From e7b7947adf13ec1dcb8c126a4373fa29baaecb63 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Tue, 29 Sep 2020 13:23:56 +0200
Subject: Added tests for wasserstein distance with tensorflow

---
 src/python/CMakeLists.txt | 8 ++++++++
 1 file changed, 8 insertions(+)

(limited to 'src/python/CMakeLists.txt')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 4f26481e..cc71503f 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -103,6 +103,9 @@ if(PYTHONINTERP_FOUND)
     if(EAGERPY_FOUND)
       add_gudhi_debug_info("EagerPy version ${EAGERPY_VERSION}")
     endif()
+    if(TENSORFLOW_FOUND)
+      add_gudhi_debug_info("TensorFlow version ${TENSORFLOW_VERSION}")
+    endif()
 
     set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
     set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
@@ -501,6 +504,11 @@ if(PYTHONINTERP_FOUND)
       endif()
       add_gudhi_py_test(test_wasserstein_barycenter)
     endif()
+    if(OT_FOUND)
+      if(TENSORFLOW_FOUND AND EAGERPY_FOUND)
+        add_gudhi_py_test(test_wasserstein_with_tensors)
+      endif()
+    endif()
 
     # Representations
     if(SKLEARN_FOUND AND MATPLOTLIB_FOUND)
-- 
cgit v1.2.3


From f0beb329f5a1767e4e0a0575ef3e078bf4563a44 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Mon, 5 Oct 2020 11:12:44 +0200
Subject: code review: move test_wasserstein_distance_grad from
 test_wasserstein_distance.py to test_wasserstein_with_tensors.py

---
 src/python/CMakeLists.txt                        |  5 +++--
 src/python/test/test_wasserstein_distance.py     | 24 ----------------------
 src/python/test/test_wasserstein_with_tensors.py | 26 ++++++++++++++++++++++--
 3 files changed, 27 insertions(+), 28 deletions(-)

(limited to 'src/python/CMakeLists.txt')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index cc71503f..c09996fe 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -499,13 +499,14 @@ if(PYTHONINTERP_FOUND)
 
     # Wasserstein
     if(OT_FOUND AND PYBIND11_FOUND)
-      if(TORCH_FOUND AND EAGERPY_FOUND)
+      # EagerPy dependency because of enable_autodiff=True
+      if(EAGERPY_FOUND)
         add_gudhi_py_test(test_wasserstein_distance)
       endif()
       add_gudhi_py_test(test_wasserstein_barycenter)
     endif()
     if(OT_FOUND)
-      if(TENSORFLOW_FOUND AND EAGERPY_FOUND)
+      if(TORCH_FOUND AND TENSORFLOW_FOUND AND EAGERPY_FOUND)
         add_gudhi_py_test(test_wasserstein_with_tensors)
       endif()
     endif()
diff --git a/src/python/test/test_wasserstein_distance.py b/src/python/test/test_wasserstein_distance.py
index 90d26809..e3b521d6 100755
--- a/src/python/test/test_wasserstein_distance.py
+++ b/src/python/test/test_wasserstein_distance.py
@@ -97,27 +97,3 @@ def test_wasserstein_distance_pot():
 def test_wasserstein_distance_hera():
     _basic_wasserstein(hera_wrap(delta=1e-12), 1e-12, test_matching=False)
     _basic_wasserstein(hera_wrap(delta=.1), .1, test_matching=False)
-
-def test_wasserstein_distance_grad():
-    import torch
-
-    diag1 = torch.tensor([[2.7, 3.7], [9.6, 14.0], [34.2, 34.974]], requires_grad=True)
-    diag2 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True)
-    diag3 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True)
-    assert diag1.grad is None and diag2.grad is None and diag3.grad is None
-    dist12 = pot(diag1, diag2, internal_p=2, order=2, enable_autodiff=True)
-    dist30 = pot(diag3, torch.tensor([]), internal_p=2, order=2, enable_autodiff=True)
-    dist12.backward()
-    dist30.backward()
-    assert not torch.isnan(diag1.grad).any() and not torch.isnan(diag2.grad).any() and not torch.isnan(diag3.grad).any()
-    diag4 = torch.tensor([[0., 10.]], requires_grad=True)
-    diag5 = torch.tensor([[1., 11.], [3., 4.]], requires_grad=True)
-    dist45 = pot(diag4, diag5, internal_p=1, order=1, enable_autodiff=True)
-    assert dist45 == 3.
-    dist45.backward()
-    assert np.array_equal(diag4.grad, [[-1., -1.]])
-    assert np.array_equal(diag5.grad, [[1., 1.], [-1., 1.]])
-    diag6 = torch.tensor([[5., 10.]], requires_grad=True)
-    pot(diag6, diag6, internal_p=2, order=2, enable_autodiff=True).backward()
-    # https://github.com/jonasrauber/eagerpy/issues/6
-    # assert np.array_equal(diag6.grad, [[0., 0.]])
diff --git a/src/python/test/test_wasserstein_with_tensors.py b/src/python/test/test_wasserstein_with_tensors.py
index 8957705d..e3f1411a 100755
--- a/src/python/test/test_wasserstein_with_tensors.py
+++ b/src/python/test/test_wasserstein_with_tensors.py
@@ -10,10 +10,32 @@
 
 from gudhi.wasserstein import wasserstein_distance as pot
 import numpy as np
+import torch
+import tensorflow as tf
 
-def test_wasserstein_distance_grad_tensorflow():
-    import tensorflow as tf
+def test_wasserstein_distance_grad():
+    diag1 = torch.tensor([[2.7, 3.7], [9.6, 14.0], [34.2, 34.974]], requires_grad=True)
+    diag2 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True)
+    diag3 = torch.tensor([[2.8, 4.45], [9.5, 14.1]], requires_grad=True)
+    assert diag1.grad is None and diag2.grad is None and diag3.grad is None
+    dist12 = pot(diag1, diag2, internal_p=2, order=2, enable_autodiff=True)
+    dist30 = pot(diag3, torch.tensor([]), internal_p=2, order=2, enable_autodiff=True)
+    dist12.backward()
+    dist30.backward()
+    assert not torch.isnan(diag1.grad).any() and not torch.isnan(diag2.grad).any() and not torch.isnan(diag3.grad).any()
+    diag4 = torch.tensor([[0., 10.]], requires_grad=True)
+    diag5 = torch.tensor([[1., 11.], [3., 4.]], requires_grad=True)
+    dist45 = pot(diag4, diag5, internal_p=1, order=1, enable_autodiff=True)
+    assert dist45 == 3.
+    dist45.backward()
+    assert np.array_equal(diag4.grad, [[-1., -1.]])
+    assert np.array_equal(diag5.grad, [[1., 1.], [-1., 1.]])
+    diag6 = torch.tensor([[5., 10.]], requires_grad=True)
+    pot(diag6, diag6, internal_p=2, order=2, enable_autodiff=True).backward()
+    # https://github.com/jonasrauber/eagerpy/issues/6
+    # assert np.array_equal(diag6.grad, [[0., 0.]])
 
+def test_wasserstein_distance_grad_tensorflow():
     with tf.GradientTape() as tape:
         diag4 = tf.convert_to_tensor(tf.Variable(initial_value=np.array([[0., 10.]]),           trainable=True))
         diag5 = tf.convert_to_tensor(tf.Variable(initial_value=np.array([[1., 11.], [3., 4.]]), trainable=True))
-- 
cgit v1.2.3


From ef30f636af892a2e226162af9072f0741caba886 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Tue, 3 Nov 2020 22:46:50 +0100
Subject: import matplotlib only when necessary in examples, in function of
 args. Tests are without matplotlib, so no need to test if present

---
 src/python/CMakeLists.txt                          | 76 ++++++++++------------
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...arcode_persistence_from_perseus_file_example.py |  2 +-
 ...istence_from_correlation_matrix_file_example.py |  2 +-
 ...ersistence_from_distance_matrix_file_example.py |  2 +-
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...complex_plain_homology_from_off_file_example.py |  2 +-
 9 files changed, 42 insertions(+), 50 deletions(-)

(limited to 'src/python/CMakeLists.txt')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index c09996fe..1f101d87 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -345,29 +345,27 @@ if(PYTHONINTERP_FOUND)
                COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
                -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
-      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
-        # Tangential
-        add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
-                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
-                 --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+      # Tangential
+      add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+               --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 
         add_gudhi_py_test(test_tangential_complex)
 
-        # Witness complex AND Subsampling
-        add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
-                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
-                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
-        add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
-                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
-                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-      endif()
+      # Witness complex
+      add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+      add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
 
       # Subsampling
       add_gudhi_py_test(test_subsampling)
@@ -422,13 +420,11 @@ if(PYTHONINTERP_FOUND)
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
                COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
-      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
-        add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+      add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
                COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
                --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
-      endif()
       add_gudhi_py_test(test_alpha_complex)
     endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
 
@@ -445,30 +441,26 @@ if(PYTHONINTERP_FOUND)
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
              --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
 
-    if(NUMPY_FOUND)
-      add_test(NAME random_cubical_complex_persistence_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
-               10 10 10)
-    endif()
+    add_test(NAME random_cubical_complex_persistence_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
+             10 10 10)
 
     add_gudhi_py_test(test_cubical_complex)
 
     # Rips
-    if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
-      add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
-               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
+    add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
 
-      add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
-               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
-    endif()
+    add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
 
     add_test(NAME rips_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
index 727af4fa..1e0273b3 100755
--- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -3,7 +3,6 @@
 import argparse
 import errno
 import os
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -65,6 +64,7 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
+            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index e1e572df..4e97cfe3 100755
--- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -3,7 +3,6 @@
 import argparse
 import errno
 import os
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -82,6 +81,7 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
+            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index 58cb2bb5..29076c74 100755
--- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -3,7 +3,6 @@
 import argparse
 import errno
 import os
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -79,6 +78,7 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
+            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
index 499171df..ee3290c6 100755
--- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
+++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import argparse
-import matplotlib.pyplot as plot
 import errno
 import os
 import gudhi
@@ -75,6 +74,7 @@ if is_file_perseus(args.file):
     print("betti_numbers()=")
     print(periodic_cubical_complex.betti_numbers())
     if args.no_barcode == False:
+        import matplotlib.pyplot as plot
         gudhi.plot_persistence_barcode(diag)
         plot.show()
 else:
diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
index 1acb187c..ea2eb7e1 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -2,7 +2,6 @@
 
 import sys
 import argparse
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
@@ -84,5 +83,6 @@ invert_diag = [
 ]
 
 if args.no_diagram == False:
+    import matplotlib.pyplot as plot
     gudhi.plot_persistence_diagram(invert_diag, band=args.band)
     plot.show()
diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index 79ccca96..236d085d 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import argparse
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
@@ -60,5 +59,6 @@ print("betti_numbers()=")
 print(simplex_tree.betti_numbers())
 
 if args.no_diagram == False:
+    import matplotlib.pyplot as plot
     gudhi.plot_persistence_diagram(diag, band=args.band)
     plot.show()
diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
index 6f992508..e80233a9 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -3,7 +3,6 @@
 import argparse
 import errno
 import os
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -70,6 +69,7 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
+            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
index 85bade4a..a4b4e9f5 100755
--- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
+++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -3,7 +3,6 @@
 import argparse
 import errno
 import os
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -62,6 +61,7 @@ with open(args.file, "r") as f:
         print(st.betti_numbers())
 
         if args.no_diagram == False:
+            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-- 
cgit v1.2.3


From 4d26e7220bdd9a3f95beacd8a33b0fbda461ebfa Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Tue, 3 Nov 2020 22:49:56 +0100
Subject: Revert "import matplotlib only when necessary in examples, in
 function of args. Tests are without matplotlib, so no need to test if
 present"

This reverts commit ef30f636af892a2e226162af9072f0741caba886.
---
 src/python/CMakeLists.txt                          | 76 ++++++++++++----------
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...arcode_persistence_from_perseus_file_example.py |  2 +-
 ...istence_from_correlation_matrix_file_example.py |  2 +-
 ...ersistence_from_distance_matrix_file_example.py |  2 +-
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...complex_plain_homology_from_off_file_example.py |  2 +-
 9 files changed, 50 insertions(+), 42 deletions(-)

(limited to 'src/python/CMakeLists.txt')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 1f101d87..c09996fe 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -345,27 +345,29 @@ if(PYTHONINTERP_FOUND)
                COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
                -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
-      # Tangential
-      add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
-               --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+        # Tangential
+        add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+                 --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 
         add_gudhi_py_test(test_tangential_complex)
 
-      # Witness complex
-      add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
-               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
-      add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
-               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+        # Witness complex AND Subsampling
+        add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+        add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+      endif()
 
       # Subsampling
       add_gudhi_py_test(test_subsampling)
@@ -420,11 +422,13 @@ if(PYTHONINTERP_FOUND)
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
                COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
-      add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+        add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
                COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
                --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+      endif()
       add_gudhi_py_test(test_alpha_complex)
     endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
 
@@ -441,26 +445,30 @@ if(PYTHONINTERP_FOUND)
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
              --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
 
-    add_test(NAME random_cubical_complex_persistence_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
-             10 10 10)
+    if(NUMPY_FOUND)
+      add_test(NAME random_cubical_complex_persistence_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
+               10 10 10)
+    endif()
 
     add_gudhi_py_test(test_cubical_complex)
 
     # Rips
-    add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
+    if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+      add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
 
-    add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
+      add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
+    endif()
 
     add_test(NAME rips_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
index 1e0273b3..727af4fa 100755
--- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -3,6 +3,7 @@
 import argparse
 import errno
 import os
+import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -64,7 +65,6 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index 4e97cfe3..e1e572df 100755
--- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -3,6 +3,7 @@
 import argparse
 import errno
 import os
+import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -81,7 +82,6 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index 29076c74..58cb2bb5 100755
--- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -3,6 +3,7 @@
 import argparse
 import errno
 import os
+import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -78,7 +79,6 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
index ee3290c6..499171df 100755
--- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
+++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import argparse
+import matplotlib.pyplot as plot
 import errno
 import os
 import gudhi
@@ -74,7 +75,6 @@ if is_file_perseus(args.file):
     print("betti_numbers()=")
     print(periodic_cubical_complex.betti_numbers())
     if args.no_barcode == False:
-        import matplotlib.pyplot as plot
         gudhi.plot_persistence_barcode(diag)
         plot.show()
 else:
diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
index ea2eb7e1..1acb187c 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -2,6 +2,7 @@
 
 import sys
 import argparse
+import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
@@ -83,6 +84,5 @@ invert_diag = [
 ]
 
 if args.no_diagram == False:
-    import matplotlib.pyplot as plot
     gudhi.plot_persistence_diagram(invert_diag, band=args.band)
     plot.show()
diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index 236d085d..79ccca96 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import argparse
+import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
@@ -59,6 +60,5 @@ print("betti_numbers()=")
 print(simplex_tree.betti_numbers())
 
 if args.no_diagram == False:
-    import matplotlib.pyplot as plot
     gudhi.plot_persistence_diagram(diag, band=args.band)
     plot.show()
diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
index e80233a9..6f992508 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -3,6 +3,7 @@
 import argparse
 import errno
 import os
+import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -69,7 +70,6 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
index a4b4e9f5..85bade4a 100755
--- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
+++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -3,6 +3,7 @@
 import argparse
 import errno
 import os
+import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -61,7 +62,6 @@ with open(args.file, "r") as f:
         print(st.betti_numbers())
 
         if args.no_diagram == False:
-            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-- 
cgit v1.2.3


From 92361d9a117a33e0d922417cfbb2e1653f2537df Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Wed, 4 Nov 2020 07:58:01 +0100
Subject: import matplotlib only when necessary in examples, in function of
 args. Tests are without matplotlib, so no need to test if present

---
 src/python/CMakeLists.txt                          | 90 ++++++++++------------
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...arcode_persistence_from_perseus_file_example.py |  2 +-
 ...istence_from_correlation_matrix_file_example.py |  2 +-
 ...ersistence_from_distance_matrix_file_example.py |  2 +-
 ...ex_diagram_persistence_from_off_file_example.py |  2 +-
 ...complex_plain_homology_from_off_file_example.py |  2 +-
 9 files changed, 49 insertions(+), 57 deletions(-)

(limited to 'src/python/CMakeLists.txt')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index c09996fe..56b6876c 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -345,29 +345,27 @@ if(PYTHONINTERP_FOUND)
                COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
                -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
-      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
-        # Tangential
-        add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
-                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
-                 --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
-
-        add_gudhi_py_test(test_tangential_complex)
-
-        # Witness complex AND Subsampling
-        add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
-                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
-                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
-        add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
-                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-                 COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-                 ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
-                 --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-      endif()
+      # Tangential
+      add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+               --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+
+      add_gudhi_py_test(test_tangential_complex)
+
+      # Witness complex
+      add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+      add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
 
       # Subsampling
       add_gudhi_py_test(test_subsampling)
@@ -422,13 +420,11 @@ if(PYTHONINTERP_FOUND)
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
                COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
-      if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
-        add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
-               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
-      endif()
+      add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
       add_gudhi_py_test(test_alpha_complex)
     endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
 
@@ -445,30 +441,26 @@ if(PYTHONINTERP_FOUND)
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
              --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
 
-    if(NUMPY_FOUND)
-      add_test(NAME random_cubical_complex_persistence_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
-               10 10 10)
-    endif()
+    add_test(NAME random_cubical_complex_persistence_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
+             10 10 10)
 
     add_gudhi_py_test(test_cubical_complex)
 
     # Rips
-    if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
-      add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
-               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
+    add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
 
-      add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-               ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
-               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
-    endif()
+    add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
 
     add_test(NAME rips_complex_from_points_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
index 727af4fa..1e0273b3 100755
--- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -3,7 +3,6 @@
 import argparse
 import errno
 import os
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -65,6 +64,7 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
+            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index e1e572df..4e97cfe3 100755
--- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -3,7 +3,6 @@
 import argparse
 import errno
 import os
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -82,6 +81,7 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
+            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index 58cb2bb5..29076c74 100755
--- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -3,7 +3,6 @@
 import argparse
 import errno
 import os
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -79,6 +78,7 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
+            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
index 499171df..ee3290c6 100755
--- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
+++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import argparse
-import matplotlib.pyplot as plot
 import errno
 import os
 import gudhi
@@ -75,6 +74,7 @@ if is_file_perseus(args.file):
     print("betti_numbers()=")
     print(periodic_cubical_complex.betti_numbers())
     if args.no_barcode == False:
+        import matplotlib.pyplot as plot
         gudhi.plot_persistence_barcode(diag)
         plot.show()
 else:
diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
index 1acb187c..ea2eb7e1 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -2,7 +2,6 @@
 
 import sys
 import argparse
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
@@ -84,5 +83,6 @@ invert_diag = [
 ]
 
 if args.no_diagram == False:
+    import matplotlib.pyplot as plot
     gudhi.plot_persistence_diagram(invert_diag, band=args.band)
     plot.show()
diff --git a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index 79ccca96..236d085d 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import argparse
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
@@ -60,5 +59,6 @@ print("betti_numbers()=")
 print(simplex_tree.betti_numbers())
 
 if args.no_diagram == False:
+    import matplotlib.pyplot as plot
     gudhi.plot_persistence_diagram(diag, band=args.band)
     plot.show()
diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
index 6f992508..e80233a9 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -3,7 +3,6 @@
 import argparse
 import errno
 import os
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -70,6 +69,7 @@ with open(args.file, "r") as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
+            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
index 85bade4a..a4b4e9f5 100755
--- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
+++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -3,7 +3,6 @@
 import argparse
 import errno
 import os
-import matplotlib.pyplot as plot
 import gudhi
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
@@ -62,6 +61,7 @@ with open(args.file, "r") as f:
         print(st.betti_numbers())
 
         if args.no_diagram == False:
+            import matplotlib.pyplot as plot
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-- 
cgit v1.2.3


From 366813c651d871c5b95d9bc8e7ea227f8015fc55 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Tue, 8 Dec 2020 16:35:48 +0100
Subject: rollback test_representation and a CGAL condition to launch it

---
 src/python/CMakeLists.txt               |  2 +-
 src/python/test/test_representations.py | 10 +---------
 2 files changed, 2 insertions(+), 10 deletions(-)

(limited to 'src/python/CMakeLists.txt')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 56b6876c..4dca3908 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -504,7 +504,7 @@ if(PYTHONINTERP_FOUND)
     endif()
 
     # Representations
-    if(SKLEARN_FOUND AND MATPLOTLIB_FOUND)
+    if(SKLEARN_FOUND AND MATPLOTLIB_FOUND AND NOT CGAL_VERSION VERSION_LESS 4.11.0)
       add_gudhi_py_test(test_representations)
     endif()
 
diff --git a/src/python/test/test_representations.py b/src/python/test/test_representations.py
index 8ebd7888..43c914f3 100755
--- a/src/python/test/test_representations.py
+++ b/src/python/test/test_representations.py
@@ -41,15 +41,7 @@ def test_multiple():
     assert d1 == pytest.approx(d2)
     assert d3 == pytest.approx(d2, abs=1e-5)  # Because of 0 entries (on the diagonal)
     d1 = pairwise_persistence_diagram_distances(l1, l2, metric="wasserstein", order=2, internal_p=2)
-    mode = ""
-    try:
-        import ot
-        mode = "pot"
-    except ImportError:
-        print("POT is not available, try with hera")
-        mode = "hera"
-    
-    d2 = WassersteinDistance(order=2, internal_p=2, mode=mode, n_jobs=4).fit(l2).transform(l1)
+    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=0.02)
 
-- 
cgit v1.2.3


From dbfe80623c89904ed18fbc8b408858175dbd0474 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Tue, 8 Dec 2020 16:42:52 +0100
Subject: do not launch test_representation when no pot

---
 src/python/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'src/python/CMakeLists.txt')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 4dca3908..2d5f793a 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -504,7 +504,7 @@ if(PYTHONINTERP_FOUND)
     endif()
 
     # Representations
-    if(SKLEARN_FOUND AND MATPLOTLIB_FOUND AND NOT CGAL_VERSION VERSION_LESS 4.11.0)
+    if(SKLEARN_FOUND AND MATPLOTLIB_FOUND AND OT_FOUND AND NOT CGAL_VERSION VERSION_LESS 4.11.0)
       add_gudhi_py_test(test_representations)
     endif()
 
-- 
cgit v1.2.3


From fda0084941ece5d41a258d19ca4eb0b3d87384a4 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Wed, 9 Dec 2020 09:41:13 +0100
Subject: Fix #388

---
 src/cmake/modules/GUDHI_third_party_libraries.cmake |  1 -
 src/python/CMakeLists.txt                           |  1 +
 src/python/gudhi/simplex_tree.pxd                   |  2 ++
 src/python/gudhi/simplex_tree.pyx                   |  3 +++
 src/python/include/Simplex_tree_interface.h         | 10 +++++++++-
 src/python/test/test_simplex_tree.py                | 14 +++++++++-----
 6 files changed, 24 insertions(+), 7 deletions(-)

(limited to 'src/python/CMakeLists.txt')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index e2684aa4..e1566877 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -58,7 +58,6 @@ endif(WITH_GUDHI_USE_TBB)
 set(CGAL_WITH_EIGEN3_VERSION 0.0.0)
 find_package(Eigen3 3.1.0)
 if (EIGEN3_FOUND)
-  add_definitions(-DGUDHI_USE_EIGEN3)
   include( ${EIGEN3_USE_FILE} )
   set(CGAL_WITH_EIGEN3_VERSION ${CGAL_VERSION})
 endif (EIGEN3_FOUND)
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 2d5f793a..45c89609 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -133,6 +133,7 @@ if(PYTHONINTERP_FOUND)
       add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}")
       # No problem, even if no CGAL found
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
+      set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_EIGEN3', ")
     endif (EIGEN3_FOUND)
 
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'off_reader', ")
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 3c4cbed3..283830ff 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -74,6 +74,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension) nogil
         Simplex_tree_skeleton_iterator get_skeleton_iterator_end(int dimension) nogil
         pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] get_boundary_iterators(vector[int] simplex) nogil except +
+    
+    cdef int _GUDHI_USE_EIGEN3
 
 cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
     cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index 7d6ab89a..eb44c0fc 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -17,6 +17,9 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
 
+# For unitary tests purpose
+__GUDHI_USE_EIGEN3 = _GUDHI_USE_EIGEN3
+
 # SimplexTree python interface
 cdef class SimplexTree:
     """The simplex tree is an efficient and flexible data structure for
diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h
index 2bd704b4..50592e25 100644
--- a/src/python/include/Simplex_tree_interface.h
+++ b/src/python/include/Simplex_tree_interface.h
@@ -27,6 +27,12 @@
 
 namespace Gudhi {
 
+#ifdef GUDHI_USE_EIGEN3
+const int _GUDHI_USE_EIGEN3 = 1;
+#else
+const int _GUDHI_USE_EIGEN3 = 0;
+#endif
+
 template<typename SimplexTreeOptions = Simplex_tree_options_full_featured>
 class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
  public:
@@ -191,7 +197,9 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     }
     return collapsed_stree_ptr;
 #else
-    return this;
+    // If no Eigen3, return a copy, as it will be deleted in pyx
+    Simplex_tree_interface* collapsed_stree_ptr = new Simplex_tree_interface(*this);
+    return collapsed_stree_ptr;
 #endif
   }
 
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index 3b23fa0b..15b472ee 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -8,7 +8,7 @@
       - YYYY/MM Author: Description of the modification
 """
 
-from gudhi import SimplexTree
+from gudhi import SimplexTree, simplex_tree
 import pytest
 
 __author__ = "Vincent Rouvreau"
@@ -353,11 +353,15 @@ def test_collapse_edges():
 
     assert st.num_simplices() == 10
 
+    # If no Eigen3, collapse_edges just return a copy, no action. Maybe it would require some user warning
     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.
+    if simplex_tree.__GUDHI_USE_EIGEN3:
+        assert st.num_simplices() == 9
+        assert st.find([1, 3]) == False
+        for simplex in st.get_skeleton(0):
+            assert simplex[1] == 1.
+    else:
+        assert st.num_simplices() == 10
 
 def test_reset_filtration():
     st = SimplexTree()
-- 
cgit v1.2.3


From 957da77f9484972ce34d0415502887f92080878e Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Fri, 11 Dec 2020 09:38:12 +0100
Subject: code review: GUDHI_USE_EIGEN3 generated by CMake in __init__.py as
 suggested and roll back the other solution

---
 src/python/CMakeLists.txt                   | 2 ++
 src/python/gudhi/__init__.py.in             | 4 ++++
 src/python/gudhi/simplex_tree.pxd           | 2 --
 src/python/gudhi/simplex_tree.pyx           | 3 ---
 src/python/include/Simplex_tree_interface.h | 6 ------
 src/python/test/test_simplex_tree.py        | 4 ++--
 6 files changed, 8 insertions(+), 13 deletions(-)

(limited to 'src/python/CMakeLists.txt')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 45c89609..5a245aac 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -129,11 +129,13 @@ if(PYTHONINTERP_FOUND)
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
     endif()
 
+    set(GUDHI_USE_EIGEN3 "False")
     if (EIGEN3_FOUND)
       add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}")
       # No problem, even if no CGAL found
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_EIGEN3', ")
+      set(GUDHI_USE_EIGEN3 "True")
     endif (EIGEN3_FOUND)
 
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'off_reader', ")
diff --git a/src/python/gudhi/__init__.py.in b/src/python/gudhi/__init__.py.in
index 79e12fbc..3043201a 100644
--- a/src/python/gudhi/__init__.py.in
+++ b/src/python/gudhi/__init__.py.in
@@ -23,6 +23,10 @@ __all__ = [@GUDHI_PYTHON_MODULES@ @GUDHI_PYTHON_MODULES_EXTRA@]
 __available_modules = ''
 __missing_modules = ''
 
+# For unitary tests purpose
+# could use "if 'collapse_edges' in gudhi.__all__" when collapse edges will have a python module
+__GUDHI_USE_EIGEN3 = @GUDHI_USE_EIGEN3@
+
 # Try to import * from gudhi.__module_name for default modules.
 # Extra modules require an explicit import by the user (mostly because of
 # unusual dependencies, but also to avoid cluttering namespace gudhi and
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 283830ff..3c4cbed3 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -74,8 +74,6 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension) nogil
         Simplex_tree_skeleton_iterator get_skeleton_iterator_end(int dimension) nogil
         pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] get_boundary_iterators(vector[int] simplex) nogil except +
-    
-    cdef int _GUDHI_USE_EIGEN3
 
 cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
     cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index eb44c0fc..7d6ab89a 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -17,9 +17,6 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
 
-# For unitary tests purpose
-__GUDHI_USE_EIGEN3 = _GUDHI_USE_EIGEN3
-
 # SimplexTree python interface
 cdef class SimplexTree:
     """The simplex tree is an efficient and flexible data structure for
diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h
index 50592e25..82444609 100644
--- a/src/python/include/Simplex_tree_interface.h
+++ b/src/python/include/Simplex_tree_interface.h
@@ -27,12 +27,6 @@
 
 namespace Gudhi {
 
-#ifdef GUDHI_USE_EIGEN3
-const int _GUDHI_USE_EIGEN3 = 1;
-#else
-const int _GUDHI_USE_EIGEN3 = 0;
-#endif
-
 template<typename SimplexTreeOptions = Simplex_tree_options_full_featured>
 class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
  public:
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index 15b472ee..0c072baa 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -8,7 +8,7 @@
       - YYYY/MM Author: Description of the modification
 """
 
-from gudhi import SimplexTree, simplex_tree
+from gudhi import SimplexTree, __GUDHI_USE_EIGEN3
 import pytest
 
 __author__ = "Vincent Rouvreau"
@@ -355,7 +355,7 @@ def test_collapse_edges():
 
     # If no Eigen3, collapse_edges just return a copy, no action. Maybe it would require some user warning
     st.collapse_edges()
-    if simplex_tree.__GUDHI_USE_EIGEN3:
+    if __GUDHI_USE_EIGEN3:
         assert st.num_simplices() == 9
         assert st.find([1, 3]) == False
         for simplex in st.get_skeleton(0):
-- 
cgit v1.2.3


From ba3be8d118a9720677b7776ae9a22c10cfcc0cef Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Fri, 11 Dec 2020 17:49:00 +0100
Subject: code review: else branch

---
 src/python/CMakeLists.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'src/python/CMakeLists.txt')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 5a245aac..5c1402a6 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -129,13 +129,14 @@ if(PYTHONINTERP_FOUND)
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ")
     endif()
 
-    set(GUDHI_USE_EIGEN3 "False")
     if (EIGEN3_FOUND)
       add_gudhi_debug_info("Eigen3 version ${EIGEN3_VERSION}")
       # No problem, even if no CGAL found
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_EIGEN3', ")
       set(GUDHI_USE_EIGEN3 "True")
+    else (EIGEN3_FOUND)
+      set(GUDHI_USE_EIGEN3 "False")
     endif (EIGEN3_FOUND)
 
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'off_reader', ")
-- 
cgit v1.2.3