Merge master and resolve conflicts

3 files changed, 48 insertions, 3 deletions

diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py
index a4ee260b..814f8289 100755
--- a/src/python/test/test_alpha_complex.py
+++ b/src/python/test/test_alpha_complex.py
@@ -198,8 +198,7 @@ def test_delaunay_complex():
         _delaunay_complex(precision)
 
 def _3d_points_on_a_plane(precision, default_filtration_value):
-    alpha = gd.AlphaComplex(off_file=gd.__root_source_dir__ + '/data/points/alphacomplexdoc.off',
-                         precision = precision)
+    alpha = gd.AlphaComplex(off_file='alphacomplexdoc.off', precision = precision)
 
     simplex_tree = alpha.create_simplex_tree(default_filtration_value = default_filtration_value)
     assert simplex_tree.dimension() == 2
@@ -207,6 +206,18 @@ def _3d_points_on_a_plane(precision, default_filtration_value):
     assert simplex_tree.num_simplices() == 25
 
 def test_3d_points_on_a_plane():
+    off_file = open("alphacomplexdoc.off", "w")
+    off_file.write("OFF         \n" \
+                   "7 0 0       \n" \
+                   "1.0 1.0  0.0\n" \
+                   "7.0 0.0  0.0\n" \
+                   "4.0 6.0  0.0\n" \
+                   "9.0 6.0  0.0\n" \
+                   "0.0 14.0 0.0\n" \
+                   "2.0 19.0 0.0\n" \
+                   "9.0 17.0 0.0\n"  )
+    off_file.close()
+
     for default_filtration_value in [True, False]:
         for precision in ['fast', 'safe', 'exact']:
             _3d_points_on_a_plane(precision, default_filtration_value)
diff --git a/src/python/test/test_representations.py b/src/python/test/test_representations.py
index 589cee00..e5c211a0 100755
--- a/src/python/test/test_representations.py
+++ b/src/python/test/test_representations.py
@@ -4,6 +4,8 @@ import matplotlib.pyplot as plt
 import numpy as np
 import pytest
 
+from sklearn.cluster import KMeans
+
 
 def test_representations_examples():
     # Disable graphics for testing purposes
@@ -15,6 +17,7 @@ def test_representations_examples():
     return None
 
 
+from gudhi.representations.vector_methods import Atol
 from gudhi.representations.metrics import *
 from gudhi.representations.kernel_methods import *
 
@@ -41,3 +44,17 @@ def test_multiple():
     d2 = WassersteinDistance(order=2, internal_p=2, n_jobs=4).fit(l2).transform(l1)
     print(d1.shape, d2.shape)
     assert d1 == pytest.approx(d2, rel=.02)
+
+
+def test_dummy_atol():
+    a = np.array([[1, 2, 4], [1, 4, 0], [1, 0, 4]])
+    b = np.array([[4, 2, 0], [4, 4, 0], [4, 0, 2]])
+    c = np.array([[3, 2, -1], [1, 2, -1]])
+
+    for weighting_method in ["cloud", "iidproba"]:
+        for contrast in ["gaussian", "laplacian", "indicator"]:
+            atol_vectoriser = Atol(quantiser=KMeans(n_clusters=1, random_state=202006), weighting_method=weighting_method, contrast=contrast)
+            atol_vectoriser.fit([a, b, c])
+            atol_vectoriser(a)
+            atol_vectoriser.transform(X=[a, b, c])
+
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index 1ca84c10..6f1d01cc 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -341,6 +341,24 @@ def test_simplices_iterator():
         print("filtration is: ", simplex[1])
         assert st.filtration(simplex[0]) == simplex[1]
 
+def test_collapse_edges():
+    st = SimplexTree()
+    
+    assert st.insert([0, 1], filtration=1.0) == True
+    assert st.insert([1, 2], filtration=1.0) == True
+    assert st.insert([2, 3], filtration=1.0) == True
+    assert st.insert([0, 3], filtration=1.0) == True
+    assert st.insert([0, 2], filtration=2.0) == True
+    assert st.insert([1, 3], filtration=2.0) == True
+
+    assert st.num_simplices() == 10
+
+    st.collapse_edges()
+    assert st.num_simplices() == 9
+    assert st.find([1, 3]) == False
+    for simplex in st.get_skeleton(0):
+        assert simplex[1] == 1.
+
 def test_reset_filtration():
     st = SimplexTree()
     
@@ -361,4 +379,3 @@ def test_reset_filtration():
                 assert st.filtration(simplex[0]) >= 1.
             else:
                 assert st.filtration(simplex[0]) == 0.
-