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.github/scripts/get_package_id.py:14:5: D401 First line of docstring should be in imperative mood: "Function to collect GHCR packages for a given owner & tag."
.github/scripts/get_package_id.py:35:9: D401 First line of docstring should be in imperative mood: "Method to make API call and return response, given a URL."
.github/scripts/get_package_id.py:85:5: D401 First line of docstring should be in imperative mood: "Function to return a package ID given an image version tag."
.github/scripts/get_package_id.py:109:5: RET505 Unnecessary `else` after `return` statement
.github/scripts/get_package_id.py:114:25: PLR2004 Magic value used in comparison, consider replacing 4 with a constant variable
CPAC/__init__.py:17:1: D205 1 blank line required between summary line and description
CPAC/__main__.py:1:1: D100 Missing docstring in public module
CPAC/__main__.py:51:5: D103 Missing docstring in public function
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CPAC/__main__.py:133:5: D103 Missing docstring in public function
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CPAC/__main__.py:402:20: A002 Argument `object` is shadowing a Python builtin
CPAC/__main__.py:420:5: D103 Missing docstring in public function
CPAC/__main__.py:429:5: D103 Missing docstring in public function
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CPAC/__main__.py:450:5: D103 Missing docstring in public function
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CPAC/__main__.py:481:5: D103 Missing docstring in public function
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CPAC/__main__.py:546:5: D103 Missing docstring in public function
CPAC/__main__.py:553:5: D103 Missing docstring in public function
CPAC/__main__.py:611:5: D103 Missing docstring in public function
CPAC/__main__.py:617:5: D103 Missing docstring in public function
CPAC/alff/__init__.py:1:1: D104 Missing docstring in public package
CPAC/alff/alff.py:1:1: D100 Missing docstring in public module
CPAC/alff/alff.py:256:5: D103 Missing docstring in public function
CPAC/alff/alff.py:304:5: D103 Missing docstring in public function
CPAC/alff/utils.py:1:1: D100 Missing docstring in public module
CPAC/alff/utils.py:5:5: D401 First line of docstring should be in imperative mood: "Method to return option string for 3dTstat."
CPAC/anat_preproc/__init__.py:1:1: D104 Missing docstring in public package
CPAC/anat_preproc/anat_preproc.py:1:1: D100 Missing docstring in public module
CPAC/anat_preproc/anat_preproc.py:41:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:198:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:240:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:514:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:706:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:800:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:847:5: D205 1 blank line required between summary line and description
CPAC/anat_preproc/anat_preproc.py:896:12: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:896:15: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:896:20: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:896:22: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:896:26: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:896:39: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:896:44: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:896:64: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:896:67: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
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CPAC/anat_preproc/anat_preproc.py:907:12: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:907:16: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
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CPAC/anat_preproc/anat_preproc.py:907:33: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:907:50: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:907:53: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:907:66: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:907:76: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:907:82: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:931:15: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:931:35: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:931:40: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:963:26: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:963:29: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:963:31: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:963:34: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:963:54: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:963:57: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:963:78: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:963:98: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:963:101: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:963:122: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:963:125: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:989:18: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:989:24: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:989:45: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:989:54: RUF003 Comment contains ambiguous ` ` (NO-BREAK SPACE). Did you mean ` ` (SPACE)?
CPAC/anat_preproc/anat_preproc.py:1023:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1159:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1340:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1405:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1445:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1493:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1547:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1597:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1646:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1675:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1706:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1739:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1775:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1792:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1811:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1828:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1847:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1864:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1888:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1905:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1928:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1949:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1974:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:1998:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2021:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2047:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2069:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2097:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2129:5: D205 1 blank line required between summary line and description
CPAC/anat_preproc/anat_preproc.py:2182:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2213:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2249:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2277:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2315:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2356:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2397:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2417:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2441:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2455:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2471:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2485:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2501:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2515:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2533:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2547:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2569:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2615:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2647:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2684:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2742:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2885:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:2935:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:3056:5: D103 Missing docstring in public function
CPAC/anat_preproc/anat_preproc.py:3141:5: D103 Missing docstring in public function
CPAC/anat_preproc/ants.py:3:1: D205 1 blank line required between summary line and description
CPAC/anat_preproc/ants.py:66:5: PLR0913 Too many arguments in function definition (15 > 10)
CPAC/anat_preproc/ants.py:83:5: D205 1 blank line required between summary line and description
CPAC/anat_preproc/ants.py:83:5: D401 First line of docstring should be in imperative mood: "A Nipype implementation of the official ANTs' ``antsBrainExtraction.sh``"
CPAC/anat_preproc/ants.py:457:5: D205 1 blank line required between summary line and description
CPAC/anat_preproc/ants.py:457:5: D401 First line of docstring should be in imperative mood: "Implements supersteps 6 and 7 of ``antsBrainExtraction.sh``,"
CPAC/anat_preproc/ants.py:732:9: E741 Ambiguous variable name: `l`
CPAC/anat_preproc/ants.py:743:5: D401 First line of docstring should be in imperative mood: "Ensures the mask headers make sense and match those of the T1w."
CPAC/anat_preproc/lesion_preproc.py:1:1: D100 Missing docstring in public module
CPAC/anat_preproc/lesion_preproc.py:10:5: D205 1 blank line required between summary line and description
CPAC/anat_preproc/lesion_preproc.py:41:5: RET505 Unnecessary `else` after `return` statement
CPAC/anat_preproc/lesion_preproc.py:46:5: D205 1 blank line required between summary line and description
CPAC/anat_preproc/lesion_preproc.py:46:5: D401 First line of docstring should be in imperative mood: "The main purpose of this workflow is to process lesions masks."
CPAC/anat_preproc/tests/__init__.py:1:1: D104 Missing docstring in public package
CPAC/anat_preproc/tests/test_anat_preproc.py:1:1: D100 Missing docstring in public module
CPAC/anat_preproc/tests/test_anat_preproc.py:3:1: F403 `from nose.tools import *` used; unable to detect undefined names
CPAC/anat_preproc/tests/test_anat_preproc.py:10:7: D101 Missing docstring in public class
CPAC/anat_preproc/tests/test_anat_preproc.py:59:9: D401 First line of docstring should be in imperative mood: "Deletes the workflow object."
CPAC/anat_preproc/tests/test_anat_preproc.py:93:33: PLR2004 Magic value used in comparison, consider replacing 3 with a constant variable
CPAC/anat_preproc/tests/test_anat_preproc.py:95:9: E722 Do not use bare `except`
CPAC/anat_preproc/tests/test_anat_preproc.py:202:21: PLR5501 Use `elif` instead of `else` then `if`, to reduce indentation
CPAC/anat_preproc/tests/test_anat_preproc.py:203:38: PLR2004 Magic value used in comparison, consider replacing 3 with a constant variable
CPAC/anat_preproc/tests/test_anat_preproc.py:245:41: PLR2004 Magic value used in comparison, consider replacing 0.95 with a constant variable
CPAC/anat_preproc/tests/test_anat_preproc.py:272:41: PLR2004 Magic value used in comparison, consider replacing 0.97 with a constant variable
CPAC/anat_preproc/utils.py:1:1: D100 Missing docstring in public module
CPAC/anat_preproc/utils.py:7:5: D103 Missing docstring in public function
CPAC/anat_preproc/utils.py:8:15: F821 Undefined name `os`
CPAC/anat_preproc/utils.py:8:28: F821 Undefined name `os`
CPAC/anat_preproc/utils.py:80:9: F821 Undefined name `loadtxt`
CPAC/anat_preproc/utils.py:82:10: F821 Undefined name `matrix`
CPAC/anat_preproc/utils.py:83:10: F821 Undefined name `matrix`
CPAC/anat_preproc/utils.py:84:10: F821 Undefined name `matrix`
CPAC/anat_preproc/utils.py:86:12: F821 Undefined name `linalg`
CPAC/anat_preproc/utils.py:92:17: F821 Undefined name `linalg`
CPAC/anat_preproc/utils.py:93:17: F821 Undefined name `multiply`
CPAC/anat_preproc/utils.py:94:17: F821 Undefined name `linalg`
CPAC/anat_preproc/utils.py:95:11: F821 Undefined name `cross`
CPAC/anat_preproc/utils.py:96:11: F821 Undefined name `mat`
CPAC/anat_preproc/utils.py:96:15: F821 Undefined name `zeros`
CPAC/anat_preproc/utils.py:102:17: F821 Undefined name `linalg`
CPAC/anat_preproc/utils.py:103:17: F821 Undefined name `multiply`
CPAC/anat_preproc/utils.py:104:17: F821 Undefined name `linalg`
CPAC/anat_preproc/utils.py:105:11: F821 Undefined name `cross`
CPAC/anat_preproc/utils.py:106:11: F821 Undefined name `mat`
CPAC/anat_preproc/utils.py:106:15: F821 Undefined name `zeros`
CPAC/anat_preproc/utils.py:110:10: F821 Undefined name `matrix`
CPAC/anat_preproc/utils.py:110:17: F821 Undefined name `eye`
CPAC/anat_preproc/utils.py:114:10: F821 Undefined name `matrix`
CPAC/anat_preproc/utils.py:114:17: F821 Undefined name `eye`
CPAC/anat_preproc/utils.py:127:5: F821 Undefined name `savetxt`
CPAC/anat_preproc/utils.py:133:5: D401 First line of docstring should be in imperative mood: "Function to return various hemisphere-specific FreeSurfer outputs."
CPAC/anat_preproc/utils.py:163:9: D401 First line of docstring should be in imperative mood: "Returns a function interface for split_hemi."
CPAC/anat_preproc/utils.py:205:5: PLR0913 Too many arguments in function definition (21 > 10)
CPAC/anat_preproc/utils.py:228:5: D401 First line of docstring should be in imperative mood: "Method to return option string for 3dSkullStrip."
CPAC/anat_preproc/utils.py:386:5: D401 First line of docstring should be in imperative mood: "Method to convert files from mgz to nifti format."
CPAC/anat_preproc/utils.py:419:5: D103 Missing docstring in public function
CPAC/anat_preproc/utils.py:431:5: D103 Missing docstring in public function
CPAC/anat_preproc/utils.py:445:5: D103 Missing docstring in public function
CPAC/anat_preproc/utils.py:466:1: E402 Module level import not at top of file
CPAC/anat_preproc/utils.py:467:1: E402 Module level import not at top of file
CPAC/anat_preproc/utils.py:468:1: E402 Module level import not at top of file
CPAC/anat_preproc/utils.py:473:7: D101 Missing docstring in public class
CPAC/anat_preproc/utils.py:490:7: D101 Missing docstring in public class
CPAC/anat_preproc/utils.py:495:5: D205 1 blank line required between summary line and description
CPAC/aroma/__init__.py:1:1: D104 Missing docstring in public package
CPAC/aroma/aroma.py:1:1: D100 Missing docstring in public module
CPAC/aroma/aroma.py:9:5: D205 1 blank line required between summary line and description
CPAC/aroma/aroma_test.py:3:1: D205 1 blank line required between summary line and description
CPAC/aroma/aroma_test.py:3:1: D404 First word of the docstring should not be "This"
CPAC/aroma/aroma_test.py:36:5: D103 Missing docstring in public function
CPAC/aroma/aroma_test.py:101:5: RET505 Unnecessary `else` after `return` statement
CPAC/connectome/__init__.py:1:1: D104 Missing docstring in public package
CPAC/connectome/connectivity_matrix.py:40:5: D401 First line of docstring should be in imperative mood: "Helper function to create connectome file filename."
CPAC/connectome/connectivity_matrix.py:64:5: D401 First line of docstring should be in imperative mood: "Helper function to get tool's method string."
CPAC/connectome/connectivity_matrix.py:96:5: D401 First line of docstring should be in imperative mood: "Function to compute a connectome matrix using Nilearn."
CPAC/connectome/connectivity_matrix.py:140:5: D103 Missing docstring in public function
CPAC/connectome/connectivity_matrix.py:213:5: D103 Missing docstring in public function
CPAC/cwas/__init__.py:1:1: D104 Missing docstring in public package
CPAC/cwas/cwas.py:1:1: D100 Missing docstring in public module
CPAC/cwas/cwas.py:18:5: D205 1 blank line required between summary line and description
CPAC/cwas/cwas.py:18:5: D401 First line of docstring should be in imperative mood: "Creates a joint mask (intersection) common to all the subjects in a provided list"
CPAC/cwas/cwas.py:44:5: D103 Missing docstring in public function
CPAC/cwas/cwas.py:50:5: D103 Missing docstring in public function
CPAC/cwas/cwas.py:64:5: D103 Missing docstring in public function
CPAC/cwas/cwas.py:72:5: D103 Missing docstring in public function
CPAC/cwas/cwas.py:89:5: D401 First line of docstring should be in imperative mood: "Performs CWAS for a group of subjects."
CPAC/cwas/cwas.py:123:5: E722 Do not use bare `except`
CPAC/cwas/cwas.py:168:34: PLR2004 Magic value used in comparison, consider replacing 2 with a constant variable
CPAC/cwas/cwas.py:194:5: D103 Missing docstring in public function
CPAC/cwas/cwas.py:200:5: D103 Missing docstring in public function
CPAC/cwas/cwas.py:207:5: D103 Missing docstring in public function
CPAC/cwas/cwas.py:247:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:1:1: D100 Missing docstring in public module
CPAC/cwas/mdmr.py:4:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:11:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:16:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:19:5: E741 Ambiguous variable name: `I`
CPAC/cwas/mdmr.py:25:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:32:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:38:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:43:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:53:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:55:5: E741 Ambiguous variable name: `I`
CPAC/cwas/mdmr.py:65:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:73:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:79:5: D103 Missing docstring in public function
CPAC/cwas/mdmr.py:99:37: NPY002 Replace legacy `np.random.permutation` call with `np.random.Generator`
CPAC/cwas/pipeline.py:1:1: D100 Missing docstring in public module
CPAC/cwas/tests/__init__.py:1:1: D104 Missing docstring in public package
CPAC/cwas/tests/features/steps/base_cwas.py:1:1: D100 Missing docstring in public module
CPAC/cwas/tests/features/steps/base_cwas.py:5:5: D205 1 blank line required between summary line and description
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:1:1: F403 `from base_cwas import *` used; unable to detect undefined names
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:1:1: D100 Missing docstring in public module
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:6:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:7:5: F405 `importr` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:9:13: F405 `op` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:10:13: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:10:22: F405 `robjects` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:11:20: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:15:13: F405 `op` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:16:12: F405 `nib` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:17:20: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:21:13: F405 `op` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:22:17: F405 `nib` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:44:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:44:5: F811 Redefinition of unused `step` from line 6
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:47:21: F405 `calc_subdists` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:51:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:51:5: F811 Redefinition of unused `step` from line 44
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:54:25: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:55:13: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:57:13: F405 `custom_corrcoef` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:61:14: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:62:14: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:63:17: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:68:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:68:5: F811 Redefinition of unused `step` from line 51
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:69:12: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:70:5: F405 `assert_that` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:74:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:74:5: F811 Redefinition of unused `step` from line 68
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:84:13: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:84:21: F405 `custom_corrcoef` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:85:21: PLR2004 Magic value used in comparison, consider replacing 0.99 with a constant variable
CPAC/cwas/tests/features/steps/step_conn-dists_connectir.py:86:5: F405 `assert_that` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_dists.py:1:1: F403 `from base_cwas import *` used; unable to detect undefined names
CPAC/cwas/tests/features/steps/step_dists.py:1:1: D100 Missing docstring in public module
CPAC/cwas/tests/features/steps/step_dists.py:6:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_dists.py:10:21: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_dists.py:15:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_dists.py:15:5: F811 Redefinition of unused `step` from line 6
CPAC/cwas/tests/features/steps/step_dists.py:16:21: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_dists.py:18:28: F405 `compute_distances` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_dists.py:22:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_dists.py:22:5: F811 Redefinition of unused `step` from line 15
CPAC/cwas/tests/features/steps/step_dists.py:23:25: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_dists.py:25:36: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_dists.py:29:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_dists.py:29:5: F811 Redefinition of unused `step` from line 22
CPAC/cwas/tests/features/steps/step_dists.py:30:12: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_dists.py:31:5: F405 `assert_that` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:1:1: F403 `from base_cwas import *` used; unable to detect undefined names
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:1:1: D100 Missing docstring in public module
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:6:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:8:13: F405 `op` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:8:21: F405 `op` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:9:5: F405 `importr` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:10:13: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:10:22: F405 `robjects` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:11:20: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:15:13: F405 `op` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:16:25: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:17:9: F405 `robjects` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:22:13: F405 `op` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:23:13: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:23:22: F405 `robjects` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:25:17: F405 `op` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:26:9: F405 `robjects` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:27:18: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:27:27: F405 `robjects` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:32:13: F405 `op` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:33:13: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:33:22: F405 `robjects` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:38:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:38:5: F811 Redefinition of unused `step` from line 6
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:43:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:43:5: F811 Redefinition of unused `step` from line 38
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:44:26: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:49:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:49:5: F811 Redefinition of unused `step` from line 43
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:51:30: F405 `calc_mdmrs` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:57:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:57:5: F811 Redefinition of unused `step` from line 49
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:59:26: F405 `mdmr` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:71:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:71:5: F811 Redefinition of unused `step` from line 57
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:72:12: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:73:5: F405 `assert_that` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:77:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:77:5: F811 Redefinition of unused `step` from line 71
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:78:12: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:79:5: F405 `assert_that` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:83:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:83:5: F811 Redefinition of unused `step` from line 77
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:84:12: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:85:5: F405 `assert_that` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:89:5: D103 Missing docstring in public function
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:89:5: F811 Redefinition of unused `step` from line 83
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:90:12: F405 `np` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:91:5: F405 `assert_that` may be undefined, or defined from star imports
CPAC/cwas/tests/features/steps/step_mdmrs_connectir.py:91:23: F405 `greater_than` may be undefined, or defined from star imports
CPAC/cwas/tests/test_cwas.py:1:1: D100 Missing docstring in public module
CPAC/cwas/tests/test_cwas.py:7:5: D103 Missing docstring in public function
CPAC/cwas/tests/test_cwas.py:13:5: D103 Missing docstring in public function
CPAC/cwas/tests/test_cwas.py:20:5: D205 1 blank line required between summary line and description
CPAC/cwas/tests/test_cwas.py:38:9: D102 Missing docstring in public method
CPAC/cwas/tests/test_cwas.py:45:9: D102 Missing docstring in public method
CPAC/cwas/tests/test_cwas.py:85:17: E741 Ambiguous variable name: `l`
CPAC/cwas/tests/test_cwas.py:120:9: D205 1 blank line required between summary line and description
CPAC/cwas/tests/test_cwas.py:120:9: D401 First line of docstring should be in imperative mood: "This runs distances and MDMR with connectir."
CPAC/cwas/tests/test_cwas.py:120:9: D404 First word of the docstring should not be "This"
CPAC/cwas/tests/test_cwas.py:159:9: D401 First line of docstring should be in imperative mood: "This will compare the output from the CPAC python vs the R connectir."
CPAC/cwas/tests/test_cwas.py:159:9: D404 First word of the docstring should not be "This"
CPAC/cwas/tests/test_cwas.py:242:60: PLR2004 Magic value used in comparison, consider replacing 0.99 with a constant variable
CPAC/cwas/tests/test_cwas.py:245:60: PLR2004 Magic value used in comparison, consider replacing 0.99 with a constant variable
CPAC/cwas/tests/test_cwas.py:248:54: PLR2004 Magic value used in comparison, consider replacing 0.01 with a constant variable
CPAC/cwas/tests/test_cwas.py:251:54: PLR2004 Magic value used in comparison, consider replacing 0.05 with a constant variable
CPAC/cwas/tests/test_cwas.py:255:5: D103 Missing docstring in public function
CPAC/cwas/tests/test_cwas.py:293:5: D103 Missing docstring in public function
CPAC/cwas/tests/test_cwas.py:305:47: E741 Ambiguous variable name: `l`
CPAC/cwas/tests/test_cwas.py:309:12: F821 Undefined name `nb`
CPAC/cwas/tests/test_cwas.py:313:9: F821 Undefined name `nb`
CPAC/cwas/tests/test_cwas.py:334:14: F821 Undefined name `robjects`
CPAC/cwas/tests/test_cwas.py:335:17: F821 Undefined name `dmats`
CPAC/cwas/tests/test_mdmr_cython.py:1:1: D100 Missing docstring in public module
CPAC/cwas/tests/test_mdmr_cython.py:7:5: D103 Missing docstring in public function
CPAC/cwas/tests/test_pipeline_cwas.py:1:1: D100 Missing docstring in public module
CPAC/cwas/tests/test_pipeline_cwas.py:14:5: D103 Missing docstring in public function
CPAC/cwas/tests/test_pipeline_cwas.py:22:5: E722 Do not use bare `except`
CPAC/cwas/tests/test_pipeline_cwas.py:37:26: PLR2004 Magic value used in comparison, consider replacing 2 with a constant variable
CPAC/distortion_correction/__init__.py:1:1: D104 Missing docstring in public package
CPAC/distortion_correction/distortion_correction.py:1:1: D100 Missing docstring in public module
CPAC/distortion_correction/distortion_correction.py:41:5: D103 Missing docstring in public function
CPAC/distortion_correction/distortion_correction.py:65:5: D205 1 blank line required between summary line and description
CPAC/distortion_correction/distortion_correction.py:146:23: F823 Local variable `afni` referenced before assignment
CPAC/distortion_correction/distortion_correction.py:274:5: D205 1 blank line required between summary line and description
CPAC/distortion_correction/distortion_correction.py:334:5: D103 Missing docstring in public function
CPAC/distortion_correction/distortion_correction.py:353:5: D103 Missing docstring in public function
CPAC/distortion_correction/distortion_correction.py:387:5: D205 1 blank line required between summary line and description
CPAC/distortion_correction/distortion_correction.py:575:5: PLR0915 Too many statements (137 > 100)
CPAC/distortion_correction/distortion_correction.py:576:5: D205 1 blank line required between summary line and description
CPAC/distortion_correction/tests/__init__.py:1:1: D104 Missing docstring in public package
CPAC/distortion_correction/tests/test_distortion_correction.py:1:1: D100 Missing docstring in public module
CPAC/distortion_correction/tests/test_distortion_correction.py:18:5: D401 First line of docstring should be in imperative mood: "Created on Thu Nov  9 10:36:37 2017."
CPAC/distortion_correction/tests/test_distortion_correction.py:101:5: RET505 Unnecessary `else` after `return` statement
CPAC/distortion_correction/tests/test_distortion_correction.py:106:5: D103 Missing docstring in public function
CPAC/distortion_correction/tests/test_distortion_correction.py:125:5: D103 Missing docstring in public function
CPAC/distortion_correction/tests/test_distortion_correction.py:141:20: F821 Undefined name `create_func_preproc`
CPAC/distortion_correction/tests/test_distortion_correction.py:148:12: F821 Undefined name `blip_distcor_wf`
CPAC/distortion_correction/tests/test_distortion_correction.py:166:5: D103 Missing docstring in public function
CPAC/distortion_correction/tests/test_distortion_correction.py:181:20: F821 Undefined name `create_func_preproc`
CPAC/distortion_correction/tests/test_distortion_correction.py:188:12: F821 Undefined name `blip_distcor_wf`
CPAC/distortion_correction/utils.py:1:1: D100 Missing docstring in public module
CPAC/distortion_correction/utils.py:16:5: D103 Missing docstring in public function
CPAC/distortion_correction/utils.py:38:5: D103 Missing docstring in public function
CPAC/distortion_correction/utils.py:52:16: F821 Undefined name `jac_out`
CPAC/distortion_correction/utils.py:59:5: D103 Missing docstring in public function
CPAC/distortion_correction/utils.py:247:5: D205 1 blank line required between summary line and description
CPAC/distortion_correction/utils.py:286:5: D103 Missing docstring in public function
CPAC/distortion_correction/utils.py:305:5: D103 Missing docstring in public function
CPAC/distortion_correction/utils.py:363:5: D103 Missing docstring in public function
CPAC/easy_thresh/__init__.py:1:1: D104 Missing docstring in public package
CPAC/easy_thresh/easy_thresh.py:1:1: D100 Missing docstring in public module
CPAC/easy_thresh/easy_thresh.py:13:5: D205 1 blank line required between summary line and description
CPAC/easy_thresh/easy_thresh.py:372:5: D103 Missing docstring in public function
CPAC/easy_thresh/easy_thresh.py:415:5: D205 1 blank line required between summary line and description
CPAC/easy_thresh/easy_thresh.py:415:5: D401 First line of docstring should be in imperative mood: "Method to call fsl fslcpgeom command to copy"
CPAC/easy_thresh/easy_thresh.py:451:5: D205 1 blank line required between summary line and description
CPAC/easy_thresh/easy_thresh.py:451:5: D401 First line of docstring should be in imperative mood: "Method to get the standard brain image from FSL"
CPAC/easy_thresh/easy_thresh.py:488:5: D205 1 blank line required between summary line and description
CPAC/easy_thresh/easy_thresh.py:488:5: D401 First line of docstring should be in imperative mood: "Simple method to return tuple of z_threhsold"
CPAC/func_preproc/func_ingress.py:1:1: D100 Missing docstring in public module
CPAC/func_preproc/func_ingress.py:24:5: D103 Missing docstring in public function
CPAC/func_preproc/func_motion.py:132:5: D205 1 blank line required between summary line and description
CPAC/func_preproc/func_motion.py:150:34: PLR2004 Magic value used in comparison, consider replacing 3 with a constant variable
CPAC/func_preproc/func_motion.py:152:36: PLR2004 Magic value used in comparison, consider replacing 4 with a constant variable
CPAC/func_preproc/func_motion.py:163:27: PLR2004 Magic value used in comparison, consider replacing 40 with a constant variable
CPAC/func_preproc/func_motion.py:222:5: D103 Missing docstring in public function
CPAC/func_preproc/func_motion.py:241:5: D103 Missing docstring in public function
CPAC/func_preproc/func_motion.py:285:5: D103 Missing docstring in public function
CPAC/func_preproc/func_motion.py:307:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:36:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:44:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:178:5: D401 First line of docstring should be in imperative mood: "Reference `DCAN lab BOLD mask <https://github.com/DCAN-Labs/DCAN-HCP/blob/master/fMRIVolume/scripts/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh>`_."
CPAC/func_preproc/func_preproc.py:380:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:445:5: D205 1 blank line required between summary line and description
CPAC/func_preproc/func_preproc.py:445:5: D401 First line of docstring should be in imperative mood: "Method to get the first and the last slice for"
CPAC/func_preproc/func_preproc.py:482:22: PLR2004 Magic value used in comparison, consider replacing 4 with a constant variable
CPAC/func_preproc/func_preproc.py:507:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:546:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:569:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:604:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:646:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:700:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:739:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:764:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:943:5: D205 1 blank line required between summary line and description
CPAC/func_preproc/func_preproc.py:1141:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:1285:5: D205 1 blank line required between summary line and description
CPAC/func_preproc/func_preproc.py:1378:5: D205 1 blank line required between summary line and description
CPAC/func_preproc/func_preproc.py:1458:5: D205 1 blank line required between summary line and description
CPAC/func_preproc/func_preproc.py:1594:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:1625:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:1648:5: D103 Missing docstring in public function
CPAC/func_preproc/func_preproc.py:1673:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:1:1: D100 Missing docstring in public module
CPAC/func_preproc/utils.py:10:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:20:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:45:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:53:20: F821 Undefined name `os`
CPAC/func_preproc/utils.py:54:13: F821 Undefined name `os`
CPAC/func_preproc/utils.py:55:13: F821 Undefined name `os`
CPAC/func_preproc/utils.py:68:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:69:16: F821 Undefined name `os`
CPAC/func_preproc/utils.py:70:9: F821 Undefined name `os`
CPAC/func_preproc/utils.py:70:22: F821 Undefined name `os`
CPAC/func_preproc/utils.py:92:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:97:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:102:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:102:5: F811 Redefinition of unused `degrees_to_mm` from line 92
CPAC/func_preproc/utils.py:107:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:107:5: F811 Redefinition of unused `mm_to_degrees` from line 97
CPAC/func_preproc/utils.py:112:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:112:5: F811 Redefinition of unused `degrees_to_mm` from line 102
CPAC/func_preproc/utils.py:117:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:117:5: F811 Redefinition of unused `mm_to_degrees` from line 107
CPAC/func_preproc/utils.py:122:5: D103 Missing docstring in public function
CPAC/func_preproc/utils.py:203:21: F821 Undefined name `os`
CPAC/func_preproc/utils.py:203:34: F821 Undefined name `os`
CPAC/func_preproc/utils.py:204:19: F821 Undefined name `os`
CPAC/func_preproc/utils.py:204:32: F821 Undefined name `os`
CPAC/func_preproc/utils.py:232:30: F821 Undefined name `os`
CPAC/func_preproc/utils.py:233:9: F821 Undefined name `os`
CPAC/func_preproc/utils.py:233:47: F821 Undefined name `os`
CPAC/generate_motion_statistics/generate_motion_statistics.py:38:5: D205 1 blank line required between summary line and description
CPAC/generate_motion_statistics/generate_motion_statistics.py:38:5: D401 First line of docstring should be in imperative mood: "The main purpose of this workflow is to get various statistical measures"
CPAC/generate_motion_statistics/generate_motion_statistics.py:359:5: D401 First line of docstring should be in imperative mood: "Method to calculate Framewise Displacement (FD)  as per Power et al., 2012."
CPAC/generate_motion_statistics/generate_motion_statistics.py:403:25: F821 Undefined name `affine`
CPAC/generate_motion_statistics/generate_motion_statistics.py:403:35: F821 Undefined name `rms`
CPAC/generate_motion_statistics/generate_motion_statistics.py:406:5: D401 First line of docstring should be in imperative mood: "Method to calculate framewise displacement as per Jenkinson et al. 2002."
CPAC/generate_motion_statistics/generate_motion_statistics.py:524:5: D401 First line of docstring should be in imperative mood: "Method to calculate all the movement parameters."
CPAC/generate_motion_statistics/generate_motion_statistics.py:589:63: PLR2004 Magic value used in comparison, consider replacing 0.1 with a constant variable
CPAC/generate_motion_statistics/generate_motion_statistics.py:624:31: E721 Do not compare types, use `isinstance()`
CPAC/generate_motion_statistics/generate_motion_statistics.py:633:5: D401 First line of docstring should be in imperative mood: "Method to generate Power parameters for scrubbing."
CPAC/generate_motion_statistics/generate_motion_statistics.py:701:31: E721 Do not compare types, use `isinstance()`
CPAC/generate_motion_statistics/generate_motion_statistics.py:707:5: D103 Missing docstring in public function
CPAC/generate_motion_statistics/generate_motion_statistics.py:715:7: D101 Missing docstring in public class
CPAC/generate_motion_statistics/generate_motion_statistics.py:740:16: RUF012 Mutable class attributes should be annotated with `typing.ClassVar`
CPAC/generate_motion_statistics/generate_motion_statistics.py:756:7: D101 Missing docstring in public class
CPAC/generate_motion_statistics/generate_motion_statistics.py:760:7: D101 Missing docstring in public class
CPAC/generate_motion_statistics/generate_motion_statistics.py:767:5: D401 First line of docstring should be in imperative mood: "Method to calculate DVARS as per power's method."
CPAC/generate_motion_statistics/generate_motion_statistics.py:808:5: D401 First line of docstring should be in imperative mood: "Method to append all the motion and power parameters into 2 files."
CPAC/generate_motion_statistics/generate_motion_statistics.py:852:42: PLR2004 Magic value used in comparison, consider replacing 5 with a constant variable
CPAC/generate_motion_statistics/generate_motion_statistics.py:862:42: PLR2004 Magic value used in comparison, consider replacing 4 with a constant variable
CPAC/generate_motion_statistics/test/test_dvars.py:1:1: D100 Missing docstring in public module
CPAC/generate_motion_statistics/test/test_dvars.py:8:1: NPY002 Replace legacy `np.random.seed` call with `np.random.Generator`
CPAC/generate_motion_statistics/test/test_dvars.py:11:5: D103 Missing docstring in public function
CPAC/generate_motion_statistics/test/test_dvars.py:14:16: NPY002 Replace legacy `np.random.uniform` call with `np.random.Generator`
CPAC/generate_motion_statistics/utils.py:112:5: D205 1 blank line required between summary line and description
CPAC/group_analysis/__init__.py:1:1: D104 Missing docstring in public package
CPAC/group_analysis/group_analysis.py:1:1: D100 Missing docstring in public module
CPAC/group_analysis/group_analysis.py:9:5: D205 1 blank line required between summary line and description
CPAC/group_analysis/group_analysis.py:9:5: D401 First line of docstring should be in imperative mood: "Method to create operation string"
CPAC/group_analysis/group_analysis.py:36:5: E722 Do not use bare `except`
CPAC/group_analysis/group_analysis.py:41:5: D205 1 blank line required between summary line and description
CPAC/group_analysis/group_analysis.py:66:5: D205 1 blank line required between summary line and description
CPAC/group_analysis/group_analysis.py:456:5: PLR0913 Too many arguments in function definition (12 > 10)
CPAC/group_analysis/group_analysis.py:470:5: D205 1 blank line required between summary line and description
CPAC/image_utils/__init__.py:1:1: D104 Missing docstring in public package
CPAC/image_utils/spatial_smoothing.py:1:1: D100 Missing docstring in public module
CPAC/image_utils/spatial_smoothing.py:24:5: D205 1 blank line required between summary line and description
CPAC/image_utils/spatial_smoothing.py:42:5: D103 Missing docstring in public function
CPAC/image_utils/statistical_transforms.py:1:1: D100 Missing docstring in public module
CPAC/image_utils/statistical_transforms.py:25:5: D103 Missing docstring in public function
CPAC/image_utils/statistical_transforms.py:48:5: D103 Missing docstring in public function
CPAC/image_utils/tests/__init__.py:1:1: D104 Missing docstring in public package
CPAC/image_utils/tests/test_smooth.py:1:1: D100 Missing docstring in public module
CPAC/image_utils/tests/test_smooth.py:12:5: D103 Missing docstring in public function
CPAC/image_utils/tests/test_smooth.py:68:84: PLR2004 Magic value used in comparison, consider replacing 0.99 with a constant variable
CPAC/image_utils/tests/test_smooth.py:74:5: D103 Missing docstring in public function
CPAC/image_utils/tests/test_smooth.py:143:60: PLR2004 Magic value used in comparison, consider replacing 0.99 with a constant variable
CPAC/info.py:35:1: D205 1 blank line required between summary line and description
CPAC/info.py:35:1: D404 First word of the docstring should not be "This"
CPAC/isc/__init__.py:1:1: D104 Missing docstring in public package
CPAC/isc/isc.py:1:1: D100 Missing docstring in public module
CPAC/isc/isc.py:7:5: D103 Missing docstring in public function
CPAC/isc/isc.py:8:22: PLR2004 Magic value used in comparison, consider replacing 3 with a constant variable
CPAC/isc/isc.py:44:5: D103 Missing docstring in public function
CPAC/isc/isc.py:48:5: D103 Missing docstring in public function
CPAC/isc/isfc.py:1:1: D100 Missing docstring in public module
CPAC/isc/isfc.py:7:5: D103 Missing docstring in public function
CPAC/isc/isfc.py:8:22: PLR2004 Magic value used in comparison, consider replacing 3 with a constant variable
CPAC/isc/isfc.py:46:5: D103 Missing docstring in public function
CPAC/isc/isfc.py:50:5: D103 Missing docstring in public function
CPAC/isc/pipeline.py:1:1: D100 Missing docstring in public module
CPAC/isc/pipeline.py:29:5: D103 Missing docstring in public function
CPAC/isc/pipeline.py:52:5: D103 Missing docstring in public function
CPAC/isc/pipeline.py:105:5: D103 Missing docstring in public function
CPAC/isc/pipeline.py:128:5: D103 Missing docstring in public function
CPAC/isc/pipeline.py:142:5: D103 Missing docstring in public function
CPAC/isc/pipeline.py:150:5: D103 Missing docstring in public function
CPAC/isc/pipeline.py:159:5: D103 Missing docstring in public function
CPAC/isc/pipeline.py:173:5: D103 Missing docstring in public function
CPAC/isc/pipeline.py:181:5: D103 Missing docstring in public function
CPAC/isc/tests/__init__.py:1:1: D104 Missing docstring in public package
CPAC/isc/tests/test_pipeline_isc.py:1:1: D100 Missing docstring in public module
CPAC/isc/tests/test_pipeline_isc.py:8:5: D103 Missing docstring in public function
CPAC/isc/tests/test_pipeline_isc.py:11:29: NPY002 Replace legacy `np.random.uniform` call with `np.random.Generator`
CPAC/isc/tests/test_pipeline_isc.py:19:5: D103 Missing docstring in public function
CPAC/isc/tests/test_pipeline_isc.py:22:29: NPY002 Replace legacy `np.random.uniform` call with `np.random.Generator`
CPAC/isc/utils.py:1:1: D100 Missing docstring in public module
CPAC/isc/utils.py:7:5: D103 Missing docstring in public function
CPAC/isc/utils.py:13:5: D103 Missing docstring in public function
CPAC/isc/utils.py:32:5: D103 Missing docstring in public function
CPAC/longitudinal_pipeline/longitudinal_preproc.py:1:1: D100 Missing docstring in public module
CPAC/longitudinal_pipeline/longitudinal_preproc.py:16:5: D103 Missing docstring in public function
CPAC/longitudinal_pipeline/longitudinal_preproc.py:32:5: D103 Missing docstring in public function
CPAC/longitudinal_pipeline/longitudinal_preproc.py:59:5: D103 Missing docstring in public function
CPAC/longitudinal_pipeline/longitudinal_preproc.py:66:5: D205 1 blank line required between summary line and description
CPAC/longitudinal_pipeline/longitudinal_preproc.py:112:5: D205 1 blank line required between summary line and description
CPAC/longitudinal_pipeline/longitudinal_preproc.py:112:5: D414 Section has no content ("Returns")
CPAC/longitudinal_pipeline/longitudinal_preproc.py:152:5: D205 1 blank line required between summary line and description
CPAC/longitudinal_pipeline/longitudinal_preproc.py:321:5: PLR0913 Too many arguments in function definition (11 > 10)
CPAC/longitudinal_pipeline/longitudinal_preproc.py:334:5: D205 1 blank line required between summary line and description
CPAC/longitudinal_pipeline/longitudinal_preproc.py:402:5: PLR5501 Use `elif` instead of `else` then `if`, to reduce indentation
CPAC/longitudinal_pipeline/longitudinal_preproc.py:424:9: F821 Undefined name `warnings`
CPAC/longitudinal_pipeline/longitudinal_preproc.py:562:5: D205 1 blank line required between summary line and description
CPAC/longitudinal_pipeline/longitudinal_preproc.py:562:5: D414 Section has no content ("Returns")
CPAC/longitudinal_pipeline/longitudinal_workflow.py:1:1: D100 Missing docstring in public module
CPAC/longitudinal_pipeline/longitudinal_workflow.py:60:5: D103 Missing docstring in public function
CPAC/longitudinal_pipeline/longitudinal_workflow.py:83:5: D205 1 blank line required between summary line and description
CPAC/longitudinal_pipeline/longitudinal_workflow.py:83:5: D414 Section has no content ("Returns")
CPAC/longitudinal_pipeline/longitudinal_workflow.py:100:5: E722 Do not use bare `except`
CPAC/longitudinal_pipeline/longitudinal_workflow.py:163:5: D205 1 blank line required between summary line and description
CPAC/longitudinal_pipeline/longitudinal_workflow.py:210:5: D103 Missing docstring in public function
CPAC/longitudinal_pipeline/longitudinal_workflow.py:220:5: D103 Missing docstring in public function
CPAC/longitudinal_pipeline/longitudinal_workflow.py:239:5: D103 Missing docstring in public function
CPAC/longitudinal_pipeline/longitudinal_workflow.py:266:5: D103 Missing docstring in public function
CPAC/longitudinal_pipeline/longitudinal_workflow.py:337:5: D103 Missing docstring in public function
CPAC/longitudinal_pipeline/longitudinal_workflow.py:393:5: PLR0915 Too many statements (109 > 100)
CPAC/longitudinal_pipeline/longitudinal_workflow.py:394:5: D205 1 blank line required between summary line and description
CPAC/longitudinal_pipeline/longitudinal_workflow.py:690:5: D205 1 blank line required between summary line and description
CPAC/longitudinal_pipeline/longitudinal_workflow.py:755:50: F821 Undefined name `connect_func_ingress`
CPAC/longitudinal_pipeline/longitudinal_workflow.py:766:36: F821 Undefined name `connect_func_init`
CPAC/longitudinal_pipeline/longitudinal_workflow.py:771:36: F821 Undefined name `connect_func_preproc`
CPAC/longitudinal_pipeline/longitudinal_workflow.py:776:36: F821 Undefined name `connect_distortion_correction`
CPAC/longitudinal_pipeline/longitudinal_workflow.py:801:5: D205 1 blank line required between summary line and description
CPAC/longitudinal_pipeline/longitudinal_workflow.py:832:5: D103 Missing docstring in public function
CPAC/longitudinal_pipeline/longitudinal_workflow.py:889:17: PLW2901 `for` loop variable `strat` overwritten by assignment target
CPAC/longitudinal_pipeline/longitudinal_workflow.py:969:21: PLW2901 `for` loop variable `strat` overwritten by assignment target
CPAC/longitudinal_pipeline/longitudinal_workflow.py:1125:5: D205 1 blank line required between summary line and description
CPAC/median_angle/median_angle.py:1:1: D100 Missing docstring in public module
CPAC/median_angle/median_angle.py:7:5: D205 1 blank line required between summary line and description
CPAC/median_angle/median_angle.py:7:5: D401 First line of docstring should be in imperative mood: "Performs median angle correction on fMRI data.  Median angle correction algorithm"
CPAC/median_angle/median_angle.py:92:5: D401 First line of docstring should be in imperative mood: "Calculates median angle parameters of a subject."
CPAC/median_angle/median_angle.py:135:5: D205 1 blank line required between summary line and description
CPAC/median_angle/median_angle.py:135:5: D401 First line of docstring should be in imperative mood: "Calculates a target angle based on median angle parameters of"
CPAC/network_centrality/__init__.py:1:1: D104 Missing docstring in public package
CPAC/network_centrality/network_centrality.py:1:1: D100 Missing docstring in public module
CPAC/network_centrality/pipeline.py:1:1: D100 Missing docstring in public module
CPAC/network_centrality/pipeline.py:39:5: D400 First line should end with a period
CPAC/network_centrality/tests/test_network_centrality.py:1:1: D100 Missing docstring in public module
CPAC/network_centrality/tests/test_network_centrality.py:51:5: D205 1 blank line required between summary line and description
CPAC/network_centrality/utils.py:1:1: D100 Missing docstring in public module
CPAC/network_centrality/utils.py:31:5: D401 First line of docstring should be in imperative mood: "Method to calculate correlation threshold from p_value."
CPAC/network_centrality/utils.py:50:23: ICN001 `nibabel` should be imported as `nib`
CPAC/network_centrality/utils.py:81:5: D401 First line of docstring should be in imperative mood: "Function to actually do the list merging."
CPAC/network_centrality/utils.py:261:29: PLR2004 Magic value used in comparison, consider replacing 3 with a constant variable
CPAC/network_centrality/utils.py:271:33: PLR2004 Magic value used in comparison, consider replacing 3 with a constant variable
CPAC/network_centrality/utils.py:273:34: PLR2004 Magic value used in comparison, consider replacing 3 with a constant variable
CPAC/network_centrality/utils.py:323:8: E721 Do not compare types, use `isinstance()`
CPAC/network_centrality/utils.py:325:8: E721 Do not compare types, use `isinstance()`
CPAC/network_centrality/utils.py:332:10: E721 Do not compare types, use `isinstance()`
CPAC/network_centrality/utils.py:390:5: D205 1 blank line required between summary line and description
CPAC/network_centrality/utils.py:411:5: D205 1 blank line required between summary line and description
CPAC/nuisance/__init__.py:1:1: D104 Missing docstring in public package
CPAC/nuisance/bandpass.py:1:1: D100 Missing docstring in public module
CPAC/nuisance/bandpass.py:8:5: D103 Missing docstring in public function
CPAC/nuisance/bandpass.py:48:5: D401 First line of docstring should be in imperative mood: "Performs ideal bandpass filtering on each voxel time-series."
CPAC/nuisance/bandpass.py:76:28: PLR2004 Magic value used in comparison, consider replacing 20.0 with a constant variable
CPAC/nuisance/nuisance.py:1:1: D100 Missing docstring in public module
CPAC/nuisance/nuisance.py:63:5: D205 1 blank line required between summary line and description
CPAC/nuisance/nuisance.py:63:5: D401 First line of docstring should be in imperative mood: "Function to handle selecting appropriate blocks based on"
CPAC/nuisance/nuisance.py:106:5: D103 Missing docstring in public function
CPAC/nuisance/nuisance.py:184:5: PLR0913 Too many arguments in function definition (11 > 10)
CPAC/nuisance/nuisance.py:184:5: PLR0915 Too many statements (119 > 100)
CPAC/nuisance/nuisance.py:197:5: D205 1 blank line required between summary line and description
CPAC/nuisance/nuisance.py:242:5: E722 Do not use bare `except`
CPAC/nuisance/nuisance.py:248:38: PLR2004 Magic value used in comparison, consider replacing 4 with a constant variable
CPAC/nuisance/nuisance.py:248:71: PLR2004 Magic value used in comparison, consider replacing 2 with a constant variable
CPAC/nuisance/nuisance.py:296:16: E721 Do not compare types, use `isinstance()`
CPAC/nuisance/nuisance.py:350:20: E721 Do not compare types, use `isinstance()`
CPAC/nuisance/nuisance.py:395:13: E722 Do not use bare `except`
CPAC/nuisance/nuisance.py:429:13: E722 Do not use bare `except`
CPAC/nuisance/nuisance.py:506:5: PLR0912 Too many branches (64 > 50)
CPAC/nuisance/nuisance.py:506:5: PLR0915 Too many statements (219 > 100)
CPAC/nuisance/nuisance.py:514:5: D205 1 blank line required between summary line and description
CPAC/nuisance/nuisance.py:973:16: E721 Do not compare types, use `isinstance()`
CPAC/nuisance/nuisance.py:1103:16: E721 Do not compare types, use `isinstance()`
CPAC/nuisance/nuisance.py:1142:16: E721 Do not compare types, use `isinstance()`
CPAC/nuisance/nuisance.py:1263:24: E721 Do not compare types, use `isinstance()`
CPAC/nuisance/nuisance.py:1643:5: D103 Missing docstring in public function
CPAC/nuisance/nuisance.py:1810:5: PLR5501 Use `elif` instead of `else` then `if`, to reduce indentation
CPAC/nuisance/nuisance.py:1824:5: D103 Missing docstring in public function
CPAC/nuisance/nuisance.py:1956:5: D103 Missing docstring in public function
CPAC/nuisance/nuisance.py:2003:5: D103 Missing docstring in public function
CPAC/nuisance/nuisance.py:2074:5: D103 Missing docstring in public function
CPAC/nuisance/nuisance.py:2127:5: D103 Missing docstring in public function
CPAC/nuisance/nuisance.py:2198:5: D103 Missing docstring in public function
CPAC/nuisance/nuisance.py:2235:5: D103 Missing docstring in public function
CPAC/nuisance/nuisance.py:2274…

.circleci/main.yml

@@ -1,4 +1,4 @@
---- 
+---
 version: 2.1
 # Singularity started failing to set up on Circle circa May 2023, so those tests are currently disabled
 
@@ -139,7 +139,7 @@ commands:
             pip install -r dev/circleci_data/requirements.txt
       - save_cache:
           key: pip-ci-requirements-{{ checksum "dev/circleci_data/requirements.txt" }}-3.10.10
-          paths: 
+          paths:
             - /opt/circleci/.pyenv/versions/3.10.10
   set-up-variant:
     parameters:
@@ -237,7 +237,7 @@ jobs:
           path: test-results
       - save_cache:
           key: coverage-docker-<< parameters.variant >>-{{ .Revision }}
-          paths: 
+          paths:
             - .coverage.docker
             - .coverage.docker-<< parameters.variant >>
   pytest-singularity:
@@ -266,7 +266,7 @@ jobs:
           path: test-results
       - save_cache:
           key: coverage-singularity-<< parameters.variant >>-{{ .Revision }}
-          paths: 
+          paths:
             - .coverage.singularity
             - .coverage.singularity-<<parameters.variant >>
 workflows:

.github/Dockerfiles/AFNI.16.2.07.neurodocker-xenial.Dockerfile

@@ -29,4 +29,4 @@ USER root
 
 COPY --from=AFNI /opt/afni-latest/ /usr/lib/afni/bin/
 
-USER c-pac_user
+USER c-pac_user

.github/Dockerfiles/FreeSurfer.6.0.1-min-xenial.Dockerfile

@@ -9,4 +9,4 @@ LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A
 FreeSurfer 6.0.1-min stage"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
 COPY --from=FreeSurfer /opt/freesurfer /opt/freesurfer
-COPY dev/docker_data/license.txt /opt/freesurfer/license.txt
+COPY dev/docker_data/license.txt /opt/freesurfer/license.txt

.github/Dockerfiles/ICA-AROMA.0.4.3-beta-bionic.Dockerfile

@@ -23,4 +23,4 @@ USER c-pac_user
 FROM scratch
 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 ICA-AROMA 0.4.3-beta stage"
-COPY --from=ICA-AROMA /opt/ICA-AROMA/ /opt/ICA-AROMA/
+COPY --from=ICA-AROMA /opt/ICA-AROMA/ /opt/ICA-AROMA/

.github/Dockerfiles/ICA-AROMA.0.4.4-beta-jammy.Dockerfile

@@ -26,4 +26,4 @@ USER c-pac_user
 FROM scratch
 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 ICA-AROMA 0.4.4-beta stage"
-COPY --from=ICA-AROMA /opt/ICA-AROMA/ /opt/ICA-AROMA/
+COPY --from=ICA-AROMA /opt/ICA-AROMA/ /opt/ICA-AROMA/

.github/Dockerfiles/ICA-AROMA.0.4.5-xenial.Dockerfile

@@ -26,4 +26,4 @@ FROM scratch
 LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
 ICA-AROMA 0.4.5 stage"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
-COPY --from=ICA-AROMA /opt/ICA-AROMA/ /opt/ICA-AROMA/
+COPY --from=ICA-AROMA /opt/ICA-AROMA/ /opt/ICA-AROMA/

.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile

@@ -80,4 +80,4 @@ RUN ldconfig \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/pip/*
 
 # Set user
-USER c-pac_user
+USER c-pac_user

.github/Dockerfiles/base-ABCD-HCP.Dockerfile

@@ -96,4 +96,4 @@ RUN locale-gen --purge en_US.UTF-8 \
   && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # set user
-USER c-pac_user
+USER c-pac_user

.github/Dockerfiles/base-fMRIPrep-LTS.Dockerfile

@@ -68,7 +68,7 @@ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
 
 # Installing and setting up AFNI
 COPY --from=AFNI /lib/x86_64-linux-gnu/ld* /lib/x86_64-linux-gnu/
-COPY --from=AFNI /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/ 
+COPY --from=AFNI /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
 COPY --from=AFNI /lib64/ld* /lib64/
 COPY --from=AFNI /usr/lib/afni/bin/ /usr/lib/afni/bin/
 COPY --from=AFNI /usr/lib/x86_64-linux-gnu/lib*so* /usr/lib/x86_64-linux-gnu/
@@ -92,7 +92,7 @@ COPY --from=c3d /usr/bin/c3d_* /usr/bin/
 COPY --from=c3d /usr/share/doc/convert3d /usr/share/doc/convert3d
 COPY --from=c3d /usr/lib/c3d_gui-1.1.0/Convert3DGUI /usr/lib/c3d_gui-1.1.0/Convert3DGUI
 
-# Installing and setting up FSL 
+# Installing and setting up FSL
 COPY --from=FSL /etc/fsl /etc/fsl
 COPY --from=FSL /usr/lib/fsl /usr/lib/fsl
 COPY --from=FSL /usr/lib/libnewmat.so.10 /usr/lib/libnewmat.so.10

.github/Dockerfiles/connectome-workbench.1.3.2-1.neurodebian-bionic.Dockerfile

@@ -26,4 +26,4 @@ COPY --from=base /usr/share/applications/connectome-workbench.desktop /usr/share
 COPY --from=base /usr/share/bash-completion/completions/wb* /usr/share/bash_completion/completions/
 COPY --from=base /usr/share/doc/connectome-workbench /usr/share/doc/connectome-workbench
 COPY --from=base /usr/share/man/man1/wb_* /usr/share/man/man1/
-COPY --from=base /usr/share/pixmaps/connectome-workbench.png /usr/share/pixmaps/connectome-workbench.png
+COPY --from=base /usr/share/pixmaps/connectome-workbench.png /usr/share/pixmaps/connectome-workbench.png

.github/Dockerfiles/connectome-workbench.1.3.2-2.neurodebian-xenial.Dockerfile

@@ -24,4 +24,4 @@ COPY --from=base /usr/share/applications/connectome-workbench.desktop /usr/share
 COPY --from=base /usr/share/bash-completion/completions/wb* /usr/share/bash-completion/completions/
 COPY --from=base /usr/share/doc/connectome-workbench /usr/share/doc/connectome-workbench
 COPY --from=base /usr/share/man/man1/wb_* /usr/share/man/man1/
-COPY --from=base /usr/share/pixmaps/connectome-workbench.png /usr/share/pixmaps/connectome-workbench.png
+COPY --from=base /usr/share/pixmaps/connectome-workbench.png /usr/share/pixmaps/connectome-workbench.png

.github/Dockerfiles/msm.2.0-bionic.Dockerfile

@@ -53,4 +53,4 @@ LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A
 msm v2.0 stage \
     Multimodal Surface Matching with Higher order Clique Reduction Version 2.00 (Feb 2017)"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
-COPY --from=MSM /opt/msm/Ubuntu/msm /opt/msm/Ubuntu/msm
+COPY --from=MSM /opt/msm/Ubuntu/msm /opt/msm/Ubuntu/msm

.github/README/README.md

@@ -50,9 +50,9 @@ flowchart LR
       end
       subgraph build_and_test.yml
         ubuntu[[Ubnutu]]-->stages[[stages]]-->build-base[[build-base]]-->build-base-standard[[build-base-standard]]
-        
+
         Circle_tests[[Circle_tests]]
-      
+
         build-base-standard-->C-PAC
         C-PAC[[C-PAC]]-->bCPAC
         C-PAC-->Circle_tests
@@ -164,7 +164,7 @@ in the commit message. For this to work, all of these must be true:
    ```YAML
    strategy:
      matrix:
-       Dockerfile: 
+       Dockerfile:
    ```
 
    in a job in a [workflow](../workflows) file.

.github/scripts/autoversioning.sh

@@ -59,4 +59,4 @@ cp .github/Dockerfiles/C-PAC.develop-jammy.Dockerfile Dockerfile
 cp .github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile variant-ABCD-HCP.Dockerfile
 cp .github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile variant-fMRIPrep-LTS.Dockerfile
 cp .github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile variant-lite.Dockerfile
-git add *Dockerfile
+git add *Dockerfile

.github/scripts/freesurfer-prune

@@ -6,4 +6,4 @@ do
     echo "Deleting $FILE"
     rm -rf $FILE || true
   fi
-done
+done

.github/scripts/get_package_id.py

@@ -1,16 +1,17 @@
-"""Get Package ID
+"""Get Package ID.
 
 Script to get GHCR ID string for a given owner + image tag
 
 Usage: python get_package_id.py $OWNER $IMAGE_TAG $VERSION_TAG
 """
 import os
-import requests
 import sys
 
+import requests
+
 
 def get_packages(owner, tag, api_token=None):
-    """Function to collect GHCR packages for a given owner & tag
+    """Function to collect GHCR packages for a given owner & tag.
 
     Parameters
     ----------
@@ -28,10 +29,10 @@ def get_packages(owner, tag, api_token=None):
     list
     """
     if api_token is None:
-        api_token = os.environ.get('GITHUB_TOKEN', '')
+        api_token = os.environ.get("GITHUB_TOKEN", "")
 
     def fetch(url):
-        """Method to make API call and return response, given a URL
+        """Method to make API call and return response, given a URL.
 
         Parameters
         ----------
@@ -42,37 +43,46 @@ def fetch(url):
         dict or list
         """
         response = requests.get(
-            url,
-            headers={'Authorization': f'token {api_token}'}).json()
-        if isinstance(response, dict) and response.get(
-            'message', ''
-        ) == 'Bad credentials':
-            raise PermissionError('\n'.join([
-                ': '.join([
-                    response['message'],
-                    api_token if api_token else '[no token provided]'
-                ]),
-                'Either set GITHUB_TOKEN to a personal access token with '
-                'read.packages permissions or explicitly pass one as a fourth '
-                'positional argument:\n'
-                '`python get_package_id.py $OWNER $IMAGE_TAG '
-                '$VERSION_TAG $GITHUB_TOKEN`'
-            ]))
+            url, headers={"Authorization": f"token {api_token}"}
+        ).json()
+        if (
+            isinstance(response, dict)
+            and response.get("message", "") == "Bad credentials"
+        ):
+            raise PermissionError(
+                "\n".join(
+                    [
+                        ": ".join(
+                            [
+                                response["message"],
+                                api_token if api_token else "[no token provided]",
+                            ]
+                        ),
+                        "Either set GITHUB_TOKEN to a personal access token with "
+                        "read.packages permissions or explicitly pass one as a fourth "
+                        "positional argument:\n"
+                        "`python get_package_id.py $OWNER $IMAGE_TAG "
+                        "$VERSION_TAG $GITHUB_TOKEN`",
+                    ]
+                )
+            )
         return response
+
     _packages = fetch(
-        f'https://api.github.com/orgs/{owner}/packages/container/'
-        f'{tag}/versions')
+        f"https://api.github.com/orgs/{owner}/packages/container/" f"{tag}/versions"
+    )
     packages = []
     for _package in _packages:
-        if _package.get('message', 'Not Found') == 'Not Found':
+        if _package.get("message", "Not Found") == "Not Found":
             packages += fetch(
-                f'https://api.github.com/users/{owner}/packages/container/'
-                f'{tag}/versions')
+                f"https://api.github.com/users/{owner}/packages/container/"
+                f"{tag}/versions"
+            )
     return packages
 
 
 def id_from_tag(owner, image, tag, api_token=None):
-    """Function to return a package ID given an image version tag
+    """Function to return a package ID given an image version tag.
 
     Parameters
     ----------
@@ -89,17 +99,19 @@ def id_from_tag(owner, image, tag, api_token=None):
         GitHub API personal access token with read.packages permission
     """
     packages = get_packages(owner, image, api_token)
-    versions = [image['id'] for image in packages if tag in image.get(
-        'metadata', {}
-    ).get('container', {}).get('tags', [])]
+    versions = [
+        image["id"]
+        for image in packages
+        if tag in image.get("metadata", {}).get("container", {}).get("tags", [])
+    ]
     if len(versions):
         return versions[0]
     else:
-        raise LookupError(f'Image not found: ghcr.io/{owner}/{image}:{tag}')
+        raise LookupError(f"Image not found: ghcr.io/{owner}/{image}:{tag}")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     if len(sys.argv) == 4:
-        print(id_from_tag(*sys.argv[1:]))
+        pass
     else:
-        print(__doc__)
+        pass

.github/scripts/get_pr_base_shas.py

@@ -14,16 +14,4 @@
 
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
-"""Get base SHAs for open PRs"""
-import os
-from github import Github
-
-print(' '.join([
-    pr.base.sha for pr in Github(os.environ.get(
-        'GITHUB_TOKEN'
-    )).get_repo(os.environ.get(
-        'GITHUB_REPOSITORY'
-    )).get_commit(os.environ.get(
-        'GITHUB_SHA'
-    )).get_pulls()
-]))
+"""Get base SHAs for open PRs."""

.github/scripts/local_ghcr

@@ -3,22 +3,17 @@ import sys
 
 
 def replace_primary_repo(yaml_string, local_owner):
-    return yaml_string.replace('ghcr.io/fcp-indi',
-                               f'ghcr.io/{local_owner.lower()}')
+    return yaml_string.replace("ghcr.io/fcp-indi", f"ghcr.io/{local_owner.lower()}")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     if len(sys.argv) != 4:
-        raise SyntaxError('Usage: local_ghcr $FILE $OWNER $DOCKER_TAG')
+        raise SyntaxError("Usage: local_ghcr $FILE $OWNER $DOCKER_TAG")
     file, owner, tag = sys.argv[1:]
-    dockerfiles = '.github/Dockerfiles'
-    new_Dockerfile = replace_primary_repo(
-        open(file, 'r').read(),
-        owner.lower()
-    )
-    if '-lite-' in file:
+    dockerfiles = ".github/Dockerfiles"
+    new_Dockerfile = replace_primary_repo(open(file, "r").read(), owner.lower())
+    if "-lite-" in file:
         tag = tag.lower().split("c-pac:")[1][:-5]
-        if tag != 'latest-lite':
-            new_Dockerfile = new_Dockerfile.replace(':latest-bionic',
-                                                    f':{tag}')
-    open(file, 'w').write(new_Dockerfile)
+        if tag != "latest-lite":
+            new_Dockerfile = new_Dockerfile.replace(":latest-bionic", f":{tag}")
+    open(file, "w").write(new_Dockerfile)

.github/stage_requirements/ABCD-HCP.txt

@@ -6,4 +6,4 @@ connectome-workbench.1.3.2-1.neurodebian-bionic
 FSL.5.0.10-bionic
 ICA-AROMA.0.4.3-beta-bionic
 msm.2.0-bionic
-Ubuntu.bionic-non-free
+Ubuntu.bionic-non-free

.github/stage_requirements/fMRIPrep-LTS.txt

@@ -6,4 +6,4 @@ connectome-workbench.1.3.2-2.neurodebian-xenial
 FSL.5.0.9-5.neurodebian-xenial
 ICA-AROMA.0.4.5-xenial
 msm.2.0-bionic
-Ubuntu.xenial-20200114
+Ubuntu.xenial-20200114

.github/stage_requirements/lite.txt

@@ -1,4 +1,4 @@
 base-lite
 AFNI.23.3.09-jammy
 ICA-AROMA.0.4.4-beta-jammy
-Ubuntu.jammy-non-free
+Ubuntu.jammy-non-free

.github/stage_requirements/phase_one.txt

@@ -1,4 +1,4 @@
 FSL.data
 Ubuntu.bionic-non-free
 Ubuntu.jammy-non-free
-Ubuntu.xenial-20200114
+Ubuntu.xenial-20200114

.github/stage_requirements/phase_three.txt

@@ -1,3 +1,3 @@
 lite
 ABCD-HCP
-fMRIPrep-LTS
+fMRIPrep-LTS

.github/stage_requirements/phase_two.txt

@@ -13,4 +13,4 @@ FSL.6.0.6.5-jammy
 ICA-AROMA.0.4.3-beta-bionic
 ICA-AROMA.0.4.4-beta-jammy
 ICA-AROMA.0.4.5-xenial
-msm.2.0-bionic
+msm.2.0-bionic

.github/workflows/build_and_test.yml

@@ -96,7 +96,7 @@ jobs:
             ${{ env.DOCKER_TAG }}
           cache-from: type=gha
           cache-to: type=gha,mode=min,compression=zstd
-  
+
   stages:
     name: Build C-PAC Docker stage images for dependencies
     needs: Ubuntu

.github/workflows/delete_images.yml

@@ -36,7 +36,7 @@ jobs:
           fi
           TAG=${GITHUB_REF_NAME}
           TAG=$TAG$VARIANT
-          
+
           VERSION_ID=$(python .github/scripts/get_package_id.py $OWNER $IMAGE $TAG)
           curl \
             -u ${GITHUB_TOKEN}: \