bump version, merge pull request #9 from AMYPAD/devel

.github/workflows/test.yml

@@ -15,13 +15,27 @@ jobs:
     - uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python }}
+    - name: set PYSHA
+      run: echo "PYSHA=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
+    - uses: actions/cache@v1
+      with:
+        path: ~/.cache/pre-commit
+        key: pre-commit|${{ env.PYSHA }}|${{ hashFiles('.pre-commit-config.yaml') }}
     - run: pip install -U .[dev]
     - run: python setup.py sdist bdist_wheel
     - run: twine check dist/*
-    - run: flake8 .
-    - if: |
-        ! startsWith(matrix.python, '2')
-      run: black --check .
+    - 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
+      env:
+        REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    - if: startsWith(matrix.python, '3')
+      run: pre-commit run -a --show-diff-on-failure
+    - if: startsWith(matrix.python, '2')
+      run: pre-commit run -a --show-diff-on-failure isort
   test:
     runs-on: [self-hosted, matlab]
     name: Test matlab
@@ -41,6 +55,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
     - uses: casperdcl/deploy-pypi@v1
       with:
         build: true
@@ -60,7 +76,7 @@ jobs:
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
       with:
         tag_name: ${{ github.ref }}
-        release_name: miutil ${{ github.ref }} beta
+        release_name: spm12 ${{ github.ref }} beta
         body_path: _CHANGES.md
         draft: true
     - uses: actions/upload-release-asset@v1

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+default_language_version:
+  python: python3
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.4.0
+  hooks:
+  - id: check-added-large-files
+  - id: check-case-conflict
+  - id: check-docstring-first
+  - id: check-executables-have-shebangs
+  - id: check-toml
+  - id: check-yaml
+  - id: end-of-file-fixer
+  - id: mixed-line-ending
+  - id: trailing-whitespace
+- hooks:
+  - id: flake8
+    additional_dependencies:
+    - flake8-bugbear
+    - flake8-comprehensions
+    - flake8-debugger
+    - flake8-string-format
+  repo: https://gitlab.com/pycqa/flake8
+  rev: 3.8.4
+- hooks:
+  - id: black
+  repo: https://github.com/psf/black
+  rev: 19.10b0
+- hooks:
+  - id: isort
+  repo: https://github.com/timothycrosley/isort
+  rev: 5.6.4

LICENCE.md

@@ -1,7 +1,7 @@
 Copyright 2020 AMYPAD
 
 Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
+you may not use this project except in compliance with the License.
 You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0

pyproject.toml

@@ -5,3 +5,6 @@ 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']

setup.cfg

@@ -17,6 +17,7 @@ platforms = any
 provides = spm12
 classifiers =
     Development Status :: 4 - Beta
+    Intended Audience :: Developers
     Intended Audience :: Education
     Intended Audience :: Healthcare Industry
     Intended Audience :: Science/Research
@@ -33,24 +34,23 @@ classifiers =
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Topic :: Scientific/Engineering :: Medical Science Apps.
+    Topic :: Software Development :: Libraries
+    Topic :: System :: Installation/Setup
 [options]
 zip_safe = False
 setup_requires = setuptools>=42; setuptools_scm[toml]>=3.4
-include_package_data = True
-packages = find:
 install_requires =
     argopt
     miutil[nii]>=0.1.0,!=0.4.0,!=0.4.1
+    setuptools  # pkg_resources
     brainweb>=1.6.2
     numpy
     scipy
-[options.entry_points]
-console_scripts =
-    spm12 = spm12.cli:main
+include_package_data = True
+packages = find:
 [options.extras_require]
 dev =
-    black; python_version >= "3.0"
-    flake8
+    pre-commit
     twine
     wheel
     pytest
@@ -61,13 +61,20 @@ dev =
 demo =
     miutil[plot]>=0.3.0
     matplotlib
+[options.entry_points]
+console_scripts =
+    spm12 = spm12.cli:main
 [options.package_data]
 * = *.md, *.rst, *.m
 
+[bdist_wheel]
+universal = 1
+
 [flake8]
 max_line_length = 88
-extend-ignore = E203
+extend-ignore = E203,P1
 exclude = .git,__pycache__,build,dist,.eggs
 
-[bdist_wheel]
-universal = 1
+[isort]
+profile = black
+known_first_party = spm12,tests

setup.py

@@ -1,3 +1,3 @@
 from setuptools import setup
 
-setup()
+setup(use_scm_version=True)

spm12/__main__.py

@@ -1,6 +1,7 @@
+#!/usr/bin/env python
 import sys
 
 from .cli import main
 
-if __name__ == "__main__":
+if __name__ == "__main__":  # pragma: no cover
     sys.exit(main(sys.argv[1:]))

spm12/regseg.py

@@ -1,13 +1,13 @@
-from textwrap import dedent
 import errno
 import logging
 import os
 import shutil
+from textwrap import dedent
 
-from miutil import create_dir, hasext
-from miutil.imio import nii
 import numpy as np
 import scipy.ndimage as ndi
+from miutil import create_dir, hasext
+from miutil.imio import nii
 
 from .utils import ensure_spm
 
@@ -302,13 +302,11 @@ def resample_spm(
         fout = os.path.join(opth, fimout)
     elif pickname == "ref":
         fout = os.path.join(
-            opth,
-            "affine_ref-" + nii.file_parts(imrefu)[1] + fcomment + ".nii.gz",
+            opth, "affine_ref-" + nii.file_parts(imrefu)[1] + fcomment + ".nii.gz",
         )
     elif pickname == "flo":
         fout = os.path.join(
-            opth,
-            "affine_flo-" + nii.file_parts(imflo)[1] + fcomment + ".nii.gz",
+            opth, "affine_flo-" + nii.file_parts(imflo)[1] + fcomment + ".nii.gz",
         )
     # change the file name
     os.rename(fim + ".gz", fout)

spm12/utils.py

@@ -1,10 +1,10 @@
+import logging
 from functools import lru_cache, wraps
 from os import path
-from pkg_resources import resource_filename
 from textwrap import dedent
-import logging
 
 from miutil.mlab import get_engine
+from pkg_resources import resource_filename
 
 __all__ = ["get_matlab", "ensure_spm"]
 PATH_M = resource_filename(__name__, "")
@@ -32,9 +32,10 @@ def ensure_spm(name=None, cache="~/.spm12", version=12):
     if not eng.exist("spm_jobman"):
         log.warn("MATLAB could not find SPM.")
         try:
-            from brainweb import get_file
             from zipfile import ZipFile
 
+            from brainweb import get_file
+
             log.info("Downloading to %s", cache)
             fname = get_file(
                 "spm12.zip",
@@ -50,7 +51,7 @@ def ensure_spm(name=None, cache="~/.spm12", version=12):
             if not eng.exist("spm_jobman"):
                 raise RuntimeError("MATLAB could not find SPM.")
             log.info("Installed")
-        except:  # NOQA: E722
+        except:  # NOQA: E722,B001
             raise ImportError(
                 dedent(
                     """\

tests/__main__.py

@@ -1,5 +1,5 @@
-from os import chdir, path
 import sys
+from os import chdir, path
 from subprocess import check_call
 
 chdir(path.dirname(path.dirname(path.abspath(__file__))))

tests/test_main.py

@@ -1,5 +1,5 @@
-from pytest import skip
 from miutil.mlab import matlabroot
+from pytest import skip
 
 
 def test_cli():

tests/test_regseg.py

@@ -1,11 +1,10 @@
-from os import path, getenv
+from os import getenv, path
 from textwrap import dedent
 
-from miutil import tmpdir
-from miutil.imio import nii
-
 import numpy as np
 import pytest
+from miutil import tmpdir
+from miutil.imio import nii
 
 from spm12 import regseg
 
@@ -53,14 +52,7 @@ def assert_equal_arrays(x, y, nmse_tol=0, denan=True):
         y: {:.3g}/{:.3g}/{:.3g}({:.3g})
         """
         ).format(
-            x.min(),
-            x.mean(),
-            x.max(),
-            x.std(),
-            y.min(),
-            y.mean(),
-            y.max(),
-            y.std(),
+            x.min(), x.mean(), x.max(), x.std(), y.min(), y.mean(), y.max(), y.std(),
         )
     )