pre-commit: update linters (black=>yapf, mbeautify)

.pre-commit-config.yaml

@@ -37,11 +37,17 @@ repos:
     - flake8-debugger
     - flake8-isort
     - flake8-string-format
-- repo: https://github.com/psf/black
-  rev: 21.7b0
+- repo: https://github.com/google/yapf
+  rev: v0.32.0
   hooks:
-  - id: black
+  - id: yapf
+    args: [-i]
+    additional_dependencies: [toml]
 - repo: https://github.com/PyCQA/isort
   rev: 5.10.1
   hooks:
   - id: isort
+- hooks:
+  - id: mbeautify
+  repo: https://github.com/AMYPAD/miutil
+  rev: v0.9.1

LICENCE.md

@@ -1,4 +1,4 @@
-Copyright 2020 AMYPAD
+Copyright 2020-2022 AMYPAD
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this project except in compliance with the License.

setup.cfg

@@ -68,12 +68,24 @@ exclude=tests
 universal=1
 
 [flake8]
-max_line_length=88
-extend-ignore=E203,P1
+max_line_length=99
+extend-ignore=P1,E261
 exclude=.git,__pycache__,build,dist,.eggs
 
+[yapf]
+spaces_before_comment=15, 20
+arithmetic_precedence_indication=true
+allow_split_before_dict_value=false
+coalesce_brackets=True
+column_limit=99
+each_dict_entry_on_separate_line=False
+space_between_ending_comma_and_closing_bracket=False
+split_before_named_assigns=False
+split_before_closing_bracket=False
+
 [isort]
 profile=black
+line_length=99
 known_first_party=spm12,tests
 
 [tool:pytest]

spm12/__init__.py

@@ -1,5 +1,5 @@
-from .regseg import *  # NOQA
-from .utils import *  # NOQA
+from .regseg import *  # yapf: disable # NOQA
+from .utils import *  # yapf: disable # NOQA
 
 # version detector. Precedence: installed dist, git, 'UNKNOWN'
 try:

spm12/__main__.py

@@ -3,5 +3,5 @@
 
 from .cli import main
 
-if __name__ == "__main__":  # pragma: no cover
+if __name__ == "__main__": # pragma: no cover
     sys.exit(main(sys.argv[1:]))

spm12/amypad_coreg.m

@@ -1,28 +1,28 @@
 function [M, x] = amypad_coreg(imref, imflo, costfun, sep, tol, fwhm, params, graphics, visual)
-    if visual>0
-        Fgraph = spm_figure('GetWin','Graphics');
-        Finter = spm_figure('GetWin','Interactive');
-    end
+if visual > 0
+    Fgraph = spm_figure('GetWin', 'Graphics');
+    Finter = spm_figure('GetWin', 'Interactive');
+end
 
-    cflags.cost_fun = costfun;
-    cflags.sep = sep;
-    cflags.tol = tol;
-    cflags.fwhm = fwhm;
-    cflags.params = params;
-    cflags.graphics = graphics;
+cflags.cost_fun = costfun;
+cflags.sep = sep;
+cflags.tol = tol;
+cflags.fwhm = fwhm;
+cflags.params = params;
+cflags.graphics = graphics;
 
-    VG = strcat(imref,',1');
-    VF = strcat(imflo,',1');
+VG = strcat(imref, ',1');
+VF = strcat(imflo, ',1');
 
-    %disp('Matlab internal reference image:'); disp(imref);
-    %disp('Matlab internal floating image:'); disp(imflo);
-    %disp(cflags);
-    %disp(tol);
+%disp('Matlab internal reference image:'); disp(imref);
+%disp('Matlab internal floating image:'); disp(imflo);
+%disp(cflags);
+%disp(tol);
 
-    spm_jobman('initcfg')
-    x = spm_coreg(VG, VF, cflags);
-    M = spm_matrix(x);
+spm_jobman('initcfg')
+x = spm_coreg(VG, VF, cflags);
+M = spm_matrix(x);
 
-    %disp('translations and rotations:'); disp(x);
-    %disp('affine matrix:'); disp(M);
+%disp('translations and rotations:'); disp(x);
+%disp('affine matrix:'); disp(M);
 end

spm12/amypad_coreg_modify_affine.m

@@ -1,7 +1,7 @@
 function out = amypad_coreg_modify_affine(imflo, M)
-    VF = strcat(imflo,',1');
-    MM = zeros(4,4);
-    MM(:,:) = spm_get_space(VF);
-    spm_get_space(VF, M\MM(:,:));
-    out = 0;
+VF = strcat(imflo, ',1');
+MM = zeros(4, 4);
+MM(:, :) = spm_get_space(VF);
+spm_get_space(VF, M \ MM(:, :));
+out = 0;
 end

spm12/amypad_normw.m

@@ -1,10 +1,10 @@
 function out = amypad_normw(def_file, flist4norm)
-    job.subj.def = {def_file};
-    job.subj.resample = flist4norm;
-    job.woptions.bb = [NaN, NaN, NaN; NaN, NaN, NaN];
-    job.woptions.vox = [2, 2, 2];
-    job.woptions.interp = 4;
-    job.woptions.prefix = 'w';
-    spm_run_norm(job);
-    out=0;
+job.subj.def = {def_file};
+job.subj.resample = flist4norm;
+job.woptions.bb = [NaN, NaN, NaN; NaN, NaN, NaN];
+job.woptions.vox = [2, 2, 2];
+job.woptions.interp = 4;
+job.woptions.prefix = 'w';
+spm_run_norm(job);
+out = 0;
 end

spm12/amypad_resample.m

@@ -1,23 +1,23 @@
 function out = amypad_resample(imref, imflo, M, f_mask, f_mean, f_interp, f_which, f_prefix)
-    %-Reslicing parameters
-    rflags.mask = f_mask;
-    rflags.mean = f_mean;
-    rflags.interp = f_interp;
-    rflags.which = f_which;
-    rflags.wrap = [0 0 0];
-    rflags.prefix = f_prefix;
+%-Reslicing parameters
+rflags.mask = f_mask;
+rflags.mean = f_mean;
+rflags.interp = f_interp;
+rflags.which = f_which;
+rflags.wrap = [0, 0, 0];
+rflags.prefix = f_prefix;
 
-    VG = strcat(imref,',1');
-    VF = strcat(imflo,',1');
+VG = strcat(imref, ',1');
+VF = strcat(imflo, ',1');
 
-    % disp('Matlab internal reference image:'); disp(imref);
-    % disp('Matlab internal floating image:'); disp(imflo);
-    % disp(rflags)
+% disp('Matlab internal reference image:'); disp(imref);
+% disp('Matlab internal floating image:'); disp(imflo);
+% disp(rflags)
 
-    MM = zeros(4,4);
-    MM(:, :) = spm_get_space(VF);
-    spm_get_space(VF, M\MM(:, :));
-    P = {VG; VF};
-    spm_reslice(P, rflags);
-    out = 0;
+MM = zeros(4, 4);
+MM(:, :) = spm_get_space(VF);
+spm_get_space(VF, M \ MM(:, :));
+P = {VG; VF};
+spm_reslice(P, rflags);
+out = 0;
 end

spm12/amypad_seg.m

@@ -1,46 +1,46 @@
-function [param,invdef,fordef] = amypad_seg(f_mri, spm_path, nat_gm, nat_wm, nat_csf, store_fwd, store_inv, visual)
-    job.channel.vols = {strcat(f_mri,',1')};
-    job.channel.biasreg = 0.001;
-    job.channel.biasfwhm = 60;
-    job.channel.write = [0, 0];
-    job.tissue(1).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,1']};
-    job.tissue(1).ngaus = 1;
-    job.tissue(1).native = [nat_gm, 0];
-    job.tissue(1).warped = [0, 0];
-    job.tissue(2).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,2']};
-    job.tissue(2).ngaus = 1;
-    job.tissue(2).native = [nat_wm, 0];
-    job.tissue(2).warped = [0, 0];
-    job.tissue(3).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,3']};
-    job.tissue(3).ngaus = 2;
-    job.tissue(3).native = [nat_csf, 0];
-    job.tissue(3).warped = [0, 0];
-    job.tissue(4).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,4']};
-    job.tissue(4).ngaus = 3;
-    job.tissue(4).native = [0, 0];
-    job.tissue(4).warped = [0, 0];
-    job.tissue(5).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,5']};
-    job.tissue(5).ngaus = 4;
-    job.tissue(5).native = [0, 0];
-    job.tissue(5).warped = [0, 0];
-    job.tissue(6).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,6']};
-    job.tissue(6).ngaus = 2;
-    job.tissue(6).native = [0, 0];
-    job.tissue(6).warped = [0, 0];
-    job.warp.mrf = 1;
-    job.warp.cleanup = 1;
-    job.warp.reg = [0, 0.001, 0.5, 0.05, 0.2];
-    job.warp.affreg = 'mni';
-    job.warp.fwhm = 0;
-    job.warp.samp = 3;
-    job.warp.write = [store_fwd, store_inv];
-    if visual>0
-        Finter = spm_figure('GetWin','Interactive');
-    end
-    spm_jobman('initcfg');
-    segout = spm_preproc_run(job);
-    param  = segout.param{1};
-    invdef = segout.invdef{1};
-    fordef = segout.fordef{1};
-    %disp(segout);
+function [param, invdef, fordef] = amypad_seg(f_mri, spm_path, nat_gm, nat_wm, nat_csf, store_fwd, store_inv, visual)
+job.channel.vols = {strcat(f_mri, ',1')};
+job.channel.biasreg = 0.001;
+job.channel.biasfwhm = 60;
+job.channel.write = [0, 0];
+job.tissue(1).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,1']};
+job.tissue(1).ngaus = 1;
+job.tissue(1).native = [nat_gm, 0];
+job.tissue(1).warped = [0, 0];
+job.tissue(2).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,2']};
+job.tissue(2).ngaus = 1;
+job.tissue(2).native = [nat_wm, 0];
+job.tissue(2).warped = [0, 0];
+job.tissue(3).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,3']};
+job.tissue(3).ngaus = 2;
+job.tissue(3).native = [nat_csf, 0];
+job.tissue(3).warped = [0, 0];
+job.tissue(4).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,4']};
+job.tissue(4).ngaus = 3;
+job.tissue(4).native = [0, 0];
+job.tissue(4).warped = [0, 0];
+job.tissue(5).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,5']};
+job.tissue(5).ngaus = 4;
+job.tissue(5).native = [0, 0];
+job.tissue(5).warped = [0, 0];
+job.tissue(6).tpm = {[spm_path, filesep, 'tpm', filesep, 'TPM.nii,6']};
+job.tissue(6).ngaus = 2;
+job.tissue(6).native = [0, 0];
+job.tissue(6).warped = [0, 0];
+job.warp.mrf = 1;
+job.warp.cleanup = 1;
+job.warp.reg = [0, 0.001, 0.5, 0.05, 0.2];
+job.warp.affreg = 'mni';
+job.warp.fwhm = 0;
+job.warp.samp = 3;
+job.warp.write = [store_fwd, store_inv];
+if visual > 0
+    Finter = spm_figure('GetWin', 'Interactive');
+end
+spm_jobman('initcfg');
+segout = spm_preproc_run(job);
+param = segout.param{1};
+invdef = segout.invdef{1};
+fordef = segout.fordef{1};
+%disp(segout);
 end

spm12/cli.py

@@ -19,9 +19,7 @@
 
 
 def main(argv=None):
-    logging.basicConfig(
-        level=logging.DEBUG, format="%(levelname)s:%(funcName)s:%(message)s"
-    )
+    logging.basicConfig(level=logging.DEBUG, format="%(levelname)s:%(funcName)s:%(message)s")
     args = argopt(__doc__).parse_args(argv)
     log.info(args)
     if isinstance(args.command, str):