yifan0330 made their first contribution in https://github.com/neurostuff/NiMARE/pull/749 +- @ghisvail made their first contribution in https://github.com/neurostuff/NiMARE/pull/751 +- @WillForan made their first contribution in https://github.com/neurostuff/NiMARE/pull/753 -## [0.0.12rc1](https://github.com/neurostuff/NiMARE/compare/0.0.11...0.0.12rc1) - 2022-02-15 +**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.12...0.0.13 -This release candidate continues to optimize certain elements of NiMARE processing for its NeuroLibre preprint. +## [0.0.12](https://github.com/neurostuff/NiMARE/compare/0.0.11...0.0.12) - 2022-07-22 + +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 #### ๐Ÿ›  Breaking Changes - Replace multiprocessing with joblib for parallelization and change n_cores default to 1 by @tsalo in https://github.com/neurostuff/NiMARE/pull/597 +- Incorporate joblib into ALESubtraction and fix SCALE docstring by @tsalo in https://github.com/neurostuff/NiMARE/pull/641 +- Stop storing MetaResults as attributes of fitted Estimators by @tsalo in https://github.com/neurostuff/NiMARE/pull/657 +- Refactor Correctors and remove statsmodels requirement by @tsalo in https://github.com/neurostuff/NiMARE/pull/679 + +#### ๐ŸŽ‰ Exciting New Features + +- Add FocusCounter diagnostic tool by @tsalo in https://github.com/neurostuff/NiMARE/pull/649 +- Support cluster-level Monte Carlo FWE correction in the MKDAChi2 Estimator by @tsalo in https://github.com/neurostuff/NiMARE/pull/650 +- Support `vfwe_only` in CBMAEstimator even when `null_method` isn't `montecarlo` by @tsalo in https://github.com/neurostuff/NiMARE/pull/678 +- Add warning when coordinates dataset contains both positive and negative z_stats by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/699 +- Add parameter estimate standard error to IBMA results by @tsalo in https://github.com/neurostuff/NiMARE/pull/691 +- Use sparse array in ALE, ALESubtraction, SCALE, KDA, and MKDADensity by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/725 #### ๐Ÿ› Bug Fixes - Retain updated Estimator in Corrector-generated MetaResults by @tsalo in https://github.com/neurostuff/NiMARE/pull/633 +- Do not inherit IBMAEstimator's aggressive_mask from previous Datasets by @tsalo in https://github.com/neurostuff/NiMARE/pull/652 +- Use beta maps in PermutedOLS instead of z maps by @tsalo in https://github.com/neurostuff/NiMARE/pull/715 #### Other Changes - Reduce SCALE memory usage by @tsalo in https://github.com/neurostuff/NiMARE/pull/632 - Improve memory management in MKDAChi2 Estimator by @tsalo in https://github.com/neurostuff/NiMARE/pull/638 +- Remove Peaks2Maps-related tests by @tsalo in https://github.com/neurostuff/NiMARE/pull/643 +- Disable MA map pre-generation in CorrelationDecoder by @tsalo in https://github.com/neurostuff/NiMARE/pull/637 +- Switch testing from CircleCI to GitHub Actions by @tsalo in https://github.com/neurostuff/NiMARE/pull/642 +- Override unusable methods and improve documentation by @tsalo in https://github.com/neurostuff/NiMARE/pull/645 +- Document other meta-analysis tools outside our ecosystem by @tsalo in https://github.com/neurostuff/NiMARE/pull/654 +- Reorganize and streamline examples by @tsalo in https://github.com/neurostuff/NiMARE/pull/656 +- Convert CBMAEstimator method to function by @tsalo in https://github.com/neurostuff/NiMARE/pull/658 +- Add explicit support for Python 3.10 by @tsalo in https://github.com/neurostuff/NiMARE/pull/648 +- Use BibTeX citations in documentation by @tsalo in https://github.com/neurostuff/NiMARE/pull/670 +- Replace relative imports with absolute ones by @tsalo in https://github.com/neurostuff/NiMARE/pull/674 +- Simplify organization of base classes by @tsalo in https://github.com/neurostuff/NiMARE/pull/675 +- Note why we don't implement TFCE in NiMARE (currently) by @tsalo in https://github.com/neurostuff/NiMARE/pull/680 +- Dropping the memory-mapping option for Estimators and kernel transformers by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/681 +- Optimize locating coordinates in convert_neurosynth_to_dataset by @ryanhammonds in https://github.com/neurostuff/NiMARE/pull/682 +- Reduce memory usage of `KernelTransformer.transform` and `meta.utils.compute_kda_ma` by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/676 +- Generate automatic CHANGELOG from release note and add it to docs by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/684 +- Add manual changelog to documentation by @tsalo in https://github.com/neurostuff/NiMARE/pull/635 +- Automatically update `CHANGELOG.md` for prereleases as well by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/688 +- Fix tag-name issue in update-changelog workflow by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/689 +- Optimize numpy operations in MKDADensity Estimator and (M)KDAKernel by @adelavega in https://github.com/neurostuff/NiMARE/pull/685 +- Add PAT to automatically commit release notes to `CHANGELOG.md` by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/695 +- Fix CHANGELOG formatting issues by @JulioAPeraza in https://github.com/neurostuff/NiMARE/pull/701 +- Add citation information to documentation by @tsalo in https://github.com/neurostuff/NiMARE/pull/712 +- Add a glossary page to the documentation by @tsalo in https://github.com/neurostuff/NiMARE/pull/706 +- Remove extraneous `copy()` statements by @jdkent in https://github.com/neurostuff/NiMARE/pull/662 +- Add information about maintaining NiMARE to developer's guide by @tsalo in https://github.com/neurostuff/NiMARE/pull/703 +- Pin minimum version of pandas by @jdkent in https://github.com/neurostuff/NiMARE/pull/722 + +### New Contributors + +- @ryanhammonds made their first contribution in https://github.com/neurostuff/NiMARE/pull/682 +- @adelavega made their first contribution in https://github.com/neurostuff/NiMARE/pull/685 -**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.11...0.0.12rc1 +**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.11...0.0.12 ## [0.0.11](https://github.com/neurostuff/NiMARE/compare/0.0.10...0.0.11) - 2022-01-06 @@ -170,20 +279,6 @@ and (3) implementing a meta-analysis model specification that can be employed wi **Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.10...0.0.11 -## [0.0.11rc1](https://github.com/neurostuff/NiMARE/compare/0.0.10...0.0.11rc1) - 2021-10-27 - -This release candidate includes certain enhancements and fixes necessary for the NiMARE software paper -(https://github.com/NBCLab/nimare-paper). - -### What's Changed - -- [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 - -**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.10...0.0.11rc1 - ## [0.0.10](https://github.com/neurostuff/NiMARE/compare/0.0.9...0.0.10) - 2021-10-06 The 0.0.10 release includes a number of bug fixes and improvements. @@ -248,44 +343,6 @@ The fetching and conversion functions also now support accessing multiple vocabu **Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.9...0.0.10 -## [0.0.10rc2](https://github.com/neurostuff/NiMARE/compare/0.0.9...0.0.11rc2) - 2021-08-10 - -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. - -### What's Changed - -- [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 - -**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.9...0.0.10rc2 - -## [0.0.10rc1](https://github.com/neurostuff/NiMARE/compare/0.0.9...0.0.10rc1) - 2021-07-15 - -This release prepares for NeuroHackademy. -The most relevant changes are the new ROIAssociationDecoder and the custom `__repr__` methods. - -### What's Changed - -- [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 - -**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.9...0.0.10rc1 - ## [0.0.9](https://github.com/neurostuff/NiMARE/compare/0.0.8...0.0.9) - 2021-07-04 This release primarily improves testing and documentation, but there are a few new features as well. @@ -313,26 +370,6 @@ enhancing NiMARE's docstrings with "versionadded" and "versionchanged" directive **Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.8...0.0.9 -## [0.0.9rc2](https://github.com/neurostuff/NiMARE/compare/0.0.8...0.0.9rc2) - 2021-06-02 - -This release candidate adds the ImageTransformer class for the OHBM tutorial. - -### What's Changed - -- [ENH] Add ImageTransformer class (#513) @tsalo - -**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.8...0.0.9rc2 - -## [0.0.9rc1](https://github.com/neurostuff/NiMARE/compare/0.0.8...0.0.9rc1) - 2021-05-27 - -This release candidate adds an overwrite option in preparation for the OHBM 2021 NiMARE tutorial. - -### What's Changed - -- [ENH] Add overwrite option to transform_images (#509) @tsalo - -**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.8...0.0.9rc1 - ## [0.0.8](https://github.com/neurostuff/NiMARE/compare/0.0.7...0.0.8) - 2021-05-17 This release includes a number of bug-fixes, along with enhancements to how many tools within NiMARE implement low-memory options. @@ -396,27 +433,6 @@ This release successfully deployed to PyPi, unlike 0.0.6. **Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.6...0.0.7 -## [0.0.7rc1](https://github.com/neurostuff/NiMARE/compare/0.0.6...0.0.7rc1) - 2021-02-25 - -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. - -### What's Changed - -- [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 - -**Full Changelog**: https://github.com/neurostuff/NiMARE/compare/0.0.6...0.0.7rc1 - ## [0.0.6](https://github.com/neurostuff/NiMARE/compare/0.0.5...0.0.6) - 2021-02-25 .. important:: \ This release was not deployed to PyPi. However, 0.0.7 is the same as 0.0.6, so just use that one. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 853e0831c..88033dc92 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -33,7 +33,7 @@ As stated in the code, severe or repeated violations by community members may re ## Asking questions about using NiMARE -Please direct usage-related questions to [NeuroStars][link_neurostars], with the ["nimare" tag][link_neurostars_nimare]. +Please direct usage-related questions to [NeuroStars][link_neurostars], with [the "Software Support" category and the "nimare" tag][link_neurostars_nimare]. The ``NiMARE`` developers follow NeuroStars, and will be able to answer your question there. ## Labels @@ -114,7 +114,7 @@ You're awesome. [link_labels]: https://github.com/neurostuff/NiMARE/labels [link_discussingissues]: https://help.github.com/articles/discussing-projects-in-issues-and-pull-requests [link_neurostars]: https://neurostars.org -[link_neurostars_nimare]: https://neurostars.org/tag/nimare +[link_neurostars_nimare]: https://neurostars.org/tags/c/software-support/234/nimare [link_pullrequest]: https://help.github.com/articles/creating-a-pull-request/ [link_fork]: https://help.github.com/articles/fork-a-repo/ diff --git a/Makefile b/Makefile index 1a4824c7f..9e4873233 100644 --- a/Makefile +++ b/Makefile @@ -9,12 +9,13 @@ help: @echo " test_performance_estimators to run performance tests on meta estimators" @echo " test_performance_correctors to run performance tests on correctors" @echo " test_performance_smoke to run performance smoke tests" + @echo " test_cbmr_importerror to run cbmr importerror tests" lint: @flake8 nimare unittest: - @py.test -m "not performance_estimators and not performance_correctors and not performance_smoke" --cov-append --cov-report=xml --cov=nimare nimare + @py.test -m "not performance_estimators and not performance_correctors and not performance_smoke and not cbmr_importerror" --cov-append --cov-report=xml --cov=nimare nimare test_performance_estimators: @py.test -m "performance_estimators" --cov-append --cov-report=xml --cov=nimare nimare @@ -24,3 +25,6 @@ test_performance_correctors: test_performance_smoke: @py.test -m "performance_smoke" --cov-append --cov-report=xml --cov=nimare nimare + +test_cbmr_importerror: + @py.test -m "cbmr_importerror" --cov-append --cov-report=xml --cov=nimare nimare diff --git a/README.md b/README.md index 5f8b18aee..4b3662024 100755 --- a/README.md +++ b/README.md @@ -3,21 +3,23 @@ A Python library for coordinate- and image-based meta-analysis. [![Latest Version](https://img.shields.io/pypi/v/nimare.svg)](https://pypi.python.org/pypi/nimare/) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/nimare.svg)](https://pypi.python.org/pypi/nimare/) +[![GitHub Repository](https://img.shields.io/badge/Source%20Code-neurostuff%2Fnimare-purple)](https://github.com/neurostuff/NiMARE) [![DOI](https://zenodo.org/badge/117724523.svg)](https://zenodo.org/badge/latestdoi/117724523) [![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT) [![Test Status](https://github.com/neurostuff/NiMARE/actions/workflows/testing.yml/badge.svg)](https://github.com/neurostuff/NiMARE/actions/workflows/testing.yml) -[![Documentation Status](https://readthedocs.org/projects/nimare/badge/?version=latest)](http://nimare.readthedocs.io/en/latest/?badge=latest) +[![Documentation Status](https://readthedocs.org/projects/nimare/badge/?version=stable)](http://nimare.readthedocs.io/en/stable/?badge=stable) [![Codecov](https://codecov.io/gh/neurostuff/NiMARE/branch/main/graph/badge.svg)](https://codecov.io/gh/neurostuff/nimare) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Join the chat at https://mattermost.brainhack.org/brainhack/channels/nimare](https://img.shields.io/badge/mattermost-join_chat%20%E2%86%92-brightgreen.svg)](https://mattermost.brainhack.org/brainhack/channels/nimare) [![RRID:SCR_017398](https://img.shields.io/badge/RRID-SCR__017398-blue.svg)](https://scicrunch.org/scicrunch/Resources/record/nlx_144509-1/SCR_017398/resolver?q=nimare&l=nimare) -[![DOI](http://neurolibre.herokuapp.com/papers/10.55458/neurolibre.00007/status.svg)](https://doi.org/10.55458/neurolibre.00007) +[![Paper](https://img.shields.io/badge/Aperture-10.52294/001c.87681-darkblue.svg)](https://doi.org/10.52294/001c.87681) +[![Preprint](https://neurolibre.org/papers/10.55458/neurolibre.00007/status.svg)](https://doi.org/10.55458/neurolibre.00007) Currently, NiMARE implements a range of image- and coordinate-based meta-analytic algorithms, as well as several methods for advanced meta-analytic methods, like automated annotation and functional decoding. ## Installation -Please see our [installation instructions](https://nimare.readthedocs.io/en/latest/installation.html) +Please see our [installation instructions](https://nimare.readthedocs.io/en/stable/installation.html) for information on how to install NiMARE. ### Installation with pip @@ -33,22 +35,20 @@ pip install git+https://github.com/neurostuff/NiMARE.git ## Citing NiMARE If you use NiMARE in your research, we recommend citing the Zenodo DOI associated with the NiMARE version you used, -as well as the NeuroLibre preprint for the NiMARE Jupyter book. +as well as the Aperture Neuro journal article for the NiMARE Jupyter book. You can find the Zenodo DOI associated with each NiMARE release at https://zenodo.org/record/6642243#.YqiXNy-B1KM. ```BibTeX -# This is the NeuroLibre preprint. -@article{Salo2022, - doi = {10.55458/neurolibre.00007}, - url = {https://doi.org/10.55458/neurolibre.00007}, - year = {2022}, - publisher = {The Open Journal}, - volume = {1}, - number = {1}, - pages = {7}, +# This is the Aperture Neuro paper. +@article{Salo2023, + doi = {10.52294/001c.87681}, + url = {https://doi.org/10.52294/001c.87681}, + year = {2023}, + volume = {3}, + pages = {1 - 32}, author = {Taylor Salo and Tal Yarkoni and Thomas E. Nichols and Jean-Baptiste Poline and Murat Bilgel and Katherine L. Bottenhorn and Dorota Jarecka and James D. Kent and Adam Kimbler and Dylan M. Nielson and Kendra M. Oudyk and Julio A. Peraza and Alexandre Pรฉrez and Puck C. Reeders and Julio A. Yanes and Angela R. Laird}, title = {NiMARE: Neuroimaging Meta-Analysis Research Environment}, - journal = {NeuroLibre} + journal = {Aperture Neuro} } # This is the Zenodo citation for version 0.0.11. diff --git a/docs/api.rst b/docs/api.rst index 8920c1e60..ebe0c762b 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -26,6 +26,7 @@ API For more information about the components of coordinate-based meta-analysis in NiMARE, see :doc:`cbma`. + .. automodule:: nimare.meta :no-members: :no-inherited-members: @@ -41,6 +42,7 @@ For more information about the components of coordinate-based meta-analysis in N meta.cbma.mkda meta.cbma.base meta.kernel + meta.cbmr .. _api_results_ref: @@ -167,6 +169,29 @@ For more information about functional characterization analysis, see :doc:`decod io.convert_neurovault_to_dataset +.. _api_nimads_ref: + +:mod:`nimare.nimads`: NeuroImaging Meta-Analysis Data Structure +--------------------------------------------------------------- +.. automodule:: nimare.nimads + :no-members: + :no-inherited-members: + +.. currentmodule:: nimare + +.. autosummary:: + :toctree: generated/ + :template: class.rst + + nimads.Studyset + nimads.Annotation + nimads.Study + nimads.Analysis + nimads.Condition + nimads.Image + nimads.Point + + .. _api_transforms_ref: :mod:`nimare.transforms`: Data transforms @@ -307,9 +332,26 @@ For more information about fetching data from the internet, see :ref:`fetching t :toctree: generated/ :template: function.rst - workflows.ale_sleuth_workflow workflows.macm_workflow + workflows.cbma.CBMAWorkflow + workflows.cbma.PairwiseCBMAWorkflow + workflows.ibma.IBMAWorkflow + workflows.misc.conjunction_analysis + +:mod:`nimare.reports`: NiMARE report +-------------------------------------------------- + +.. automodule:: nimare.reports + :no-members: + :no-inherited-members: + +.. currentmodule:: nimare + +.. autosummary:: + :toctree: generated/ + :template: function.rst + reports.run_reports .. _api_base_ref: @@ -326,4 +368,4 @@ For more information about fetching data from the internet, see :ref:`fetching t :template: class.rst base.NiMAREBase - base.Estimator + estimator.Estimator diff --git a/docs/cbma.rst b/docs/cbma.rst index e7cc1bf11..190fdf09d 100644 --- a/docs/cbma.rst +++ b/docs/cbma.rst @@ -170,6 +170,12 @@ The Monte Carlo FWE correction approach implemented in NiMARE produces three new although there is a closed pull request with an implementation that worked at the time it was closed (see `#655 `_). + +.. admonition:: Where is SDM? + + Seed Based *d* Mapping (SDM) is currently not implemented in NiMARE because the source code is not publicly available. + To follow the current discussion on SDM in the context of NiMARE, see `#183 `_. + References ---------- .. footbibliography:: diff --git a/docs/conf.py b/docs/conf.py index f755d1c8d..674716a49 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -174,7 +174,7 @@ "matplotlib": ("https://matplotlib.org/", (None, "https://matplotlib.org/objects.inv")), "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None), "nibabel": ("https://nipy.org/nibabel/", None), - "nilearn": ("http://nilearn.github.io/", None), + "nilearn": ("http://nilearn.github.io/stable/", None), "pymare": ("https://pymare.readthedocs.io/en/latest/", None), "skimage": ("https://scikit-image.org/docs/stable/", None), } @@ -209,7 +209,7 @@ # ----------------------------------------------------------------------------- # sphinxcontrib-bibtex # ----------------------------------------------------------------------------- -bibtex_bibfiles = ["./references.bib"] +bibtex_bibfiles = ["../nimare/resources/references.bib"] bibtex_style = "unsrt" bibtex_reference_style = "author_year" bibtex_footbibliography_header = "" diff --git a/docs/index.rst b/docs/index.rst index 71caa82de..6bddbf4da 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -16,6 +16,10 @@ To install NiMARE check out our `installation guide`_. :target: https://pypi.python.org/pypi/nimare/ :alt: PyPI - Python Version +.. image:: https://img.shields.io/badge/Source%20Code-neurostuff%2Fnimare-purple + :target: https://github.com/neurostuff/NiMARE + :alt: GitHub Repository + .. image:: https://zenodo.org/badge/117724523.svg :target: https://zenodo.org/badge/latestdoi/117724523 :alt: DOI @@ -28,8 +32,8 @@ To install NiMARE check out our `installation guide`_. :target: https://github.com/neurostuff/NiMARE/actions/workflows/testing.yml :alt: Test Status -.. image:: https://readthedocs.org/projects/nimare/badge/?version=latest - :target: http://nimare.readthedocs.io/en/latest/?badge=latest +.. image:: https://readthedocs.org/projects/nimare/badge/?version=stable + :target: http://nimare.readthedocs.io/en/stable/?badge=stable :alt: Documentation Status .. image:: https://codecov.io/gh/neurostuff/NiMARE/branch/main/graph/badge.svg @@ -48,7 +52,11 @@ To install NiMARE check out our `installation guide`_. :target: https://scicrunch.org/scicrunch/Resources/record/nlx_144509-1/SCR_017398/resolver?q=nimare&l=nimare :alt: RRID:SCR_017398 -.. image:: http://neurolibre.herokuapp.com/papers/10.55458/neurolibre.00007/status.svg +.. image:: https://img.shields.io/badge/Aperture-10.52294/001c.87681-darkblue.svg + :target: https://doi.org/10.52294/001c.87681 + :alt: Aperture paper + +.. image:: https://neurolibre.org/papers/10.55458/neurolibre.00007/status.svg :target: https://doi.org/10.55458/neurolibre.00007 :alt: NeuroLibre preprint @@ -61,24 +69,22 @@ Citing NiMARE ------------- If you use NiMARE in your research, we recommend citing the Zenodo DOI associated with the NiMARE version you used, -as well as the NeuroLibre preprint for the NiMARE Jupyter book. +as well as the Aperture Neuro journal article for the NiMARE Jupyter book. You can find the Zenodo DOI associated with each NiMARE release at https://zenodo.org/record/6642243#.YqiXNy-B1KM. .. code-block:: bibtex :caption: BibTeX entries for NiMARE version 0.0.11. - # This is the NeuroLibre preprint. - @article{Salo2022, - doi = {10.55458/neurolibre.00007}, - url = {https://doi.org/10.55458/neurolibre.00007}, - year = {2022}, - publisher = {The Open Journal}, - volume = {1}, - number = {1}, - pages = {7}, - author = {Taylor Salo and Tal Yarkoni and Thomas E. Nichols and Jean-Baptiste Poline and Murat Bilgel and Katherine L. Bottenhorn and Dorota Jarecka and James D. Kent and Adam Kimbler and Dylan M. Nielson and Kendra M. Oudyk and Julio A. Peraza and Alexandre Pรฉrez and Puck C. Reeders and Julio A. Yanes and Angela R. Laird}, - title = {NiMARE: Neuroimaging Meta-Analysis Research Environment}, - journal = {NeuroLibre} + # This is the Aperture Neuro paper. + @article{Salo2023, + doi = {10.52294/001c.87681}, + url = {https://doi.org/10.52294/001c.87681}, + year = {2023}, + volume = {3}, + pages = {1 - 32}, + author = {Taylor Salo and Tal Yarkoni and Thomas E. Nichols and Jean-Baptiste Poline and Murat Bilgel and Katherine L. Bottenhorn and Dorota Jarecka and James D. Kent and Adam Kimbler and Dylan M. Nielson and Kendra M. Oudyk and Julio A. Peraza and Alexandre Pรฉrez and Puck C. Reeders and Julio A. Yanes and Angela R. Laird}, + title = {NiMARE: Neuroimaging Meta-Analysis Research Environment}, + journal = {Aperture Neuro} } # This is the Zenodo citation for version 0.0.11. diff --git a/docs/installation.rst b/docs/installation.rst index 69507915e..5bf659c6b 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -15,9 +15,13 @@ If you want to use the most up-to-date version, you can install from the ``main` pip install git+https://github.com/neurostuff/NiMARE.git -NiMARE requires Python >=3.6 and a number of packages. +NiMARE requires Python ``>=3.8`` and a number of packages. For a complete list, please see ``nimare/setup.cfg``. +.. note:: + We only support Python versions that are part of the Python release cycle (i.e., 3.8, 3.9, + 3.10, and 3.11). For more information, see `Python Supported Versions`_. + What Next? ---------- diff --git a/docs/links.rst b/docs/links.rst index ebc720893..76a28a9e0 100644 --- a/docs/links.rst +++ b/docs/links.rst @@ -68,6 +68,8 @@ .. _PyMARE: https://pymare.readthedocs.io/en/latest/ +.. _Python Supported Versions: https://devguide.python.org/versions/#supported-versions + .. _scikit-learn: https://scikit-learn.org/stable/developers/index.html .. _Scribe: https://brainmap.org/scribe/ diff --git a/docs/outputs.rst b/docs/outputs.rst index 0690ee3e5..ab25b7f62 100644 --- a/docs/outputs.rst +++ b/docs/outputs.rst @@ -11,11 +11,13 @@ File names NiMARE-generated files, especially ones made by meta-analyses, follow a naming convention somewhat based on BIDS. -Here is the basic naming convention for statistical maps: +Here is the basic naming convention for statistical maps and tables: .. code-block:: Text - [_desc-