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Update bokeh requirement from <=3.4.1,>=1.0.0 to <=3.5.0,>=3.5.0 #1109

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merged 2 commits into from
Jul 8, 2024

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Updates the requirements on bokeh to permit the latest version.

Changelog

Sourced from bokeh's changelog.

2024-07-04 3.5:

  • bugfixes:

    • #8766 [component: bokehjs] box_select not working as active_drag for gridplot
    • #12638 [component: bokehjs] Make Slider and Image available in BokehJS (JS only)
    • #13515 [component: tests] CI unit-test on Python 3.9 fails systematically
    • #13623 [component: bokehjs] [BUG] TextAreaInput resizable=False doesn't set resize: none
    • #13720 [component: docs] Explanation is part of the code block in the latex_axis_labels_titles_labels example
    • #13766 [component: bokehjs] [BUG] Dropdown doesnt update properly when .menu changed in 3.4
    • #13771 [component: bokehjs] GMap example not showing glyphs
    • #13787 [component: bokehjs] [BUG] DataTable inside Dialog
    • #13789 [component: docs] [BUG] JS errors on Bokeh docs page
    • #13824 [component: docs] activate pydata-sphinx-theme version banner
    • #13834 [component: build] bokehjs' build fails on Windows with no explanation
    • #13844 [component: build] [BUG] cannot build environment with pixi due to firefox =>96 constraint
    • #13848 Can't build extensions on Windows
    • #13852 [component: bokehjs] [BUG] and ignored in tooltips on Firefox
    • #13878 [component: bokehjs] Bokeh.Plotting.figure.circle in bokehjs can't find x and y in a ColumnDataSource
    • #13894 [component: bokehjs] Tooltip is initially attached to the DOM when it shouldn't be
    • #13895 [component: bokehjs] Inner canvas layers need overflow: hidden after PR #13863
    • #13897 [component: docs] [BUG] Typing of layouts.gridplot expects wrong type if ncols given
    • #13902 Release build fails after PR #13901
    • #13910 [component: tests] Tests/CI fail due to a regression in requests 2.32.0
    • #13912 [component: bokehjs] [BUG] Dialog and Datatable don't get along well
    • #13919 [component: bokehjs] [BUG] Bokeh 3.5 no longer allow custom properties for HTMLAttr
    • #13923 [component: bokehjs] Tooltip.content doesn't rebuild views on change
    • #13948 [component: docs] Version banner warns about unknown version on latest docs after 3.4.2 release
    • #13951 [component: bokehjs] [BUG] Image Glyph causing tons of unnecessary calls to set_data
    • #13822 [component: docs] remove consecutive "the" and fix typos in touched files
    • #13879 [component: docs] Fix broken example in user guide advanced bokehjs
    • #13884 [component: docs] silence warning in theme_glyphs.py
    • #13908 [component: bokehjs] Fix CartesianFrame's position and generalize rendering_target()
    • #13926 [component: docs] Remove blob/main and tree/master from references
    • #13927 [component: docs] update path in readme for server examples
    • #13939 [component: docs] correct version string to match dev name from switcher.json
    • #13940 [component: bokehjs] Fix initialization of AjaxDataSource and add tests
  • features:

    • #8289 [component: bokehjs] Permanent labels on Networkx graph
    • #10439 [component: bokehjs] Activate wheel zoom by default with BokehJS
    • #12185 [component: bokehjs] [FEATURE] Legend click events
    • #12759 [component: bokehjs] [FEATURE] Support using CSS Variables in place of colors
    • #13599 [FEATURE] Support formatters when using Template as HoverTool
    • #13646 [FEATURE] Support BoxSelectTool-like range-setting for the RangeTool
    • #13652 [FEATURE] HTMLLabel to support stylesheets and css_classes
    • #13673 [FEATURE] Add Carbon Theme
    • #13728 [FEATURE] Create option for wheel zoom tool to apply only to subplot nearest to the cursor position
    • #13792 [component: server] [FEATURE] Allow bokeh server embed script to forward credentials
    • #13861 [FEATURE] Support directory upload and clearing inputs from Python for FileInput widget
    • #13935 [FEATURE] Allow extensions to register server side events

... (truncated)

Commits
  • c9f67a2 Deployment updates for release 3.5.0
  • f84ee3b Final preparations for 3.5.0 release (#13961)
  • 10c4904 Merge deployment staging branch staging-3.5.0rc2
  • c3ba286 Deployment updates for release 3.5.0rc2
  • 2e34a08 Implement data inheritance in ImageBase._set_data() (#13952)
  • 2d1351e add release to project configuration (#13949)
  • 45c796f Merge deployment staging branch staging-3.5.0rc1
  • 4217685 Deployment updates for release 3.5.0rc1
  • 548285f Fixing dropdowns (#13833)
  • ac18777 Add support for resize and drag handles to BoxAnnotation (#13906)
  • Additional commits viewable in compare view

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Updates the requirements on [bokeh](https://github.com/bokeh/bokeh) to permit the latest version.
- [Changelog](https://github.com/bokeh/bokeh/blob/branch-3.6/docs/CHANGELOG)
- [Commits](bokeh/bokeh@1.0.0...3.5.0)

---
updated-dependencies:
- dependency-name: bokeh
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added ignore-for-release maintenance issues related to versioning, dependencies, and other related elements labels Jul 8, 2024
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@tsalo tsalo left a comment

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I manually changed the minimum version and now it works.

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I just viewed the report with bokeh 3.5.0 and it looks fine.

@handwerkerd handwerkerd merged commit 18081c6 into main Jul 8, 2024
14 checks passed
@dependabot dependabot bot deleted the dependabot/pip/bokeh-lte-3.5.0-and-gte-3.5.0 branch July 8, 2024 20:29
BahmanTahayori pushed a commit to BahmanTahayori/tedana_florey that referenced this pull request Aug 30, 2024
* Limit current adaptive mask method to brain mask (ME-ICA#1060)

* Limit adaptive mask calculation to brain mask.

Limit adaptive mask calculation to brain mask.

Expand on logic of first adaptive mask method.

Update tedana/utils.py

Improve docstring.

Update test.

Add decreasing-signal-based adaptive mask.

Keep removing.

Co-Authored-By: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Use `compute_epi_mask` in t2smap workflow.

* Try fixing the tests.

* Fix make_adaptive_mask.

* Update test_utils.py

* Update test_utils.py

* Improve docstring.

* Update utils.py

* Update test_utils.py

* Revert "Update test_utils.py"

This reverts commit 259b002.

* Don't take absolute value of echo means.

* Log echo-wise thresholds in adaptive mask.

* Add comment about non-zero voxels.

* Update utils.py

* Update test_utils.py

* Update test_utils.py

* Update test_utils.py

* Log the thresholds again.

* Address review.

* Fix test.

---------

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Update nilearn requirement from <=0.10.3,>=0.7 to >=0.7,<=0.10.4 (ME-ICA#1077)

* Add adaptive mask plot to report (ME-ICA#1073)

* Update scikit-learn requirement (ME-ICA#1075)

Updates the requirements on [scikit-learn](https://github.com/scikit-learn/scikit-learn) to permit the latest version.
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@0.21.0...1.4.2)

---
updated-dependencies:
- dependency-name: scikit-learn
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Update pandas requirement from <=2.2.1,>=2.0 to >=2.0,<=2.2.2 (ME-ICA#1076)

Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v2.0.0...v2.2.2)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Update bokeh requirement from <=3.4.0,>=1.0.0 to >=1.0.0,<=3.4.1 (ME-ICA#1078)

Updates the requirements on [bokeh](https://github.com/bokeh/bokeh) to permit the latest version.
- [Changelog](https://github.com/bokeh/bokeh/blob/branch-3.5/docs/CHANGELOG)
- [Commits](bokeh/bokeh@1.0.0...3.4.1)

---
updated-dependencies:
- dependency-name: bokeh
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Load user-defined mask as expected by plot_adaptive_mask (ME-ICA#1079)

* DOC desc-optcomDenoised -> desc-denoised (ME-ICA#1080)

* docs: add mvdoc as a contributor for code, bug, and doc (ME-ICA#1082)

* docs: update README.md

* docs: update .all-contributorsrc

---------

Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>

* Identify the last good echo in adaptive mask instead of sum of good echoes (ME-ICA#1061)

* Limit adaptive mask calculation to brain mask.

Limit adaptive mask calculation to brain mask.

Expand on logic of first adaptive mask method.

Update tedana/utils.py

Improve docstring.

Update test.

Add decreasing-signal-based adaptive mask.

Keep removing.

Co-Authored-By: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Use `compute_epi_mask` in t2smap workflow.

* Try fixing the tests.

* Fix make_adaptive_mask.

* Update test_utils.py

* Update test_utils.py

* Improve docstring.

* Identify the last good echo instead of sum.

Improve docstring.

Update test_utils.py

Update test_utils.py

Fix make_adaptive_mask.

Try fixing the tests.

Use `compute_epi_mask` in t2smap workflow.

Limit adaptive mask calculation to brain mask.

Limit adaptive mask calculation to brain mask.

Expand on logic of first adaptive mask method.

Update tedana/utils.py

Improve docstring.

Update test.

Add decreasing-signal-based adaptive mask.

Keep removing.

Co-Authored-By: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Fix.

* Update utils.py

* Update utils.py

* Try fixing.

* Update utils.py

* Update utils.py

* add checks

* Just loop over voxels.

* Update utils.py

* Update utils.py

* Update test_utils.py

* Revert "Update test_utils.py"

This reverts commit 259b002.

* Update test_utils.py

* Update test_utils.py

* Remove checks.

* Don't take absolute value of echo means.

* Log echo-wise thresholds in adaptive mask.

* Add comment about non-zero voxels.

* Update utils.py

* Update utils.py

* Update test_utils.py

* Update test_utils.py

* Update test_utils.py

* Log the thresholds again.

* Update test_utils.py

* Update test_utils.py

* Update test_utils.py

* Add simulated data to adaptive mask test.

* Clean up the tests.

* Add value that tests the base mask.

* Remove print in test.

* Update tedana/utils.py

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Update tedana/utils.py

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

---------

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Output RMSE map and time series for decay model fit (ME-ICA#1044)

* Draft function to calculate decay model fit.

* Calculate root mean squared error instead.

* Incorporate metrics.

* Output RMSE results.

* Output results in tedana.

* Hopefully fix things.

* Update decay.py

* Try improving performance.

* Update decay.py

* Fix again.

* Use tqdm.

* Update decay.py

* Update decay.py

* Update decay.py

* Update expected outputs.

* Add figures.

* Update outputs.

* Include global signal in confounds file.

* Update fiu_four_echo_outputs.txt

* Rename function.

* Rename function.

* Update tedana.py

* Update tedana/decay.py

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Update decay.py

* Update decay.py

* Whoops.

* Apply suggestions from code review

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Fix things maybe.

* Fix things.

* Update decay.py

* Remove any files that are built through appending.

* Update outputs.

* Add section on plots to docs.

* Fix the description.

* Update docs/outputs.rst

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Update docs/outputs.rst

* Fix docstring.

---------

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* minimum nilearn 0.10.3 (ME-ICA#1094)

* Use nearest-neighbors interpolation in `plot_component` (ME-ICA#1098)

* Use nearest-neighbors interpolation in plot_stat_map.

* Only use NN interp for component maps.

* Update scipy requirement from <=1.13.0,>=1.2.0 to >=1.2.0,<=1.13.1 (ME-ICA#1100)

Updates the requirements on [scipy](https://github.com/scipy/scipy) to permit the latest version.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.2.0...v1.13.1)

---
updated-dependencies:
- dependency-name: scipy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Update scikit-learn requirement from <=1.4.2,>=0.21 to >=0.21,<=1.5.0 (ME-ICA#1101)

Updates the requirements on [scikit-learn](https://github.com/scikit-learn/scikit-learn) to permit the latest version.
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@0.21.0...1.5.0)

---
updated-dependencies:
- dependency-name: scikit-learn
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Update numpy requirement from <=1.26.4,>=1.16 to >=1.16,<=2.0.0 (ME-ICA#1104)

* Update numpy requirement from <=1.26.4,>=1.16 to >=1.16,<=2.0.0

Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.16.0...v2.0.0)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Use np.nan instead of np.NaN

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>

* Filter out non-diagonal affine warning (ME-ICA#1103)

* Filter out non-diagonal affine warning.

* Fix warning capture.

* Update tedana/reporting/static_figures.py

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Update static_figures.py

---------

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Update bokeh requirement from <=3.4.1,>=1.0.0 to <=3.5.0,>=3.5.0 (ME-ICA#1109)

* Update bokeh requirement from <=3.4.1,>=1.0.0 to <=3.5.0,>=3.5.0

Updates the requirements on [bokeh](https://github.com/bokeh/bokeh) to permit the latest version.
- [Changelog](https://github.com/bokeh/bokeh/blob/branch-3.6/docs/CHANGELOG)
- [Commits](bokeh/bokeh@1.0.0...3.5.0)

---
updated-dependencies:
- dependency-name: bokeh
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Update pyproject.toml

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>

* Update scikit-learn requirement from <=1.5.0,>=0.21 to <=1.5.1,>=1.5.1 (ME-ICA#1108)

* Update scikit-learn requirement from <=1.5.0,>=0.21 to <=1.5.1,>=1.5.1

Updates the requirements on [scikit-learn](https://github.com/scikit-learn/scikit-learn) to permit the latest version.
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@0.21.0...1.5.1)

---
updated-dependencies:
- dependency-name: scikit-learn
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Update pyproject.toml to restore minimum version of scikit-learn

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Update scipy requirement from <=1.13.1,>=1.2.0 to <=1.14.0,>=1.14.0 (ME-ICA#1106)

* Update scipy requirement from <=1.13.1,>=1.2.0 to <=1.14.0,>=1.14.0

Updates the requirements on [scipy](https://github.com/scipy/scipy) to permit the latest version.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.2.0...v1.14.0)

---
updated-dependencies:
- dependency-name: scipy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Update pyproject.toml to retain minimum version of scipy

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>
Co-authored-by: Eneko Uruñuela <e.urunuela@icloud.com>

* Update numpy requirement from <=2.0.0,>=1.16 to >=1.16,<=2.0.1 (ME-ICA#1112)

Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.16.0...v2.0.1)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Cleaning up installation instructions (ME-ICA#1113)

* install instructions

* Update docs/installation.rst

Co-authored-by: Taylor Salo <tsalo90@gmail.com>

* Update docs/installation.rst

Co-authored-by: Eneko Uruñuela <e.urunuela@icloud.com>

---------

Co-authored-by: Taylor Salo <tsalo90@gmail.com>
Co-authored-by: Eneko Uruñuela <e.urunuela@icloud.com>

* Update bokeh requirement from <=3.5.0,>=1.0.0 to >=1.0.0,<=3.5.1 (ME-ICA#1116)

Updates the requirements on [bokeh](https://github.com/bokeh/bokeh) to permit the latest version.
- [Changelog](https://github.com/bokeh/bokeh/blob/3.5.1/docs/CHANGELOG)
- [Commits](bokeh/bokeh@1.0.0...3.5.1)

---
updated-dependencies:
- dependency-name: bokeh
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Update list of multi-echo datasets (ME-ICA#1115)

* Generate metrics from external regressors using F stats (ME-ICA#1064)

* Get required metrics from decision tree.

* Continue changes.

* More updates.

* Store necessary_metrics as a list.

* Update selection_nodes.py

* Update selection_utils.py

* Update across the package.

* Keep updating.

* Update tedana.py

* Add extra metrics to list.

* Update ica_reclassify.py

* Draft metric-based regressor correlations.

* Fix typo.

* Work on trees.

* Expand regular expressions in trees.

* Fix up the expansion.

* Really fix it though.

* Fix style issue.

* Added external regress integration test

* Got intregration test with external regressors working

* Added F tests and options

* added corr_no_detrend.json

* updated names and reporting

* Run black.

* Address style issues.

* Try fixing test bugs.

* Update test_component_selector.py

* Update component_selector.py

* Use component table directly in selectcomps2use.

* Fix.

* Include generated metrics in necessary metrics.

* Update component_selector.py

* responding to feedback from tsalo

* Update component_selector.py

* Update test_component_selector.py

* fixed some testing failures

* fixed test_check_null_succeeds

* fixed ica_reclassify bug and selector_properties test

* ComponentSelector initialized before loading data

* fixed docstrings

* updated building decision tree docs

* using external regressors and most tests passing

* removed corr added tasks

* fit_model moved to stats

* removed and cleaned up external_regressors_config option

* Added task regressors and some tests. Now alll in decision tree

* cleaning up decision tree json files

* removed mot12_csf.json changed task to signal

* fixed tests with task_keep signal

* Update tedana/metrics/external.py

Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>

* Update tedana/metrics/_utils.py

Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>

* Update tedana/metrics/collect.py

Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>

* Update tedana/metrics/external.py

Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>

* Update tedana/metrics/external.py

Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>

* Responding to review comments

* reworded docstring

* Added type hints to external.py

* fixed external.py type hints

* type hints to _utils collect and component_selector

* type hints and doc improvements in selection_utils

* no expand_node recursion

* removed expand_nodes expand_node expand_dict

* docstring lines break on punctuation

* updating external tests and docs

* moved test data downloading to tests.utils.py and started test for fit_regressors

* fixed bug where task regressors retained in partial models

* matched testing external regressors to included mixing and fixed bugs

* Made single function for detrending regressors

* added tests for external fit_regressors and fix_mixing_to_regressors

* Full tests in test_external_metrics.py

* adding tests

* fixed extern regress validation warnings and added tests

* sorting set values for test outputs

* added to test_metrics

* Added docs to building_decision_trees.rst

* Added motion task decision tree flow chart

* made recommended change to external_regressor_config

* Finished documentation and renamed demo decision trees

* added link to example external regressors tsv file

* Apply suggestions from code review

Fixed nuissance typos

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* Minor documentation edits

---------

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* Link to the open-multi-echo-data website (ME-ICA#1117)

* Update multi-echo.rst

* Update multi-echo.rst

* Refactor `metrics.dependence` module (ME-ICA#1088)

* Add type hints to metric functions.

* Use keyword arguments.

* Update tests.

* Update dependence.py

* Update collect.py

* Fix other stuff.

* documentation and resource updates (ME-ICA#1114)

* documentation and resource updates

* Fixed citation numbering and updated posters

---------

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handwerkerd added a commit that referenced this pull request Sep 23, 2024
…sults (#1013)

* Add robustica method

* Incorporation of major comments regarding robustica addition

Manual modification of commit f2cdb4e to remove unwanted file additions.

* Add robustica 0.1.3 to dependency list

Cherry-pick of 41354cb.

* Multiple fixes to RobustICA addition from code review

From: BahmanTahayori#2.

Co-authored-by: Robert E. Smith <robert.smith@florey.edu.au>

* Specify magic number fixed seed of 42 as a constant

Cherry-pick of da1b128 (with modification).

* Updated

* Robustica Updates

* Incorporating the third round of Robert E. Smith's comments

* Enhance the "ica_method" description suggested by D. Handwerker

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Enhancing the "n_robust_runs" description suggested by D. Handwerkerd

Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* RobustICA: Restructure code loop over robust methods (#4)

* RobustICA: Restructure code loop over robust methods

* Addressing the issue with try/except

---------

Co-authored-by: Bahman <tahayori@gmail.com>

* Applied suggested changes

In this commit, some of the comments from Daniel Handwerker and Robert
Smith were incorporated.

* Incorporating more comments

* Fixing the problem of argument parser for n_robust_runs.

* Removing unnecessary tests from the test_integration. There are 3
  tests for echo as before, but the ica_method is robustica for five and
three echos and fatsica for the four echo test.

* Adding already requested changes

* fixed failing tests

* updated documentation in faq.rst

* more documentation changes

* Update docs/faq.rst

Co-authored-by: Robert Smith <robert.smith@florey.edu.au>

* Update docs/faq.rst

Co-authored-by: Robert Smith <robert.smith@florey.edu.au>

* Aligning robustICA with current Main + (#5)

* Limit current adaptive mask method to brain mask (#1060)

* Limit adaptive mask calculation to brain mask.

Limit adaptive mask calculation to brain mask.

Expand on logic of first adaptive mask method.

Update tedana/utils.py

Improve docstring.

Update test.

Add decreasing-signal-based adaptive mask.

Keep removing.

Co-Authored-By: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Use `compute_epi_mask` in t2smap workflow.

* Try fixing the tests.

* Fix make_adaptive_mask.

* Update test_utils.py

* Update test_utils.py

* Improve docstring.

* Update utils.py

* Update test_utils.py

* Revert "Update test_utils.py"

This reverts commit 259b002.

* Don't take absolute value of echo means.

* Log echo-wise thresholds in adaptive mask.

* Add comment about non-zero voxels.

* Update utils.py

* Update test_utils.py

* Update test_utils.py

* Update test_utils.py

* Log the thresholds again.

* Address review.

* Fix test.

---------

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* Update nilearn requirement from <=0.10.3,>=0.7 to >=0.7,<=0.10.4 (#1077)

* Add adaptive mask plot to report (#1073)

* Update scikit-learn requirement (#1075)

Updates the requirements on [scikit-learn](https://github.com/scikit-learn/scikit-learn) to permit the latest version.
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* Update pandas requirement from <=2.2.1,>=2.0 to >=2.0,<=2.2.2 (#1076)

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* Update bokeh requirement from <=3.4.0,>=1.0.0 to >=1.0.0,<=3.4.1 (#1078)

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* Load user-defined mask as expected by plot_adaptive_mask (#1079)

* DOC desc-optcomDenoised -> desc-denoised (#1080)

* docs: add mvdoc as a contributor for code, bug, and doc (#1082)

* docs: update README.md

* docs: update .all-contributorsrc

---------

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* Identify the last good echo in adaptive mask instead of sum of good echoes (#1061)

* Limit adaptive mask calculation to brain mask.

Limit adaptive mask calculation to brain mask.

Expand on logic of first adaptive mask method.

Update tedana/utils.py

Improve docstring.

Update test.

Add decreasing-signal-based adaptive mask.

Keep removing.

Co-Authored-By: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Use `compute_epi_mask` in t2smap workflow.

* Try fixing the tests.

* Fix make_adaptive_mask.

* Update test_utils.py

* Update test_utils.py

* Improve docstring.

* Identify the last good echo instead of sum.

Improve docstring.

Update test_utils.py

Update test_utils.py

Fix make_adaptive_mask.

Try fixing the tests.

Use `compute_epi_mask` in t2smap workflow.

Limit adaptive mask calculation to brain mask.

Limit adaptive mask calculation to brain mask.

Expand on logic of first adaptive mask method.

Update tedana/utils.py

Improve docstring.

Update test.

Add decreasing-signal-based adaptive mask.

Keep removing.

Co-Authored-By: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>

* Fix.

* Update utils.py

* Update utils.py

* Try fixing.

* Update utils.py

* Update utils.py

* add checks

* Just loop over voxels.

* Update utils.py

* Update utils.py

* Update test_utils.py

* Revert "Update test_utils.py"

This reverts commit 259b002.

* Update test_utils.py

* Update test_utils.py

* Remove checks.

* Don't take absolute value of echo means.

* Log echo-wise thresholds in adaptive mask.

* Add comment about non-zero voxels.

* Update utils.py

* Update utils.py

* Update test_utils.py

* Update test_utils.py

* Update test_utils.py

* Log the thresholds again.

* Update test_utils.py

* Update test_utils.py

* Update test_utils.py

* Add simulated data to adaptive mask test.

* Clean up the tests.

* Add value that tests the base mask.

* Remove print in test.

* Update tedana/utils.py

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* Update tedana/utils.py

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---------

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* Output RMSE map and time series for decay model fit (#1044)

* Draft function to calculate decay model fit.

* Calculate root mean squared error instead.

* Incorporate metrics.

* Output RMSE results.

* Output results in tedana.

* Hopefully fix things.

* Update decay.py

* Try improving performance.

* Update decay.py

* Fix again.

* Use tqdm.

* Update decay.py

* Update decay.py

* Update decay.py

* Update expected outputs.

* Add figures.

* Update outputs.

* Include global signal in confounds file.

* Update fiu_four_echo_outputs.txt

* Rename function.

* Rename function.

* Update tedana.py

* Update tedana/decay.py

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* Update decay.py

* Update decay.py

* Whoops.

* Apply suggestions from code review

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* Fix things maybe.

* Fix things.

* Update decay.py

* Remove any files that are built through appending.

* Update outputs.

* Add section on plots to docs.

* Fix the description.

* Update docs/outputs.rst

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* Update docs/outputs.rst

* Fix docstring.

---------

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* minimum nilearn 0.10.3 (#1094)

* Use nearest-neighbors interpolation in `plot_component` (#1098)

* Use nearest-neighbors interpolation in plot_stat_map.

* Only use NN interp for component maps.

* Update scipy requirement from <=1.13.0,>=1.2.0 to >=1.2.0,<=1.13.1 (#1100)

Updates the requirements on [scipy](https://github.com/scipy/scipy) to permit the latest version.
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* Update scikit-learn requirement from <=1.4.2,>=0.21 to >=0.21,<=1.5.0 (#1101)

Updates the requirements on [scikit-learn](https://github.com/scikit-learn/scikit-learn) to permit the latest version.
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* Update numpy requirement from <=1.26.4,>=1.16 to >=1.16,<=2.0.0 (#1104)

* Update numpy requirement from <=1.26.4,>=1.16 to >=1.16,<=2.0.0

Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
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* Use np.nan instead of np.NaN

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* Filter out non-diagonal affine warning (#1103)

* Filter out non-diagonal affine warning.

* Fix warning capture.

* Update tedana/reporting/static_figures.py

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* Update static_figures.py

---------

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* Update bokeh requirement from <=3.4.1,>=1.0.0 to <=3.5.0,>=3.5.0 (#1109)

* Update bokeh requirement from <=3.4.1,>=1.0.0 to <=3.5.0,>=3.5.0

Updates the requirements on [bokeh](https://github.com/bokeh/bokeh) to permit the latest version.
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* Update scikit-learn requirement from <=1.5.0,>=0.21 to <=1.5.1,>=1.5.1 (#1108)

* Update scikit-learn requirement from <=1.5.0,>=0.21 to <=1.5.1,>=1.5.1

Updates the requirements on [scikit-learn](https://github.com/scikit-learn/scikit-learn) to permit the latest version.
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* Update scipy requirement from <=1.13.1,>=1.2.0 to <=1.14.0,>=1.14.0 (#1106)

* Update scipy requirement from <=1.13.1,>=1.2.0 to <=1.14.0,>=1.14.0

Updates the requirements on [scipy](https://github.com/scipy/scipy) to permit the latest version.
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* Update numpy requirement from <=2.0.0,>=1.16 to >=1.16,<=2.0.1 (#1112)

Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
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* Cleaning up installation instructions (#1113)

* install instructions

* Update docs/installation.rst

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* Update docs/installation.rst

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* Update bokeh requirement from <=3.5.0,>=1.0.0 to >=1.0.0,<=3.5.1 (#1116)

Updates the requirements on [bokeh](https://github.com/bokeh/bokeh) to permit the latest version.
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* Update list of multi-echo datasets (#1115)

* Generate metrics from external regressors using F stats (#1064)

* Get required metrics from decision tree.

* Continue changes.

* More updates.

* Store necessary_metrics as a list.

* Update selection_nodes.py

* Update selection_utils.py

* Update across the package.

* Keep updating.

* Update tedana.py

* Add extra metrics to list.

* Update ica_reclassify.py

* Draft metric-based regressor correlations.

* Fix typo.

* Work on trees.

* Expand regular expressions in trees.

* Fix up the expansion.

* Really fix it though.

* Fix style issue.

* Added external regress integration test

* Got intregration test with external regressors working

* Added F tests and options

* added corr_no_detrend.json

* updated names and reporting

* Run black.

* Address style issues.

* Try fixing test bugs.

* Update test_component_selector.py

* Update component_selector.py

* Use component table directly in selectcomps2use.

* Fix.

* Include generated metrics in necessary metrics.

* Update component_selector.py

* responding to feedback from tsalo

* Update component_selector.py

* Update test_component_selector.py

* fixed some testing failures

* fixed test_check_null_succeeds

* fixed ica_reclassify bug and selector_properties test

* ComponentSelector initialized before loading data

* fixed docstrings

* updated building decision tree docs

* using external regressors and most tests passing

* removed corr added tasks

* fit_model moved to stats

* removed and cleaned up external_regressors_config option

* Added task regressors and some tests. Now alll in decision tree

* cleaning up decision tree json files

* removed mot12_csf.json changed task to signal

* fixed tests with task_keep signal

* Update tedana/metrics/external.py

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* Update tedana/metrics/_utils.py

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* Update tedana/metrics/collect.py

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* Update tedana/metrics/external.py

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* Update tedana/metrics/external.py

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* Responding to review comments

* reworded docstring

* Added type hints to external.py

* fixed external.py type hints

* type hints to _utils collect and component_selector

* type hints and doc improvements in selection_utils

* no expand_node recursion

* removed expand_nodes expand_node expand_dict

* docstring lines break on punctuation

* updating external tests and docs

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* fixed bug where task regressors retained in partial models

* matched testing external regressors to included mixing and fixed bugs

* Made single function for detrending regressors

* added tests for external fit_regressors and fix_mixing_to_regressors

* Full tests in test_external_metrics.py

* adding tests

* fixed extern regress validation warnings and added tests

* sorting set values for test outputs

* added to test_metrics

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* Added motion task decision tree flow chart

* made recommended change to external_regressor_config

* Finished documentation and renamed demo decision trees

* added link to example external regressors tsv file

* Apply suggestions from code review

Fixed nuissance typos

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* Minor documentation edits

---------

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* Link to the open-multi-echo-data website (#1117)

* Update multi-echo.rst

* Update multi-echo.rst

* Refactor `metrics.dependence` module (#1088)

* Add type hints to metric functions.

* Use keyword arguments.

* Update tests.

* Update dependence.py

* Update collect.py

* Fix other stuff.

* documentation and resource updates (#1114)

* documentation and resource updates

* Fixed citation numbering and updated posters

---------

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* Adding already requested changes

* fixed failing tests

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* align with main

* fixed ica.py docstring error

* added scikit-learn-extra to pyproject and changed ref name

* increment circleci version keys

* Removing the scikit-learn-extra dependency

* Updating pyproject.toml file

* Minor changes to make the help more readable

* Minor changes

* upgrading to robustica 0.1.4

* Update docs

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* updating utils.py, toml file and the docs

* minor change to utils.py

* Incorporating Eneko's comments

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* Added a warning when the clustering method is changed

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Co-authored-by: Robert E. Smith <robert.smith@florey.edu.au>
Co-authored-by: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>
Co-authored-by: handwerkerd <dan.handwerker@gmail.com>
Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Matteo Visconti di Oleggio Castello <mvdoc@users.noreply.github.com>
Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: Eneko Uruñuela <e.urunuela@icloud.com>
Co-authored-by: Taylor Salo <tsalo90@gmail.com>
Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
Co-authored-by: Neha Reddy <nreddy@northwestern.edu>
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