Merge pull request #10 from AMYPAD/devel

.github/workflows/test.yml

@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: ['2.7', '3.7']
+        python: [2.7, 3.6, 3.9]
     name: Check py${{ matrix.python }}
     steps:
     - uses: actions/checkout@v2
@@ -27,9 +27,7 @@ jobs:
     - uses: reviewdog/action-setup@v1
     - if: github.event_name != 'schedule'
       run: |
-        set -o pipefail
-        pre-commit run -a flake8 | \
-          reviewdog -f=pep8 -name=flake8 -tee -reporter=github-check -filter-mode nofilter
+        pre-commit run -a flake8 | reviewdog -f=pep8 -name=flake8 -tee -reporter=github-check -filter-mode nofilter
       env:
         REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     - if: startsWith(matrix.python, '3')
@@ -44,7 +42,7 @@ jobs:
       with:
         fetch-depth: 0
     - run: pip install -U .[dev]
-    - run: python -m tests --cov-report=term-missing --cov-report=xml
+    - run: pytest
     - run: codecov
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

pyproject.toml

@@ -7,4 +7,4 @@ write_to = "spm12/_dist_ver.py"
 write_to_template = "__version__ = '{version}'\n"
 
 [tool.black]
-target-version = ['py27', 'py36']
+target_version = ["py27", "py36", "py38"]

setup.cfg

@@ -1,21 +1,21 @@
 [metadata]
-name = spm12
-description = Statistical Parametric Mapping
-long_description = file: README.rst
-long_description_content_type = text/x-rst
-license = Apache 2.0
-license_file = LICENCE.md
-url = https://github.com/AMYPAD/SPM12
-project_urls =
+name=spm12
+description=Statistical Parametric Mapping
+long_description=file: README.rst
+long_description_content_type=text/x-rst
+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
-    Upstream Project = https://www.fil.ion.ucl.ac.uk/spm
-maintainer = Casper da Costa-Luis
-maintainer_email = casper.dcl@physics.org
-keywords = fMRI, PET, SPECT, EEG, MEG
-platforms = any
-provides = spm12
-classifiers =
+    Upstream Project=https://www.fil.ion.ucl.ac.uk/spm
+maintainer=Casper da Costa-Luis
+maintainer_email=casper.dcl@physics.org
+keywords=fMRI, PET, SPECT, EEG, MEG
+platforms=any
+provides=spm12
+classifiers=
     Development Status :: 4 - Beta
     Intended Audience :: Developers
     Intended Audience :: Education
@@ -38,18 +38,18 @@ classifiers =
     Topic :: System :: Installation/Setup
 [options]
 zip_safe = False
-setup_requires = setuptools>=42; setuptools_scm[toml]>=3.4
-install_requires =
+setup_requires=setuptools>=42; wheel; setuptools_scm[toml]>=3.4
+install_requires=
     argopt
     miutil[nii]>=0.1.0,!=0.4.0,!=0.4.1
     setuptools  # pkg_resources
     brainweb>=1.6.2
     numpy
     scipy
-include_package_data = True
-packages = find:
+include_package_data=True
+packages=find:
 [options.extras_require]
-dev =
+dev=
     pre-commit
     twine
     wheel
@@ -58,23 +58,26 @@ dev =
     pytest-timeout
     pytest-xdist
     codecov
-demo =
+demo=
     miutil[plot]>=0.3.0
     matplotlib
 [options.entry_points]
 console_scripts =
-    spm12 = spm12.cli:main
+    spm12=spm12.cli:main
 [options.package_data]
-* = *.md, *.rst, *.m
+*=*.md, *.rst, *.m
 
 [bdist_wheel]
 universal = 1
 
 [flake8]
-max_line_length = 88
-extend-ignore = E203,P1
-exclude = .git,__pycache__,build,dist,.eggs
+max_line_length=88
+extend-ignore=E203,P1
+exclude=.git,__pycache__,build,dist,.eggs
 
 [isort]
-profile = black
-known_first_party = spm12,tests
+profile=black
+known_first_party=spm12,tests
+
+[tool:pytest]
+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

tests/test_regseg.py

@@ -34,6 +34,9 @@
 """
     % HOME,
 )
+no_matlab_warn = pytest.mark.filterwarnings(
+    "ignore:.*collections.abc:DeprecationWarning"
+)
 
 
 def assert_equal_arrays(x, y, nmse_tol=0, denan=True):
@@ -58,6 +61,7 @@ def assert_equal_arrays(x, y, nmse_tol=0, denan=True):
 
 
 @skip_no_data
+@no_matlab_warn
 def test_resample():
     with tmpdir() as outpath:
         res = regseg.resample_spm(PET, MRI, MRI2PET, outpath=outpath)
@@ -68,6 +72,7 @@ def test_resample():
 
 
 @skip_no_data
+@no_matlab_warn
 def test_coreg():
     with tmpdir() as outpath:
         res = regseg.coreg_spm(PET, MRI, outpath=outpath)