Code review: rename get_simplex_filtration with get_simplex_and_filtration. Remove exception raise. Fix failed tests. Reword documentation

5 files changed, 141 insertions, 117 deletions

diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py
index 3761fe16..ceead919 100755
--- a/src/python/test/test_alpha_complex.py
+++ b/src/python/test/test_alpha_complex.py
@@ -40,19 +40,21 @@ def test_infinite_alpha():
     assert simplex_tree.num_simplices() == 11
     assert simplex_tree.num_vertices() == 4
 
-    assert simplex_tree.get_filtration() == [
-        ([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),
-    ]
+    filtration_generator = simplex_tree.get_filtration()
+    assert(next(filtration_generator) == ([0], 0.0))
+    assert(next(filtration_generator) == ([1], 0.0))
+    assert(next(filtration_generator) == ([2], 0.0))
+    assert(next(filtration_generator) == ([3], 0.0))
+    assert(next(filtration_generator) == ([0, 1], 0.25))
+    assert(next(filtration_generator) == ([0, 2], 0.25))
+    assert(next(filtration_generator) == ([1, 3], 0.25))
+    assert(next(filtration_generator) == ([2, 3], 0.25))
+    assert(next(filtration_generator) == ([1, 2], 0.5))
+    assert(next(filtration_generator) == ([0, 1, 2], 0.5))
+    assert(next(filtration_generator) == ([1, 2, 3], 0.5))
+    with pytest.raises(StopIteration):
+        next(filtration_generator)
+
     assert simplex_tree.get_star([0]) == [
         ([0], 0.0),
         ([0, 1], 0.25),
@@ -105,16 +107,18 @@ def test_filtered_alpha():
     else:
         assert False
 
-    assert simplex_tree.get_filtration() == [
-        ([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),
-    ]
+    filtration_generator = simplex_tree.get_filtration()
+    assert(next(filtration_generator) == ([0], 0.0))
+    assert(next(filtration_generator) == ([1], 0.0))
+    assert(next(filtration_generator) == ([2], 0.0))
+    assert(next(filtration_generator) == ([3], 0.0))
+    assert(next(filtration_generator) == ([0, 1], 0.25))
+    assert(next(filtration_generator) == ([0, 2], 0.25))
+    assert(next(filtration_generator) == ([1, 3], 0.25))
+    assert(next(filtration_generator) == ([2, 3], 0.25))
+    with pytest.raises(StopIteration):
+        next(filtration_generator)
+
     assert simplex_tree.get_star([0]) == [([0], 0.0), ([0, 1], 0.25), ([0, 2], 0.25)]
     assert simplex_tree.get_cofaces([0], 1) == [([0, 1], 0.25), ([0, 2], 0.25)]
 
diff --git a/src/python/test/test_euclidean_witness_complex.py b/src/python/test/test_euclidean_witness_complex.py
index c18d2484..16ff1ef4 100755
--- a/src/python/test/test_euclidean_witness_complex.py
+++ b/src/python/test/test_euclidean_witness_complex.py
@@ -9,6 +9,7 @@
 """
 
 import gudhi
+import pytest
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
@@ -40,15 +41,16 @@ def test_witness_complex():
     assert landmarks[1] == euclidean_witness_complex.get_point(1)
     assert landmarks[2] == euclidean_witness_complex.get_point(2)
 
-    assert simplex_tree.get_filtration() == [
-        ([0], 0.0),
-        ([1], 0.0),
-        ([0, 1], 0.0),
-        ([2], 0.0),
-        ([0, 2], 0.0),
-        ([1, 2], 0.0),
-        ([0, 1, 2], 0.0),
-    ]
+    filtration_generator = simplex_tree.get_filtration()
+    assert(next(filtration_generator) == ([0], 0.0))
+    assert(next(filtration_generator) == ([1], 0.0))
+    assert(next(filtration_generator) == ([0, 1], 0.0))
+    assert(next(filtration_generator) == ([2], 0.0))
+    assert(next(filtration_generator) == ([0, 2], 0.0))
+    assert(next(filtration_generator) == ([1, 2], 0.0))
+    assert(next(filtration_generator) == ([0, 1, 2], 0.0))
+    with pytest.raises(StopIteration):
+        next(filtration_generator)
 
 
 def test_empty_euclidean_strong_witness_complex():
@@ -78,18 +80,24 @@ def test_strong_witness_complex():
     assert landmarks[1] == euclidean_strong_witness_complex.get_point(1)
     assert landmarks[2] == euclidean_strong_witness_complex.get_point(2)
 
-    assert simplex_tree.get_filtration() == [([0], 0.0), ([1], 0.0), ([2], 0.0)]
+    filtration_generator = simplex_tree.get_filtration()
+    assert(next(filtration_generator) == ([0], 0.0))
+    assert(next(filtration_generator) == ([1], 0.0))
+    assert(next(filtration_generator) == ([2], 0.0))
+    with pytest.raises(StopIteration):
+        next(filtration_generator)
 
     simplex_tree = euclidean_strong_witness_complex.create_simplex_tree(
         max_alpha_square=100.0
     )
 
-    assert simplex_tree.get_filtration() == [
-        ([0], 0.0),
-        ([1], 0.0),
-        ([2], 0.0),
-        ([1, 2], 15.0),
-        ([0, 2], 34.0),
-        ([0, 1], 37.0),
-        ([0, 1, 2], 37.0),
-    ]
+    filtration_generator = simplex_tree.get_filtration()
+    assert(next(filtration_generator) == ([0], 0.0))
+    assert(next(filtration_generator) == ([1], 0.0))
+    assert(next(filtration_generator) == ([2], 0.0))
+    assert(next(filtration_generator) == ([1, 2], 15.0))
+    assert(next(filtration_generator) == ([0, 2], 34.0))
+    assert(next(filtration_generator) == ([0, 1], 37.0))
+    assert(next(filtration_generator) == ([0, 1, 2], 37.0))
+    with pytest.raises(StopIteration):
+        next(filtration_generator)
diff --git a/src/python/test/test_rips_complex.py b/src/python/test/test_rips_complex.py
index b02a68e1..bd31c47c 100755
--- a/src/python/test/test_rips_complex.py
+++ b/src/python/test/test_rips_complex.py
@@ -10,6 +10,7 @@
 
 from gudhi import RipsComplex
 from math import sqrt
+import pytest
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
@@ -32,18 +33,20 @@ def test_rips_from_points():
     assert simplex_tree.num_simplices() == 10
     assert simplex_tree.num_vertices() == 4
 
-    assert simplex_tree.get_filtration() == [
-        ([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),
-    ]
+    filtration_generator = simplex_tree.get_filtration()
+    assert(next(filtration_generator) == ([0], 0.0))
+    assert(next(filtration_generator) == ([1], 0.0))
+    assert(next(filtration_generator) == ([2], 0.0))
+    assert(next(filtration_generator) == ([3], 0.0))
+    assert(next(filtration_generator) == ([0, 1], 1.0))
+    assert(next(filtration_generator) == ([0, 2], 1.0))
+    assert(next(filtration_generator) == ([1, 3], 1.0))
+    assert(next(filtration_generator) == ([2, 3], 1.0))
+    assert(next(filtration_generator) == ([1, 2], 1.4142135623730951))
+    assert(next(filtration_generator) == ([0, 3], 1.4142135623730951))
+    with pytest.raises(StopIteration):
+        next(filtration_generator)
+
     assert simplex_tree.get_star([0]) == [
         ([0], 0.0),
         ([0, 1], 1.0),
@@ -95,18 +98,20 @@ def test_rips_from_distance_matrix():
     assert simplex_tree.num_simplices() == 10
     assert simplex_tree.num_vertices() == 4
 
-    assert simplex_tree.get_filtration() == [
-        ([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),
-    ]
+    filtration_generator = simplex_tree.get_filtration()
+    assert(next(filtration_generator) == ([0], 0.0))
+    assert(next(filtration_generator) == ([1], 0.0))
+    assert(next(filtration_generator) == ([2], 0.0))
+    assert(next(filtration_generator) == ([3], 0.0))
+    assert(next(filtration_generator) == ([0, 1], 1.0))
+    assert(next(filtration_generator) == ([0, 2], 1.0))
+    assert(next(filtration_generator) == ([1, 3], 1.0))
+    assert(next(filtration_generator) == ([2, 3], 1.0))
+    assert(next(filtration_generator) == ([1, 2], 1.4142135623730951))
+    assert(next(filtration_generator) == ([0, 3], 1.4142135623730951))
+    with pytest.raises(StopIteration):
+        next(filtration_generator)
+
     assert simplex_tree.get_star([0]) == [
         ([0], 0.0),
         ([0, 1], 1.0),
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index 1822c43b..0f3db7ac 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -9,6 +9,7 @@
 """
 
 from gudhi import SimplexTree
+import pytest
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
@@ -126,55 +127,58 @@ def test_expansion():
 
     assert st.num_vertices() == 7
     assert st.num_simplices() == 17
-    assert st.get_filtration() == [
-        ([2], 0.1),
-        ([3], 0.1),
-        ([2, 3], 0.1),
-        ([0], 0.2),
-        ([0, 2], 0.2),
-        ([1], 0.3),
-        ([0, 1], 0.3),
-        ([1, 3], 0.4),
-        ([1, 2], 0.5),
-        ([5], 0.6),
-        ([6], 0.6),
-        ([5, 6], 0.6),
-        ([4], 0.7),
-        ([2, 4], 0.7),
-        ([0, 3], 0.8),
-        ([4, 6], 0.9),
-        ([3, 6], 1.0),
-    ]
+
+    filtration_generator = st.get_filtration()
+    assert(next(filtration_generator) == ([2], 0.1))
+    assert(next(filtration_generator) == ([3], 0.1))
+    assert(next(filtration_generator) == ([2, 3], 0.1))
+    assert(next(filtration_generator) == ([0], 0.2))
+    assert(next(filtration_generator) == ([0, 2], 0.2))
+    assert(next(filtration_generator) == ([1], 0.3))
+    assert(next(filtration_generator) == ([0, 1], 0.3))
+    assert(next(filtration_generator) == ([1, 3], 0.4))
+    assert(next(filtration_generator) == ([1, 2], 0.5))
+    assert(next(filtration_generator) == ([5], 0.6))
+    assert(next(filtration_generator) == ([6], 0.6))
+    assert(next(filtration_generator) == ([5, 6], 0.6))
+    assert(next(filtration_generator) == ([4], 0.7))
+    assert(next(filtration_generator) == ([2, 4], 0.7))
+    assert(next(filtration_generator) == ([0, 3], 0.8))
+    assert(next(filtration_generator) == ([4, 6], 0.9))
+    assert(next(filtration_generator) == ([3, 6], 1.0))
+    with pytest.raises(StopIteration):
+        next(filtration_generator)
 
     st.expansion(3)
     assert st.num_vertices() == 7
     assert st.num_simplices() == 22
     st.initialize_filtration()
 
-    assert st.get_filtration() == [
-        ([2], 0.1),
-        ([3], 0.1),
-        ([2, 3], 0.1),
-        ([0], 0.2),
-        ([0, 2], 0.2),
-        ([1], 0.3),
-        ([0, 1], 0.3),
-        ([1, 3], 0.4),
-        ([1, 2], 0.5),
-        ([0, 1, 2], 0.5),
-        ([1, 2, 3], 0.5),
-        ([5], 0.6),
-        ([6], 0.6),
-        ([5, 6], 0.6),
-        ([4], 0.7),
-        ([2, 4], 0.7),
-        ([0, 3], 0.8),
-        ([0, 1, 3], 0.8),
-        ([0, 2, 3], 0.8),
-        ([0, 1, 2, 3], 0.8),
-        ([4, 6], 0.9),
-        ([3, 6], 1.0),
-    ]
+    filtration_generator = st.get_filtration()
+    assert(next(filtration_generator) == ([2], 0.1))
+    assert(next(filtration_generator) == ([3], 0.1))
+    assert(next(filtration_generator) == ([2, 3], 0.1))
+    assert(next(filtration_generator) == ([0], 0.2))
+    assert(next(filtration_generator) == ([0, 2], 0.2))
+    assert(next(filtration_generator) == ([1], 0.3))
+    assert(next(filtration_generator) == ([0, 1], 0.3))
+    assert(next(filtration_generator) == ([1, 3], 0.4))
+    assert(next(filtration_generator) == ([1, 2], 0.5))
+    assert(next(filtration_generator) == ([0, 1, 2], 0.5))
+    assert(next(filtration_generator) == ([1, 2, 3], 0.5))
+    assert(next(filtration_generator) == ([5], 0.6))
+    assert(next(filtration_generator) == ([6], 0.6))
+    assert(next(filtration_generator) == ([5, 6], 0.6))
+    assert(next(filtration_generator) == ([4], 0.7))
+    assert(next(filtration_generator) == ([2, 4], 0.7))
+    assert(next(filtration_generator) == ([0, 3], 0.8))
+    assert(next(filtration_generator) == ([0, 1, 3], 0.8))
+    assert(next(filtration_generator) == ([0, 2, 3], 0.8))
+    assert(next(filtration_generator) == ([0, 1, 2, 3], 0.8))
+    assert(next(filtration_generator) == ([4, 6], 0.9))
+    assert(next(filtration_generator) == ([3, 6], 1.0))
+    with pytest.raises(StopIteration):
+        next(filtration_generator)
 
 
 def test_automatic_dimension():
diff --git a/src/python/test/test_tangential_complex.py b/src/python/test/test_tangential_complex.py
index e650e99c..90e2c75b 100755
--- a/src/python/test/test_tangential_complex.py
+++ b/src/python/test/test_tangential_complex.py
@@ -9,6 +9,7 @@
 """
 
 from gudhi import TangentialComplex, SimplexTree
+import pytest
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
@@ -37,14 +38,16 @@ def test_tangential():
     assert st.num_simplices() == 6
     assert st.num_vertices() == 4
 
-    assert st.get_filtration() == [
-        ([0], 0.0),
-        ([1], 0.0),
-        ([2], 0.0),
-        ([0, 2], 0.0),
-        ([3], 0.0),
-        ([1, 3], 0.0),
-    ]
+    filtration_generator = st.get_filtration()
+    assert(next(filtration_generator) == ([0], 0.0))
+    assert(next(filtration_generator) == ([1], 0.0))
+    assert(next(filtration_generator) == ([2], 0.0))
+    assert(next(filtration_generator) == ([0, 2], 0.0))
+    assert(next(filtration_generator) == ([3], 0.0))
+    assert(next(filtration_generator) == ([1, 3], 0.0))
+    with pytest.raises(StopIteration):
+        next(filtration_generator)
+
     assert st.get_cofaces([0], 1) == [([0, 2], 0.0)]
 
     assert point_list[0] == tc.get_point(0)