Enabling flake and mypy checks on CI

setup.cfg

@@ -1,2 +1,25 @@
 [metadata]
-description-file = README.md
+description-file = README.md
+
+[flake8]
+max-line-length = 120
+exclude = topology.py
+max-complexity = 15
+
+[mypy-topopy.topology]
+ignore_errors = True
+
+[mypy-networkx.*]
+ignore_missing_imports = True
+
+[mypy-nglpy.*]
+ignore_missing_imports = True
+
+[mypy-numpy.*]
+ignore_missing_imports = True
+
+[mypy-scipy.*]
+ignore_missing_imports = True
+
+[mypy-sklearn.*]
+ignore_missing_imports = True

topopy/ContourTree.py

@@ -6,8 +6,8 @@
 
 import networkx as nx
 
-from . import MergeTree
-from . import TopologicalObject
+from .MergeTree import MergeTree
+from .TopologicalObject import TopologicalObject
 
 
 class ContourTree(TopologicalObject):

topopy/MergeTree.py

@@ -1,9 +1,9 @@
 import sys
 import time
 
-from .topology import MergeTreeFloat, vectorFloat, vectorString
+from .topology import MergeTreeFloat, vectorFloat
 
-from . import TopologicalObject
+from .TopologicalObject import TopologicalObject
 
 
 class MergeTree(TopologicalObject):

topopy/MorseComplex.py

@@ -6,7 +6,7 @@
 import numpy as np
 
 from .topology import MorseComplexFloat, vectorFloat, mapIntSetInt
-from . import TopologicalObject
+from .TopologicalObject import TopologicalObject
 
 
 class MorseComplex(TopologicalObject):
@@ -375,7 +375,6 @@ def get_label(self, indices=None):
         partitions = self.get_partitions(self.persistence)
         labels = self.X.shape[0] * [None]
         for label, partition_indices in partitions.items():
-            partIndices = partitions[label]
             for idx in np.intersect1d(partition_indices, indices):
                 labels[idx] = label
 

topopy/MorseSmaleComplex.py

@@ -5,8 +5,8 @@
 
 import numpy as np
 
-from . import TopologicalObject
-from . import MorseComplex
+from .TopologicalObject import TopologicalObject
+from .MorseComplex import MorseComplex
 
 
 class MorseSmaleComplex(TopologicalObject):

topopy/tests/test_functions.py

@@ -507,11 +507,12 @@ def gerber2(_x):
         + (1. / 1.) * np.exp(-((y - .75) ** 2) / 0.01)
     )
 
+
 def gerber_different_heights(_x):
     x, y = unpack2D(_x)
     return (
         (1. / 1.) * np.exp(-((x - .25) ** 2) / 0.09)
         + (1. / 4.) * np.exp(-((y - .25) ** 2) / 0.09)
         + (1. / 3.) * np.exp(-((x - .75) ** 2) / 0.01)
         + (1. / 2.) * np.exp(-((y - .75) ** 2) / 0.01)
-    )
+    )

travis.sh

@@ -1,8 +1,8 @@
 set -e
 set -x
 
-# mypy topopy
-# flake8
+mypy topopy
+flake8
 coverage run --source topopy setup.py test
 deploy/test.sh