MCR support

.github/workflows/test.yml

@@ -2,17 +2,11 @@ name: Test
 on: [push, pull_request]
 jobs:
   check:
-    if: github.event_name != 'push' || github.ref != 'refs/heads/devel'
+    if: github.event_name != 'pull_request' || github.repository_owner != 'AMYPAD'
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python: [2.7, 3.6, 3.9]
-    name: Check py${{ matrix.python }}
     steps:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python }}
     - name: set PYSHA
       run: echo "PYSHA=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
     - uses: actions/cache@v1
@@ -22,7 +16,7 @@ jobs:
     - name: dependencies
       run: pip install -U pre-commit
     - uses: reviewdog/action-setup@v1
-    - if: github.event_name != 'schedule'
+    - if: github.event_name == 'push' || github.event_name == 'pull_request'
       name: comment
       run: |
         if [[ $EVENT == pull_request ]]; then
@@ -35,15 +29,14 @@ jobs:
       env:
         REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         EVENT: ${{ github.event_name }}
-    - if: startsWith(matrix.python, '3')
-      run: pre-commit run -a --show-diff-on-failure
+    - run: SKIP=mbeautify pre-commit run -a --show-diff-on-failure
   test:
-    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
+    if: github.event_name != 'pull_request' || github.repository_owner != 'AMYPAD'
+    name: py${{ matrix.python }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python: [2.7, 3.6, 3.9]
-    name: Test py${{ matrix.python }}
     steps:
     - uses: actions/checkout@v2
       with:
@@ -56,22 +49,25 @@ jobs:
       run: pytest --durations-min=1
     - if: startsWith(matrix.python, '2')
       run: pytest
-    - run: codecov
+    - uses: codecov/codecov-action@v1
   matlab:
-    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
+    if: github.event_name != 'pull_request' || github.repository_owner != 'AMYPAD'
+    name: matlab py${{ matrix.python }}
     runs-on: [self-hosted, python, matlab]
-    name: Test matlab
+    strategy:
+      matrix:
+        python: [3.9]
     steps:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
     - name: Run setup-python
-      run: setup-python -p3.7
+      run: setup-python -p${{ matrix.python }}
     - run: pip install -U .[dev]
     - run: pytest --durations-min=1
-    - run: codecov
+    - uses: codecov/codecov-action@v1
     - name: Post Run setup-python
-      run: setup-python -p3.7 -Dr
+      run: setup-python -p${{ matrix.python }} -Dr
       if: ${{ always() }}
   deploy:
     needs: [check, test, matlab]
@@ -85,7 +81,8 @@ jobs:
     - id: dist
       uses: casperdcl/deploy-pypi@v2
       with:
-        pip: true
+        requirements: twine setuptools wheel setuptools_scm[toml]
+        build: true
         gpg_key: ${{ secrets.GPG_KEY }}
         password: ${{ secrets.PYPI_TOKEN }}
         upload: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags') }}

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.1.0
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -21,25 +21,33 @@ repos:
   - id: todo
     name: Check TODO
     language: pygrep
+    args: [-i]
     entry: TODO
     types: [text]
     exclude: ^(.pre-commit-config.yaml|.github/workflows/test.yml)$
-    args: [-i]
 - repo: https://gitlab.com/pycqa/flake8
   rev: 3.9.2
   hooks:
   - id: flake8
     args: [-j8]
     additional_dependencies:
+    - flake8-broken-line
     - flake8-bugbear
     - flake8-comprehensions
     - 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: 5.9.3
+  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.

pyproject.toml

@@ -1,10 +1,6 @@
 [build-system]
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"]
-build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 write_to = "spm12/_dist_ver.py"
 write_to_template = "__version__ = '{version}'\n"
-
-[tool.black]
-target_version = ["py27", "py36", "py38"]

setup.cfg

@@ -7,8 +7,8 @@ license=Apache 2.0
 license_file=LICENCE.md
 url=https://github.com/AMYPAD/SPM12
 project_urls=
-    Changelog = https://github.com/AMYPAD/SPM12/releases
-    Documentation = https://github.com/AMYPAD/SPM12/#SPM12
+    Changelog=https://github.com/AMYPAD/SPM12/releases
+    Documentation=https://github.com/AMYPAD/SPM12/#SPM12
     Upstream Project=https://www.fil.ion.ucl.ac.uk/spm
 maintainer=Casper da Costa-Luis
 maintainer_email=casper.dcl@physics.org
@@ -36,48 +36,56 @@ classifiers=
     Topic :: Software Development :: Libraries
     Topic :: System :: Installation/Setup
 [options]
-zip_safe = False
+zip_safe=False
 setup_requires=setuptools>=42; wheel; setuptools_scm[toml]>=3.4
 install_requires=
     argopt
-    miutil[nii,web]>=0.7.2
-    setuptools  # pkg_resources
+    miutil[nii,web]>=0.8.0
     numpy
     scipy
+    setuptools
 include_package_data=True
 packages=find:
 python_requires=>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*
 [options.extras_require]
 dev=
-    pre-commit
-    twine
-    wheel
     pytest
     pytest-cov
     pytest-timeout
     pytest-xdist
-    codecov
 demo=
     miutil[plot]>=0.3.0
     matplotlib
 [options.entry_points]
-console_scripts =
+console_scripts=
     spm12=spm12.cli:main
 [options.packages.find]
 exclude=tests
 [options.package_data]
 *=*.md, *.rst, *.m
 
 [bdist_wheel]
-universal = 1
+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