Merge pull request #12 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: ${{ secrets.GITHUB_TOKEN }}
     - if: startsWith(matrix.python, '3')
@@ -40,7 +38,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [2.7, 3.7]
+        python: [2.7, 3.5, 3.6, 3.9]
     name: Test py${{ matrix.python }}
     steps:
     - uses: actions/checkout@v2
@@ -50,7 +48,10 @@ jobs:
       with:
         python-version: ${{ matrix.python }}
     - run: pip install -U .[dev]
-    - run: python -m tests --cov-report=term-missing --cov-report=xml
+    - if: startsWith(matrix.python, '3')
+      run: pytest --durations-min=1
+    - if: startsWith(matrix.python, '2')
+      run: pytest
     - run: codecov
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
@@ -62,7 +63,7 @@ jobs:
       with:
         fetch-depth: 0
     - run: pip install -U .[dev,cuda]
-    - run: python -m tests --cov-report=term-missing --cov-report=xml
+    - run: pytest --durations-min=1
     - run: codecov
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

miutil/cuinfo.py

@@ -6,6 +6,7 @@
 Options:
   -n, --num-devices   : print number of devices (ignores `-d`)
   -f, --nvcc-flags    : print out flags for use nvcc compilation
+  -c, --compute       : print out compute capabilities (strip periods)
   -d ID, --dev-id ID  : select device ID [default: None:int] for all
 """
 import pynvml
@@ -72,6 +73,9 @@ def main(*args, **kwargs):
     if args.nvcc_flags:
         print(" ".join(sorted(set(map(nvcc_flags, devices)))[::-1]))
         noargs = False
+    if args.compute:
+        print(" ".join(sorted({"%d%d" % compute_capability(i) for i in devices})[::-1]))
+        noargs = False
     if noargs:
         for dev_id in devices:
             print(

miutil/fdio.py

@@ -1,4 +1,5 @@
 import logging
+from collections import Iterable
 from contextlib import contextmanager
 from os import makedirs, path
 from shutil import rmtree
@@ -19,13 +20,18 @@ def create_dir(pth):
         try:
             makedirs(pth)
         except Exception as exc:
-            log.warn("cannot create:%s:%s" % (pth, exc))
+            log.warning("cannot create:%s:%s" % (pth, exc))
+
+
+def is_iter(x):
+    return isinstance(x, Iterable) and not isinstance(x, (str, bytes))
 
 
 def hasext(fname, ext):
-    if ext[0] != ".":
-        ext = "." + ext
-    return path.splitext(fspath(fname))[1].lower() == ext.lower()
+    if not is_iter(ext):
+        ext = (ext,)
+    ext = (("" if i[0] == "." else ".") + i.lower() for i in ext)
+    return fspath(fname).lower().endswith(tuple(ext))
 
 
 @contextmanager

miutil/mlab/__init__.py

@@ -31,7 +31,7 @@ def get_engine(name=None):
         from matlab import engine
     except ImportError:
         try:
-            log.warn(
+            log.warning(
                 dedent(
                     """\
                 Python could not find the MATLAB engine.
@@ -125,5 +125,5 @@ def _install_engine():
         try:
             return check_output_u8(cmd, cwd=src)
         except CalledProcessError:
-            log.warn("Normal install failed. Attempting `--user` install.")
+            log.warning("Normal install failed. Attempting `--user` install.")
             return check_output_u8(cmd + ["--user"], cwd=src)

miutil/mlab/beautify.py

@@ -17,7 +17,7 @@
 from . import get_engine
 
 log = logging.getLogger(__name__)
-MBEAUTIFIER_REV = "73bc3da7df39a60aab859a2cb86dd82b4d284312"
+MBEAUTIFIER_REV = "9c3c82387ec3c0fb29e707ebd060e8e2ca9ea6f2"
 
 
 @lru_cache()
@@ -26,7 +26,7 @@ def ensure_mbeautifier(*args, **kwargs):
     eng = get_engine(*args, **kwargs)
     fn = get_file(
         "MBeautifier-%s.zip" % MBEAUTIFIER_REV[:7],
-        "https://github.com/AMYPAD/MBeautifier/archive/%s.zip" % MBEAUTIFIER_REV,
+        "https://github.com/davidvarga/MBeautifier/archive/%s.zip" % MBEAUTIFIER_REV,
     )
     outpath = path.join(path.dirname(fn), "MBeautifier-%s" % MBEAUTIFIER_REV)
     if not path.exists(outpath):
@@ -46,7 +46,10 @@ def main(*args, **kwargs):
 
     for fn in tmap(path.abspath, args.mfile):
         log.debug("file:%s", fn)
-        formatter(fn, fn, nargout=0)
+        try:
+            formatter(fn, fn, nargout=0)
+        except Exception as exc:
+            log.error("file:%s:\n%s", fn, exc)
 
 
 if __name__ == "__main__":  # pragma: no cover

pyproject.toml

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

setup.cfg

@@ -1,20 +1,20 @@
 [metadata]
-name = miutil
-description = Medical imaging utilities for the AMYPAD and NiftyPET projects
-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/miutil
-project_urls =
+name=miutil
+description=Medical imaging utilities for the AMYPAD and NiftyPET projects
+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/miutil
+project_urls=
     Changelog = https://github.com/AMYPAD/miutil/releases
     Documentation = https://github.com/AMYPAD/miutil/#miutil
-maintainer = Casper da Costa-Luis
-maintainer_email = casper.dcl@physics.org
-keywords = fMRI, PET, SPECT, EEG, MEG
-platforms = any
-provides = miutil
-classifiers =
+maintainer=Casper da Costa-Luis
+maintainer_email=casper.dcl@physics.org
+keywords=fMRI, PET, SPECT, EEG, MEG
+platforms=any
+provides=miutil
+classifiers=
     Development Status :: 4 - Beta
     Intended Audience :: Developers
     Environment :: GPU
@@ -41,14 +41,11 @@ classifiers =
     Topic :: System :: Installation/Setup
     Topic :: Utilities
 [options]
-zip_safe = False
-setup_requires = setuptools>=42; setuptools_scm[toml]>=3.4
-install_requires =
-    argparse; python_version == "2.6"
-include_package_data = True
-packages = find:
+setup_requires=setuptools>=42; wheel; setuptools_scm[toml]>=3.4
+packages=find:
+python_requires=>=2.7
 [options.extras_require]
-dev =
+dev=
     pre-commit
     twine
     wheel
@@ -66,17 +63,18 @@ mbeautify = argopt; %(web)s
 console_scripts =
     cuinfo = miutil.cuinfo:main
     mbeautify = miutil.mlab.beautify:main
-[options.package_data]
-* = *.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 = miutil,tests
+profile=black
+known_first_party=miutil,tests
+
+[tool:pytest]
+addopts=-v --tb=short -rxs -W=error --log-level=debug -n=auto --durations=0 --cov=miutil --cov-report=term-missing --cov-report=xml

tests/test_cuinfo.py

@@ -46,3 +46,7 @@ def test_cuinfo_cli(capsys):
     cuinfo.main(["--nvcc-flags"])
     out, _ = capsys.readouterr()
     assert not devices or out.startswith("-gencode=")
+
+    cuinfo.main(["--compute"])
+    out, _ = capsys.readouterr()
+    assert not devices or all(map(int, out.split(" ")))

tests/test_fdio.py

@@ -7,34 +7,34 @@
 
 def test_create_dir(tmp_path, caplog):
     tmpdir = tmp_path / "create_dir"
-    assert not path.exists(fdio.fspath(tmpdir))
+    assert not tmpdir.exists()
     fdio.create_dir(tmpdir)
-    tmpdir = fdio.fspath(tmpdir)
-    assert path.exists(tmpdir)
-    rmtree(tmpdir, True)
+    assert tmpdir.exists() and tmpdir.is_dir()
+    rmtree(fdio.fspath(tmpdir), True)
 
-    with open(tmpdir, "w") as fd:
+    with open(fdio.fspath(tmpdir), "w") as fd:
         fd.write("dummy file")
     with caplog.at_level(logging.INFO):
         assert "cannot create" not in caplog.text
         fdio.create_dir(tmpdir)
         assert "cannot create" in caplog.text
 
-    assert path.exists(tmpdir)
+    assert tmpdir.exists()
 
 
 def test_hasext():
     for fname, ext in [
+        (".baz", ".baz"),
         ("foo.bar", ".bar"),
         ("foo.bar", "bar"),
-        ("foo.bar.baz", "baz"),
+        ("foo.bar.baz", "bar.baz"),
         ("foo/bar.baz", "baz"),
+        ("foo.bar.baz", "baz"),
     ]:
         assert fdio.hasext(fname, ext)
 
     for fname, ext in [
         ("foo.bar", "baz"),
-        ("foo.bar.baz", "bar.baz"),
         ("foo", "foo"),
     ]:
         assert not fdio.hasext(fname, ext)

tests/test_web.py

@@ -1,18 +1,14 @@
-from os import path
-
 from pytest import importorskip
 
-from miutil import fspath
-
 web = importorskip("miutil.web")
 
 
 def test_get_file(tmp_path):
     tmpdir = tmp_path / "get_file"
-    assert not path.exists(fspath(tmpdir))
+    assert not tmpdir.exists()
     web.get_file(
         "README.rst",
         "https://github.com/AMYPAD/miutil/raw/master/README.rst",
         cache_dir=tmpdir,
     )
-    assert path.exists(fspath(tmpdir / "README.rst"))
+    assert (tmpdir / "README.rst").is_file()