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-rw-r--r--.github/for_maintainers/new_gudhi_version_creation.md4
-rw-r--r--.github/workflows/pip-packaging-linux.yml34
-rw-r--r--src/Persistent_cohomology/example/CMakeLists.txt2
-rw-r--r--src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h2
-rw-r--r--src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h18
-rw-r--r--src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp35
-rw-r--r--src/Spatial_searching/include/gudhi/Kd_tree_search.h2
-rw-r--r--src/common/doc/installation.h8
-rw-r--r--src/python/doc/installation.rst9
-rw-r--r--src/python/gudhi/cubical_complex.pyx6
-rw-r--r--src/python/gudhi/periodic_cubical_complex.pyx6
-rw-r--r--src/python/gudhi/simplex_tree.pxd2
-rw-r--r--src/python/gudhi/simplex_tree.pyx6
-rw-r--r--src/python/setup.py.in2
14 files changed, 90 insertions, 46 deletions
diff --git a/.github/for_maintainers/new_gudhi_version_creation.md b/.github/for_maintainers/new_gudhi_version_creation.md
index d6c4cdd3..3e5295c5 100644
--- a/.github/for_maintainers/new_gudhi_version_creation.md
+++ b/.github/for_maintainers/new_gudhi_version_creation.md
@@ -128,5 +128,5 @@ docker image on docker hub.
## Mail sending
Send version mail to the following lists :
-* gudhi-devel@lists.gforge.inria.fr
-* gudhi-users@lists.gforge.inria.fr (not for release candidate)
+* gudhi-devel@inria.fr
+* gudhi-users@inria.fr (not for release candidate)
diff --git a/.github/workflows/pip-packaging-linux.yml b/.github/workflows/pip-packaging-linux.yml
index 0fa2c083..6ce0ba89 100644
--- a/.github/workflows/pip-packaging-linux.yml
+++ b/.github/workflows/pip-packaging-linux.yml
@@ -14,18 +14,6 @@ jobs:
- uses: actions/checkout@v1
with:
submodules: true
- - name: Build wheel for Python 3.5
- run: |
- mkdir build_35
- cd build_35
- cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON35/bin/python ..
- cd src/python
- $PYTHON35/bin/python setup.py bdist_wheel
- auditwheel repair dist/*.whl
- - name: Install and test wheel for Python 3.5
- run: |
- $PYTHON35/bin/python -m pip install --user pytest build_35/src/python/dist/*.whl
- $PYTHON35/bin/python -m pytest src/python/test/test_alpha_complex.py
- name: Build wheel for Python 3.6
run: |
mkdir build_36
@@ -74,13 +62,25 @@ jobs:
run: |
$PYTHON39/bin/python -m pip install --user pytest build_39/src/python/dist/*.whl
$PYTHON39/bin/python -m pytest src/python/test/test_alpha_complex.py
+ - name: Build wheel for Python 3.10
+ run: |
+ mkdir build_310
+ cd build_310
+ cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON310/bin/python ..
+ cd src/python
+ $PYTHON310/bin/python setup.py bdist_wheel
+ auditwheel repair dist/*.whl
+ - name: Install and test wheel for Python 3.10
+ run: |
+ $PYTHON310/bin/python -m pip install --user pytest build_310/src/python/dist/*.whl
+ $PYTHON310/bin/python -m pytest src/python/test/test_alpha_complex.py
- name: Publish on PyPi
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
run: |
- $PYTHON39/bin/python -m twine upload build_35/src/python/wheelhouse/*
- $PYTHON39/bin/python -m twine upload build_36/src/python/wheelhouse/*
- $PYTHON39/bin/python -m twine upload build_37/src/python/wheelhouse/*
- $PYTHON39/bin/python -m twine upload build_38/src/python/wheelhouse/*
- $PYTHON39/bin/python -m twine upload build_39/src/python/wheelhouse/*
+ $PYTHON36/bin/python -m twine upload build_36/src/python/wheelhouse/*
+ $PYTHON36/bin/python -m twine upload build_37/src/python/wheelhouse/*
+ $PYTHON36/bin/python -m twine upload build_38/src/python/wheelhouse/*
+ $PYTHON36/bin/python -m twine upload build_39/src/python/wheelhouse/*
+ $PYTHON36/bin/python -m twine upload build_310/src/python/wheelhouse/*
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index c68c6524..3e7e9369 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -11,7 +11,7 @@ if (TBB_FOUND)
target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES})
endif()
add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $<TARGET_FILE:persistence_from_simple_simplex_tree>
- "1" "0")
+ "2" "0")
if(TARGET Boost::program_options)
add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp)
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index d34ee07d..d428e497 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -100,7 +100,7 @@ class Persistent_cohomology {
ds_rank_(num_simplices_), // union-find
ds_parent_(num_simplices_), // union-find
ds_repr_(num_simplices_, NULL), // union-find -> annotation vectors
- dsets_(&ds_rank_[0], &ds_parent_[0]), // union-find
+ dsets_(ds_rank_.data(), ds_parent_.data()), // union-find
cam_(), // collection of annotation vectors
zero_cocycles_(), // union-find -> Simplex_key of creator for 0-homology
transverse_idx_(), // key -> row
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
index 0673625c..8ec89e41 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
@@ -13,6 +13,7 @@
#include <utility>
#include <vector>
+#include <stdexcept>
namespace Gudhi {
@@ -34,14 +35,29 @@ class Field_Zp {
void init(int charac) {
assert(charac > 0); // division by zero + non negative values
+
Prime = charac;
+
+ // Check that the provided prime is less than the maximum allowed as int, calculation below, and 'plus_times_equal' function : 46337 ; i.e (max_prime-1)*max_prime <= INT_MAX
+ if(Prime > 46337)
+ throw std::invalid_argument("Maximum homology_coeff_field allowed value is 46337");
+
+ // Check for primality
+ if (Prime <= 1)
+ throw std::invalid_argument("homology_coeff_field must be a prime number");
+
inverse_.clear();
inverse_.reserve(charac);
inverse_.push_back(0);
for (int i = 1; i < Prime; ++i) {
int inv = 1;
- while (((inv * i) % Prime) != 1)
+ int mult = inv * i;
+ while ( (mult % Prime) != 1) {
++inv;
+ if(mult == Prime)
+ throw std::invalid_argument("homology_coeff_field must be a prime number");
+ mult = inv * i;
+ }
inverse_.push_back(inv);
}
}
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
index fe3f8517..041cb0fd 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
@@ -146,9 +146,14 @@ void test_rips_persistence_in_dimension(int dimension) {
std::clog << "str_rips_persistence=" << str_rips_persistence << std::endl;
}
+BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_0 )
+{
+ BOOST_CHECK_THROW(test_rips_persistence_in_dimension(0), std::invalid_argument);
+}
+
BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_1 )
{
- test_rips_persistence_in_dimension(1);
+ BOOST_CHECK_THROW(test_rips_persistence_in_dimension(1), std::invalid_argument);
}
BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_2 )
@@ -161,15 +166,35 @@ BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_3 )
test_rips_persistence_in_dimension(3);
}
+BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_4 )
+{
+ BOOST_CHECK_THROW(test_rips_persistence_in_dimension(4), std::invalid_argument);
+}
+
BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_5 )
{
test_rips_persistence_in_dimension(5);
}
-// TODO(VR): not working from 6
-// std::string str_rips_persistence = test_rips_persistence(6, 0);
-// TODO(VR): division by zero
-// std::string str_rips_persistence = test_rips_persistence(0, 0);
+BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_6 )
+{
+ BOOST_CHECK_THROW(test_rips_persistence_in_dimension(6), std::invalid_argument);
+}
+
+BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_11 )
+{
+ test_rips_persistence_in_dimension(11);
+}
+
+BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_13 )
+{
+ test_rips_persistence_in_dimension(13);
+}
+
+BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_46349 )
+{
+ BOOST_CHECK_THROW(test_rips_persistence_in_dimension(46349), std::invalid_argument);
+}
/** SimplexTree minimal options to test the limits.
*
diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
index a50a8537..6fb611f2 100644
--- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h
+++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h
@@ -139,7 +139,7 @@ class Kd_tree_search {
}
template <typename Coord_iterator>
- bool contains_point_given_as_coordinates(Coord_iterator pi, Coord_iterator CGAL_UNUSED) const {
+ bool contains_point_given_as_coordinates(Coord_iterator pi, Coord_iterator) const {
FT distance = 0;
auto ccci = traits.construct_cartesian_const_iterator_d_object();
auto ci = ccci(c);
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index 610aa17e..5d40a48e 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -243,10 +243,12 @@ make \endverbatim
* Witness_complex/example_nearest_landmark_table.cpp</a>
*
* \section Contributions Bug reports and contributions
- * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to:
- * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+ * Please help us improving the quality of the GUDHI library.
+ * You may <a href="https://github.com/GUDHI/gudhi-devel/issues">report bugs</a> or
+ * <a href="https://gudhi.inria.fr/contact/">contact us</a> for any suggestions.
*
- * GUDHI is open to external contributions. If you want to join our development team, please contact us.
+ * GUDHI is open to external contributions. If you want to join our development team, please take some time to read our
+ * <a href="https://github.com/GUDHI/gudhi-devel/blob/master/.github/CONTRIBUTING.md">contributing guide</a>.
*
*/
diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst
index 451ae020..cb7700ce 100644
--- a/src/python/doc/installation.rst
+++ b/src/python/doc/installation.rst
@@ -398,8 +398,9 @@ TensorFlow
Bug reports and contributions
*****************************
-Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to:
+Please help us improving the quality of the GUDHI library.
+You may `report bugs <https://github.com/GUDHI/gudhi-devel/issues>`_ or
+`contact us <https://gudhi.inria.fr/contact/>`_ for any suggestions.
- Contact: gudhi-users@lists.gforge.inria.fr
-
-GUDHI is open to external contributions. If you want to join our development team, please contact us.
+GUDHI is open to external contributions. If you want to join our development team, please take some time to read our
+`contributing guide <https://github.com/GUDHI/gudhi-devel/blob/master/.github/CONTRIBUTING.md>`_.
diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 28fbe3af..97c69a2d 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -35,7 +35,7 @@ cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
cdef cppclass Cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Cubical_complex_interface<>>":
Cubical_complex_persistence_interface(Bitmap_cubical_complex_base_interface * st, bool persistence_dim_max) nogil
- void compute_persistence(int homology_coeff_field, double min_persistence) nogil
+ void compute_persistence(int homology_coeff_field, double min_persistence) nogil except+
vector[pair[int, pair[double, double]]] get_persistence() nogil
vector[vector[int]] cofaces_of_cubical_persistence_pairs() nogil
vector[int] betti_numbers() nogil
@@ -147,7 +147,7 @@ cdef class CubicalComplex:
:func:`persistence` returns.
:param homology_coeff_field: The homology coefficient field. Must be a
- prime number
+ prime number. Default value is 11. Max is 46337.
:type homology_coeff_field: int.
:param min_persistence: The minimum persistence value to take into
account (strictly greater than min_persistence). Default value is
@@ -169,7 +169,7 @@ cdef class CubicalComplex:
"""This function computes and returns the persistence of the complex.
:param homology_coeff_field: The homology coefficient field. Must be a
- prime number
+ prime number. Default value is 11. Max is 46337.
:type homology_coeff_field: int.
:param min_persistence: The minimum persistence value to take into
account (strictly greater than min_persistence). Default value is
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index d353d2af..ef1d3080 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -32,7 +32,7 @@ cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
cdef cppclass Periodic_cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Cubical_complex_interface<Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>>>":
Periodic_cubical_complex_persistence_interface(Periodic_cubical_complex_base_interface * st, bool persistence_dim_max) nogil
- void compute_persistence(int homology_coeff_field, double min_persistence) nogil
+ void compute_persistence(int homology_coeff_field, double min_persistence) nogil except +
vector[pair[int, pair[double, double]]] get_persistence() nogil
vector[vector[int]] cofaces_of_cubical_persistence_pairs() nogil
vector[int] betti_numbers() nogil
@@ -148,7 +148,7 @@ cdef class PeriodicCubicalComplex:
:func:`persistence` returns.
:param homology_coeff_field: The homology coefficient field. Must be a
- prime number
+ prime number. Default value is 11. Max is 46337.
:type homology_coeff_field: int.
:param min_persistence: The minimum persistence value to take into
account (strictly greater than min_persistence). Default value is
@@ -170,7 +170,7 @@ cdef class PeriodicCubicalComplex:
"""This function computes and returns the persistence of the complex.
:param homology_coeff_field: The homology coefficient field. Must be a
- prime number
+ prime number. Default value is 11. Max is 46337.
:type homology_coeff_field: int.
:param min_persistence: The minimum persistence value to take into
account (strictly greater than min_persistence). Default value is
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 3b8ea4f9..006a24ed 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -78,7 +78,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
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>>":
Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max) nogil
- void compute_persistence(int homology_coeff_field, double min_persistence) nogil
+ void compute_persistence(int homology_coeff_field, double min_persistence) nogil except +
vector[pair[int, pair[double, double]]] get_persistence() nogil
vector[int] betti_numbers() nogil
vector[int] persistent_betti_numbers(double from_value, double to_value) nogil
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index be08a3a1..9c51cb46 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -412,7 +412,7 @@ cdef class SimplexTree:
"""This function retrieves good values for extended persistence, and separate the diagrams into the Ordinary,
Relative, Extended+ and Extended- subdiagrams.
- :param homology_coeff_field: The homology coefficient field. Must be a prime number. Default value is 11.
+ :param homology_coeff_field: The homology coefficient field. Must be a prime number. Default value is 11. Max is 46337.
:type homology_coeff_field: int
:param min_persistence: The minimum persistence value (i.e., the absolute value of the difference between the
persistence diagram point coordinates) to take into account (strictly greater than min_persistence).
@@ -449,7 +449,7 @@ cdef class SimplexTree:
"""This function computes and returns the persistence of the simplicial complex.
:param homology_coeff_field: The homology coefficient field. Must be a
- prime number. Default value is 11.
+ prime number. Default value is 11. Max is 46337.
:type homology_coeff_field: int
:param min_persistence: The minimum persistence value to take into
account (strictly greater than min_persistence). Default value is
@@ -472,7 +472,7 @@ cdef class SimplexTree:
when you do not want the list :func:`persistence` returns.
:param homology_coeff_field: The homology coefficient field. Must be a
- prime number. Default value is 11.
+ prime number. Default value is 11. Max is 46337.
:type homology_coeff_field: int
:param min_persistence: The minimum persistence value to take into
account (strictly greater than min_persistence). Default value is
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 759ec8d8..c400b601 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -71,7 +71,7 @@ setup(
name = 'gudhi',
packages=find_packages(), # find_namespace_packages(include=["gudhi*"])
author='GUDHI Editorial Board',
- author_email='gudhi-contact@lists.gforge.inria.fr',
+ author_email='gudhi-contact@inria.fr',
version='@GUDHI_VERSION@',
url='https://gudhi.inria.fr/',
project_urls={
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-09 02:06:14 +0000