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-rw-r--r--src/python/CMakeLists.txt4
-rw-r--r--src/python/doc/installation.rst16
-rwxr-xr-xsrc/python/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py5
-rw-r--r--src/python/gudhi/clustering/tomato.py4
-rw-r--r--src/python/gudhi/point_cloud/knn.py2
-rw-r--r--src/python/gudhi/simplex_tree.pxd2
-rw-r--r--src/python/gudhi/simplex_tree.pyx2
-rw-r--r--src/python/setup.py.in9
-rwxr-xr-xsrc/python/test/test_reader_utils.py2
-rwxr-xr-xsrc/python/test/test_rips_complex.py21
-rwxr-xr-xsrc/python/test/test_tomato.py2
11 files changed, 41 insertions, 28 deletions
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 73303a24..bc9a3b7b 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -274,8 +274,6 @@ if(PYTHONINTERP_FOUND)
add_custom_target(python ALL DEPENDS gudhi.so
COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
- install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
-
set(GUDHI_PYTHON_PATH_ENV "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH}")
# Documentation generation is available through sphinx - requires all modules
# Make it first as sphinx test is by far the longest test which is nice when testing in parallel
@@ -459,7 +457,7 @@ if(PYTHONINTERP_FOUND)
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${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)
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -s , -e 12.0 -d 3)
add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst
index 66efe45a..9c16b04e 100644
--- a/src/python/doc/installation.rst
+++ b/src/python/doc/installation.rst
@@ -41,7 +41,7 @@ there.
The library uses c++14 and requires `Boost <https://www.boost.org/>`_ :math:`\geq` 1.56.0,
`CMake <https://www.cmake.org/>`_ :math:`\geq` 3.5 to generate makefiles,
-`NumPy <http://numpy.org>`_, `Cython <https://www.cython.org/>`_ and
+`NumPy <http://numpy.org>`_ :math:`\geq` 1.15.0, `Cython <https://www.cython.org/>`_ and
`pybind11 <https://github.com/pybind/pybind11>`_ to compile
the GUDHI Python module.
It is a multi-platform library and compiles on Linux, Mac OSX and Visual
@@ -99,20 +99,14 @@ Or install it definitely in your Python packages folder:
.. code-block:: bash
cd /path-to-gudhi/build/python
- # May require sudo or administrator privileges
- make install
+ python setup.py install # add --user to the command if you do not have the permission
+ # Or 'pip install .'
.. note::
- :code:`make install` is only a
- `CMake custom targets <https://cmake.org/cmake/help/latest/command/add_custom_target.html>`_
- to shortcut :code:`python setup.py install` command.
It does not take into account :code:`CMAKE_INSTALL_PREFIX`.
- But one can use :code:`python setup.py install ...` specific options in the python directory:
-
-.. code-block:: bash
-
- python setup.py install --prefix /home/gudhi # Install in /home/gudhi directory
+ But one can use
+ `alternate location installation <https://docs.python.org/3/install/#alternate-installation>`_.
Test suites
===========
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..8a9cc857 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
@@ -21,11 +21,12 @@ parser = argparse.ArgumentParser(
description="RipsComplex creation from " "a distance matrix read in a csv file.",
epilog="Example: "
"example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py "
- "-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3"
+ "-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -s , -e 12.0 -d 3"
"- Constructs a Rips complex with the "
"distance matrix from the given csv file.",
)
parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-s", "--separator", type=str, required=True)
parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
parser.add_argument("-d", "--max_dimension", type=int, default=1)
parser.add_argument("-b", "--band", type=float, default=0.0)
@@ -44,7 +45,7 @@ print("RipsComplex creation from distance matrix read in a csv file")
message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
print(message)
-distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file)
+distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file, separator=args.separator)
rips_complex = gudhi.RipsComplex(
distance_matrix=distance_matrix, max_edge_length=args.max_edge_length
)
diff --git a/src/python/gudhi/clustering/tomato.py b/src/python/gudhi/clustering/tomato.py
index fbba3cc8..d0e9995c 100644
--- a/src/python/gudhi/clustering/tomato.py
+++ b/src/python/gudhi/clustering/tomato.py
@@ -271,7 +271,7 @@ class Tomato:
l = self.max_weight_per_cc_.min()
r = self.max_weight_per_cc_.max()
if self.diagram_.size > 0:
- plt.plot(self.diagram_[:, 0], self.diagram_[:, 1], "ro")
+ plt.plot(self.diagram_[:, 0], self.diagram_[:, 1], "o", color="red")
l = min(l, self.diagram_[:, 1].min())
r = max(r, self.diagram_[:, 0].max())
if l == r:
@@ -283,7 +283,7 @@ class Tomato:
l, r = -1.0, 1.0
plt.plot([l, r], [l, r])
plt.plot(
- self.max_weight_per_cc_, numpy.full(self.max_weight_per_cc_.shape, 1.1 * l - 0.1 * r), "ro", color="green"
+ self.max_weight_per_cc_, numpy.full(self.max_weight_per_cc_.shape, 1.1 * l - 0.1 * r), "o", color="green"
)
plt.show()
diff --git a/src/python/gudhi/point_cloud/knn.py b/src/python/gudhi/point_cloud/knn.py
index 994be3b6..829bf1bf 100644
--- a/src/python/gudhi/point_cloud/knn.py
+++ b/src/python/gudhi/point_cloud/knn.py
@@ -111,7 +111,7 @@ class KNearestNeighbors:
nargs = {
k: v for k, v in self.params.items() if k in {"p", "n_jobs", "metric_params", "algorithm", "leaf_size"}
}
- self.nn = NearestNeighbors(self.k, metric=self.metric, **nargs)
+ self.nn = NearestNeighbors(n_neighbors=self.k, metric=self.metric, **nargs)
self.nn.fit(X)
if self.params["implementation"] == "hnsw":
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 000323af..3b8ea4f9 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -44,7 +44,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>":
- Simplex_tree() nogil
+ Simplex_tree_interface_full_featured() nogil
double simplex_filtration(vector[int] simplex) nogil
void assign_simplex_filtration(vector[int] simplex, double filtration) nogil
void initialize_filtration() nogil
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index d7991417..be08a3a1 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -11,7 +11,7 @@ from cython.operator import dereference, preincrement
from libc.stdint cimport intptr_t
import numpy
from numpy import array as np_array
-cimport simplex_tree
+cimport gudhi.simplex_tree
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 98d058fc..759ec8d8 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -41,10 +41,9 @@ for module in cython_modules:
libraries=libraries,
library_dirs=library_dirs,
include_dirs=include_dirs,
- runtime_library_dirs=runtime_library_dirs,
- cython_directives = {'language_level': str(sys.version_info[0])},))
+ runtime_library_dirs=runtime_library_dirs,))
-ext_modules = cythonize(ext_modules)
+ext_modules = cythonize(ext_modules, compiler_directives={'language_level': str(sys.version_info[0])})
for module in pybind11_modules:
my_include_dirs = include_dirs + [pybind11.get_include(False), pybind11.get_include(True)]
@@ -86,7 +85,7 @@ setup(
long_description_content_type='text/x-rst',
long_description=long_description,
ext_modules = ext_modules,
- install_requires = ['numpy >= 1.9',],
- setup_requires = ['cython','numpy >= 1.9','pybind11',],
+ install_requires = ['numpy >= 1.15.0',],
+ setup_requires = ['cython','numpy >= 1.15.0','pybind11',],
package_data={"": ["*.dll"], },
)
diff --git a/src/python/test/test_reader_utils.py b/src/python/test/test_reader_utils.py
index 90da6651..e96e0569 100755
--- a/src/python/test/test_reader_utils.py
+++ b/src/python/test/test_reader_utils.py
@@ -30,7 +30,7 @@ def test_full_square_distance_matrix_csv_file():
test_file.write("0;1;2;3;\n1;0;4;5;\n2;4;0;6;\n3;5;6;0;")
test_file.close()
matrix = gudhi.read_lower_triangular_matrix_from_csv_file(
- csv_file="full_square_distance_matrix.csv"
+ csv_file="full_square_distance_matrix.csv", separator=";"
)
assert matrix == [[], [1.0], [2.0, 4.0], [3.0, 5.0, 6.0]]
diff --git a/src/python/test/test_rips_complex.py b/src/python/test/test_rips_complex.py
index b86e7498..a2f43a1b 100755
--- a/src/python/test/test_rips_complex.py
+++ b/src/python/test/test_rips_complex.py
@@ -133,3 +133,24 @@ def test_filtered_rips_from_distance_matrix():
assert simplex_tree.num_simplices() == 8
assert simplex_tree.num_vertices() == 4
+
+
+def test_sparse_with_multiplicity():
+ points = [
+ [3, 4],
+ [0.1, 2],
+ [0.1, 2],
+ [0.1, 2],
+ [0.1, 2],
+ [0.1, 2],
+ [0.1, 2],
+ [0.1, 2],
+ [0.1, 2],
+ [0.1, 2],
+ [0.1, 2],
+ [3, 4.1],
+ ]
+ rips = RipsComplex(points=points, sparse=0.01)
+ simplex_tree = rips.create_simplex_tree(max_dimension=2)
+ assert simplex_tree.num_simplices() == 7
+ diag = simplex_tree.persistence()
diff --git a/src/python/test/test_tomato.py b/src/python/test/test_tomato.py
index ecab03c4..c571f799 100755
--- a/src/python/test/test_tomato.py
+++ b/src/python/test/test_tomato.py
@@ -37,7 +37,7 @@ def test_tomato_1():
t = Tomato(metric="euclidean", graph_type="radius", r=4.7, k=4)
t.fit(a)
assert t.max_weight_per_cc_.size == 2
- assert np.array_equal(t.neighbors_, [[0, 1, 2], [0, 1, 2], [0, 1, 2], [3, 4, 5, 6], [3, 4, 5], [3, 4, 5], [3, 6]])
+ assert t.neighbors_ == [[0, 1, 2], [0, 1, 2], [0, 1, 2], [3, 4, 5, 6], [3, 4, 5], [3, 4, 5], [3, 6]]
t.plot_diagram()
t = Tomato(graph_type="radius", r=4.7, k=4, symmetrize_graph=True)
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-31 10:16:52 +0000