bump version, merge pull request #19 from AMYPAD/devel

.github/workflows/test.yml

@@ -1,10 +1,12 @@
 name: Test
-on: [push, pull_request]
+on:
+  push:
+  pull_request:
+  schedule: [{cron: '10 23 * * 6'}]  # M H d m w (Sat at 23:10)
 jobs:
   check:
     if: github.event_name != 'pull_request' || !contains('OWNER,MEMBER,COLLABORATOR', github.event.pull_request.author_association)
     runs-on: ubuntu-latest
-    name: Check
     steps:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
@@ -19,7 +21,7 @@ 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 [[ $EVENT == pull_request ]]; then
@@ -35,11 +37,11 @@ jobs:
     - run: pre-commit run -a --show-diff-on-failure
   test:
     if: github.event_name != 'pull_request' || !contains('OWNER,MEMBER,COLLABORATOR', github.event.pull_request.author_association)
+    name: py${{ matrix.python }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [3.7, '3.10']
-    name: Test py${{ matrix.python }}
+        python: [3.7, 3.11]
     steps:
     - uses: actions/checkout@v3
       with:
@@ -49,22 +51,25 @@ jobs:
         python-version: ${{ matrix.python }}
     - run: pip install -U .[dev]
     - run: pytest --durations-min=1
-    - run: codecov
+    - uses: codecov/codecov-action@v3
   matlab:
     if: github.event_name != 'pull_request' || !contains('OWNER,MEMBER,COLLABORATOR', github.event.pull_request.author_association)
+    name: MATLAB py${{ matrix.python }}
     runs-on: [self-hosted, python, matlab]
-    name: Test matlab
+    strategy:
+      matrix:
+        python: [3.7, 3.8]
     steps:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
     - name: Run setup-python
-      run: setup-python -p3.7
-    - run: pip install -U .[dev]
+      run: setup-python -p${{ matrix.python }}
+    - run: pip install -U .[dev] 'setuptools<66'  # ignore matlab engine PEP440 non-compliance https://github.com/pypa/setuptools/issues/3772
     - run: pytest --durations-min=1
-    - run: codecov
+    - uses: codecov/codecov-action@v3
     - name: Post Run setup-python
-      run: setup-python -p3.7 -Dr
+      run: setup-python -p${{ matrix.python }} -Dr
       if: ${{ always() }}
   deploy:
     needs: [check, test, matlab]
@@ -75,6 +80,8 @@ jobs:
       with:
         fetch-depth: 0
     - uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
     - id: dist
       uses: casperdcl/deploy-pypi@v2
       with:
@@ -83,10 +90,10 @@ jobs:
         password: ${{ secrets.PYPI_TOKEN }}
         upload: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags') }}
     - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-      name: release
+      name: Release
       run: |
         changelog=$(git log --pretty='format:%d%n- %s%n%b---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD)
         tag="${GITHUB_REF#refs/tags/}"
         gh release create --title "spm12 $tag beta" --draft --notes "$changelog" "$tag" dist/${{ steps.dist.outputs.whl }} dist/${{ steps.dist.outputs.whl_asc }}
       env:
-        GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
+        GH_TOKEN: ${{ github.token }}

.gitignore

@@ -1,9 +1,9 @@
 *.py[cod]
 __pycache__/
 /spm12/_dist_ver.py
-/.eggs/
-/*.egg-info/
+/*.egg*/
 /build/
 /dist/
 /.coverage*
 /coverage.xml
+/.pytest_cache/

.pre-commit-config.yaml

@@ -36,11 +36,14 @@ repos:
     - flake8-comprehensions
     - flake8-debugger
     - flake8-isort
+    - flake8-pyproject
     - flake8-string-format
-- repo: https://github.com/psf/black
-  rev: 22.12.0
+- repo: https://github.com/google/yapf
+  rev: v0.33.0
   hooks:
-  - id: black
+  - id: yapf
+    args: [-i]
+    additional_dependencies: [toml]
 - repo: https://github.com/PyCQA/isort
   rev: 5.12.0
   hooks:

LICENCE.md

@@ -1,4 +1,4 @@
-Copyright 2020 AMYPAD
+Copyright 2020-23 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

@@ -6,6 +6,84 @@ build-backend = "setuptools.build_meta"
 write_to = "spm12/_dist_ver.py"
 write_to_template = "__version__ = '{version}'\n"
 
-[tool.black]
-target_version = ["py36", "py310"]
+[tool.setuptools.packages.find]
+exclude = ["tests"]
+
+[tool.setuptools.package-data]
+"*" = ["*.md", "*.rst", "*.m"]
+
+[project.urls]
+documentation = "https://github.com/AMYPAD/SPM12/#SPM12"
+repository = "https://github.com/AMYPAD/SPM12"
+changelog = "https://github.com/AMYPAD/SPM12/releases"
+upstream-project = "https://www.fil.ion.ucl.ac.uk/spm"
+
+[project]
+name = "spm12"
+dynamic = ["version"]
+maintainers = [{name = "Casper da Costa-Luis", email = "casper.dcl@physics.org"}]
+description = "Statistical Parametric Mapping"
+readme = "README.rst"
+requires-python = ">=3.7"
+keywords = ["fMRI", "PET", "SPECT", "EEG", "MEG"]
+license = {text = "Apache-2.0"}
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Other Scripting Engines",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+    "Topic :: Software Development :: Libraries",
+    "Topic :: System :: Installation/Setup"]
+dependencies = ['importlib_resources; python_version < "3.9"', "argopt", "miutil[nii,web]>=0.12.0", "numpy", "scipy"]
+
+[project.optional-dependencies]
+dev = ["pytest>=6", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+demo = ["miutil[plot]>=0.3.0", "matplotlib"]
+
+[project.scripts]
+spm12 = "spm12.cli:main"
+
+[tool.flake8]
+max_line_length = 99
+extend_ignore = ["E261"]
+exclude = [".git", "__pycache__", "build", "dist", ".eggs"]
+
+[tool.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
+blank_line_before_nested_class_or_def = false
+
+[tool.isort]
+profile = "black"
 line_length = 99
+multi_line_output = 4
+known_first_party = ["spm12", "tests"]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+timeout = 300
+log_level = "INFO"
+python_files = ["tests/test_*.py"]
+testpaths = ["tests"]
+addopts = "-v --tb=short -rxs -W=error --log-level=debug -n=auto --durations=0 --durations-min=1 --cov=spm12 --cov-report=term-missing --cov-report=xml"
+filterwarnings = ["ignore:numpy.ufunc size changed.*:RuntimeWarning"]

spm12/__init__.py

@@ -1,5 +1,5 @@
-from .regseg import *  # NOQA
-from .utils import *  # NOQA
+from .regseg import *  # NOQA, yapf: disable
+from .utils import *  # NOQA, yapf: disable
 
 # 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_normw.m

@@ -3,9 +3,11 @@
     job.subj.resample = flist4norm;
     %job.woptions.bb = [NaN, NaN, NaN; NaN, NaN, NaN];
     job.woptions.bb = bbox;
-    job.woptions.vox = [voxsz, voxsz, voxsz];
+    job.woptions.vox = voxsz; %[voxsz, voxsz, voxsz];
     job.woptions.interp = intrp;
     job.woptions.prefix = 'w';
+
+    addpath(fullfile(spm('Dir'),'config'));
     spm_run_norm(job);
     out=0;
 end

spm12/cli.py

@@ -16,5 +16,5 @@ def main(argv=None):
     logging.basicConfig(level=logging.DEBUG, format="%(levelname)s:%(funcName)s:%(message)s")
     args = argopt(__doc__).parse_args(argv)
     ensure_spm(cache=args.cache, version=args.spm_version)
-    print("SPM{v} is successfully installed".format(v=args.spm_version))
+    print(f"SPM{args.spm_version} is successfully installed")
     return 0