Ecosyste.ms: Issues

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GitHub / ME-ICA/tedana issues and pull requests

#1067 - Draft March 2024 newsletter

Issue - State: closed - Opened by handwerkerd 11 months ago
Labels: discussion, community

#1066 - Changes to --tedpca option

Pull Request - State: open - Opened by Lestropie 11 months ago - 16 comments

#1064 - Generate metrics from external regressors using F stats

Pull Request - State: closed - Opened by handwerkerd 11 months ago - 18 comments

#1063 - dynamics reports crashing with bokeh 3.4.0

Issue - State: closed - Opened by handwerkerd 11 months ago - 2 comments
Labels: bug, good first issue, reports

#1062 - March 2024 Developers call

Issue - State: closed - Opened by handwerkerd 11 months ago
Labels: discussion, community

#1061 - Identify the last good echo in adaptive mask instead of sum of good echoes

Pull Request - State: closed - Opened by tsalo 11 months ago - 1 comment
Labels: bug

#1060 - Limit current adaptive mask method to brain mask

Pull Request - State: closed - Opened by tsalo 11 months ago - 7 comments
Labels: bug, breaking change

#1059 - Adaptive mask is generated using whole acquisition matrix, instead of brain mask

Issue - State: closed - Opened by tsalo 11 months ago - 1 comment
Labels: bug

#1058 - killed

Issue - State: closed - Opened by bedardp2 11 months ago

#1057 - Add `--masktype` option to control adaptive mask method

Pull Request - State: closed - Opened by tsalo 11 months ago - 4 comments
Labels: enhancement

#1056 - Support ICA on complex-valued data

Issue - State: closed - Opened by tsalo 11 months ago - 1 comment
Labels: enhancement, discussion, decomposition, effort: high, impact: medium

#1055 - Update nibabel requirement from <=5.2.0,>=2.5.1 to >=2.5.1,<=5.2.1

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: maintenance, ignore-for-release

#1054 - Detrending & tedana (or detrended variance explained)

Issue - State: open - Opened by handwerkerd 12 months ago - 9 comments
Labels: enhancement, effort: medium, impact: medium

#1053 - Censoring data within tedana

Issue - State: open - Opened by handwerkerd 12 months ago - 7 comments
Labels: enhancement, effort: high, impact: medium

#1052 - Limit selection node functions to minimal inputs

Issue - State: open - Opened by tsalo 12 months ago - 1 comment
Labels: refactoring

#1051 - Rename ComponentSelector to DecisionTree

Issue - State: open - Opened by tsalo 12 months ago - 1 comment
Labels: refactoring

#1050 - Enforce equal figure width in HTML report

Issue - State: closed - Opened by tsalo 12 months ago - 1 comment
Labels: enhancement, reports

#1049 - Improve multi-echo acquisition recommendations

Issue - State: open - Opened by tsalo 12 months ago - 5 comments
Labels: documentation, discussion

#1048 - Update pandas requirement from <=2.2.0,>=2.0 to >=2.0,<=2.2.1

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: maintenance, ignore-for-release

#1047 - RobustICA behaviour on non-convergence

Issue - State: open - Opened by Lestropie 12 months ago - 3 comments

#1045 - Improve component plots

Pull Request - State: closed - Opened by tsalo 12 months ago - 5 comments
Labels: enhancement, reports

#1044 - Output RMSE map and time series for decay model fit

Pull Request - State: closed - Opened by tsalo 12 months ago - 9 comments
Labels: enhancement

#1043 - Document decision tree steps in report and remove log_extra_report

Pull Request - State: closed - Opened by handwerkerd 12 months ago - 4 comments
Labels: refactoring

#1042 - Check orientation of brain/acquisition in figures

Issue - State: closed - Opened by tsalo 12 months ago
Labels: enhancement, reports

#1041 - Add a check on volumes and TE input order

Issue - State: open - Opened by tsalo 12 months ago
Labels: bug

#1040 - Add T2* and S0 figures

Pull Request - State: closed - Opened by tsalo 12 months ago - 13 comments
Labels: enhancement, reports

#1039 - docs: add martaarbizu as a contributor for code

Pull Request - State: closed - Opened by allcontributors[bot] 12 months ago - 1 comment

#1038 - Update nilearn requirement from <=0.10.2,>=0.7 to >=0.7,<=0.10.3

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 5 comments
Labels: maintenance, ignore-for-release

#1037 - Update scikit-learn requirement from <=1.4.0,>=0.21 to >=0.21,<=1.4.1.post1

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: maintenance, ignore-for-release

#1036 - Update mapca requirement from <=0.0.4,>=0.0.4 to >=0.0.4,<=0.0.5

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 2 comments
Labels: maintenance, ignore-for-release

#1035 - Update numpy requirement from <=1.26.3,>=1.16 to >=1.16,<=1.26.4

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: maintenance, ignore-for-release

#1034 - Refactor `ComponentSelector` to match sklearn's `DecisionTreeClassifier`

Issue - State: open - Opened by tsalo 12 months ago
Labels: refactoring, TE-dependence

#1033 - Remove accepted and rejected time series from the standard file outputs and change denoised time series name (updated)

Pull Request - State: closed - Opened by handwerkerd 12 months ago - 3 comments
Labels: breaking change

#1032 - docs: add martinezeguiluz as a contributor for code

Pull Request - State: closed - Opened by allcontributors[bot] 12 months ago - 1 comment

#1031 - Fix error on empty input file & pre-commit updated to black version 24.2.0

Pull Request - State: closed - Opened by handwerkerd 12 months ago - 5 comments

#1030 - Support YAMLs for config files

Issue - State: open - Opened by tsalo 12 months ago - 4 comments
Labels: enhancement, documentation

#1029 - Pin maximum versions of dependencies in pyproject.toml

Pull Request - State: closed - Opened by tsalo 12 months ago - 7 comments
Labels: maintenance, ignore-for-release

#1028 - Switch to pinning maximum versions in pyproject.toml

Issue - State: closed - Opened by tsalo 12 months ago

#1027 - February 2024 Developers call

Issue - State: closed - Opened by handwerkerd 12 months ago
Labels: discussion, community

#1026 - Bump actions/checkout from 2 to 4

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 2 comments
Labels: maintenance, ignore-for-release

#1025 - Bump actions/setup-python from 2 to 5

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 2 comments
Labels: maintenance, ignore-for-release

#1024 - Add Dependabot config and switch Release Drafter to Changelog config

Pull Request - State: closed - Opened by tsalo almost 1 year ago - 2 comments
Labels: maintenance

#1023 - Decompose, and classify components from, FIT-T2* and FIT-S0

Issue - State: open - Opened by tsalo about 1 year ago - 10 comments
Labels: enhancement, question, discussion, decomposition

#1022 - Support complex-valued decomposition on analytic signal to account for lagged signals

Issue - State: open - Opened by tsalo about 1 year ago - 1 comment
Labels: enhancement, discussion, decomposition, effort: high, impact: high

#1021 - Allow for correlations with regressors in decision tree

Pull Request - State: closed - Opened by tsalo about 1 year ago - 10 comments
Labels: enhancement

#1020 - Reformat with new version of black

Pull Request - State: closed - Opened by tsalo about 1 year ago - 2 comments
Labels: refactoring

#1019 - mapca error

Issue - State: closed - Opened by rhl508 about 1 year ago - 6 comments

#1018 - docs: add goodalse2019 as a contributor for doc, ideas, and question

Pull Request - State: closed - Opened by allcontributors[bot] about 1 year ago - 1 comment

#1017 - [DOC] Replaced newsletter with Google Groups

Pull Request - State: closed - Opened by goodalse2019 about 1 year ago - 7 comments

#1016 - [DOC] Replace newsletter as Google Group

Pull Request - State: closed - Opened by goodalse2019 about 1 year ago - 1 comment

#1015 - January 2024 Developers call

Issue - State: closed - Opened by handwerkerd about 1 year ago
Labels: discussion, community

#1014 - Adding python library version numbers

Pull Request - State: closed - Opened by handwerkerd about 1 year ago - 1 comment
Labels: reports, effort: low, impact: medium, maintenance

#1013 - Adding robustica option to ICA decomposition to achieve consistent results

Pull Request - State: closed - Opened by BahmanTahayori about 1 year ago - 12 comments

#1012 - Fixed Inappropriate Logical Expression

Pull Request - State: closed - Opened by fazledyn-or about 1 year ago - 1 comment

#1011 - TinyLetter shutting down

Issue - State: closed - Opened by handwerkerd about 1 year ago - 5 comments
Labels: discussion, community, priority: medium

#1010 - Fixing ica_reclassify CLI documentation typo

Pull Request - State: closed - Opened by handwerkerd about 1 year ago - 1 comment
Labels: documentation

#1009 - Add option to classify components based on their correlation with regressors

Issue - State: closed - Opened by eurunuela about 1 year ago
Labels: enhancement, priority: low, effort: high, impact: high

#1008 - [ENH] Allow for correlations with regressors in decision tree

Pull Request - State: closed - Opened by eurunuela about 1 year ago - 7 comments

#1007 - Fix error on empty input file

Pull Request - State: closed - Opened by martinezeguiluz about 1 year ago - 1 comment

#1006 - Remove accepted and rejected time series from the standard file outputs and change denoised time series name

Pull Request - State: closed - Opened by martaarbizu about 1 year ago - 6 comments
Labels: breaking change

#1004 - docs: add effigies as a contributor for code

Pull Request - State: closed - Opened by allcontributors[bot] about 1 year ago - 1 comment

#1003 - docs: add bpinsard as a contributor for code

Pull Request - State: closed - Opened by allcontributors[bot] about 1 year ago - 4 comments

#1002 - Fix style issues 2

Pull Request - State: closed - Opened by martaarbizu about 1 year ago

#1001 - Fix Bibtex rendering in reports

Pull Request - State: closed - Opened by eurunuela about 1 year ago - 8 comments

#999 - MNT: Test on 3.11 and 3.12

Pull Request - State: closed - Opened by effigies about 1 year ago - 7 comments
Labels: testing, maintenance

#998 - MNT: Uncap dependencies

Pull Request - State: closed - Opened by effigies about 1 year ago - 3 comments

#997 - Test project board automatization

Issue - State: closed - Opened by eurunuela about 1 year ago - 1 comment
Labels: documentation

#996 - November 2023 Developers Call

Issue - State: closed - Opened by handwerkerd about 1 year ago
Labels: discussion, community

#995 - remove unecessary copy of large data

Pull Request - State: closed - Opened by bpinsard over 1 year ago - 10 comments

#994 - Exclude tests folder from precommit hooks.

Pull Request - State: closed - Opened by eurunuela over 1 year ago - 2 comments

#993 - Search on tedana.readthedocs.io is hanging

Issue - State: closed - Opened by handwerkerd over 1 year ago - 4 comments
Labels: bug, help wanted, good first issue, documentation, priority: medium, effort: medium, impact: high

#992 - Create a GitHub Action to automatically add issues to projects

Pull Request - State: closed - Opened by eurunuela over 1 year ago - 10 comments

#991 - Get parameter visualization back into the documentation

Issue - State: open - Opened by handwerkerd over 1 year ago - 1 comment
Labels: documentation, priority: medium, effort: medium, impact: medium

#990 - Revisit documentation recommendations for alignment

Issue - State: open - Opened by handwerkerd over 1 year ago - 1 comment
Labels: documentation, priority: low, effort: low, impact: low

#986 - Fix reference rendering in HTML report

Issue - State: closed - Opened by handwerkerd over 1 year ago - 4 comments
Labels: bug, good first issue, reports, priority: medium, effort: medium, impact: low

#985 - Make it clearer in CONTRIBUTING.md how devs can make pre-commit work

Pull Request - State: closed - Opened by eurunuela over 1 year ago - 2 comments

#984 - October 2023 Developers Call and meeting time poll

Issue - State: closed - Opened by handwerkerd over 1 year ago
Labels: discussion, community

#983 - Add .pre-commit-config.yaml

Pull Request - State: closed - Opened by eurunuela over 1 year ago - 2 comments

#982 - Remove `log_extra_report` from decision tree configs

Issue - State: closed - Opened by tsalo over 1 year ago - 1 comment
Labels: refactoring

#981 - Add prefix to pre-defined ICA mixing matrix

Issue - State: open - Opened by tsalo over 1 year ago
Labels: bug

#980 - What to do if a provided ICA mixing matrix doesn't result in likely BOLD components

Issue - State: open - Opened by handwerkerd over 1 year ago - 1 comment
Labels: decomposition, priority: medium, effort: low, impact: low

#979 - Color is wrong in component classification pie charts

Issue - State: closed - Opened by yonestar over 1 year ago - 2 comments

#978 - September 2023 Developers Call

Issue - State: closed - Opened by handwerkerd over 1 year ago - 10 comments
Labels: discussion, community

#977 - Split out reports dependencies

Pull Request - State: open - Opened by tsalo over 1 year ago - 2 comments

#976 - Fragile dependencies

Issue - State: closed - Opened by effigies over 1 year ago - 2 comments

#975 - Add PCA methods to report

Issue - State: open - Opened by eurunuela over 1 year ago - 5 comments
Labels: enhancement, discussion

#974 - ica_reclassify Errors on Empty Input File

Issue - State: closed - Opened by rylandm over 1 year ago
Labels: bug, good first issue

#973 - Add pre-commit to automatically fix style issue before pushing commits

Pull Request - State: closed - Opened by eurunuela over 1 year ago - 3 comments

#972 - Proposal to add pre-commits to tedana

Issue - State: closed - Opened by eurunuela over 1 year ago - 3 comments
Labels: discussion, priority: low, effort: low, impact: low, maintenance

#971 - Add minimally-processed Reddy dataset to datasets module

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: priority: low, effort: medium, impact: medium, datasets

#970 - Lint codebase with additional style restrictions

Pull Request - State: closed - Opened by tsalo over 1 year ago - 23 comments
Labels: testing, refactoring

#969 - Generate metrics based on decision tree

Pull Request - State: closed - Opened by tsalo over 1 year ago - 16 comments
Labels: enhancement, refactoring

#968 - [FIX] Styling issues and make RTD build work

Pull Request - State: closed - Opened by eurunuela over 1 year ago - 4 comments
Labels: maintenance

#967 - Style test is not passing

Issue - State: closed - Opened by eurunuela over 1 year ago - 2 comments
Labels: bug, priority: high, effort: low, impact: medium, maintenance

#966 - [FIX] Make RTD build work

Pull Request - State: closed - Opened by eurunuela over 1 year ago - 2 comments

#965 - Remove RefLGR from code and refs field from decision trees

Pull Request - State: closed - Opened by tsalo over 1 year ago - 8 comments
Labels: bug

#964 - Add minimally-processed CAT-D dataset to datasets module

Issue - State: closed - Opened by tsalo over 1 year ago
Labels: priority: low, effort: medium, impact: medium, datasets

#963 - Add prefix to all output files

Pull Request - State: closed - Opened by tsalo over 1 year ago - 13 comments
Labels: enhancement, breaking change