TVB-2719 Add 100% test coverage

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+plugins = Cython.Coverage

.gitignore

@@ -8,9 +8,10 @@ __pycache__/
 
 # Distribution / packaging
 dist/
+*.egg-info
 
 # coverage file
-.coverage
+.coverage*
 
 # PyCharm generated configuration
 .idea/
@@ -30,3 +31,6 @@ env
 # Shared object files
 *.so
 *.pyd
+
+# generated file during compilation
+gdist.cpp

.travis.yml

@@ -3,16 +3,20 @@ notifications:
 
 install:
   - pip3 install .
-  # - python setup.py build_ext --inplace
 script:
-  - pip3 install pytest~=3.6.1
-  - pytest
+  - pip3 install pytest
+  - if [ "${TRAVIS_OS_NAME}" = "linux" ]; then pytest --cov=gdist; else pytest; fi
 
 jobs:
   include:
     - name: "Python 3.8 on Xenial Linux"
       language: python
+      os: linux
       python: 3.8
+      env: COVERAGE=1
+      before_install: pip3 install pytest-cov codecov
+      before_script: python3 setup.py clean --all build_ext --force --inplace
+      after_success: codecov
     - name: "Python 3.8.0 on Windows"
       os: windows
       language: shell

data/flat_triangular_mesh_no_target.txt

@@ -0,0 +1,121 @@
+0.000000000000000000e+00
+1.999999999999999556e-01
+3.999999999999999667e-01
+5.999999999999998668e-01
+7.999999999999998224e-01
+9.999999999999997780e-01
+1.199999999999999734e+00
+1.399999999999999689e+00
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gdist.pyx

@@ -1,5 +1,4 @@
 # -*- coding: utf-8 -*-
-# cython: language_level=3
 #
 #
 # TheVirtualBrain-Framework Package. This package holds all Data Management, and
@@ -171,10 +170,10 @@ def compute_gdist(numpy.ndarray[numpy.float64_t, ndim=2] vertices,
     cdef vector[unsigned] faces
 
     if source_indices is None:
-        source_indices = numpy.arange(0, dtype=numpy.int32)  # default to 0
+        source_indices = numpy.arange(1, dtype=numpy.int32)  # default to 0
     if target_indices is None:
         propagate_on_max_distance = True
-        target_indices = numpy.arange(vertices.size(), dtype=numpy.int32)
+        target_indices = numpy.arange(vertices.shape[0], dtype=numpy.int32)
 
     for k in vertices.flatten():
         points.push_back(k)

setup.py

@@ -41,10 +41,24 @@
 """
 
 import os
-import numpy
 import shutil
 import setuptools
+
+import numpy
 from Cython.Distutils import build_ext
+from Cython.Build.Dependencies import cythonize
+
+
+compiler_directives = {
+    'language_level': 3,
+}
+
+# Disable assertions; one is failing geodesic_mesh.h:405
+define_macros = [('NDEBUG', 1)]
+
+if 'COVERAGE' in os.environ:
+    compiler_directives['linetrace'] = True
+    define_macros.append(("CYTHON_TRACE_NOGIL", "1"))
 
 GEODESIC_NAME = "gdist"
 
@@ -53,8 +67,7 @@
         name=GEODESIC_NAME,  # Name of extension
         sources=["gdist.pyx"],  # Filename of Cython source
         language="c++",  # Cython create C++ source
-        # Disable assertions; one is failing geodesic_mesh.h:405
-        define_macros=[('NDEBUG', 1)],
+        define_macros=define_macros,
         extra_compile_args=['--std=c++14'],
         extra_link_args=['--std=c++14'],
         include_dirs=[numpy.get_include(), "geodesic_library"],
@@ -73,12 +86,26 @@
 with open(os.path.join(os.path.dirname(__file__), 'README.rst')) as fd:
     DESCRIPTION = fd.read()
 
+class new_build_ext(build_ext):
+    def finalize_options(self):
+        self.distribution.ext_modules = cythonize(
+            self.distribution.ext_modules,
+            compiler_directives=compiler_directives,
+            annotate=False,
+        )
+        if not self.include_dirs:
+            self.include_dirs = []
+        elif isinstance(self.include_dirs, str):
+            self.include_dirs = [self.include_dirs]
+        self.include_dirs.append(numpy.get_include())
+        super().finalize_options()
+
 setuptools.setup(
     name="tvb-" + GEODESIC_NAME,
     version='2.1.0',
     ext_modules=GEODESIC_MODULE,
     include_dirs=INCLUDE_DIRS,
-    cmdclass={'build_ext': build_ext},
+    cmdclass={"build_ext": new_build_ext},
     install_requires=INSTALL_REQUIREMENTS,
     description="Compute geodesic distances",
     long_description=DESCRIPTION,
@@ -88,8 +115,3 @@
     url='https://github.com/the-virtual-brain/tvb-gdist',
     keywords="gdist geodesic distance geo tvb"
 )
-
-shutil.rmtree('tvb_gdist.egg-info', True)
-if os.path.exists(GEODESIC_NAME + '.cpp'):
-    os.remove(GEODESIC_NAME + '.cpp')
-shutil.rmtree('build', True)

tests/test_gdist.py

@@ -71,6 +71,21 @@ def test_flat_triangular_mesh_1_indexed(self):
         )
         np.testing.assert_array_almost_equal(distance, [0.2])
 
+    def test_flat_triangular_mesh_no_target(self):
+        data = np.loadtxt("data/flat_triangular_mesh.txt", skiprows=1)
+        vertices = data[0:121].astype(np.float64)
+        triangles = data[121:].astype(np.int32)
+        source = None
+        target = None
+        distance = gdist.compute_gdist(
+            vertices,
+            triangles,
+            source,
+            target,
+        )
+        expected = np.loadtxt("data/flat_triangular_mesh_no_target.txt")
+        np.testing.assert_array_almost_equal(distance, expected)
+
     def test_hedgehog_mesh(self):
         data = np.loadtxt("data/hedgehog_mesh.txt", skiprows=1)
         vertices = data[0:300].astype(np.float64)