gudhi-devel
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GUDHI
The GUDHI library is a generic open source C++ library, with a Python interface, for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding.
I'm currently working on comparing the open source implementations of the Mapper algorithm[^1] and the python binding for Gudhi's cover complexes has very unusual performance characteristics in my tests. I...
https://github.com/GUDHI/gudhi-devel/blob/71beeb391cef793836e2d91598f9f942748edbb0/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h#L254 We should add the corresponding typedefs directly so we don't need to derive from it.
According to [https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.cKDTree.query.html#scipy.spatial.cKDTree.query](kdtree query documentation), `n_jobs` is deprecated starting from scipy>=1.9.0. With scipy 1.9.0, this leads to an error in `test_tomato.py`: ``` gudhi/point_cloud/knn.py:318: in transform distances, neighbors = self.kdtree.query(X, k=self.k,...
After [3.0.0 python documentation](https://gudhi.inria.fr/python/3.0.0/), sphinx search tool is broken. sphinx was 1.7.4 On [3.1.0 python documentation](https://gudhi.inria.fr/python/3.1.0/), search tool is no more working, with sphinx 2.3.0. A good start would be...
With sphinx >= 5.0.0, in generated `sphinx/_static/classic.css` file, one can see: ```css div.document { display: flex; background-color: white; } ``` which leads to the same issue than [this python-docs-theme issue](https://github.com/python/python-docs-theme/issues/92)....
Seems to be quite faster on OSx with ninja. 1h02m51s without, versus 43m27s with ninja. TODO: try on windows also
Added Embedded_cubical_complex to compute hybrid_transforms
[PeriodicCubicalComplex.cofaces_of_persistence_pairs](https://gudhi.inria.fr/python/latest/periodic_cubical_complex_ref.html#gudhi.PeriodicCubicalComplex.cofaces_of_persistence_pairs) and [CubicalComplex.cofaces_of_persistence_pairs](https://gudhi.inria.fr/python/latest/cubical_complex_ref.html#gudhi.CubicalComplex.cofaces_of_persistence_pairs) require a note to explain that cofaces_of_persistence_pairs requires [compute_persistence()](https://gudhi.inria.fr/python/latest/cubical_complex_ref.html#gudhi.CubicalComplex.compute_persistence) function to be launched first. (cf. [betti numbers method](https://gudhi.inria.fr/python/latest/cubical_complex_ref.html#gudhi.CubicalComplex.betti_numbers))
On the page documentation bage index.html we see:  this information is correct but we see here 2 header types: - a "group" header:  - a "package" header ...
When looking at the page class_gudhi_1_1cech__complex_1_1_cech__complex.html we see:  in my personal opinion, this doesn't look nice. I would have expected something more in the standard doxygen style like: ...