FIX: Deprecated args (#252)

Author: larsoner

.travis.yml

@@ -2,37 +2,28 @@ language: c
 sudo: false
 
 env:
-    global: PYTHON_VERSION=2.7
+    global: PYTHON_VERSION=3.6
+            CONDA_DEPENDENCIES="numpy scipy matplotlib pyqt>=5.9 coverage pytest pytest-cov flake8 pygments traits traitsui pyface"
+            PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio"
             DISPLAY=:99.0
 
 matrix:
     include:
-        # Full (Linux, 3.6)
+        # Full
         - os: linux
-          env: CONDA_ENVIRONMENT="environment.yml"
           addons:
             apt:
               packages:
                 - mencoder
 
-        # Full (Linux, 2.7)
+        # 2.7, no mencoder
         - os: linux
-          env: CONDA_DEPENDENCIES="numpy scipy matplotlib mayavi flake8 pytest pytest-cov coverage"
-               PIP_DEPENDENCIES="codecov nibabel imageio"
-          addons:
-            apt:
-              packages:
-                - mencoder
-
-        # Minimal (no mencoder)
-        - os: linux
-          env: CONDA_DEPENDENCIES="numpy scipy matplotlib mayavi flake8 pytest pytest-cov coverage"
-               PIP_DEPENDENCIES="codecov nibabel"
+          env: PYTHON_VERSION=2.7
+               CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8 mayavi"
+               PIP_DEPENDENCIES="codecov pytest-sugar faulthandler pytest-faulthandler nibabel imageio"
 
         # OSX
         - os: osx
-          env: CONDA_DEPENDENCIES="numpy scipy matplotlib mayavi flake8 pytest pytest-cov coverage"
-               PIP_DEPENDENCIES="codecov nibabel imageio"
 
 # Setup anaconda
 before_install:
@@ -47,6 +38,10 @@ before_install:
       fi;
     - git clone https://github.com/astropy/ci-helpers.git
     - source ci-helpers/travis/setup_conda.sh
+    - if [ "$PYTHON_VERSION" != "2.7" ]; then
+        pip install vtk;
+        pip install mayavi;
+      fi;
 
 install:
     - python setup.py build
@@ -68,7 +63,7 @@ before_script:
 
 script:
     - cd ${SRC_DIR}
-    - pytest surfer --cov=surfer
+    - pytest surfer --cov=surfer -v
     - make flake
 
 after_success:

appveyor.yml

@@ -6,7 +6,7 @@ environment:
 install:
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
   - "python --version"
-  - "pip install numpy scipy matplotlib nose pillow pytest pytest-cov coverage imageio codecov pyqt5==5.9"
+  - "pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio codecov pyqt5==5.9"
   - "pip install traits traitsui pyface vtk mayavi nibabel"
   - "python -c \"import imageio; imageio.plugins.ffmpeg.download()\""
   - "powershell make/get_fsaverage.ps1"
@@ -18,7 +18,7 @@ build: false  # Not a C# project, build stuff at the test step instead.
 
 test_script:
   # Run the project tests
-  - "pytest surfer --cov=surfer"
+  - "pytest surfer --cov=surfer -v"
 
 on_success:
   - "codecov"

environment.yml

@@ -1,2 +1,11 @@
 [tool:pytest]
 addopts = --showlocals --durations=10 --doctest-modules -rs --cov-report= --doctest-ignore-import-errors
+filterwarnings =
+    error::
+    ignore:Importing from numpy.testing.decorators is deprecated, import from numpy.testing instead.:DeprecationWarning
+    ignore:use "HasTraits.trait_.et" instead:DeprecationWarning
+    ignore:np.loads is deprecated, use pickle.loads instead:DeprecationWarning
+    ignore:can't resolve package from __spec__ or __package__, falling back on __name__ and __path__:ImportWarning
+    ignore:The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead:DeprecationWarning
+    ignore:elementwise == comparison failed:DeprecationWarning
+    ignore:Matplotlib is building the font cache using fc-list. This may take a moment.:UserWarning

setup.cfg

@@ -8,7 +8,8 @@
 from mayavi import mlab
 import nibabel as nib
 import numpy as np
-from numpy.testing import assert_array_equal
+from numpy.testing import assert_array_equal, assert_array_less
+
 from unittest import SkipTest
 
 from surfer import Brain, io, utils
@@ -27,13 +28,12 @@ def _set_backend(backend=None):
     """Use testing backend for Windows."""
     only_test = (sys.platform == 'win32' or
                  (os.getenv('TRAVIS', 'false') == 'true' and
-                  sys.version[0] == '3'))
+                  sys.platform == 'linux') and sys.version[0] == '3')
     if backend is None:
         backend = 'test' if only_test else 'auto'
-    else:
-        if only_test:
-            raise SkipTest('non-testing backend crashes on Windows and '
-                           'Travis Py3k')
+    if only_test and backend != 'test':
+        raise SkipTest('non-testing backend crashes on Windows and '
+                       'Travis Py3k')
     mlab.options.backend = backend
 
 
@@ -64,18 +64,11 @@ def check_view(brain, view):
 @requires_fsaverage()
 def test_offscreen():
     """Test offscreen rendering."""
-    if os.getenv('TRAVIS', 'false') == 'true':
-        if sys.platform == 'darwin':
-            raise SkipTest('Offscreen Travis tests fail on OSX')
-        if sys.version[0] == '3':
-            raise SkipTest('Offscreen Travis tests fail on Py3k')
     _set_backend()
     brain = Brain(*std_args, offscreen=True)
-    # Sometimes the first screenshot is rendered with a different
-    # resolution on OS X
-    brain.screenshot()
     shot = brain.screenshot()
-    assert_array_equal(shot.shape, (800, 800, 3))
+    assert_array_less((400, 400, 2), shot.shape)
+    assert_array_less(shot.shape, (801, 801, 4))
     brain.close()
 
 
@@ -93,8 +86,6 @@ def test_image(tmpdir):
     brain.close()
 
     brain = Brain(*std_args, size=100)
-    if sys.platform == 'darwin' and os.getenv('TRAVIS', '') == 'true':
-        raise SkipTest('image saving on OSX travis is not supported')
     brain.save_image(tmp_name)
     brain.save_image(tmp_name, 'rgba', True)
     brain.screenshot()
@@ -138,7 +129,8 @@ def test_brains():
         brain = Brain(subject_id, hemi, surf, title=title, cortex=cort,
                       alpha=alpha, size=s, background=bg, foreground=fg,
                       figure=fig, subjects_dir=sd)
-        brain.set_distance()
+        with np.errstate(invalid='ignore'):  # encountered in double_scalars
+            brain.set_distance()
         brain.close()
     brain = Brain(subject_id, hemi, surf, subjects_dir=sd,
                   interaction='terrain')
@@ -374,8 +366,6 @@ def test_movie(tmpdir):
                    smoothing_steps=10, time=time, time_label='time=%0.2f ms')
     brain.scale_data_colormap(fmin=13, fmid=18, fmax=22, transparent=True)
 
-    if sys.platform == 'darwin' and os.getenv('TRAVIS', '') == 'true':
-        raise SkipTest('movie saving on OSX Travis is not supported')
     # save movies with different options
     dst = str(tmpdir.join('test.mov'))
     # test the number of frames in the movie

surfer/tests/test_viz.py

@@ -332,6 +332,28 @@ def set_log_file(fname=None, output_format='%(message)s', overwrite=None):
     logger.addHandler(lh)
 
 
+if hasattr(inspect, 'signature'):  # py35
+    def _get_args(function, varargs=False):
+        params = inspect.signature(function).parameters
+        args = [key for key, param in params.items()
+                if param.kind not in (param.VAR_POSITIONAL, param.VAR_KEYWORD)]
+        if varargs:
+            varargs = [param.name for param in params.values()
+                       if param.kind == param.VAR_POSITIONAL]
+            if len(varargs) == 0:
+                varargs = None
+            return args, varargs
+        else:
+            return args
+else:
+    def _get_args(function, varargs=False):
+        out = inspect.getargspec(function)  # args, varargs, keywords, defaults
+        if varargs:
+            return out[:2]
+        else:
+            return out[0]
+
+
 def verbose(function):
     """Decorator to allow functions to override default log level
 
@@ -348,7 +370,7 @@ def verbose(function):
         None defaults to using the current log level [e.g., set using
         mne.set_log_level()].
     """
-    arg_names = inspect.getargspec(function).args
+    arg_names = _get_args(function)
     # this wrap allows decorated functions to be pickled (e.g., for parallel)
 
     @wraps(function)