Pytest unitary tests

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1333 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0f0b284583267400574c2c2f644d5a99dfb6032e

5 files changed, 209 insertions, 205 deletions

diff --git a/src/cython/test/test_alpha_complex.py b/src/cython/test/test_alpha_complex.py
index a1e57294..13c6f7e8 100755
--- a/src/cython/test/test_alpha_complex.py
+++ b/src/cython/test/test_alpha_complex.py
@@ -1,6 +1,4 @@
-import unittest
-
-import gudhi
+from gudhi import AlphaComplex
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -29,56 +27,60 @@ __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
 
-class TestAlphaComplex(unittest.TestCase):
-
-    def test_infinite_alpha(self):
-        point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
-        alpha_complex = gudhi.AlphaComplex(points=point_list)
-
-        self.assertEqual(alpha_complex.num_simplices(), 11)
-        self.assertEqual(alpha_complex.num_vertices(), 4)
-
-        self.assertEqual(alpha_complex.get_filtered_tree(),
-                         [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
-                          ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25),
-                          ([2, 3], 0.25), ([1, 2], 0.5), ([0, 1, 2], 0.5),
-                          ([1, 2, 3], 0.5)])
-        self.assertEqual(alpha_complex.get_star_tree([0]),
-                         [([0], 0.0), ([0, 1], 0.25), ([0, 1, 2], 0.5),
-                         ([0, 2], 0.25)])
-        self.assertEqual(alpha_complex.get_coface_tree([0], 1),
-                         [([0, 1], 0.25), ([0, 2], 0.25)])
-
-        self.assertEqual(point_list[0], alpha_complex.get_point(0))
-        self.assertEqual(point_list[1], alpha_complex.get_point(1))
-        self.assertEqual(point_list[2], alpha_complex.get_point(2))
-        self.assertEqual(point_list[3], alpha_complex.get_point(3))
-        self.assertEqual([], alpha_complex.get_point(4))
-        self.assertEqual([], alpha_complex.get_point(125))
-
-    def test_filtered_alpha(self):
-        point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
-        filtered_alpha = gudhi.AlphaComplex(points=point_list,
-                                            max_alpha_square=0.25)
-
-        self.assertEqual(filtered_alpha.num_simplices(), 8)
-        self.assertEqual(filtered_alpha.num_vertices(), 4)
-
-        self.assertEqual(point_list[0], filtered_alpha.get_point(0))
-        self.assertEqual(point_list[1], filtered_alpha.get_point(1))
-        self.assertEqual(point_list[2], filtered_alpha.get_point(2))
-        self.assertEqual(point_list[3], filtered_alpha.get_point(3))
-        self.assertEqual([], filtered_alpha.get_point(4))
-        self.assertEqual([], filtered_alpha.get_point(125))
-
-        self.assertEqual(filtered_alpha.get_filtered_tree(),
-                         [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
-                          ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25),
-                          ([2, 3], 0.25)])
-        self.assertEqual(filtered_alpha.get_star_tree([0]),
-                         [([0], 0.0), ([0, 1], 0.25), ([0, 2], 0.25)])
-        self.assertEqual(filtered_alpha.get_coface_tree([0], 1),
-                         [([0, 1], 0.25), ([0, 2], 0.25)])
-
-if __name__ == '__main__':
-    unittest.main()
+def test_empty_alpha():
+    alpha_complex = AlphaComplex()
+    assert alpha_complex.__is_defined() == True
+    assert alpha_complex.__is_persistence_defined() == False
+    assert alpha_complex.num_simplices() == 0
+    assert alpha_complex.num_vertices() == 0
+
+def test_infinite_alpha():
+    point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
+    alpha_complex = AlphaComplex(points=point_list)
+    assert alpha_complex.__is_defined() == True
+    assert alpha_complex.__is_persistence_defined() == False
+
+    assert alpha_complex.num_simplices() == 11
+    assert alpha_complex.num_vertices() == 4
+ 
+    assert alpha_complex.get_filtered_tree() == \
+           [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
+            ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25),
+            ([2, 3], 0.25), ([1, 2], 0.5), ([0, 1, 2], 0.5),
+            ([1, 2, 3], 0.5)]
+    assert alpha_complex.get_star_tree([0]) == \
+           [([0], 0.0), ([0, 1], 0.25), ([0, 1, 2], 0.5),
+           ([0, 2], 0.25)]
+    assert alpha_complex.get_coface_tree([0], 1) == \
+           [([0, 1], 0.25), ([0, 2], 0.25)]
+ 
+    assert point_list[0] == alpha_complex.get_point(0)
+    assert point_list[1] == alpha_complex.get_point(1)
+    assert point_list[2] == alpha_complex.get_point(2)
+    assert point_list[3] == alpha_complex.get_point(3)
+    assert alpha_complex.get_point(4) == []
+    assert alpha_complex.get_point(125) == []
+
+def test_filtered_alpha():
+    point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
+    filtered_alpha = AlphaComplex(points=point_list,
+                                  max_alpha_square=0.25)
+
+    assert filtered_alpha.num_simplices() == 8
+    assert filtered_alpha.num_vertices() == 4
+
+    assert point_list[0] == filtered_alpha.get_point(0)
+    assert point_list[1] == filtered_alpha.get_point(1)
+    assert point_list[2] == filtered_alpha.get_point(2)
+    assert point_list[3] == filtered_alpha.get_point(3)
+    assert filtered_alpha.get_point(4) == []
+    assert filtered_alpha.get_point(125) == []
+
+    assert filtered_alpha.get_filtered_tree() == \
+           [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
+            ([0, 1], 0.25), ([0, 2], 0.25), ([1, 3], 0.25),
+            ([2, 3], 0.25)]
+    assert filtered_alpha.get_star_tree([0]) == \
+           [([0], 0.0), ([0, 1], 0.25), ([0, 2], 0.25)]
+    assert filtered_alpha.get_coface_tree([0], 1) == \
+           [([0, 1], 0.25), ([0, 2], 0.25)]
diff --git a/src/cython/test/test_mini_simplex_tree.py b/src/cython/test/test_mini_simplex_tree.py
index ec1f5044..e44bfdbc 100755
--- a/src/cython/test/test_mini_simplex_tree.py
+++ b/src/cython/test/test_mini_simplex_tree.py
@@ -1,6 +1,4 @@
-import unittest
-
-import gudhi
+from gudhi import MiniSimplexTree
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -29,27 +27,24 @@ __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
 
-class TestMiniSimplexTree(unittest.TestCase):
-
-    def test_mini(self):
-        triangle012 = [0, 1, 2]
-        edge03 = [0, 3]
-        mini_st = gudhi.MiniSimplexTree()
-        self.assertTrue(mini_st.insert(triangle012))
-        self.assertTrue(mini_st.insert(edge03))
-        # FIXME: Remove this line
-        mini_st.set_dimension(2)
-
-        edge02 = [0, 2]
-        self.assertTrue(mini_st.find(edge02))
-        self.assertEqual(mini_st.get_coface_tree(edge02, 1),
-                         [([0, 1, 2], 0.0)])
-
-        # remove_maximal_simplex test
-        self.assertEqual(mini_st.get_coface_tree(triangle012, 1), [])
-        mini_st.remove_maximal_simplex(triangle012)
-        self.assertTrue(mini_st.find(edge02))
-        self.assertFalse(mini_st.find(triangle012))
-
-if __name__ == '__main__':
-    unittest.main()
+def test_mini():
+    triangle012 = [0, 1, 2]
+    edge03 = [0, 3]
+    mini_st = MiniSimplexTree()
+    assert mini_st.__is_defined() == True
+    assert mini_st.__is_persistence_defined() == False
+    assert mini_st.insert(triangle012) == True
+    assert mini_st.insert(edge03) == True
+    # FIXME: Remove this line
+    mini_st.set_dimension(2)
+
+    edge02 = [0, 2]
+    assert mini_st.find(edge02) == True
+    assert mini_st.get_coface_tree(edge02, 1) == \
+            [([0, 1, 2], 0.0)]
+
+    # remove_maximal_simplex test
+    assert mini_st.get_coface_tree(triangle012, 1) == []
+    mini_st.remove_maximal_simplex(triangle012)
+    assert mini_st.find(edge02) == True
+    assert mini_st.find(triangle012) == False
diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py
index ecc676c7..877289cf 100755
--- a/src/cython/test/test_rips_complex.py
+++ b/src/cython/test/test_rips_complex.py
@@ -1,6 +1,4 @@
-import unittest
-
-import gudhi
+from gudhi import RipsComplex
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -29,33 +27,39 @@ __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
 
-class TestRipsComplex(unittest.TestCase):
-
-    def test_rips(self):
-        point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
-        rips_complex = gudhi.RipsComplex(points=point_list, max_dimension=1,
-                                         max_edge_length=42)
-
-        self.assertEqual(rips_complex.num_simplices(), 10)
-        self.assertEqual(rips_complex.num_vertices(), 4)
-
-        self.assertEqual(rips_complex.get_filtered_tree(),
-                         [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
-                          ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0),
-                          ([2, 3], 1.0), ([1, 2], 1.4142135623730951),
-                          ([0, 3], 1.4142135623730951)])
-        self.assertEqual(rips_complex.get_star_tree([0]),
-                         [([0], 0.0), ([0, 1], 1.0), ([0, 2], 1.0),
-                          ([0, 3], 1.4142135623730951)])
-        self.assertEqual(rips_complex.get_coface_tree([0], 1),
-                         [([0, 1], 1.0), ([0, 2], 1.0),
-                          ([0, 3], 1.4142135623730951)])
-
-        filtered_rips = gudhi.RipsComplex(points=point_list, max_dimension=1,
-                                          max_edge_length=1.0)
-
-        self.assertEqual(filtered_rips.num_simplices(), 8)
-        self.assertEqual(filtered_rips.num_vertices(), 4)
-
-if __name__ == '__main__':
-    unittest.main()
+def test_empty_rips():
+    rips_complex = RipsComplex()
+    assert rips_complex.__is_defined() == True
+    assert rips_complex.__is_persistence_defined() == False
+
+def test_rips():
+    point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
+    rips_complex = RipsComplex(points=point_list, max_dimension=1,
+                               max_edge_length=42)
+    assert rips_complex.__is_defined() == True
+    assert rips_complex.__is_persistence_defined() == False
+
+    assert rips_complex.num_simplices() == 10
+    assert rips_complex.num_vertices() == 4
+
+    assert rips_complex.get_filtered_tree() == \
+           [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
+            ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0),
+            ([2, 3], 1.0), ([1, 2], 1.4142135623730951),
+            ([0, 3], 1.4142135623730951)]
+    assert rips_complex.get_star_tree([0]) == \
+           [([0], 0.0), ([0, 1], 1.0), ([0, 2], 1.0),
+            ([0, 3], 1.4142135623730951)]
+    assert rips_complex.get_coface_tree([0], 1) == \
+           [([0, 1], 1.0), ([0, 2], 1.0),
+            ([0, 3], 1.4142135623730951)]
+
+def test_filtered_rips():
+    point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
+    filtered_rips = RipsComplex(points=point_list, max_dimension=1,
+                                      max_edge_length=1.0)
+    assert filtered_rips.__is_defined() == True
+    assert filtered_rips.__is_persistence_defined() == False
+
+    assert filtered_rips.num_simplices() == 8
+    assert filtered_rips.num_vertices() == 4
diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py
index 7663ed70..0b9899f8 100755
--- a/src/cython/test/test_simplex_tree.py
+++ b/src/cython/test/test_simplex_tree.py
@@ -1,6 +1,4 @@
-import unittest
-
-import gudhi
+from gudhi import SimplexTree
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -29,63 +27,72 @@ __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
 
-class TestSimplexTree(unittest.TestCase):
-
-    def test_insertion(self):
-        st = gudhi.SimplexTree()
-
-        # insert test
-        self.assertTrue(st.insert([0, 1]))
-        self.assertTrue(st.insert([0, 1, 2], filtration=4.0))
-        self.assertEqual(st.num_simplices(), 7)
-        self.assertEqual(st.num_vertices(), 3)
-
-        # find test
-        self.assertTrue(st.find([0, 1, 2]))
-        self.assertTrue(st.find([0, 1]))
-        self.assertTrue(st.find([0, 2]))
-        self.assertTrue(st.find([0]))
-        self.assertTrue(st.find([1]))
-        self.assertTrue(st.find([2]))
-        self.assertFalse(st.find([3]))
-        self.assertFalse(st.find([0, 3]))
-        self.assertFalse(st.find([1, 3]))
-        self.assertFalse(st.find([2, 3]))
-
-        # filtration test
-        st.set_filtration(5.0)
-        st.initialize_filtration()
-        self.assertEqual(st.get_filtration(), 5.0)
-        self.assertEqual(st.filtration([0, 1, 2]), 4.0)
-        self.assertEqual(st.filtration([0, 2]), 4.0)
-        self.assertEqual(st.filtration([1, 2]), 4.0)
-        self.assertEqual(st.filtration([2]), 4.0)
-        self.assertEqual(st.filtration([0, 1]), 0.0)
-        self.assertEqual(st.filtration([0]), 0.0)
-        self.assertEqual(st.filtration([1]), 0.0)
-
-        # skeleton_tree test
-        self.assertEqual(st.get_skeleton_tree(2),
-                         [([0, 1, 2], 4.0), ([0, 1], 0.0), ([0, 2], 4.0),
-                          ([0], 0.0), ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)])
-        self.assertEqual(st.get_skeleton_tree(1),
-                         [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0),
-                          ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)])
-        self.assertEqual(st.get_skeleton_tree(0),
-                         [([0], 0.0), ([1], 0.0), ([2], 4.0)])
-
-        # remove_maximal_simplex test
-        self.assertEqual(st.get_coface_tree([0, 1, 2], 1), [])
-        st.remove_maximal_simplex([0, 1, 2])
-        self.assertEqual(st.get_skeleton_tree(2),
-                         [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0),
-                          ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)])
-        self.assertFalse(st.find([0, 1, 2]))
-        self.assertTrue(st.find([0, 1]))
-        self.assertTrue(st.find([0, 2]))
-        self.assertTrue(st.find([0]))
-        self.assertTrue(st.find([1]))
-        self.assertTrue(st.find([2]))
-
-if __name__ == '__main__':
-    unittest.main()
+def test_insertion():
+    st = SimplexTree()
+    assert st.__is_defined() == True
+    assert st.__is_persistence_defined() == False
+
+    # insert test
+    assert st.insert([0, 1]) == True
+    assert st.insert([0, 1, 2], filtration=4.0) == True
+    # FIXME: Remove this line
+    st.set_dimension(2)
+    assert st.num_simplices() == 7
+    assert st.num_vertices() == 3
+
+    # find test
+    assert st.find([0, 1, 2]) == True
+    assert st.find([0, 1]) == True
+    assert st.find([0, 2]) == True
+    assert st.find([0]) == True
+    assert st.find([1]) == True
+    assert st.find([2]) == True
+    assert st.find([3])    == False
+    assert st.find([0, 3]) == False
+    assert st.find([1, 3]) == False
+    assert st.find([2, 3]) == False
+
+    # filtration test
+    st.set_filtration(5.0)
+    st.initialize_filtration()
+    assert st.get_filtration() == 5.0
+    assert st.filtration([0, 1, 2]) == 4.0
+    assert st.filtration([0, 2]) == 4.0
+    assert st.filtration([1, 2]) == 4.0
+    assert st.filtration([2]) == 4.0
+    assert st.filtration([0, 1]) == 0.0
+    assert st.filtration([0]) == 0.0
+    assert st.filtration([1]) == 0.0
+
+    # skeleton_tree test
+    assert st.get_skeleton_tree(2) == \
+        [([0, 1, 2], 4.0), ([0, 1], 0.0), ([0, 2], 4.0),
+        ([0], 0.0), ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)]
+    assert st.get_skeleton_tree(1) == \
+        [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0),
+        ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)]
+    assert st.get_skeleton_tree(0) == \
+        [([0], 0.0), ([1], 0.0), ([2], 4.0)]
+
+    # remove_maximal_simplex test
+    assert st.get_coface_tree([0, 1, 2], 1) == []
+    st.remove_maximal_simplex([0, 1, 2])
+    assert st.get_skeleton_tree(2) == \
+        [([0, 1], 0.0), ([0, 2], 4.0), ([0], 0.0),
+        ([1, 2], 4.0), ([1], 0.0), ([2], 4.0)]
+    assert st.find([0, 1, 2]) == False
+    assert st.find([0, 1]) == True
+    assert st.find([0, 2]) == True
+    assert st.find([0]) == True
+    assert st.find([1]) == True
+    assert st.find([2]) == True
+
+    st.initialize_filtration()
+    assert st.persistence() == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))]
+    assert st.__is_persistence_defined() == True
+    assert st.betti_numbers() == [1, 1]
+    assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0]
+    assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0]
+    assert st.persistent_betti_numbers(3.9, 10000.0) == [1, 0]
+    assert st.persistent_betti_numbers(4.0, 10000.0) == [1, 1]
+    assert st.persistent_betti_numbers(9999.0, 10000.0) == [1, 1]
diff --git a/src/cython/test/test_witness_complex.py b/src/cython/test/test_witness_complex.py
index 2891935d..9f4a3523 100755
--- a/src/cython/test/test_witness_complex.py
+++ b/src/cython/test/test_witness_complex.py
@@ -1,6 +1,4 @@
-import unittest
-
-import gudhi
+from gudhi import WitnessComplex
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -29,31 +27,29 @@ __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
 
-class TestWitnessComplex(unittest.TestCase):
-
-    def test_witness_complex(self):
-        point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
-        witness = gudhi.WitnessComplex(points=point_list,
-                                       number_of_landmarks=10)
-
-        # FIXME: Remove this line
-        witness.set_dimension(2)
+def test_empty_witness_complex():
+    witness = WitnessComplex()
+    assert witness.__is_defined() == False
 
-        self.assertEqual(witness.num_simplices(), 13)
-        self.assertEqual(witness.num_vertices(), 10)
-        witness.initialize_filtration()
+def test_witness_complex():
+    point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
+    witness = WitnessComplex(points=point_list, number_of_landmarks=10)
+    assert witness.__is_defined() == True
 
-        self.assertEqual(witness.get_filtered_tree(),
-                         [([0], 0.0), ([1], 0.0), ([2], 0.0), ([0, 2], 0.0),
-                         ([1, 2], 0.0), ([3], 0.0), ([4], 0.0), ([3, 4], 0.0),
-                         ([5], 0.0), ([6], 0.0), ([7], 0.0), ([8], 0.0),
-                         ([9], 0.0)])
+    # FIXME: Remove this line
+    witness.set_dimension(2)
 
-        self.assertEqual(witness.get_coface_tree([2], 1),
-                         [([0, 2], 0.0), ([1, 2], 0.0)])
-        self.assertEqual(witness.get_star_tree([2]),
-                         [([0, 2], 0.0), ([1, 2], 0.0), ([2], 0.0)])
+    assert witness.num_simplices() == 13
+    assert witness.num_vertices() == 10
+    witness.initialize_filtration()
 
+    assert witness.get_filtered_tree() == \
+        [([0], 0.0), ([1], 0.0), ([2], 0.0), ([0, 2], 0.0),
+        ([1, 2], 0.0), ([3], 0.0), ([4], 0.0), ([3, 4], 0.0),
+        ([5], 0.0), ([6], 0.0), ([7], 0.0), ([8], 0.0),
+        ([9], 0.0)]
 
-if __name__ == '__main__':
-    unittest.main()
+    assert witness.get_coface_tree([2], 1) == \
+        [([0, 2], 0.0), ([1, 2], 0.0)]
+    assert witness.get_star_tree([2]) == \
+        [([0, 2], 0.0), ([1, 2], 0.0), ([2], 0.0)]