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[REF] Decision Tree Modularization#756

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tsalo merged 207 commits intoME-ICA:mainME-ICA/tedana:mainfrom jbteves:JT_DTMCopy head branch name to clipboardMay 11, 2023

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Commits on Aug 8, 2022

• Decision tree refactor with minimal and kundu

  

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• Fix commented-out tedana workflow

  

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• Appease the style checker

  

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• All tremble before the mighty linter

  

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• Actually fix incorrect style checker issue

  

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• Unfix another style checker error

  

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• Attempt to make Black happy, even though it does not actually say what's wrong

  

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Commits on Aug 9, 2022

• ran black

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• Merge pull request #10 from handwerkerd/DTM_BlackFix

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Commits on Aug 10, 2022

• Added elbows to reports

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• Merge pull request #11 from handwerkerd/AddElbowsToReport

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Commits on Aug 16, 2022

• fixing kundu tree and added calc_median

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Commits on Aug 17, 2022

• kundu.json added comment

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• kundu kappa_elbow is GTE not GT

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• kundu dtm matches main and minimal updated

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• flake8 style fixes

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Commits on Aug 18, 2022

• Merge pull request #12 from handwerkerd/harmonizing_kunduDTM_with_main

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• fixed linting

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• fixed report elbow warning

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• Merge pull request #13 from handwerkerd/harmonizing_kunduDTM_with_main

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• removed unneeded second d_table calc function

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• Merge pull request #14 from handwerkerd/harmonizing_kunduDTM_with_main

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Commits on Aug 19, 2022

• Links building decision trees to index

  

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• Adds ComponentSelector to API docs

  

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• Set language to English

  

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• Fix dead nilearn link

  

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Commits on Aug 31, 2022

• Add load_config and ComponentSelector to API docs

  

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Commits on Sep 7, 2022

• Fix mixing matrix over-save bug

  

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Commits on Sep 13, 2022

• Separately modularized kappa & rho elbow calcs and created liberal rho elbow (#15)

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Commits on Sep 15, 2022

• Enable tedana_reclassify as console script

  

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• Merge remote-tracking branch 'origin/JT_DTM' into JT_DTM

  

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Commits on Sep 22, 2022

• No errors if no xcomp but also no decide_comps (#16)

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Commits on Nov 16, 2022

• Merges main

  

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• Update tedana/io.py

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• Appease style checker

  

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• Merge remote-tracking branch 'origin/JT_DTM' into JT_DTM

  

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• Appease the style checker?

  

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• Force to use up to date setuptools; installation bug otherwise

  

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• Remove out of date make entry

  

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Commits on Nov 17, 2022

• Create functional reclassify CLI

  

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• Replace blanks with n/a

  

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• Maybe appease black

  

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Commits on Nov 18, 2022

• Fix typo

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• BIDSify some outputs

  

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• Appease black

  

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Commits on Nov 21, 2022

• Heavily revise ComponentSelector module docs

  

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Commits on Nov 23, 2022

• Fixing mid kappa A inconsistency (#17)

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• Merge branch 'main' into JT_DTM

  

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• Merge remote-tracking branch 'origin/JT_DTM' into JT_DTM

  

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• Drops 3.6 support

  

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• Remove 3.6 support from CircleCI tests

  

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• Reformat comment

  

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• Reduce line length

  

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• Update lint in Makefile

  

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• Correctly collect API submodule doc

  

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• Fix errors

  

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• Fix more sphinx

  

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Commits on Nov 29, 2022

• working on selector init documentation

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Commits on Nov 30, 2022

• Breaking up outputs.rst

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Commits on Dec 1, 2022

• partially updated output_file_descriptions.rst

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• changed n_bold_comps to n_accepted_comps

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• n_bold_comps to n_accepted_comps

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• ComponentSelector.py API docs cleaned up

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• selection_nodes decision_docs updated

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Commits on Dec 2, 2022

• selection_nodes docstrings cleaned up

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• Fixed a test for selection_nodes

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• Updated faq for tedana_reclassify and tree options

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• docstrings in tedica and other small updates

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Commits on Dec 5, 2022

• Updated docstrings in selection_utils.py

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• Update docs/output_file_descriptions.rst

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• Working on improving selector documentation (#18)

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• Merge main

  

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• Remove manual selection

  

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• Force user to pick a tree

  

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• Fix CLI test

  

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• Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs

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• Revert "Force user to pick a tree"

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• Revert "Fix CLI test"

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• Make kundu default tree

  

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• Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs

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• Attempt to fix error

  

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Commits on Dec 6, 2022

• Adds input data to registry

  

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• Revert "Adds input data to registry"

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Commits on Dec 12, 2022

• Adds input registration

  

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• Appease linter

  

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• Add class template start

  

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Commits on Dec 13, 2022

• Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs

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• Add previous workflow registry into new one

  

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• Fix failure to update tags and classifications in manual

  

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• Fix missing less likely BOOLD tag

  

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• Adds more useful reporting for unused metrics

  

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• Create generated metrics

  

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• Update line terminator

  

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• Force black to run before flake8

  

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• Updates percentile call

  

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• more doc updates

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• Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs

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• fixed meica to v2.5 in docstrings

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Commits on Dec 14, 2022

• docs building again

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Commits on Dec 15, 2022

• more updates to building decision trees

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• improved docs (#19)

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• Get rid of optional method keyword

  

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• Revert "Update line terminator"

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• Autodocument ComponentSelector methods/attributes (#20)

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• Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs

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• fixed rename of component_selector

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Commits on Dec 16, 2022

• Fixed remaining transition to component_selector (#21)

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Commits on Dec 19, 2022

• more doc updates

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• Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs

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Commits on Dec 20, 2022

• mostly classification_output_descriptions

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• Fixed io API and selector API warnings

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• message

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Commits on Dec 21, 2022

• key parts of docs all updated

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• output_file_descriptions fully updated

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• filled testing gaps for component_selector

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• Updates integration test fnames

  

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• Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs

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• Try a numpy fix

  

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• Try again

  

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• Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs

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• Remove dead code

  

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• Merge branch 'jbteves/JT_DTM' into improved_docs

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Commits on Dec 22, 2022

• full selector coverage (#23)

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• Add tedana_reclassify tests

  

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• Maybe actually add it

  

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• Change o to outdir

  

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• Fix noreports maybe

  

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• Fix tedort

  

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• CircleCI are you okay?

  

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• Circle if you keep this up I will switch to Actions

  

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• Maybe silence duecredit and re-trigger Circle

  

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• Try something else

  

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• Add references to resources package

  

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Commits on Dec 23, 2022

• Dispose of sanity check

  

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• Add more reclassify tests

  

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• Adaptive mask is not a bool

  

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• Add label for setup.cfg

  

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• Revert "Adaptive mask is not a bool"

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• Add resource files

  

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• Clarify variables

  

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• Merge branch 'main' into JT_DTM

  

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• Update date and weep

  

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Commits on Jan 4, 2023

• Fixed NoLikelyBOLDBug (#24)

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• fixed debug logging

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• Merge pull request #25 from handwerkerd/FixRedoICANoLikelyBOLD

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• Temporarily turn on force overwrite for redo ICA

  

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• Fixed I007 divergence

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• Merge remote-tracking branch 'jbteves/JT_DTM' into Fixed_I007_divergance

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Commits on Jan 5, 2023

• calc_varex_thresh now has num_highest_var_comps

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• fixed linting errors

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• Merge pull request #26 from handwerkerd/Fixed_I007_divergance

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• Update integration test data

  

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Commits on Jan 6, 2023

• Adds csv and text file reading for manual acc/rej

  

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• Add tests for CustomEncoder

  

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• Adds bibtex warning check test

  

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• Appease linter

  

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• Fix unused metrics warning

  

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• Add reclassify tests and patches to test failures

  

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Commits on Jan 10, 2023

• Make stylistic changes.

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• Remove trailing whitespace.

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Commits on Jan 11, 2023

• Spacing in io.

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• More minor changes.

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• Add custom napoleon section "Generated Files"

  

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• Replace numTrue/numFalse with n_true/n_false.

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• Replace ifTrue/ifFalse with if_true/if_false.

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• Use fill_doc.

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• Style fixes.

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• more int32

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• Merge pull request #27 from tsalo/dtm-review

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• Merge pull request #28 from handwerkerd/DTM_integer_to_int32

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• more int32 fun

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• Merge pull request #29 from handwerkerd/int32Fun

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• Appease linter

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• Fixed style issues

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• Merge main

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• Merge remote-tracking branch 'upstream/main' into pr/756

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• Add RICA to Approach section of docs

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• Fixed CI style check failure

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• DTM documentation review (#30)

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• Rename reclassify force (#32)

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• Add defaults to --help output (#31)

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• added ica_reclassify to setup.cfg

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• Using a more persistent cache for the testing data (#33)

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• Change to TestLGR.info

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Commits on Mar 15, 2023

• Fixing high variance classification mess (#34)

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• Replace versioneer with hatch (#35)

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• Fix CI (#36)

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• Add flake8-pyproject as a requirement. (#37)

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• Try fixing coverage. (#38)

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Commits on Apr 20, 2023

• Improving ica_reclassify (#39)

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• Ica reclassify registry fixes (#42)

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• Drop Python 3.6 and 3.7 support (#40)

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Commits on Apr 27, 2023

• added mixm to 4echo test (#43)

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• Updating Contributor Information (#41)

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Commits on May 4, 2023

• Added flow charts and some text (#44)

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• RTDfix (#45)

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• Update documentation (#46)

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Commits on May 9, 2023

• Output docs on one page (#47)

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Commits on May 11, 2023

• Merge branch 'main' into JT_DTM

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