Review PR for #298 #314

effigies · 2021-09-13T18:51:43Z

This is just to get CI running and provide a set of commits for @shashankbansal6's consideration.

At the moment, it's mostly refactoring cruft that no longer applies.

External review is obviously also welcome.

…or each level

…sion to use directly from git

Co-authored-by: Shashank Bansal <shashankbansal56@gmail.com>

…iverse

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

…nto enh/mutliverse

…aph instead of layout; fix init_wf test

…tadata for afni estimator

pep8speaks · 2021-09-13T18:51:51Z

Hello @effigies, Thank you for updating!

In the file fitlins/cli/run.py:

Line 23:1: F401 'bids.modeling.auto_model' imported but unused

In the file fitlins/interfaces/afni.py:

Line 268:21: E126 continuation line over-indented for hanging indent
Line 339:100: E501 line too long (105 > 99 characters)

In the file fitlins/interfaces/nistats.py:

Line 227:15: E126 continuation line over-indented for hanging indent
Line 229:21: E126 continuation line over-indented for hanging indent
Line 361:21: E126 continuation line over-indented for hanging indent
Line 367:17: E121 continuation line under-indented for hanging indent

In the file fitlins/interfaces/tests/test_afni.py:

Line 45:13: E126 continuation line over-indented for hanging indent
Line 111:13: E126 continuation line over-indented for hanging indent
Line 147:0: F541 f-string is missing placeholders

In the file fitlins/interfaces/visualizations.py:

Line 6:1: F401 'collections.namedtuple' imported but unused
Line 74:50: W291 trailing whitespace
Line 75:1: W293 blank line contains whitespace
Line 84:1: W293 blank line contains whitespace
Line 86:17: E126 continuation line over-indented for hanging indent
Line 89:1: W293 blank line contains whitespace
Line 121:50: W291 trailing whitespace
Line 122:1: W293 blank line contains whitespace
Line 131:1: W293 blank line contains whitespace
Line 133:17: E126 continuation line over-indented for hanging indent
Line 136:1: W293 blank line contains whitespace

In the file fitlins/utils/bids.py:

Line 20:1: F401 'copy' imported but unused
Line 46:71: W291 trailing whitespace
Line 47:1: W293 blank line contains whitespace

In the file fitlins/viz/reports.py:

Line 48:15: E251 unexpected spaces around keyword / parameter equals
Line 48:17: E251 unexpected spaces around keyword / parameter equals
Line 66:1: W293 blank line contains whitespace
Line 69:1: W293 blank line contains whitespace
Line 81:1: W293 blank line contains whitespace
Line 89:1: W293 blank line contains whitespace
Line 103:1: W293 blank line contains whitespace

In the file fitlins/workflows/base.py:

Line 14:5: F401 'bids.modeling.BIDSStatsModelsGraph' imported but unused
Line 84:66: E226 missing whitespace around arithmetic operator
Line 115:13: E126 continuation line over-indented for hanging indent
Line 116:100: E501 line too long (110 > 99 characters)
Line 122:13: E126 continuation line over-indented for hanging indent
Line 123:100: E501 line too long (110 > 99 characters)
Line 125:100: E501 line too long (103 > 99 characters)
Line 128:13: E126 continuation line over-indented for hanging indent
Line 129:100: E501 line too long (110 > 99 characters)
Line 130:100: E501 line too long (102 > 99 characters)
Line 133:13: E126 continuation line over-indented for hanging indent
Line 134:100: E501 line too long (110 > 99 characters)
Line 140:13: E126 continuation line over-indented for hanging indent
Line 141:100: E501 line too long (110 > 99 characters)
Line 143:100: E501 line too long (161 > 99 characters)
Line 199:100: E501 line too long (100 > 99 characters)
Line 216:50: E241 multiple spaces after ','
Line 248:17: E126 continuation line over-indented for hanging indent
Line 248:28: E251 unexpected spaces around keyword / parameter equals
Line 248:30: E251 unexpected spaces around keyword / parameter equals
Line 249:29: E251 unexpected spaces around keyword / parameter equals
Line 249:31: E251 unexpected spaces around keyword / parameter equals
Line 250:25: E251 unexpected spaces around keyword / parameter equals
Line 250:27: E251 unexpected spaces around keyword / parameter equals
Line 251:14: E126 continuation line over-indented for hanging indent
Line 259:17: E126 continuation line over-indented for hanging indent
Line 259:28: E251 unexpected spaces around keyword / parameter equals
Line 259:30: E251 unexpected spaces around keyword / parameter equals
Line 260:29: E251 unexpected spaces around keyword / parameter equals
Line 260:31: E251 unexpected spaces around keyword / parameter equals
Line 261:25: E251 unexpected spaces around keyword / parameter equals
Line 261:27: E251 unexpected spaces around keyword / parameter equals
Line 262:14: E126 continuation line over-indented for hanging indent
Line 270:17: E126 continuation line over-indented for hanging indent
Line 270:28: E251 unexpected spaces around keyword / parameter equals
Line 270:30: E251 unexpected spaces around keyword / parameter equals
Line 271:29: E251 unexpected spaces around keyword / parameter equals
Line 271:31: E251 unexpected spaces around keyword / parameter equals
Line 272:25: E251 unexpected spaces around keyword / parameter equals
Line 272:27: E251 unexpected spaces around keyword / parameter equals
Line 273:14: E126 continuation line over-indented for hanging indent
Line 286:14: E131 continuation line unaligned for hanging indent
Line 297:1: W293 blank line contains whitespace
Line 348:61: E241 multiple spaces after ','
Line 349:46: E241 multiple spaces after ','
Line 351:61: E241 multiple spaces after ','
Line 361:21: E126 continuation line over-indented for hanging indent

In the file fitlins/workflows/tests/test_base.py:

Line 3:1: F401 'bids' imported but unused

To test for issues locally, pip install flake8 and then run flake8 fitlins.

Comment last updated at 2021-09-13 20:23:55 UTC

…tine

effigies · 2021-09-13T20:44:38Z

@shashankbansal6 I think this is now a straight refactor of yours. Full diff: shashankbansal6/fitlins@enh/mutliverse...poldracklab:298-review

shashankbansal6 and others added 30 commits May 31, 2021 18:52

[WIP, RF] use a recursive function to load statsmodel data/metadata f…

f08dd79

…or each level

RF: Working l1_model refactor using the new stats model

c9c8391

ENH: Rewrite ds003 model with recent changes

08c6578

PIN: pybids @ master

6beee71

RF: init second level model

73697b6

RF: All level models working; reports are still broken

02a61db

fixed reports - added level, name to entities/patterns

f859279

use ContrastInfo from the new stats model for tests; patch pybids ver…

c8985db

…sion to use directly from git

Update examples/models/ds000003/models/model-001_smdl.json

9aefd46

Co-authored-by: Shashank Bansal <shashankbansal56@gmail.com>

Merge branch 'master' of github.com:poldracklab/fitlins into enh/mutl…

1789c2b

…iverse

Update fitlins/interfaces/nistats.py

3484870

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

Update fitlins/interfaces/bids.py

ccd878f

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

fix merge conflict on pybids package

91b3986

Merge branch 'enh/mutliverse' of github.com:shashankbansal6/fitlins i…

fb227f0

…nto enh/mutliverse

remove pymare

3577744

slight optimization - load BIDSStatsModelsGraph only once and pass gr…

d3248a5

…aph instead of layout; fix init_wf test

use review suggested cleaner way of creating all_specs

7ef332a

cleaner logic until pymare is used for meta-analysis

59bdfc9

fix viz for contrast related plots

448324d

replace . with _ for contrasts and names

16a2022

use models from examples dir for ds03_test

972adb4

fix merge conflict

fe03c05

make model_dict check explicit

38e9caa

update conftest sample model as per the new stats model

b0a0ce9

working afni estimator

3f39c3e

smoothing working for both estimators

eff0fe1

try using my own fork with updated model for ds03 tests

05f9c92

uninstall cached ds03 and reinstall forked

df433f4

fix contrast filters

576ed6f

revert all circleci config changes

b376699

shashankbansal6 and others added 10 commits July 23, 2021 13:31

attach fitlins source dir to all fitlins docker containers

1106d33

fix merge conflict from upstream/master[0.9.2]

ece620d

retry with the new fmriprep/fitlins data

d977a94

fix run_pytest

a38e587

Fix f-tests

820156c

Temporarily use pybids PR commit until merged

7139e9a

Update ds03 example model; include additional entities in contrast_me…

747c914

…tadata for afni estimator

Merge branch 'master' into enh/mutliverse

c2893dd

update pybids version

6a80cb3

Clean up output spec

684005e

effigies marked this pull request as draft September 13, 2021 18:52

effigies force-pushed the 298-review branch 3 times, most recently from f80c9b4 to 50e7d9f Compare September 13, 2021 20:11

effigies added 8 commits September 13, 2021 16:23

RF: Break _load_all_specs into primary structure and run-level subrou…

b4dda01

…tine

RF: coll -> spec

c4f84d8

RF: Raise an informative error if RepetitionTime is missing

6d5dd15

RF: Use BIDSStatsModelsNode's minimal entities

a3cdab3

RF: Remove excess variables

1b2659b

RF: step_subdir is only used in run-level setup

e5fb96f

ENH: Restore comment explaining imputation

7c2ddf1

STY: flake8

892cafe

effigies force-pushed the 298-review branch from 50e7d9f to 892cafe Compare September 13, 2021 20:23

effigies merged commit 892cafe into master Dec 7, 2021

effigies deleted the 298-review branch March 30, 2022 00:08

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Comment last updated at 2021-09-13 20:23:55 UTC

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