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[REF] Decision Tree Modularization #756

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merged 207 commits into from
May 11, 2023
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4b8e555
Decision tree refactor with minimal and kundu
Aug 8, 2022
7663afb
Fix commented-out tedana workflow
Aug 8, 2022
1284ff5
Appease the style checker
Aug 8, 2022
bfbc509
All tremble before the mighty linter
Aug 8, 2022
f01a9a9
Actually fix incorrect style checker issue
Aug 8, 2022
29b6fba
Unfix another style checker error
Aug 8, 2022
ac34882
Attempt to make Black happy, even though it does not actually say wha…
Aug 8, 2022
9e8159a
ran black
handwerkerd Aug 9, 2022
c67bfa8
Merge pull request #10 from handwerkerd/DTM_BlackFix
jbteves Aug 9, 2022
fd4abf2
Added elbows to reports
handwerkerd Aug 10, 2022
8935063
Merge pull request #11 from handwerkerd/AddElbowsToReport
jbteves Aug 10, 2022
d3f0b6b
fixing kundu tree and added calc_median
handwerkerd Aug 16, 2022
e72c1e0
kundu.json added comment
handwerkerd Aug 17, 2022
f34f1b8
kundu kappa_elbow is GTE not GT
handwerkerd Aug 17, 2022
de87de3
kundu dtm matches main and minimal updated
handwerkerd Aug 17, 2022
b7219fd
flake8 style fixes
handwerkerd Aug 17, 2022
27d5851
Merge pull request #12 from handwerkerd/harmonizing_kunduDTM_with_main
jbteves Aug 18, 2022
f81dac2
fixed linting
handwerkerd Aug 18, 2022
20548f4
fixed report elbow warning
handwerkerd Aug 18, 2022
0af24d2
Merge pull request #13 from handwerkerd/harmonizing_kunduDTM_with_main
jbteves Aug 18, 2022
2802e38
removed unneeded second d_table calc function
handwerkerd Aug 18, 2022
7018b04
Merge pull request #14 from handwerkerd/harmonizing_kunduDTM_with_main
jbteves Aug 18, 2022
92ae3eb
Links building decision trees to index
Aug 19, 2022
f8d479b
Adds ComponentSelector to API docs
Aug 19, 2022
e544bf9
Set language to English
Aug 19, 2022
617fa9a
Fix dead nilearn link
Aug 19, 2022
ed083a5
Add load_config and ComponentSelector to API docs
Aug 31, 2022
e60f87a
Fix mixing matrix over-save bug
Sep 7, 2022
800f181
Separately modularized kappa & rho elbow calcs and created liberal rh…
handwerkerd Sep 13, 2022
d1366ad
Enable tedana_reclassify as console script
Sep 15, 2022
dccc35d
Merge remote-tracking branch 'origin/JT_DTM' into JT_DTM
Sep 15, 2022
b65b133
No errors if no xcomp but also no decide_comps (#16)
handwerkerd Sep 22, 2022
31a94b0
Merges main
Nov 16, 2022
df9afbe
Update tedana/io.py
jbteves Nov 16, 2022
2c9dd19
Appease style checker
Nov 16, 2022
2e7b49f
Merge remote-tracking branch 'origin/JT_DTM' into JT_DTM
Nov 16, 2022
9ae1b90
Appease the style checker?
Nov 16, 2022
df7048a
Force to use up to date setuptools; installation bug otherwise
Nov 16, 2022
e60bb81
Remove out of date make entry
Nov 16, 2022
7073604
Create functional reclassify CLI
Nov 17, 2022
37456d2
Replace blanks with n/a
Nov 17, 2022
ae15075
Maybe appease black
Nov 17, 2022
cce4d37
Fix typo
Nov 18, 2022
2622ba5
BIDSify some outputs
Nov 18, 2022
12debd3
Appease black
Nov 18, 2022
9f59824
Heavily revise ComponentSelector module docs
Nov 21, 2022
7a5ffff
Fixing mid kappa A inconsistency (#17)
handwerkerd Nov 23, 2022
a333987
Merge branch 'main' into JT_DTM
Nov 23, 2022
bc443ab
Merge remote-tracking branch 'origin/JT_DTM' into JT_DTM
Nov 23, 2022
5a768be
Drops 3.6 support
Nov 23, 2022
e40bd60
Remove 3.6 support from CircleCI tests
Nov 23, 2022
6caeecf
Reformat comment
Nov 23, 2022
723e6af
Reduce line length
Nov 23, 2022
48bfe5a
Update lint in Makefile
Nov 23, 2022
f403e38
Correctly collect API submodule doc
Nov 23, 2022
e3db441
Fix errors
Nov 23, 2022
12169d7
Fix more sphinx
Nov 23, 2022
509affd
working on selector init documentation
handwerkerd Nov 29, 2022
4c7abce
Breaking up outputs.rst
handwerkerd Nov 30, 2022
a881b57
partially updated output_file_descriptions.rst
handwerkerd Dec 1, 2022
05757ff
changed n_bold_comps to n_accepted_comps
handwerkerd Dec 1, 2022
6d44265
n_bold_comps to n_accepted_comps
handwerkerd Dec 1, 2022
e91498e
ComponentSelector.py API docs cleaned up
handwerkerd Dec 1, 2022
d09c977
selection_nodes decision_docs updated
handwerkerd Dec 1, 2022
6dd25ff
selection_nodes docstrings cleaned up
handwerkerd Dec 2, 2022
6e597ae
Fixed a test for selection_nodes
handwerkerd Dec 2, 2022
e13d680
Updated faq for tedana_reclassify and tree options
handwerkerd Dec 2, 2022
413a1df
docstrings in tedica and other small updates
handwerkerd Dec 2, 2022
728ceb3
Updated docstrings in selection_utils.py
handwerkerd Dec 5, 2022
fe9ff44
Update docs/output_file_descriptions.rst
jbteves Dec 5, 2022
a662355
Working on improving selector documentation (#18)
handwerkerd Dec 5, 2022
9544422
Merge main
Dec 5, 2022
f7ee8db
Remove manual selection
Dec 5, 2022
4fc656f
Force user to pick a tree
Dec 5, 2022
4038336
Fix CLI test
Dec 5, 2022
95b367e
Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs
handwerkerd Dec 5, 2022
ca57825
Revert "Force user to pick a tree"
Dec 5, 2022
3a8bd8b
Revert "Fix CLI test"
Dec 5, 2022
e77cdd0
Make kundu default tree
Dec 5, 2022
a11a409
Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs
handwerkerd Dec 5, 2022
9d22468
Attempt to fix error
Dec 5, 2022
c7349bd
Adds input data to registry
Dec 6, 2022
7959f8f
Revert "Adds input data to registry"
Dec 6, 2022
5ff5883
Adds input registration
Dec 12, 2022
6fac77e
Appease linter
Dec 12, 2022
0190f72
Add class template start
Dec 12, 2022
f7d02c8
Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs
handwerkerd Dec 13, 2022
dafe703
Add previous workflow registry into new one
Dec 13, 2022
fc94f2e
Fix failure to update tags and classifications in manual
Dec 13, 2022
f87e0a2
Fix missing less likely BOOLD tag
Dec 13, 2022
7e0de9f
Adds more useful reporting for unused metrics
Dec 13, 2022
232e3f7
Create generated metrics
Dec 13, 2022
8cf697c
Update line terminator
Dec 13, 2022
347aa13
Force black to run before flake8
Dec 13, 2022
9d6a487
Updates percentile call
Dec 13, 2022
336dfa4
more doc updates
handwerkerd Dec 13, 2022
54c0c91
Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs
handwerkerd Dec 13, 2022
63446dc
fixed meica to v2.5 in docstrings
handwerkerd Dec 13, 2022
054616a
docs building again
handwerkerd Dec 14, 2022
14b3400
more updates to building decision trees
handwerkerd Dec 15, 2022
8c54a18
improved docs (#19)
handwerkerd Dec 15, 2022
e5fdec1
Get rid of optional method keyword
Dec 15, 2022
4937f76
Revert "Get rid of optional method keyword"
Dec 15, 2022
b9e17fb
Revert "Updates percentile call"
Dec 15, 2022
c96ad83
Revert "Update line terminator"
Dec 15, 2022
0505349
Autodocument ComponentSelector methods/attributes (#20)
tsalo Dec 15, 2022
4b9c051
Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs
handwerkerd Dec 15, 2022
254b26a
fixed rename of component_selector
handwerkerd Dec 15, 2022
6389822
Fixed remaining transition to component_selector (#21)
handwerkerd Dec 16, 2022
075d6e2
more doc updates
handwerkerd Dec 19, 2022
364be08
Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs
handwerkerd Dec 19, 2022
f174dac
mostly classification_output_descriptions
handwerkerd Dec 20, 2022
fc3c2a0
Fixed io API and selector API warnings
handwerkerd Dec 20, 2022
fd2dd96
message
handwerkerd Dec 20, 2022
0c28c68
key parts of docs all updated
handwerkerd Dec 21, 2022
bbdd9bb
output_file_descriptions fully updated
handwerkerd Dec 21, 2022
682f352
filled testing gaps for component_selector
handwerkerd Dec 21, 2022
2a189d8
Updates integration test fnames
Dec 21, 2022
48f6d6e
Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs
handwerkerd Dec 21, 2022
ee3d517
Try a numpy fix
Dec 21, 2022
2d5b809
Try again
Dec 21, 2022
9d116ad
Merge remote-tracking branch 'jbteves/JT_DTM' into DTM_improved_docs
handwerkerd Dec 21, 2022
a361417
Remove dead code
Dec 21, 2022
e1a69fe
Merge branch 'jbteves/JT_DTM' into improved_docs
handwerkerd Dec 21, 2022
88721ae
full selector coverage (#23)
handwerkerd Dec 22, 2022
e16c7a1
Add tedana_reclassify tests
Dec 22, 2022
00bbb9b
Actually add test to circle workflow
Dec 22, 2022
9711aef
Maybe actually add it
Dec 22, 2022
460a453
Change o to outdir
Dec 22, 2022
691d9d5
Fix noreports maybe
Dec 22, 2022
989e10e
Fix tedort
Dec 22, 2022
3c2d76f
CircleCI are you okay?
Dec 22, 2022
ad29c0d
Circle if you keep this up I will switch to Actions
Dec 22, 2022
ff1d631
Revert "Circle if you keep this up I will switch to Actions"
Dec 22, 2022
4325c32
Maybe silence duecredit and re-trigger Circle
Dec 22, 2022
003666b
Try something else
Dec 22, 2022
69356a7
Guess that wasn't legal
Dec 22, 2022
953d020
Switch main to _main
Dec 22, 2022
12b5629
Add to pyproject.toml
Dec 22, 2022
a1adaa3
Force it to be editable
Dec 22, 2022
dfe6720
Add references to resources package
Dec 22, 2022
bc9ec11
Dispose of sanity check
Dec 23, 2022
2748fd9
Add more reclassify tests
Dec 23, 2022
f7db360
Adaptive mask is not a bool
Dec 23, 2022
a842c60
Add label for setup.cfg
Dec 23, 2022
ecee71d
Revert "Adaptive mask is not a bool"
Dec 23, 2022
71d905c
Add resource files
Dec 23, 2022
e9ac5f2
Clarify variables
Dec 23, 2022
c5ec75a
Merge branch 'main' into JT_DTM
Dec 23, 2022
52a6bc8
Update date and weep
Dec 23, 2022
7628d13
Fixed NoLikelyBOLDBug (#24)
handwerkerd Jan 4, 2023
133947f
fixed debug logging
handwerkerd Jan 4, 2023
77255c1
Merge pull request #25 from handwerkerd/FixRedoICANoLikelyBOLD
jbteves Jan 4, 2023
1273718
Temporarily turn on force overwrite for redo ICA
Jan 4, 2023
05e3fc3
Fixed I007 divergence
handwerkerd Jan 4, 2023
d87ca36
Merge remote-tracking branch 'jbteves/JT_DTM' into Fixed_I007_divergance
handwerkerd Jan 4, 2023
6b19cfc
calc_varex_thresh now has num_highest_var_comps
handwerkerd Jan 5, 2023
0b3d1b8
fixed linting errors
handwerkerd Jan 5, 2023
b0bdf8a
Merge pull request #26 from handwerkerd/Fixed_I007_divergance
jbteves Jan 5, 2023
05a6b1b
Update integration test data
Jan 5, 2023
50ba4a8
Adds csv and text file reading for manual acc/rej
Jan 6, 2023
a2ec444
Add tests for CustomEncoder
Jan 6, 2023
24e3f73
Adds bibtex warning check test
Jan 6, 2023
922f336
Appease linter
Jan 6, 2023
a2524bc
Fix unused metrics warning
Jan 6, 2023
563060b
Add reclassify tests and patches to test failures
Jan 6, 2023
6d6eda4
Make stylistic changes.
tsalo Jan 10, 2023
f0caf5b
Remove trailing whitespace.
tsalo Jan 10, 2023
f0f934f
Spacing in io.
tsalo Jan 11, 2023
7ec4d81
More minor changes.
tsalo Jan 11, 2023
8a6e294
Add custom napoleon section "Generated Files"
Jan 19, 2023
5e80e9c
Replace numTrue/numFalse with n_true/n_false.
tsalo Jan 21, 2023
09a5f11
Replace ifTrue/ifFalse with if_true/if_false.
tsalo Jan 21, 2023
d0b6639
Use fill_doc.
tsalo Jan 21, 2023
e20e2ff
Style fixes.
tsalo Jan 21, 2023
1f7c07a
more int32
handwerkerd Feb 2, 2023
353f96e
Merge pull request #27 from tsalo/dtm-review
jbteves Feb 3, 2023
bdd1a9e
Merge pull request #28 from handwerkerd/DTM_integer_to_int32
jbteves Feb 3, 2023
149ec28
more int32 fun
handwerkerd Feb 3, 2023
5248ab0
Merge pull request #29 from handwerkerd/int32Fun
jbteves Feb 3, 2023
322a25f
Appease linter
jbteves Feb 3, 2023
b130e82
Fixed style issues
handwerkerd Feb 14, 2023
7c46ed4
Merge main
jbteves Feb 14, 2023
2664126
Merge remote-tracking branch 'upstream/main' into pr/756
eurunuela Feb 16, 2023
a65a4cf
Add RICA to Approach section of docs
eurunuela Feb 16, 2023
1a9ffe4
Fixed CI style check failure
handwerkerd Feb 16, 2023
f8bb798
DTM documentation review (#30)
n-reddy Feb 16, 2023
a03b120
Rename reclassify force (#32)
handwerkerd Feb 16, 2023
532dc6a
Add defaults to --help output (#31)
n-reddy Feb 17, 2023
c43befb
added ica_reclassify to setup.cfg
handwerkerd Feb 17, 2023
2dc0a5a
Using a more persistent cache for the testing data (#33)
handwerkerd Feb 28, 2023
2e45e8d
Change to TestLGR.info
handwerkerd Feb 28, 2023
8acf185
Fixing high variance classification mess (#34)
handwerkerd Mar 15, 2023
a2a30fa
Replace versioneer with hatch (#35)
tsalo Mar 16, 2023
7129854
Fix CI (#36)
tsalo Mar 16, 2023
df57b56
Add flake8-pyproject as a requirement. (#37)
tsalo Mar 28, 2023
f7cf821
Try fixing coverage. (#38)
tsalo Mar 28, 2023
ac52721
Improving ica_reclassify (#39)
handwerkerd Apr 20, 2023
b06f65a
Ica reclassify registry fixes (#42)
handwerkerd Apr 26, 2023
29eee66
Drop Python 3.6 and 3.7 support (#40)
tsalo Apr 26, 2023
a3dc1c2
added mixm to 4echo test (#43)
handwerkerd Apr 27, 2023
3e48d9f
Updating Contributor Information (#41)
handwerkerd May 1, 2023
1e7ee6e
Added flow charts and some text (#44)
handwerkerd May 4, 2023
5921237
RTDfix (#45)
handwerkerd May 4, 2023
26ff954
Update documentation (#46)
tsalo May 8, 2023
bc1cf40
Output docs on one page (#47)
handwerkerd May 9, 2023
8dcdafa
Merge branch 'main' into JT_DTM
tsalo May 11, 2023
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34 changes: 33 additions & 1 deletion .all-contributorsrc
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,16 @@
"question"
]
},
{
"login": "marco7877",
"name": "Marco Flores-Coronado",
"avatar_url": "https://avatars.githubusercontent.com/u/56403434?v=4",
"profile": "https://github.com/marco7877",
"contributions": [
"ideas",
"doc"
]
},
{
"login": "javiergcas",
"name": "Javier Gonzalez-Castillo",
Expand Down Expand Up @@ -78,6 +88,28 @@
"question"
]
},
{
"login": "pmolfese",
"name": "Pete Molfese",
"avatar_url": "https://avatars.githubusercontent.com/u/3665743?v=4",
"profile": "https://github.com/pmolfese",
"contributions": [
"code"
]
},
{
"login": "n-reddy",
"name": "Neha Reddy",
"avatar_url": "https://avatars.githubusercontent.com/u/58482773?v=4",
"profile": "https://github.com/n-reddy",
"contributions": [
"bug",
"doc",
"ideas",
"question",
"review"
]
},
{
"login": "tsalo",
"name": "Taylor Salo",
Expand Down Expand Up @@ -252,4 +284,4 @@
"repoHost": "https://github.com",
"skipCi": false,
"commitConvention": "angular"
}
}
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