Make pylint version compatible and remove morph-tool unnecessary depe…

…ndency

Change-Id: Icb33469addd895a63f36995e5e70c21b9920bdd0

setup.py

@@ -15,8 +15,8 @@
     author_email='lida.kanari@epfl.ch',
     install_requires=[
         'matplotlib>=1.3.1',
-        'morph-tool>=0.1.12',
         'tmd>=2.0.8',
+        'morphio>=2.3.10',
         'neurom>=1.4.15',
         'enum-compat>=0.0.1',
         'scipy>=0.13.3',

tns/extract_input/from_TMD.py

@@ -14,6 +14,6 @@ def persistent_homology_angles(pop, threshold=2, neurite_type='basals', feature=
 
     # Keep only the trees whose number of terminations is above the threshold
     # Saves the list of persistence diagrams for the selected neurite_type
-    phs = list(np.array(ph_ang)[np.where(np.array([len(p) for p in ph_ang]) > threshold)[0]])
+    phs = list(np.array(ph_ang, dtype=object)[np.where(np.array([len(p) for p in ph_ang]) > threshold)[0]])
 
     return {"persistence_diagram": phs}

tns/extract_input/from_diameter.py

@@ -72,7 +72,7 @@ def model(input_object):
         key = NEUROM_TYPE_TO_STR[neurite_type]
 
         values[key] = {"taper": taper_c,
-                       "term": [c for c in chain(*term_diam)],
+                       "term": list(chain(*term_diam)),
                        "trunk": trunk_diam,
                        "trunk_taper": trunk_taper}
 

tns/generate/algorithms/abstractgrower.py

@@ -4,7 +4,7 @@
 import copy
 
 
-class AbstractAlgo(object):
+class AbstractAlgo():
     """TreeGrower abstract class"""
     # meta class is used to define other classes
     __metaclass__ = abc.ABCMeta

tns/generate/algorithms/barcode.py

@@ -7,7 +7,7 @@
 from tns.utils import TNSError
 
 
-class Barcode(object):
+class Barcode():
     """Class to generate the barcode structure
        which is essential for the TMD based growth
        algorithms.

tns/generate/algorithms/common.py

@@ -36,7 +36,7 @@ def section_data(direction, first_point, stop_criteria, process_type):
             'process': process_type}
 
 
-class TMDStop(object):
+class TMDStop():
     '''Class to define the data for stop criteria
        based on the TMD method.
     '''

tns/generate/algorithms/tmdgrower.py

@@ -201,7 +201,7 @@ def initialize(self):
         Initializes the tree grower and
         computes the apical distance using the input barcode.
         """
-        from tmd.Topology.analysis import find_apical_point_distance_smoothed as ap_dist
+        from tmd.Topology.analysis import find_apical_point_distance_smoothed as ap_dist  # pylint: disable=C0415
         stop, num_sec = super(TMDApicalAlgo, self).initialize()
         if self.params['has_apical_tuft']:
             self.apical_point_distance_from_soma = ap_dist(self.ph_angles)

tns/generate/grower.py

@@ -18,7 +18,7 @@
 bifurcation_methods = ['symmetric', 'bio_oriented', 'directional', 'bio_smoothed']
 
 
-class NeuronGrower(object):
+class NeuronGrower():
     """
     A Grower object is a container for a Neuron, encoded in the (groups, points) structure,
     as a morphIO Morphology object. A set of input distributions that store the data
@@ -107,7 +107,7 @@ def grow(self):
         """
         self._grow_soma()
         while self.active_neurites:
-            self.next()
+            self.next()  # pylint: disable=E1102
         self._post_grow()
         self._diametrize()
         return self.neuron

tns/generate/section.py

@@ -14,7 +14,7 @@
 WEIGHTS = np.exp(np.arange(1, MEMORY + 1) - MEMORY)
 
 
-class SectionGrower(object):
+class SectionGrower():
     '''Class for the section growth
     '''
     # pylint: disable-msg=too-many-arguments

tns/generate/soma.py

@@ -14,7 +14,7 @@
 L = logging.getLogger()
 
 
-class SomaGrower(object):
+class SomaGrower():
     """Soma class"""
 
     def __init__(self, initial_point, radius=1.0, context=None):

tns/generate/tree.py

@@ -66,7 +66,7 @@ def _create_section_parameters(input_dict):
         raise TNSError(msg)
 
 
-class TreeGrower(object):
+class TreeGrower():
     """Tree class"""
 
     def __init__(self,

tns/morphmath/sample.py

@@ -5,7 +5,7 @@
 from scipy import stats
 
 
-class Distr(object):
+class Distr():
     '''Class of custom distributions
     '''
 

tns/version.py

@@ -1,2 +1,2 @@
 """ tns version """
-VERSION = "2.2.1"
+VERSION = "2.2.2.dev0"

tox.ini

@@ -19,7 +19,9 @@ indexserver =
 
 [testenv]
 basepython= python3.6
-deps = {[base]testdeps}
+deps = 
+    {[base]testdeps}
+    morph-tool>=0.1.12
 commands = nosetests tests tests/astrocyte
 
 [testenv:check-version]
@@ -30,14 +32,15 @@ commands = do_release.py -p . check-version
 [testenv:lint]
 deps =
     pycodestyle==2.4.0
-    pylint==1.9.3
+    pylint==2.5.3
 commands =
     pycodestyle {[base]name} --exclude tests
     pylint {[base]name} --ignore tests
 
 [testenv:coverage]
 deps =
     {[base]testdeps}
+    morph-tool>=0.1.12
     coverage
 commands =
     coverage run --source {[base]name} {envbindir}/nosetests