From bcc49c54943e20b117a3a83579d94f6c1b0efd04 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Sat, 4 Jan 2020 12:50:14 +0100 Subject: Link the doc for subsampling & point file readers, some reorg --- src/python/doc/diagram_readers_ref.rst | 11 ++++++++++ src/python/doc/index.rst | 40 ++++++++++++++++------------------ src/python/doc/point_cloud.rst | 22 +++++++++++++++++++ src/python/doc/point_cloud_sum.inc | 15 +++++++++++++ src/python/doc/reader_utils_ref.rst | 15 ------------- src/python/gudhi/off_reader.pyx | 2 +- src/python/gudhi/reader_utils.pyx | 6 ++--- src/python/gudhi/subsampling.pyx | 12 +++++----- 8 files changed, 77 insertions(+), 46 deletions(-) create mode 100644 src/python/doc/diagram_readers_ref.rst create mode 100644 src/python/doc/point_cloud.rst create mode 100644 src/python/doc/point_cloud_sum.inc delete mode 100644 src/python/doc/reader_utils_ref.rst diff --git a/src/python/doc/diagram_readers_ref.rst b/src/python/doc/diagram_readers_ref.rst new file mode 100644 index 00000000..c79daf9c --- /dev/null +++ b/src/python/doc/diagram_readers_ref.rst @@ -0,0 +1,11 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + +================================ +Diagram readers reference manual +================================ + +.. autofunction:: gudhi.read_persistence_intervals_grouped_by_dimension + +.. autofunction:: gudhi.read_persistence_intervals_in_dimension diff --git a/src/python/doc/index.rst b/src/python/doc/index.rst index c36a578f..9513deb0 100644 --- a/src/python/doc/index.rst +++ b/src/python/doc/index.rst @@ -6,8 +6,8 @@ GUDHI Python modules documentation :alt: Gudhi banner :figclass: align-center -Complexes -********* +Data structures for cell complexes +********************************** Cubical complexes ================= @@ -17,18 +17,26 @@ Cubical complexes Simplicial complexes ==================== +Simplex tree +------------ + +.. include:: simplex_tree_sum.inc + +Filtrations and reconstructions +******************************* + Alpha complex -------------- +============= .. include:: alpha_complex_sum.inc Rips complex ------------- +============ .. include:: rips_complex_sum.inc Witness complex ---------------- +=============== .. include:: witness_complex_sum.inc @@ -37,16 +45,10 @@ Cover complexes .. include:: nerve_gic_complex_sum.inc -Data structures and basic operations -************************************ - -Data structures -=============== - -Simplex tree ------------- +Tangential complex +================== -.. include:: simplex_tree_sum.inc +.. include:: tangential_complex_sum.inc Topological descriptors computation *********************************** @@ -56,14 +58,10 @@ Persistence cohomology .. include:: persistent_cohomology_sum.inc -Manifold reconstruction -*********************** - -Tangential complex -================== - -.. include:: tangential_complex_sum.inc +Point cloud utilities +********************* +.. include:: point_cloud_sum.inc Topological descriptors tools ***************************** diff --git a/src/python/doc/point_cloud.rst b/src/python/doc/point_cloud.rst new file mode 100644 index 00000000..6a74d253 --- /dev/null +++ b/src/python/doc/point_cloud.rst @@ -0,0 +1,22 @@ +:orphan: + +.. To get rid of WARNING: document isn't included in any toctree + +============================ +Point cloud utilities manual +============================ + +File Readers +------------ + +.. autofunction:: gudhi.read_off + +.. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file + +Subsampling +----------- + +.. automodule:: gudhi.subsampling + :members: + :special-members: + :show-inheritance: diff --git a/src/python/doc/point_cloud_sum.inc b/src/python/doc/point_cloud_sum.inc new file mode 100644 index 00000000..cefcf1c8 --- /dev/null +++ b/src/python/doc/point_cloud_sum.inc @@ -0,0 +1,15 @@ +.. table:: + :widths: 30 50 20 + + +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+ + | :math:`(x_1, x_2, \ldots, x_d)` | Utilities to process point clouds: read from file, subsample, etc. | :Author: Vincent Rouvreau | + | :math:`(y_1, y_2, \ldots, y_d)` | | | + | | | :Introduced in: GUDHI 2.0.0 | + | | | | + | | | :Copyright: MIT (`GPL v3 `_) | + | | Parts of this package require CGAL. | | + | | | :Requires: `Eigen `__ :math:`\geq` 3.1.0 and `CGAL `__ :math:`\geq` 4.11.0 | + | | | | + +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+ + | * :doc:`point_cloud` | + +----------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/python/doc/reader_utils_ref.rst b/src/python/doc/reader_utils_ref.rst deleted file mode 100644 index f3ecebad..00000000 --- a/src/python/doc/reader_utils_ref.rst +++ /dev/null @@ -1,15 +0,0 @@ -:orphan: - -.. To get rid of WARNING: document isn't included in any toctree - -============================= -Reader utils reference manual -============================= - -.. autofunction:: gudhi.read_off - -.. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file - -.. autofunction:: gudhi.read_persistence_intervals_grouped_by_dimension - -.. autofunction:: gudhi.read_persistence_intervals_in_dimension diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx index 225e981c..e45356be 100644 --- a/src/python/gudhi/off_reader.pyx +++ b/src/python/gudhi/off_reader.pyx @@ -26,7 +26,7 @@ def read_off(off_file=''): :type off_file: string :returns: The point set. - :rtype: vector[vector[double]] + :rtype: list(list(float)) """ if off_file: if os.path.isfile(off_file): diff --git a/src/python/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx index 6994c4f9..5a756e4b 100644 --- a/src/python/gudhi/reader_utils.pyx +++ b/src/python/gudhi/reader_utils.pyx @@ -34,7 +34,7 @@ def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'): :type separator: char :returns: The lower triangular matrix. - :rtype: vector[vector[double]] + :rtype: list(list(float)) """ if csv_file: if path.isfile(csv_file): @@ -45,7 +45,7 @@ def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'): def read_persistence_intervals_grouped_by_dimension(persistence_file=''): """Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death - The return value is an `map[dim, vector[pair[birth, death]]]` + The return value is a `dict(dim, list(tuple(birth, death)))` where `dim` is an `int`, `birth` a `double`, and `death` a `double`. Note: the function does not check that birth <= death. @@ -53,7 +53,7 @@ def read_persistence_intervals_grouped_by_dimension(persistence_file=''): :type persistence_file: string :returns: The persistence pairs grouped by dimension. - :rtype: map[int, vector[pair[double, double]]] + :rtype: dict(int, list(tuple(float, float))) """ if persistence_file: if path.isfile(persistence_file): diff --git a/src/python/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx index e0cd1348..04f66219 100644 --- a/src/python/gudhi/subsampling.pyx +++ b/src/python/gudhi/subsampling.pyx @@ -33,7 +33,7 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi The iteration starts with the landmark `starting point`. :param points: The input point set. - :type points: vector[vector[double]]. + :type points: list(list(float)). Or @@ -47,7 +47,7 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi index is chosen randomly. :type starting_point: unsigned. :returns: The subsample point set. - :rtype: vector[vector[double]] + :rtype: list(list(float)). """ if off_file: if os.path.isfile(off_file): @@ -74,7 +74,7 @@ def pick_n_random_points(points=None, off_file='', nb_points=0): """Subsample a point set by picking random vertices. :param points: The input point set. - :type points: vector[vector[double]]. + :type points: list(list(float)). Or @@ -84,7 +84,7 @@ def pick_n_random_points(points=None, off_file='', nb_points=0): :param nb_points: Number of points of the subsample. :type nb_points: unsigned. :returns: The subsample point set. - :rtype: vector[vector[double]] + :rtype: list(list(float)) """ if off_file: if os.path.isfile(off_file): @@ -103,7 +103,7 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): between any two points is greater than or equal to min_squared_dist. :param points: The input point set. - :type points: vector[vector[double]]. + :type points: list(list(float)). Or @@ -114,7 +114,7 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): points. :type min_squared_dist: float. :returns: The subsample point set. - :rtype: vector[vector[double]] + :rtype: list(list(float)) """ if off_file: if os.path.isfile(off_file): -- cgit v1.2.3 From 18c98020adea4a7d0c53fe4e76c92bab23e7ad76 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Thu, 9 Jan 2020 18:03:39 +0100 Subject: Spell out types as in PEP 484 but don't actually use annotations. A quick try with sphinx-autodoc-typehints failed, I didn't investigate much, it can wait. --- src/python/gudhi/off_reader.pyx | 2 +- src/python/gudhi/reader_utils.pyx | 6 +++--- src/python/gudhi/subsampling.pyx | 12 ++++++------ 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx index e45356be..3a31eba6 100644 --- a/src/python/gudhi/off_reader.pyx +++ b/src/python/gudhi/off_reader.pyx @@ -26,7 +26,7 @@ def read_off(off_file=''): :type off_file: string :returns: The point set. - :rtype: list(list(float)) + :rtype: List[List[float]] """ if off_file: if os.path.isfile(off_file): diff --git a/src/python/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx index 5a756e4b..9ced6bca 100644 --- a/src/python/gudhi/reader_utils.pyx +++ b/src/python/gudhi/reader_utils.pyx @@ -34,7 +34,7 @@ def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'): :type separator: char :returns: The lower triangular matrix. - :rtype: list(list(float)) + :rtype: List[List[float]] """ if csv_file: if path.isfile(csv_file): @@ -46,14 +46,14 @@ def read_persistence_intervals_grouped_by_dimension(persistence_file=''): """Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death The return value is a `dict(dim, list(tuple(birth, death)))` - where `dim` is an `int`, `birth` a `double`, and `death` a `double`. + where `dim` is an `int`, `birth` a `float`, and `death` a `float`. Note: the function does not check that birth <= death. :param persistence_file: A persistence file style name. :type persistence_file: string :returns: The persistence pairs grouped by dimension. - :rtype: dict(int, list(tuple(float, float))) + :rtype: Dict[int, List[Tuple[float, float]]] """ if persistence_file: if path.isfile(persistence_file): diff --git a/src/python/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx index 04f66219..f50f4b0c 100644 --- a/src/python/gudhi/subsampling.pyx +++ b/src/python/gudhi/subsampling.pyx @@ -33,7 +33,7 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi The iteration starts with the landmark `starting point`. :param points: The input point set. - :type points: list(list(float)). + :type points: Iterable[Iterable[float]]. Or @@ -47,7 +47,7 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi index is chosen randomly. :type starting_point: unsigned. :returns: The subsample point set. - :rtype: list(list(float)). + :rtype: List[List[float]]. """ if off_file: if os.path.isfile(off_file): @@ -74,7 +74,7 @@ def pick_n_random_points(points=None, off_file='', nb_points=0): """Subsample a point set by picking random vertices. :param points: The input point set. - :type points: list(list(float)). + :type points: Iterable[Iterable[float]]. Or @@ -84,7 +84,7 @@ def pick_n_random_points(points=None, off_file='', nb_points=0): :param nb_points: Number of points of the subsample. :type nb_points: unsigned. :returns: The subsample point set. - :rtype: list(list(float)) + :rtype: List[List[float]] """ if off_file: if os.path.isfile(off_file): @@ -103,7 +103,7 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): between any two points is greater than or equal to min_squared_dist. :param points: The input point set. - :type points: list(list(float)). + :type points: Iterable[Iterable[float]]. Or @@ -114,7 +114,7 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): points. :type min_squared_dist: float. :returns: The subsample point set. - :rtype: list(list(float)) + :rtype: List[List[float]] """ if off_file: if os.path.isfile(off_file): -- cgit v1.2.3 From 2f7f4d84df64172c1af8b8741112c6dd9c883944 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Thu, 9 Jan 2020 18:22:24 +0100 Subject: Move point utilities in the index they we between computing diagrams and using diagrams, it looked strange --- src/python/doc/index.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/python/doc/index.rst b/src/python/doc/index.rst index 9513deb0..3387a64f 100644 --- a/src/python/doc/index.rst +++ b/src/python/doc/index.rst @@ -58,11 +58,6 @@ Persistence cohomology .. include:: persistent_cohomology_sum.inc -Point cloud utilities -********************* - -.. include:: point_cloud_sum.inc - Topological descriptors tools ***************************** @@ -86,6 +81,11 @@ Persistence graphical tools .. include:: persistence_graphical_tools_sum.inc +Point cloud utilities +********************* + +.. include:: point_cloud_sum.inc + Bibliography ************ -- cgit v1.2.3 From 051c9760a214a11e8e4af14ae6221e34bb876350 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Thu, 9 Jan 2020 20:56:48 +0100 Subject: align text --- src/python/doc/point_cloud_sum.inc | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/python/doc/point_cloud_sum.inc b/src/python/doc/point_cloud_sum.inc index cefcf1c8..85d52de7 100644 --- a/src/python/doc/point_cloud_sum.inc +++ b/src/python/doc/point_cloud_sum.inc @@ -2,8 +2,8 @@ :widths: 30 50 20 +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+ - | :math:`(x_1, x_2, \ldots, x_d)` | Utilities to process point clouds: read from file, subsample, etc. | :Author: Vincent Rouvreau | - | :math:`(y_1, y_2, \ldots, y_d)` | | | + | | :math:`(x_1, x_2, \ldots, x_d)` | Utilities to process point clouds: read from file, subsample, etc. | :Author: Vincent Rouvreau | + | | :math:`(y_1, y_2, \ldots, y_d)` | | | | | | :Introduced in: GUDHI 2.0.0 | | | | | | | | :Copyright: MIT (`GPL v3 `_) | -- cgit v1.2.3 From f5e49792f809b198908a67e674672a676c0877ec Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Sat, 18 Jan 2020 22:56:22 +0100 Subject: Separate optional arguments from common arguments I copy-pasted what is done in RipsComplex. Before that, sphinx was grouping nb_points with off_file, as if it couldn't be used with points. --- src/python/gudhi/subsampling.pyx | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/python/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx index 4c84cb03..f77c6f75 100644 --- a/src/python/gudhi/subsampling.pyx +++ b/src/python/gudhi/subsampling.pyx @@ -40,6 +40,8 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi :param off_file: An OFF file style name. :type off_file: string + And in both cases + :param nb_points: Number of points of the subsample. :type nb_points: unsigned. :param starting_point: The iteration starts with the landmark `starting \ @@ -81,6 +83,8 @@ def pick_n_random_points(points=None, off_file='', nb_points=0): :param off_file: An OFF file style name. :type off_file: string + And in both cases + :param nb_points: Number of points of the subsample. :type nb_points: unsigned. :returns: The subsample point set. @@ -110,6 +114,8 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): :param off_file: An OFF file style name. :type off_file: string + And in both cases + :param min_squared_dist: Minimum squared distance separating the output \ points. :type min_squared_dist: float. -- cgit v1.2.3 From b36d27e63a6e60e3b84346aa3b3a95014b30068e Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Thu, 21 Nov 2019 23:49:07 +0100 Subject: Sprinkle some "except +" in cython files --- src/python/gudhi/alpha_complex.pyx | 11 +++++------ src/python/gudhi/euclidean_strong_witness_complex.pyx | 4 ++-- src/python/gudhi/euclidean_witness_complex.pyx | 4 ++-- src/python/gudhi/rips_complex.pyx | 2 +- src/python/gudhi/simplex_tree.pxd | 2 +- src/python/gudhi/strong_witness_complex.pyx | 4 ++-- src/python/gudhi/witness_complex.pyx | 4 ++-- src/python/include/Alpha_complex_interface.h | 10 +++------- 8 files changed, 18 insertions(+), 23 deletions(-) diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx index f3ca3dd5..fff3e920 100644 --- a/src/python/gudhi/alpha_complex.pyx +++ b/src/python/gudhi/alpha_complex.pyx @@ -24,11 +24,11 @@ __license__ = "GPL v3" cdef extern from "Alpha_complex_interface.h" namespace "Gudhi": cdef cppclass Alpha_complex_interface "Gudhi::alpha_complex::Alpha_complex_interface": - Alpha_complex_interface(vector[vector[double]] points) + Alpha_complex_interface(vector[vector[double]] points) except + # bool from_file is a workaround for cython to find the correct signature - Alpha_complex_interface(string off_file, bool from_file) - vector[double] get_point(int vertex) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + Alpha_complex_interface(string off_file, bool from_file) except + + vector[double] get_point(int vertex) except + + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + # AlphaComplex python interface cdef class AlphaComplex: @@ -96,8 +96,7 @@ cdef class AlphaComplex: :rtype: list of float :returns: the point. """ - cdef vector[double] point = self.thisptr.get_point(vertex) - return point + return self.thisptr.get_point(vertex) def create_simplex_tree(self, max_alpha_square = float('inf')): """ diff --git a/src/python/gudhi/euclidean_strong_witness_complex.pyx b/src/python/gudhi/euclidean_strong_witness_complex.pyx index 9889f92c..aca6084e 100644 --- a/src/python/gudhi/euclidean_strong_witness_complex.pyx +++ b/src/python/gudhi/euclidean_strong_witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "GPL v3" cdef extern from "Euclidean_strong_witness_complex_interface.h" namespace "Gudhi": cdef cppclass Euclidean_strong_witness_complex_interface "Gudhi::witness_complex::Euclidean_strong_witness_complex_interface": Euclidean_strong_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + vector[double] get_point(unsigned vertex) # EuclideanStrongWitnessComplex python interface diff --git a/src/python/gudhi/euclidean_witness_complex.pyx b/src/python/gudhi/euclidean_witness_complex.pyx index e3ce0e82..fb0c2201 100644 --- a/src/python/gudhi/euclidean_witness_complex.pyx +++ b/src/python/gudhi/euclidean_witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "GPL v3" cdef extern from "Euclidean_witness_complex_interface.h" namespace "Gudhi": cdef cppclass Euclidean_witness_complex_interface "Gudhi::witness_complex::Euclidean_witness_complex_interface": Euclidean_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + vector[double] get_point(unsigned vertex) # EuclideanWitnessComplex python interface diff --git a/src/python/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx index 722cdcdc..deb8057a 100644 --- a/src/python/gudhi/rips_complex.pyx +++ b/src/python/gudhi/rips_complex.pyx @@ -28,7 +28,7 @@ cdef extern from "Rips_complex_interface.h" namespace "Gudhi": void init_matrix(vector[vector[double]] values, double threshold) void init_points_sparse(vector[vector[double]] values, double threshold, double sparse) void init_matrix_sparse(vector[vector[double]] values, double threshold, double sparse) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) except + # RipsComplex python interface cdef class RipsComplex: diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 1066d44b..96d14079 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -39,7 +39,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": vector[pair[vector[int], double]] get_star(vector[int] simplex) vector[pair[vector[int], double]] get_cofaces(vector[int] simplex, int dimension) - void expansion(int max_dim) + void expansion(int max_dim) except + void remove_maximal_simplex(vector[int] simplex) bool prune_above_filtration(double filtration) bool make_filtration_non_decreasing() diff --git a/src/python/gudhi/strong_witness_complex.pyx b/src/python/gudhi/strong_witness_complex.pyx index 2c33c3f2..9f89d3ae 100644 --- a/src/python/gudhi/strong_witness_complex.pyx +++ b/src/python/gudhi/strong_witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "MIT" cdef extern from "Strong_witness_complex_interface.h" namespace "Gudhi": cdef cppclass Strong_witness_complex_interface "Gudhi::witness_complex::Strong_witness_complex_interface": Strong_witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + # StrongWitnessComplex python interface cdef class StrongWitnessComplex: diff --git a/src/python/gudhi/witness_complex.pyx b/src/python/gudhi/witness_complex.pyx index b032a5a1..e589d006 100644 --- a/src/python/gudhi/witness_complex.pyx +++ b/src/python/gudhi/witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "MIT" cdef extern from "Witness_complex_interface.h" namespace "Gudhi": cdef cppclass Witness_complex_interface "Gudhi::witness_complex::Witness_complex_interface": Witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + # WitnessComplex python interface cdef class WitnessComplex: diff --git a/src/python/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h index e9bbadb0..8614eee3 100644 --- a/src/python/include/Alpha_complex_interface.h +++ b/src/python/include/Alpha_complex_interface.h @@ -50,13 +50,9 @@ class Alpha_complex_interface { std::vector get_point(int vh) { std::vector vd; - try { - Point_d const& ph = alpha_complex_->get_point(vh); - for (auto coord = ph.cartesian_begin(); coord != ph.cartesian_end(); coord++) - vd.push_back(CGAL::to_double(*coord)); - } catch (std::out_of_range const&) { - // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown - } + Point_d const& ph = alpha_complex_->get_point(vh); + for (auto coord = ph.cartesian_begin(); coord != ph.cartesian_end(); coord++) + vd.push_back(CGAL::to_double(*coord)); return vd; } -- cgit v1.2.3 From d9bdb64a5bc016c5bc34f95f29773050e90aa7ed Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Fri, 22 Nov 2019 00:14:08 +0100 Subject: Adapt tests It is still failing by default, until I touch alpha_complex.pyx and rebuild it, after which it works ?! --- .../example/alpha_complex_from_points_example.py | 7 +++++- src/python/test/test_alpha_complex.py | 28 ++++++++++++++++++---- 2 files changed, 30 insertions(+), 5 deletions(-) diff --git a/src/python/example/alpha_complex_from_points_example.py b/src/python/example/alpha_complex_from_points_example.py index a746998c..844d7a82 100755 --- a/src/python/example/alpha_complex_from_points_example.py +++ b/src/python/example/alpha_complex_from_points_example.py @@ -52,4 +52,9 @@ print("star([0])=", simplex_tree.get_star([0])) print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1)) print("point[0]=", alpha_complex.get_point(0)) -print("point[5]=", alpha_complex.get_point(5)) +try: + print("point[5]=", alpha_complex.get_point(5)) +except IndexError: + pass +else: + assert False diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py index 0d9e9e45..3761fe16 100755 --- a/src/python/test/test_alpha_complex.py +++ b/src/python/test/test_alpha_complex.py @@ -65,8 +65,18 @@ def test_infinite_alpha(): assert point_list[1] == alpha_complex.get_point(1) assert point_list[2] == alpha_complex.get_point(2) assert point_list[3] == alpha_complex.get_point(3) - assert alpha_complex.get_point(4) == [] - assert alpha_complex.get_point(125) == [] + try: + alpha_complex.get_point(4) == [] + except IndexError: + pass + else: + assert False + try: + alpha_complex.get_point(125) == [] + except IndexError: + pass + else: + assert False def test_filtered_alpha(): @@ -82,8 +92,18 @@ def test_filtered_alpha(): assert point_list[1] == filtered_alpha.get_point(1) assert point_list[2] == filtered_alpha.get_point(2) assert point_list[3] == filtered_alpha.get_point(3) - assert filtered_alpha.get_point(4) == [] - assert filtered_alpha.get_point(125) == [] + try: + filtered_alpha.get_point(4) == [] + except IndexError: + pass + else: + assert False + try: + filtered_alpha.get_point(125) == [] + except IndexError: + pass + else: + assert False assert simplex_tree.get_filtration() == [ ([0], 0.0), -- cgit v1.2.3 From 6ee77c3da821256459406e87024077c48419a493 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Mon, 20 Jan 2020 20:03:56 +0100 Subject: Shuffle the modules on the main page --- src/common/doc/main_page.md | 253 +++++++++++++++++++++----------------------- 1 file changed, 123 insertions(+), 130 deletions(-) diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index 0b4bfb7a..768c5794 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -4,8 +4,8 @@ \image html "Gudhi_banner.png"



-## Complexes {#Complexes} -### Cubical complex +## Data structures for cell complexes {#Complexes} +### Cubical complexes @@ -29,246 +29,269 @@
-### Simplicial complex - -#### Alpha complex +### Simplicial complexes +#### Simplex tree
- \image html "alpha_complex_representation.png" + \image html "Simplex_tree_representation.png" - Alpha complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.
- The filtration value of each simplex is computed as the square of the circumradius of the simplex if the - circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration - values of the codimension 1 cofaces that make it not Gabriel otherwise. - All simplices that have a filtration value \f$ > \alpha^2 \f$ are removed from the Delaunay complex - when creating the simplicial complex if it is specified.
- For performances reasons, it is advised to use \ref cgal ≥ 5.0.0. + The simplex tree is an efficient and flexible + data structure for representing general (filtered) simplicial complexes. The data structure + is described in \cite boissonnatmariasimplextreealgorithmica . 		- Author: Vincent Rouvreau
- Introduced in: GUDHI 1.3.0
- Copyright: MIT [(GPL v3)](../../licensing/)
- Requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 4.11.0 + Author: Clément Maria
+ Introduced in: GUDHI 1.0.0
+ Copyright: MIT
- User manual: \ref alpha_complex + User manual: \ref simplex_tree
-#### Čech complex +#### Skeleton blocker - +
- \image html "cech_complex_representation.png" + \image html "ds_representation.png" - The Čech complex is a simplicial complex constructed from a proximity graph. - The set of all simplices is filtered by the radius of their minimal enclosing ball. + The Skeleton-Blocker data-structure proposes a light encoding for simplicial complexes by storing only an *implicit* + representation of its simplices \cite socg_blockers_2011,\cite blockers2012. Intuitively, it just stores the + 1-skeleton of a simplicial complex with a graph and the set of its "missing faces" that is very small in practice. + This data-structure handles all simplicial complexes operations such as simplex enumeration or simplex removal but + operations that are particularly efficient are operations that do not require simplex enumeration such as edge + iteration, link computation or simplex contraction. - Author: Vincent Rouvreau
- Introduced in: GUDHI 2.2.0
- Copyright: MIT [(GPL v3)](../../licensing/)
- Includes: [Miniball](https://people.inf.ethz.ch/gaertner/subdir/software/miniball.html)
+ Author: David Salinas
+ Introduced in: GUDHI 1.1.0
+ Copyright: MIT
- User manual: \ref cech_complex + User manual: \ref skbl
-#### Rips complex +#### Toplex Map
- \image html "rips_complex_representation.png" + \image html "map.png" - Rips complex is a simplicial complex constructed from a one skeleton graph.
- The filtration value of each edge is computed from a user-given distance function and is inserted until a - user-given threshold value.
- This complex can be built from a point cloud and a distance function, or from a distance matrix. + The Toplex map data structure is composed firstly of a raw storage of toplices (the maximal simplices) + and secondly of a map which associate any vertex to a set of pointers toward all toplices + containing this vertex. 		- Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse
- Introduced in: GUDHI 2.0.0
+ Author: François Godi
+ Introduced in: GUDHI 2.1.0
Copyright: MIT
- User manual: \ref rips_complex + User manual: \ref toplex_map
-#### Witness complex +#### Basic operation: contraction
- \image html "Witness_complex_representation.png" + \image html "sphere_contraction_representation.png" - Witness complex \f$ Wit(W,L) \f$ is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$. - The data structure is described in \cite boissonnatmariasimplextreealgorithmica . + The purpose of this package is to offer a user-friendly interface for edge contraction simplification of huge + simplicial complexes. It uses the \ref skbl data-structure whose size remains small during simplification of most + used geometrical complexes of topological data analysis such as the Rips or the Delaunay complexes. In practice, + the size of this data-structure is even much lower than the total number of simplices. - Author: Siargey Kachanovich
- Introduced in: GUDHI 1.3.0
- Copyright: MIT ([GPL v3](../../licensing/) for Euclidean version)
- Euclidean version requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 4.11.0 + Author: David Salinas
+ Introduced in: GUDHI 1.1.0
+ Copyright: MIT [(LGPL v3)](../../licensing/)
+ Requires: \ref cgal ≥ 4.11.0
- User manual: \ref witness_complex + User manual: \ref contr
-### Cover Complexes +## Filtrations and reconstructions +### Alpha complex +
- \image html "gicvisu.jpg" + \image html "alpha_complex_representation.png" - Nerves and Graph Induced Complexes are cover complexes, i.e. simplicial complexes that provably contain - topological information about the input data. They can be computed with a cover of the - data, that comes i.e. from the preimage of a family of intervals covering the image - of a scalar-valued function defined on the data.
+ Alpha complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.
+ The filtration value of each simplex is computed as the square of the circumradius of the simplex if the + circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration + values of the codimension 1 cofaces that make it not Gabriel otherwise. + All simplices that have a filtration value \f$ > \alpha^2 \f$ are removed from the Delaunay complex + when creating the simplicial complex if it is specified.
+ For performances reasons, it is advised to use \ref cgal ≥ 5.0.0. 		- Author: Mathieu Carrière
- Introduced in: GUDHI 2.1.0
+ Author: Vincent Rouvreau
+ Introduced in: GUDHI 1.3.0
Copyright: MIT [(GPL v3)](../../licensing/)
- Requires: \ref cgal ≥ 4.11.0 + Requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 4.11.0
- User manual: \ref cover_complex + User manual: \ref alpha_complex
-## Data structures and basic operations {#DataStructuresAndBasicOperations} +### Čech complex + + + + + + + + + + +
+ \image html "cech_complex_representation.png" + + The Čech complex is a simplicial complex constructed from a proximity graph. + The set of all simplices is filtered by the radius of their minimal enclosing ball. + + Author: Vincent Rouvreau
+ Introduced in: GUDHI 2.2.0
+ Copyright: MIT [(GPL v3)](../../licensing/)
+ Includes: [Miniball](https://people.inf.ethz.ch/gaertner/subdir/software/miniball.html)
+
+ User manual: \ref cech_complex +
-### Data structures +### Rips complex -#### Simplex tree
- \image html "Simplex_tree_representation.png" + \image html "rips_complex_representation.png" - The simplex tree is an efficient and flexible - data structure for representing general (filtered) simplicial complexes. The data structure - is described in \cite boissonnatmariasimplextreealgorithmica . + Rips complex is a simplicial complex constructed from a one skeleton graph.
+ The filtration value of each edge is computed from a user-given distance function and is inserted until a + user-given threshold value.
+ This complex can be built from a point cloud and a distance function, or from a distance matrix. 		- Author: Clément Maria
- Introduced in: GUDHI 1.0.0
+ Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse
+ Introduced in: GUDHI 2.0.0
Copyright: MIT
- User manual: \ref simplex_tree + User manual: \ref rips_complex
-#### Skeleton blocker +### Witness complex
- \image html "ds_representation.png" + \image html "Witness_complex_representation.png" - The Skeleton-Blocker data-structure proposes a light encoding for simplicial complexes by storing only an *implicit* - representation of its simplices \cite socg_blockers_2011,\cite blockers2012. Intuitively, it just stores the - 1-skeleton of a simplicial complex with a graph and the set of its "missing faces" that is very small in practice. - This data-structure handles all simplicial complexes operations such as simplex enumeration or simplex removal but - operations that are particularly efficient are operations that do not require simplex enumeration such as edge - iteration, link computation or simplex contraction. + Witness complex \f$ Wit(W,L) \f$ is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$. + The data structure is described in \cite boissonnatmariasimplextreealgorithmica . - Author: David Salinas
- Introduced in: GUDHI 1.1.0
- Copyright: MIT
+ Author: Siargey Kachanovich
+ Introduced in: GUDHI 1.3.0
+ Copyright: MIT ([GPL v3](../../licensing/) for Euclidean version)
+ Euclidean version requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 4.11.0
- User manual: \ref skbl + User manual: \ref witness_complex
-#### Toplex Map - +### Cover Complexes
- \image html "map.png" + \image html "gicvisu.jpg" - The Toplex map data structure is composed firstly of a raw storage of toplices (the maximal simplices) - and secondly of a map which associate any vertex to a set of pointers toward all toplices - containing this vertex. + Nerves and Graph Induced Complexes are cover complexes, i.e. simplicial complexes that provably contain + topological information about the input data. They can be computed with a cover of the + data, that comes i.e. from the preimage of a family of intervals covering the image + of a scalar-valued function defined on the data.
- Author: François Godi
+ Author: Mathieu Carrière
Introduced in: GUDHI 2.1.0
- Copyright: MIT
+ Copyright: MIT [(GPL v3)](../../licensing/)
+ Requires: \ref cgal ≥ 4.11.0
- User manual: \ref toplex_map + User manual: \ref cover_complex
-### Basic operations - -#### Contraction +### Tangential complex
- \image html "sphere_contraction_representation.png" + \image html "tc_examples.png" - The purpose of this package is to offer a user-friendly interface for edge contraction simplification of huge - simplicial complexes. It uses the \ref skbl data-structure whose size remains small during simplification of most - used geometrical complexes of topological data analysis such as the Rips or the Delaunay complexes. In practice, - the size of this data-structure is even much lower than the total number of simplices. + A Tangential Delaunay complex is a simplicial complex + designed to reconstruct a \f$ k \f$-dimensional manifold embedded in \f$ d \f$-dimensional Euclidean space. + The input is a point sample coming from an unknown manifold. + The running time depends only linearly on the extrinsic dimension \f$ d \f$ + and exponentially on the intrinsic dimension \f$ k \f$. - Author: David Salinas
- Introduced in: GUDHI 1.1.0
- Copyright: MIT [(LGPL v3)](../../licensing/)
- Requires: \ref cgal ≥ 4.11.0 + Author: Clément Jamin
+ Introduced in: GUDHI 2.0.0
+ Copyright: MIT [(GPL v3)](../../licensing/)
+ Requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 4.11.0
- User manual: \ref contr + User manual: \ref tangential_complex
@@ -305,36 +328,6 @@ -## Manifold reconstruction {#ManifoldReconstruction} - -### Tangential complex - - - - - - - - - - -
- \image html "tc_examples.png" - - A Tangential Delaunay complex is a simplicial complex - designed to reconstruct a \f$ k \f$-dimensional manifold embedded in \f$ d \f$-dimensional Euclidean space. - The input is a point sample coming from an unknown manifold. - The running time depends only linearly on the extrinsic dimension \f$ d \f$ - and exponentially on the intrinsic dimension \f$ k \f$. - - Author: Clément Jamin
- Introduced in: GUDHI 2.0.0
- Copyright: MIT [(GPL v3)](../../licensing/)
- Requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 4.11.0 -
- User manual: \ref tangential_complex -
- ## Topological descriptors tools {#TopologicalDescriptorsTools} ### Bottleneck distance -- cgit v1.2.3 From 82b4a1e765adc6ec9d37b1bfb09ce443f642cb08 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Mon, 20 Jan 2020 20:11:28 +0100 Subject: Missing entry in TOC --- src/common/doc/main_page.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index 768c5794..90afb05d 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -135,7 +135,7 @@ -## Filtrations and reconstructions +## Filtrations and reconstructions {#FiltrationsReconstructions} ### Alpha complex -- cgit v1.2.3 From 8c85fa3f6dcb47346f3070adc46d44c9afca2f2c Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Mon, 20 Jan 2020 20:26:18 +0100 Subject: Reorder skbl and toplexmap so that skbl is next to contractions --- src/common/doc/main_page.md | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index 90afb05d..23dd3fde 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -55,55 +55,55 @@
-#### Skeleton blocker +#### Toplex Map
- \image html "ds_representation.png" + \image html "map.png" - The Skeleton-Blocker data-structure proposes a light encoding for simplicial complexes by storing only an *implicit* - representation of its simplices \cite socg_blockers_2011,\cite blockers2012. Intuitively, it just stores the - 1-skeleton of a simplicial complex with a graph and the set of its "missing faces" that is very small in practice. - This data-structure handles all simplicial complexes operations such as simplex enumeration or simplex removal but - operations that are particularly efficient are operations that do not require simplex enumeration such as edge - iteration, link computation or simplex contraction. + The Toplex map data structure is composed firstly of a raw storage of toplices (the maximal simplices) + and secondly of a map which associate any vertex to a set of pointers toward all toplices + containing this vertex. - Author: David Salinas
- Introduced in: GUDHI 1.1.0
+ Author: François Godi
+ Introduced in: GUDHI 2.1.0
Copyright: MIT
- User manual: \ref skbl + User manual: \ref toplex_map
-#### Toplex Map +#### Skeleton blocker
- \image html "map.png" + \image html "ds_representation.png" - The Toplex map data structure is composed firstly of a raw storage of toplices (the maximal simplices) - and secondly of a map which associate any vertex to a set of pointers toward all toplices - containing this vertex. + The Skeleton-Blocker data-structure proposes a light encoding for simplicial complexes by storing only an *implicit* + representation of its simplices \cite socg_blockers_2011,\cite blockers2012. Intuitively, it just stores the + 1-skeleton of a simplicial complex with a graph and the set of its "missing faces" that is very small in practice. + This data-structure handles all simplicial complexes operations such as simplex enumeration or simplex removal but + operations that are particularly efficient are operations that do not require simplex enumeration such as edge + iteration, link computation or simplex contraction. - Author: François Godi
- Introduced in: GUDHI 2.1.0
+ Author: David Salinas
+ Introduced in: GUDHI 1.1.0
Copyright: MIT
- User manual: \ref toplex_map + User manual: \ref skbl
-- cgit v1.2.3 From dc3d21f55d3e0de311f56b2706629483f50b0258 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Mon, 20 Jan 2020 20:36:58 +0100 Subject: Link kd-tree and subsampling from the main doc --- src/common/doc/main_page.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index 23dd3fde..72bf1cef 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -383,3 +383,26 @@ + +## Point cloud utilities {#PointCloudUtils} + + + + + + + + + + +
+ \f$(x_1,\ldots\x_d)\f$ + + This contains various tools to handle point clouds: spatial searching, subsampling, etc. + + Author: Clément Jamin
+ Introduced in: GUDHI 1.3.0
+ Copyright: MIT [(GPL v3)](../../licensing/)
+
+ Manuals: \ref spatial_searching, \ref subsampling +
-- cgit v1.2.3 From 43b6452cf36e92595e4fd05bdeca6c5eeaf95e86 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Mon, 20 Jan 2020 20:55:33 +0100 Subject: Typo --- src/common/doc/main_page.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index 72bf1cef..6ea10b88 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -389,7 +389,7 @@
- \f$(x_1,\ldots\x_d)\f$ + \f$(x_1,\ldots,x_d)\f$ This contains various tools to handle point clouds: spatial searching, subsampling, etc. -- cgit v1.2.3 From 5572f6a59390d389535925b8c68de429bc32861b Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 27 Jan 2020 09:42:35 +0100 Subject: Reset for next release --- next_release.md | 24 ++++++++---------------- 1 file changed, 8 insertions(+), 16 deletions(-) diff --git a/next_release.md b/next_release.md index 08b736b1..b85afdf5 100644 --- a/next_release.md +++ b/next_release.md @@ -1,27 +1,19 @@ -We are pleased to announce the release 3.1.0 of the GUDHI library. +We are pleased to announce the release 3.X.X of the GUDHI library. As a major new feature, the GUDHI library now offers 2 new Python modules: Persistence representations and Wasserstein distance. -We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.1.0.rc1.tar.gz). +We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.X.X.tar.gz). -Below is a list of changes made since Gudhi 3.0.0: +Below is a list of changes made since Gudhi 3.1.0: -- [Persistence representations](https://gudhi.inria.fr/python/3.1.0.rc1/representations.html) (new Python module) - - Vectorizations, distances and kernels that work on persistence diagrams, compatible with scikit-learn. This module was originally available at https://github.com/MathieuCarriere/sklearn-tda and named sklearn_tda. +- [Module](link) + - ... -- [Wasserstein distance](https://gudhi.inria.fr/python/3.1.0.rc1/wasserstein_distance_user.html) (new Python module) - - The q-Wasserstein distance measures the similarity between two persistence diagrams. - -- [Alpha complex](https://gudhi.inria.fr/doc/3.1.0.rc1/group__alpha__complex.html) (new C++ interface) - - Thanks to [CGAL 5.0 Epeck_d](https://doc.cgal.org/latest/Kernel_d/structCGAL_1_1Epeck__d.html) kernel, an exact computation version of Alpha complex dD is available and the default one (even in Python). - -- [Persistence graphical tools](https://gudhi.inria.fr/python/3.1.0.rc1/persistence_graphical_tools_user.html) (new Python interface) - - Axes as a parameter allows the user to subplot graphics. - - Use matplotlib default palette (can be user defined). +- [Module](link) + - ... - Miscellaneous - - Python `read_off` function has been renamed `read_points_from_off_file` as it only reads points from OFF files. - - See the list of [bug fixes](https://github.com/GUDHI/gudhi-devel/issues?utf8=%E2%9C%93&q=is%3Aissue+label%3A3.1.0+). + - See the list of [bug fixes](https://github.com/GUDHI/gudhi-devel/issues?utf8=%E2%9C%93&q=is%3Aissue+label%3A3.X.X+). All modules are distributed under the terms of the MIT license. -- cgit v1.2.3 From 1e061ddfe473aceb8727fc5ca160193bf9d9a4fc Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 27 Jan 2020 09:44:13 +0100 Subject: Reset for next release --- next_release.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/next_release.md b/next_release.md index b85afdf5..26d4fca5 100644 --- a/next_release.md +++ b/next_release.md @@ -1,6 +1,6 @@ We are pleased to announce the release 3.X.X of the GUDHI library. -As a major new feature, the GUDHI library now offers 2 new Python modules: Persistence representations and Wasserstein distance. +As a major new feature, the GUDHI library now offers ... We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.X.X.tar.gz). -- cgit v1.2.3 From 0cbf41493cee2b9bd598557b97df9b1211da2b9d Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 30 Jan 2020 18:04:20 +0100 Subject: Use mutex from stl instead of tbb one that is deprecated --- src/Nerve_GIC/include/gudhi/GIC.h | 8 ++++---- src/Tangential_complex/include/gudhi/Tangential_complex.h | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index a47d6889..2a6d4788 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -14,7 +14,7 @@ #ifdef GUDHI_USE_TBB #include -#include +#include #endif #include @@ -459,7 +459,7 @@ class Cover_complex { // This cannot be parallelized if thread_local is not defined // thread_local is not defined for XCode < v.8 #if defined(GUDHI_USE_TBB) && defined(GUDHI_CAN_USE_CXX11_THREAD_LOCAL) - tbb::mutex deltamutex; + std::mutex deltamutex; tbb::parallel_for(0, N, [&](int i){ std::vector samples(m); SampleWithoutReplacement(n, m, samples); @@ -765,7 +765,7 @@ class Cover_complex { #ifdef GUDHI_USE_TBB if (verbose) std::cout << "Computing connected components (parallelized)..." << std::endl; - tbb::mutex covermutex, idmutex; + std::mutex covermutex, idmutex; tbb::parallel_for(0, res, [&](int i){ // Compute connected components Graph G = one_skeleton.create_subgraph(); @@ -895,7 +895,7 @@ class Cover_complex { // Compute the geodesic distances to subsamples with Dijkstra #ifdef GUDHI_USE_TBB if (verbose) std::cout << "Computing geodesic distances (parallelized)..." << std::endl; - tbb::mutex coverMutex; tbb::mutex mindistMutex; + std::mutex coverMutex; std::mutex mindistMutex; tbb::parallel_for(0, m, [&](int i){ int seed = voronoi_subsamples[i]; std::vector dmap(n); diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index f058fa9f..f007bdd5 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -60,7 +60,7 @@ #ifdef GUDHI_USE_TBB #include #include -#include +#include #endif // #define GUDHI_TC_EXPORT_NORMALS // Only for 3D surfaces (k=2, d=3) @@ -147,7 +147,7 @@ class Tangential_complex { typedef typename Tr_traits::Vector_d Tr_vector; #if defined(GUDHI_USE_TBB) - typedef tbb::mutex Mutex_for_perturb; + typedef std::mutex Mutex_for_perturb; typedef Vector Translation_for_perturb; typedef std::vector > Weights; #else -- cgit v1.2.3 From 59116c450bf912a4b446b02e55278f3ec55a90ee Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Mon, 3 Feb 2020 18:48:36 +0100 Subject: Contradictory requirements for CGAL --- src/python/doc/alpha_complex_sum.inc | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/src/python/doc/alpha_complex_sum.inc b/src/python/doc/alpha_complex_sum.inc index a1184663..b5af0d27 100644 --- a/src/python/doc/alpha_complex_sum.inc +++ b/src/python/doc/alpha_complex_sum.inc @@ -5,16 +5,13 @@ | .. figure:: | Alpha complex is a simplicial complex constructed from the finite | :Author: Vincent Rouvreau | | ../../doc/Alpha_complex/alpha_complex_representation.png | cells of a Delaunay Triangulation. | | | :alt: Alpha complex representation | | :Introduced in: GUDHI 2.0.0 | - | :figclass: align-center | The filtration value of each simplex is computed as the square of the | | - | | circumradius of the simplex if the circumsphere is empty (the simplex | :Copyright: MIT (`GPL v3 `_) | - | | is then said to be Gabriel), and as the minimum of the filtration | | - | | values of the codimension 1 cofaces that make it not Gabriel | :Requires: `Eigen `__ :math:`\geq` 3.1.0 and `CGAL `__ :math:`\geq` 4.11.0 | - | | otherwise. All simplices that have a filtration value | | - | | :math:`> \alpha^2` are removed from the Delaunay complex | | - | | when creating the simplicial complex if it is specified. | | + | :figclass: align-center | The filtration value of each simplex is computed as the **square** of | | + | | the circumradius of the simplex if the circumsphere is empty (the | :Copyright: MIT (`GPL v3 `_) | + | | simplex is then said to be Gabriel), and as the minimum of the | | + | | filtration values of the codimension 1 cofaces that make it not | :Requires: `Eigen `__ :math:`\geq` 3.1.0 and `CGAL `__ :math:`\geq` 4.11.0 | + | | Gabriel otherwise. | | | | | | - | | This package requires having CGAL version 4.7 or higher (4.8.1 is | | - | | advised for better performance). | | + | | For performances reasons, it is advised to use CGAL ≥ 5.0.0. | | +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+ | * :doc:`alpha_complex_user` | * :doc:`alpha_complex_ref` | +----------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ -- cgit v1.2.3 From 53f90be09bcfafd8edda763ba1532c519847929a Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 4 Feb 2020 16:59:49 +0100 Subject: Dockerfile_gudhi_installation for gudhi 3.1.0 version --- Dockerfile_gudhi_installation | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/Dockerfile_gudhi_installation b/Dockerfile_gudhi_installation index 9fe20730..d5d86338 100644 --- a/Dockerfile_gudhi_installation +++ b/Dockerfile_gudhi_installation @@ -50,14 +50,16 @@ RUN pip3 install \ numpy \ matplotlib \ scipy \ - Cython + Cython \ + POT \ + scikit-learn # apt clean up RUN apt autoremove && rm -rf /var/lib/apt/lists/* -RUN curl -LO "https://github.com/GUDHI/gudhi-devel/releases/download/tags%2Fgudhi-release-3.0.0/gudhi.3.0.0.tar.gz" \ -&& tar xf gudhi.3.0.0.tar.gz \ -&& cd gudhi.3.0.0 \ +RUN curl -LO "https://github.com/GUDHI/gudhi-devel/releases/download/tags%2Fgudhi-release-3.1.0/gudhi.3.1.0.tar.gz" \ +&& tar xf gudhi.3.1.0.tar.gz \ +&& cd gudhi.3.1.0 \ && mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_PYTHON=OFF -DPython_ADDITIONAL_VERSIONS=3 .. \ && make all test install \ && cmake -DWITH_GUDHI_PYTHON=ON . \ -- cgit v1.2.3 From 08596f907e5b4fb99a5c9d51799f54f1b0535071 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 4 Feb 2020 18:05:42 +0100 Subject: Fix #186 - Link with TBB for all simplex tree user --- src/Simplex_tree/example/CMakeLists.txt | 3 +++ src/Witness_complex/example/CMakeLists.txt | 10 +++++++++- src/common/doc/installation.h | 8 ++++++++ 3 files changed, 20 insertions(+), 1 deletion(-) diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index f99b164c..8a8cac58 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -16,6 +16,9 @@ endif() add_test(NAME Simplex_tree_example_simple_simplex_tree COMMAND $) add_executable ( Simplex_tree_example_mini_simplex_tree mini_simplex_tree.cpp ) +if (TBB_FOUND) + target_link_libraries(Simplex_tree_example_mini_simplex_tree ${TBB_LIBRARIES}) +endif() add_test(NAME Simplex_tree_example_mini_simplex_tree COMMAND $) # An example with Simplex-tree using CGAL alpha_shapes_3 diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index 5860f3a3..2659798e 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -12,10 +12,18 @@ install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin) # CGAL and Eigen3 are required for Euclidean version of Witness if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) + if (TBB_FOUND) + target_link_libraries(Witness_complex_example_off ${TBB_LIBRARIES}) + endif() add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp ) + if (TBB_FOUND) + target_link_libraries(Witness_complex_example_sphere ${TBB_LIBRARIES}) + endif() add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) - target_link_libraries(Witness_complex_example_strong_off) + if (TBB_FOUND) + target_link_libraries(Witness_complex_example_strong_off ${TBB_LIBRARIES}) + endif() add_test(NAME Witness_complex_example_off_test_torus COMMAND $ diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index ce2c5448..c2da1ba0 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -204,6 +204,8 @@ make doxygen * Nerve_GIC/Nerve.cpp * \li * Nerve_GIC/VoronoiGIC.cpp + * \li + * Simplex_tree/mini_simplex_tree.cpp * \li * Simplex_tree/simple_simplex_tree.cpp * \li @@ -244,6 +246,12 @@ make doxygen * Witness_complex/weak_witness_persistence.cpp * \li * Witness_complex/example_nearest_landmark_table.cpp + * \li + * Witness_complex/example_strong_witness_complex_off.cpp + * \li + * Witness_complex/example_witness_complex_off.cpp + * \li + * Witness_complex/example_witness_complex_sphere.cpp * * \section Contributions Bug reports and contributions * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: -- cgit v1.2.3 From fd6db1cb3c60199b0c7c0eafd4d10e527a505ac3 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 4 Feb 2020 21:58:52 +0100 Subject: Code review: Rollback installation as these examples are not optimized with TBB --- src/common/doc/installation.h | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index c2da1ba0..ce2c5448 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -204,8 +204,6 @@ make doxygen * Nerve_GIC/Nerve.cpp * \li * Nerve_GIC/VoronoiGIC.cpp - * \li - * Simplex_tree/mini_simplex_tree.cpp * \li * Simplex_tree/simple_simplex_tree.cpp * \li @@ -246,12 +244,6 @@ make doxygen * Witness_complex/weak_witness_persistence.cpp * \li * Witness_complex/example_nearest_landmark_table.cpp - * \li - * Witness_complex/example_strong_witness_complex_off.cpp - * \li - * Witness_complex/example_witness_complex_off.cpp - * \li - * Witness_complex/example_witness_complex_sphere.cpp * * \section Contributions Bug reports and contributions * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: -- cgit v1.2.3 From 966a8e0131cb55d815bfe6c8286c9d7865f1a32f Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 5 Feb 2020 16:09:45 +0100 Subject: Add gudhi.representations in setup.py packages --- src/python/setup.py.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 9c2124f4..f993165c 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -44,7 +44,7 @@ for module in modules: setup( name = 'gudhi', - packages=["gudhi",], + packages=["gudhi","gudhi.representations"], author='GUDHI Editorial Board', author_email='gudhi-contact@lists.gforge.inria.fr', version='@GUDHI_VERSION@', -- cgit v1.2.3 From 15e0accb230b2f618e361b96e7f7b2c766179a68 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 6 Feb 2020 10:15:04 +0100 Subject: Install version, clean compilation and test the installed version --- .circleci/config.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 5e45bc14..34910ad6 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -45,6 +45,7 @@ jobs: python: docker: - image: gudhi/ci_for_gudhi:latest + parallelism: 4 steps: - checkout - run: @@ -58,10 +59,12 @@ jobs: mkdir build; cd build; cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..; - make all; - ctest --output-on-failure; + python setup.py build_ext -j 4 --inplace; make sphinx; cp -R python/sphinx /tmp/sphinx; + python setup.py install; + python setup.py clean --all; + ctest -j 4 --output-on-failure; - store_artifacts: path: /tmp/sphinx -- cgit v1.2.3 From dc44366683dd87d362c82fe2d93cee8d52dc3f28 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 6 Feb 2020 10:53:06 +0100 Subject: must change directory to build python --- .circleci/config.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 34910ad6..4edb0e1b 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -59,6 +59,7 @@ jobs: mkdir build; cd build; cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..; + cd python; python setup.py build_ext -j 4 --inplace; make sphinx; cp -R python/sphinx /tmp/sphinx; -- cgit v1.2.3 From 4ba35f8120c897b378b84e6f0e4b955d254f683e Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 6 Feb 2020 11:10:19 +0100 Subject: Add setuptools --- Dockerfile_for_circleci_image | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile_for_circleci_image b/Dockerfile_for_circleci_image index ff4e6018..b7d0dcca 100644 --- a/Dockerfile_for_circleci_image +++ b/Dockerfile_for_circleci_image @@ -49,6 +49,7 @@ RUN apt-get install -y make \ pkg-config RUN pip3 install \ + setuptools \ numpy \ matplotlib \ scipy \ -- cgit v1.2.3 From 7833223f55ca261f4592efd7fbb1ae3002f40f3d Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 6 Feb 2020 12:49:39 +0100 Subject: Try to use a specific version of docker file --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 4edb0e1b..a166a439 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -44,7 +44,7 @@ jobs: python: docker: - - image: gudhi/ci_for_gudhi:latest + - image: gudhi/ci_for_gudhi@sha256:9c90c7965f2288470fd5b374200f5b1bc23a9bd9939ece9f1bf864a6135fccb5 parallelism: 4 steps: - checkout -- cgit v1.2.3 From b84ea8b77c759e8f8c84ca1b21f5eded3a975a50 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 6 Feb 2020 13:06:10 +0100 Subject: Use python3 --- .circleci/config.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a166a439..abcd52dd 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -60,11 +60,11 @@ jobs: cd build; cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..; cd python; - python setup.py build_ext -j 4 --inplace; + python3 setup.py build_ext -j 4 --inplace; make sphinx; cp -R python/sphinx /tmp/sphinx; - python setup.py install; - python setup.py clean --all; + python3 setup.py install; + python3 setup.py clean --all; ctest -j 4 --output-on-failure; - store_artifacts: -- cgit v1.2.3 From 9e955b7088ac19cf701b213337d8ea29355f0b40 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 6 Feb 2020 13:11:31 +0100 Subject: Rollback latest docker tag --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index abcd52dd..d9678852 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -44,7 +44,7 @@ jobs: python: docker: - - image: gudhi/ci_for_gudhi@sha256:9c90c7965f2288470fd5b374200f5b1bc23a9bd9939ece9f1bf864a6135fccb5 + - image: gudhi/ci_for_gudhi:latest parallelism: 4 steps: - checkout -- cgit v1.2.3 From 31d3c96d65737fbeb0c8762b1f7e7ac4f5aaeab8 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 6 Feb 2020 13:22:55 +0100 Subject: python change directory make copy fail --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index d9678852..f4073746 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -62,7 +62,7 @@ jobs: cd python; python3 setup.py build_ext -j 4 --inplace; make sphinx; - cp -R python/sphinx /tmp/sphinx; + cp -R sphinx /tmp/sphinx; python3 setup.py install; python3 setup.py clean --all; ctest -j 4 --output-on-failure; -- cgit v1.2.3 From 2dbe066378ed3b5b4913775873326d0d62a7f1b9 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 6 Feb 2020 13:54:13 +0100 Subject: language_level was not properly set --- src/python/setup.py.in | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/python/setup.py.in b/src/python/setup.py.in index f993165c..c434f659 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -39,8 +39,7 @@ for module in 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,)) setup( name = 'gudhi', @@ -49,7 +48,8 @@ setup( author_email='gudhi-contact@lists.gforge.inria.fr', version='@GUDHI_VERSION@', url='http://gudhi.gforge.inria.fr/', - ext_modules = cythonize(ext_modules), + ext_modules = cythonize(ext_modules, + language_level=str(sys.version_info[0])), install_requires = ['cython','numpy >= 1.9',], setup_requires = ['numpy >= 1.9',], ) -- cgit v1.2.3 From 3f5420aa5d5c9de1cd0cfe6ea1eb57a20a212c7c Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 6 Feb 2020 14:04:28 +0100 Subject: Rollback language_level --- src/python/setup.py.in | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/python/setup.py.in b/src/python/setup.py.in index c434f659..f993165c 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -39,7 +39,8 @@ for module in modules: libraries=libraries, library_dirs=library_dirs, include_dirs=include_dirs, - runtime_library_dirs=runtime_library_dirs,)) + runtime_library_dirs=runtime_library_dirs, + cython_directives = {'language_level': str(sys.version_info[0])},)) setup( name = 'gudhi', @@ -48,8 +49,7 @@ setup( author_email='gudhi-contact@lists.gforge.inria.fr', version='@GUDHI_VERSION@', url='http://gudhi.gforge.inria.fr/', - ext_modules = cythonize(ext_modules, - language_level=str(sys.version_info[0])), + ext_modules = cythonize(ext_modules), install_requires = ['cython','numpy >= 1.9',], setup_requires = ['numpy >= 1.9',], ) -- cgit v1.2.3 From 09a0757357f89ff91fdafb535a0b250b937ee88b Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 6 Feb 2020 17:09:17 +0100 Subject: 3.1.1 release candidate 1 --- CMakeGUDHIVersion.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt index ed19ecfb..ec9794ce 100644 --- a/CMakeGUDHIVersion.txt +++ b/CMakeGUDHIVersion.txt @@ -1,6 +1,6 @@ set (GUDHI_MAJOR_VERSION 3) set (GUDHI_MINOR_VERSION 1) -set (GUDHI_PATCH_VERSION 0) +set (GUDHI_PATCH_VERSION 1.rc1) set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION}) message(STATUS "GUDHI version : ${GUDHI_VERSION}") -- cgit v1.2.3 From 57eabeaa00f724fe60e1ee69b5db3c35a765e198 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 6 Feb 2020 17:16:08 +0100 Subject: Release note for version 3.1.1 --- next_release.md | 20 +++----------------- 1 file changed, 3 insertions(+), 17 deletions(-) diff --git a/next_release.md b/next_release.md index 26d4fca5..deb04085 100644 --- a/next_release.md +++ b/next_release.md @@ -1,20 +1,6 @@ -We are pleased to announce the release 3.X.X of the GUDHI library. - -As a major new feature, the GUDHI library now offers ... - -We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.X.X.tar.gz). - -Below is a list of changes made since Gudhi 3.1.0: - -- [Module](link) - - ... - -- [Module](link) - - ... - -- Miscellaneous - - See the list of [bug fixes](https://github.com/GUDHI/gudhi-devel/issues?utf8=%E2%9C%93&q=is%3Aissue+label%3A3.X.X+). +gudhi-3.1.1 is a bug-fix release. In particular, it fixes the installation of the Python representation module. +The [list of bugs that were solved since gudhi-3.1.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.1.1+is%3Aclosed) is available on GitHub. All modules are distributed under the terms of the MIT license. However, there are still GPL dependencies for many modules. We invite you to check our [license dedicated web page](https://gudhi.inria.fr/licensing/) for further details. @@ -25,4 +11,4 @@ We provide [bibtex entries](https://gudhi.inria.fr/doc/latest/_citation.html) fo Feel free to [contact us](https://gudhi.inria.fr/contact/) in case you have any questions or remarks. -For further information about downloading and installing the library ([C++](https://gudhi.inria.fr/doc/3.1.0.rc1/installation.html) or [Python](https://gudhi.inria.fr/python/3.1.0.rc1/installation.html)), please visit the [GUDHI web site](https://gudhi.inria.fr/). +For further information about downloading and installing the library ([C++](https://gudhi.inria.fr/doc/3.1.1.rc1/installation.html) or [Python](https://gudhi.inria.fr/python/3.1.1.rc1/installation.html)), please visit the [GUDHI web site](https://gudhi.inria.fr/). -- cgit v1.2.3 From cbe3d0d2b16e19048928ae308851c4312cca42c8 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 7 Feb 2020 14:37:06 +0100 Subject: Release note and Version for 3.1.1 version --- CMakeGUDHIVersion.txt | 2 +- next_release.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt index ec9794ce..0f827b9e 100644 --- a/CMakeGUDHIVersion.txt +++ b/CMakeGUDHIVersion.txt @@ -1,6 +1,6 @@ set (GUDHI_MAJOR_VERSION 3) set (GUDHI_MINOR_VERSION 1) -set (GUDHI_PATCH_VERSION 1.rc1) +set (GUDHI_PATCH_VERSION 1) set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION}) message(STATUS "GUDHI version : ${GUDHI_VERSION}") diff --git a/next_release.md b/next_release.md index deb04085..78270d15 100644 --- a/next_release.md +++ b/next_release.md @@ -11,4 +11,4 @@ We provide [bibtex entries](https://gudhi.inria.fr/doc/latest/_citation.html) fo Feel free to [contact us](https://gudhi.inria.fr/contact/) in case you have any questions or remarks. -For further information about downloading and installing the library ([C++](https://gudhi.inria.fr/doc/3.1.1.rc1/installation.html) or [Python](https://gudhi.inria.fr/python/3.1.1.rc1/installation.html)), please visit the [GUDHI web site](https://gudhi.inria.fr/). +For further information about downloading and installing the library ([C++](https://gudhi.inria.fr/doc/3.1.1/installation.html) or [Python](https://gudhi.inria.fr/python/3.1.1/installation.html)), please visit the [GUDHI web site](https://gudhi.inria.fr/). -- cgit v1.2.3