Merge remote-tracking branch 'nipy/master' into fix/mrtrix3-tckgen-option

Author: jguillon

.travis.yml

@@ -60,6 +60,9 @@ matrix:
           NIPYPE_EXTRAS="doc,tests,nipy,profiler"
           EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
           CI_SKIP_TEST=1
+  allow_failures:
+    - python: 2.7
+      env: INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,nipy,profiler" EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS" CI_SKIP_TEST=1
 
 addons:
   apt:

nipype/info.py

@@ -105,6 +105,7 @@ def get_nipype_gitversion():
 # Numpy bug in python 3.7:
 # https://www.opensourceanswers.com/blog/you-shouldnt-use-python-37-for-data-science-right-now.html
 NUMPY_MIN_VERSION_37 = '1.15.3'
+NUMPY_BAD_VERSION_27 = '1.16.0'
 SCIPY_MIN_VERSION = '0.14'
 TRAITS_MIN_VERSION = '4.6'
 DATEUTIL_MIN_VERSION = '2.2'
@@ -136,7 +137,8 @@ def get_nipype_gitversion():
 REQUIRES = [
     'nibabel>=%s' % NIBABEL_MIN_VERSION,
     'networkx>=%s' % NETWORKX_MIN_VERSION,
-    'numpy>=%s ; python_version < "3.7"' % NUMPY_MIN_VERSION,
+    'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27),
+    'numpy>=%s ; python_version > "3.0" and python_version < "3.7"' % NUMPY_MIN_VERSION,
     'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37,
     'python-dateutil>=%s' % DATEUTIL_MIN_VERSION,
     'scipy>=%s' % SCIPY_MIN_VERSION,

nipype/interfaces/ants/segmentation.py

@@ -207,13 +207,27 @@ class LaplacianThicknessInputSpec(ANTSCommandInputSpec):
         name_template='%s_thickness',
         keep_extension=True,
         hash_files=False)
-    smooth_param = traits.Float(argstr='smoothparam=%d', desc='', position=4)
+    smooth_param = traits.Float(
+        argstr='%f',
+        desc='Sigma of the Laplacian Recursive Image Filter (defaults to 1)',
+        position=4)
     prior_thickness = traits.Float(
-        argstr='priorthickval=%d', desc='', position=5)
-    dT = traits.Float(argstr='dT=%d', desc='', position=6)
-    sulcus_prior = traits.Bool(argstr='use-sulcus-prior', desc='', position=7)
-    opt_tolerance = traits.Float(
-        argstr='optional-laplacian-tolerance=%d', desc='', position=8)
+        argstr='%f',
+        desc='Prior thickness (defaults to 500)',
+        position=5)
+    dT = traits.Float(
+        argstr='%f',
+        desc='Time delta used during integration (defaults to 0.01)',
+        position=6)
+    sulcus_prior = traits.Float(
+        argstr='%f',
+        desc='Positive floating point number for sulcus prior. '
+             'Authors said that 0.15 might be a reasonable value',
+        position=7)
+    tolerance = traits.Float(
+        argstr='%f',
+        desc='Tolerance to reach during optimization (defaults to 0.001)',
+        position=8)
 
 
 class LaplacianThicknessOutputSpec(TraitedSpec):

nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py

@@ -7,7 +7,7 @@ def test_LaplacianThickness_inputs():
     input_map = dict(
         args=dict(argstr='%s', ),
         dT=dict(
-            argstr='dT=%d',
+            argstr='%f',
             position=6,
         ),
         environ=dict(
@@ -30,10 +30,6 @@ def test_LaplacianThickness_inputs():
             nohash=True,
             usedefault=True,
         ),
-        opt_tolerance=dict(
-            argstr='optional-laplacian-tolerance=%d',
-            position=8,
-        ),
         output_image=dict(
             argstr='%s',
             hash_files=False,
@@ -43,17 +39,21 @@ def test_LaplacianThickness_inputs():
             position=3,
         ),
         prior_thickness=dict(
-            argstr='priorthickval=%d',
+            argstr='%f',
             position=5,
         ),
         smooth_param=dict(
-            argstr='smoothparam=%d',
+            argstr='%f',
             position=4,
         ),
         sulcus_prior=dict(
-            argstr='use-sulcus-prior',
+            argstr='%f',
             position=7,
         ),
+        tolerance=dict(
+            argstr='%f',
+            position=8,
+        ),
     )
     inputs = LaplacianThickness.input_spec()