multipers 2.2.3__cp311-cp311-win_amd64.whl → 2.3.0__cp311-cp311-win_amd64.whl

{multipers-2.2.3.dist-info → multipers-2.3.0.dist-info}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2023 David Loiseaux
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2023 David Loiseaux
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{multipers-2.2.3.dist-info → multipers-2.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: multipers
-Version: 2.2.3
+Version: 2.3.0
 Summary: Multiparameter Topological Persistence for Machine Learning
 Author-email: David Loiseaux <david.lapous@proton.me>, Hannah Schreiber <hannah.schreiber@inria.fr>
 Maintainer-email: David Loiseaux <david.lapous@proton.me>
@@ -56,25 +56,33 @@ Requires-Dist: pykeops
 Requires-Dist: pot
 
 # multipers : Multiparameter Persistence for Machine Learning
-[![Documentation](https://img.shields.io/badge/Documentation-website-blue)](https://davidlapous.github.io/multipers)
-[![DOI](https://joss.theoj.org/papers/10.21105/joss.06773/status.svg)](https://doi.org/10.21105/joss.06773)
-[![PyPI](https://img.shields.io/pypi/v/multipers?color=green)](https://pypi.org/project/multipers)
-[![Build, test](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml/badge.svg)](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml)
-[![Downloads](https://static.pepy.tech/badge/multipers)](https://pepy.tech/project/multipers)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06773/status.svg)](https://doi.org/10.21105/joss.06773) [![Documentation](https://img.shields.io/badge/Documentation-website-blue)](https://davidlapous.github.io/multipers) [![Build, test](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml/badge.svg)](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml)
 <br>
 Scikit-style PyTorch-autodiff multiparameter persistent homology python library. 
 This library aims to provide easy to use and performant strategies for applied multiparameter topology.
-<br> Meant to be integrated in [the Gudhi library](https://gudhi.inria.fr/).
+<br> Meant to be integrated in the [Gudhi](https://gudhi.inria.fr/) library.
+
+## Compiled packages
+| Source | Version | Downloads | Platforms | 
+| --- | --- | --- | --- | 
+| [![Conda Recipe](https://img.shields.io/badge/conda-recipe-green.svg)](https://anaconda.org/conda-forge/multipers)| [![Conda Version](https://img.shields.io/conda/vn/conda-forge/multipers.svg)](https://anaconda.org/conda-forge/multipers) |  [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/multipers.svg)](https://anaconda.org/conda-forge/multipers) |[![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/multipers.svg)](https://anaconda.org/conda-forge/multipers) | 
+| [![pip Recipe](https://img.shields.io/badge/pip-package-green.svg)](https:///pypi.org/project/multipers) | [![PyPI](https://img.shields.io/pypi/v/multipers?color=green)](https://pypi.org/project/multipers) | [![ pip downloads](https://static.pepy.tech/badge/multipers)](https://pepy.tech/project/multipers) | | 
+
+
 
 ## Quick start
 This library allows computing several representations from "geometrical datasets", e.g., point clouds, images, graphs, that have multiple scales.
 We provide some *nice* pictures in the [documentation](https://davidlapous.github.io/multipers/index.html). 
 A non-exhaustive list of features can be found in the **Features** section.
 
-This library is available [on PyPI](https://pypi.org/project/multipers/) for (reasonably up to date) Linux, macOS and Windows, via
+This library is available on pip and conda-forge for (reasonably up to date) Linux, macOS and Windows, via
 ```sh
 pip install multipers
 ```
+or 
+```sh
+conda install multipers -c conda-forge
+```
 
 Windows support is experimental, and some core dependencies are not available on Windows.
 We hence recommend Windows user to use [WSL](https://learn.microsoft.com/en-us/windows/wsl/).
@@ -95,6 +103,7 @@ This library features a bunch of different functions and helpers. See below for
  - [x] [[Chunk Reduction for Multi-Parameter Persistent Homology, SOCG2019]](https://doi.org/10.4230/LIPIcs.SoCG.2019.37) Multi-filtration preprocessing algorithm for homology computations.
  - [x] [[Computing Minimal Presentations and Bigraded Betti Numbers of 2-Parameter Persistent Homology, JAAG]](https://doi.org/10.1137/20M1388425) Minimal presentation of multiparameter persistence modules, using [mpfree](https://bitbucket.org/mkerber/mpfree/src/master/). Hilbert, Rank Decomposition Signed Measures, and MMA decompositions can be computed using the mpfree backend.
  - [x] [[Delaunay Bifiltrations of Functions on Point Clouds, SODA2024]](https://epubs.siam.org/doi/10.1137/1.9781611977912.173) Provides an alternative to function rips bifiltrations, using Delaunay complexes. Very good alternative to Rips-Density like bifiltrations.
+ - [x] [[Delaunay Core Bifiltration]](https://arxiv.org/abs/2405.01214) Bifiltration for point clouds, taking into account the density. Similar to Rips-Density. 
  - [x] [[Rivet]](https://github.com/rivetTDA/rivet) Interactive two parameter persistence
  - [x] [[Kernel Operations on the GPU, with Autodiff, without Memory Overflows, JMLR]](http://jmlr.org/papers/v22/20-275.html) Although not linked, at first glance, to persistence in any way, this library allows computing blazingly fast signed measures convolutions (and more!) with custom kernels. 
  - [ ] [Backend only] [[Projected distances for multi-parameter persistence modules]](https://arxiv.org/abs/2206.08818) Provides a strategy to estimate the convolution distance between multiparameter persistence module using projected barcodes. Implementation is a WIP.
@@ -103,11 +112,12 @@ This library features a bunch of different functions and helpers. See below for
 If I missed something, or you want to add something, feel free to open an issue.
 
 ## Authors
-[David Loiseaux](https://www-sop.inria.fr/members/David.Loiseaux/index.html),<br>
+[David Loiseaux](https://davidlapous.github.io/),<br>
 [Hannah Schreiber](https://github.com/hschreiber) (Persistence backend code),<br>
 [Luis Scoccola](https://luisscoccola.com/) 
 (Möbius inversion in python, degree-rips using [persistable](https://github.com/LuisScoccola/persistable) and [RIVET](https://github.com/rivetTDA/rivet/)),<br>
-[Mathieu Carrière](https://www-sop.inria.fr/members/Mathieu.Carriere/) (Sliced Wasserstein)<br>
+[Mathieu Carrière](https://www-sop.inria.fr/members/Mathieu.Carriere/) (Sliced Wasserstein),<br>
+[Odin Hoff Gardå](https://odinhg.github.io/) (Delaunay Core bifiltration).<br>
 
 ## Citation
 Please cite this library when using it in scientific publications;
@@ -130,5 +140,5 @@ you can use the following journal bibtex entry
 ```
 ## Contributions
 Feel free to contribute, report a bug on a pipeline, or ask for documentation by opening an issue.<br>
-In particular, if you have a nice example or application that is not taken care in the documentation (see the ./docs/notebooks/ folder), please contact me to add it there.
+In particular, if you have a nice example or application that is not taken care in the documentation (see the `./docs/notebooks/` folder), please contact me to add it there.
 

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multipers/tests/test_diff_helper.py

@@ -1,73 +0,0 @@
-import gudhi as gd
-import numpy as np
-
-import multipers as mp
-
-
-
-def test_h1_rips_density():
-    num_pts = 100
-    dim = 2
-    pts = np.random.uniform(size=(num_pts, dim))
-    weights = np.random.uniform(size=num_pts)
-    st = gd.RipsComplex(points=pts).create_simplex_tree()
-    st = mp.SimplexTreeMulti(st, num_parameters=2)
-    st.fill_lowerstar(weights, parameter=1)
-    st.collapse_edges(num=100)
-    st.expansion(2)
-    # F=st.get_filtration_grid()
-    # st.grid_squeeze(F, coordinate_values=True)
-    (sm,) = mp.signed_measure(st, degree=1, plot=True, mass_default=None)
-    pts, weights = sm
-    sm_indices, unmappable_points = st.pts_to_indices(pts, simplices_dimensions=[1, 0])
-    assert len(unmappable_points) == 0, "Found unmappable points in Rips edges ?"
-    filtration_values = np.array([f for _, f in st.get_simplices()])
-    reconstructed_measure = np.asarray(
-        [
-            [filtration_values[i][parameter] for parameter, i in enumerate(indices)]
-            for indices in sm_indices
-        ]
-    )
-    assert np.array_equal(
-        reconstructed_measure, pts
-    ), "Reconstructed measure is not equal to original measure ?"
-
-
-def test_h0_rips_density():
-    num_pts = 100
-    dim = 2
-    pts = np.random.uniform(size=(num_pts, dim))
-    weights = np.random.uniform(size=num_pts)
-    st = gd.RipsComplex(points=pts).create_simplex_tree()
-    st = mp.SimplexTreeMulti(st, num_parameters=2)
-    st.fill_lowerstar(weights, parameter=1)
-    st.collapse_edges(full=True)
-    # F=st.get_filtration_grid()
-    # st.grid_squeeze(F, coordinate_values=True)
-    (sm,) = mp.signed_measure(st, degree=0, plot=True, mass_default=None)
-    pts, weights = sm
-    _, unmappable_points = st.pts_to_indices(pts, simplices_dimensions=[1, 0])
-    assert (
-        pts[unmappable_points[:, 0]][:, 0] == 0
-    ).all(), "Unmapped points of H0 have to be the nodes of the rips."
-
-
-# def test_h1_rips_density_rank():
-# 	num_pts = 100
-# 	dim=2
-# 	pts = np.random.uniform(size=(num_pts,dim))
-# 	weights = np.random.uniform(size=num_pts)
-# 	st = gd.RipsComplex(points=pts).create_simplex_tree()
-# 	st = mp.SimplexTreeMulti(st, num_parameters=2)
-# 	st.fill_lowerstar(weights, parameter=1)
-# 	st.collapse_edges(full=True)
-# 	st.expansion(2)
-# 	# F=st.get_filtration_grid()
-# 	# st.grid_squeeze(F, coordinate_values=True)
-# 	sm, = mp.signed_measure(st, degree=1, plot=True, mass_default=None, invariant="rank_invariant", resolution=20, grid_strategy="quantile")
-# 	pts, weights = sm
-# 	sm_indices, unmappable_points = signed_measure_indices(st,pts, simplices_dimensions = [1,0])
-# 	assert len(unmappable_points) == 0,  'Found unmappable points in Rips edges ?'
-# 	filtration_values = np.array([f for _,f in st.get_simplices()])
-# 	reconstructed_measure = np.asarray([[filtration_values[i][parameter%2] for parameter,i in enumerate(indices)] for indices in sm_indices])
-# 	assert np.array_equal(reconstructed_measure, pts), 'Reconstructed measure is not equal to original measure ?'

multipers/tests/test_hilbert_function.py

@@ -1,82 +0,0 @@
-import numpy as np
-
-import multipers as mp
-from multipers import signed_measure
-
-
-
-
-# def test_1(): # TODO: test integrate_measure instead
-#     st = mp.SimplexTreeMulti(num_parameters=3)
-#     st.insert([0], [1, 0, 0])
-#     st.insert([1], [0, 1, 0])
-#     st.insert([2], [0, 0, 1])
-#     st.insert([0, 1, 2], [2, 2, 2])
-#     st.make_filtration_non_decreasing()
-#     st = st.grid_squeeze(grid_strategy="exact")
-#     assert np.array_equal(
-#         hilbert_surface(st, degrees=[0])[1],
-#         np.array(
-#             [
-#                 [
-#                     [[0, 1, 1], [1, 2, 2], [1, 2, 2]],
-#                     [[1, 2, 2], [2, 3, 3], [2, 3, 3]],
-#                     [[1, 2, 2], [2, 3, 3], [2, 3, 1]],
-#                 ]
-#             ]
-#         ),
-#     )
-#     assert np.array_equal(hilbert_surface(st, degrees=[0])[1][0], euler_surface(st)[1])
-
-
-# def test_2():
-#     st = mp.SimplexTreeMulti(num_parameters=4)
-#     st.insert([0], [1, 0, 0, 0])
-#     st.insert([1], [0, 1, 0, 0])
-#     st.insert([2], [0, 0, 1, 0])
-#     st.insert([3], [0, 0, 0, 1])
-#     st.insert([0, 1, 2, 3], [2, 2, 2, 2])
-#     st.make_filtration_non_decreasing()
-#     # list(st.get_simplices())
-#     st.grid_squeeze(grid_strategy="exact")
-#     assert np.array_equal(
-#         hilbert_surface(st, degrees=[0])[1][0], (euler_surface(st)[1])
-#     )
-
-
-def test_3():
-    st = mp.SimplexTreeMulti(num_parameters=2)
-    st.insert([0, 1, 2], [1] * st.num_parameters)
-    st.remove_maximal_simplex([0, 1, 2])
-    st = st.grid_squeeze(grid_strategy="exact")
-    ((a, b),) = mp.signed_measure(st, degrees=[1], mass_default=None)
-    assert np.array_equal(a, [[1, 1]]) and np.array_equal(b, [1])
-    assert mp.signed_measure(st, degrees=[1], mass_default="inf")[0][1].sum() == 0
-
-
-def test_4():
-    st = mp.SimplexTreeMulti(num_parameters=3)
-    st.insert([0], [1, 0, 0])
-    st.insert([1], [0, 1, 0])
-    st.insert([2], [0, 0, 1])
-    st.insert([0, 1, 2], [2, 2, 2])
-    st.make_filtration_non_decreasing()
-    # list(st.get_simplices())
-    st.grid_squeeze(grid_strategy="exact")
-    assert signed_measure(st, degrees=[0], mass_default="inf")[0][1].sum() == 0
-
-
-def test_5():
-    num_param = 7
-    st = mp.SimplexTreeMulti(num_parameters=num_param)
-    for i in range(num_param):
-        f = np.zeros(num_param)
-        f[i] = 1
-        st.insert([i], f)
-    st.insert(np.arange(num_param), [2] * num_param)
-    assert not st.make_filtration_non_decreasing()
-    st.grid_squeeze()
-    (a, b), (c, d) = signed_measure(st, degrees=[0, 1])
-    assert np.all(a[-1] == 2)
-    assert np.sum(b) == 1 and b[-1] == -(num_param - 1)
-    assert c.shape == (0, num_param)

multipers/tests/test_mma.py

@@ -1,83 +0,0 @@
-import numpy as np
-import pytest
-
-import multipers as mp
-import multipers.ml.mma as mma
-from multipers.tests import random_st
-
-
-
-def test_1():
-    st = mp.SimplexTreeMulti(num_parameters=2)
-    st.insert([0], [0, 1])
-    st.insert([1], [1, 0])
-    st.insert([0, 1], [1, 1])
-    mma_pymodule = st.persistence_approximation()
-    assert np.array_equal(mma_pymodule[0].get_birth_list(), [[0.0, 1.0], [1.0, 0.0]])
-    assert np.array_equal(mma_pymodule[0].get_death_list(), [[np.inf, np.inf]])
-
-
-def test_img():
-    simplextree = mp.SimplexTreeMulti(num_parameters=4)
-    simplextree.insert([0], [1, 2, 3, 4])
-    mod = simplextree.persistence_approximation(
-        box=[[0, 0, 0, 0], [5, 5, 5, 5]], max_error=1.0
-    )
-    img = mod.representation(resolution=6, kernel="linear")
-    assert np.isclose(img[0, 2, 3, 4, 5], 0.5)
-    assert np.isclose(img[0, 1, 1, 1, 1], 0)
-    assert np.isclose(img[0, 3, 4, 5, 5], 1)
-
-
-@pytest.mark.parametrize("n_jobs", [1, 2])
-@pytest.mark.parametrize("prune_degrees_above", [0, 1, None])
-def test_pipeline1(prune_degrees_above, n_jobs):
-    args = locals()
-    st = random_st(npts=50, max_dim=1).collapse_edges(-2)
-    st.expansion(2)
-    (truc1,) = mma.FilteredComplex2MMA(**args).fit_transform([[st]])[0]
-    (truc2,) = mma.FilteredComplex2MMA(**args).fit_transform([[mp.Slicer(st)]])[0]
-    box = st.filtration_bounds()
-    st_copy = st.copy()
-    if prune_degrees_above is not None:
-        st_copy.prune_above_dimension(prune_degrees_above)
-    output = mp.module_approximation(st_copy, box=box).representation(
-        bandwidth=0.1, kernel="linear"
-    )
-    assert np.sum(output) > 0, "Invalid mma rpz"
-    assert np.array_equal(
-        truc1.representation(bandwidth=0.1, kernel="linear"),
-        truc2.representation(bandwidth=0.1, kernel="linear"),
-    ), "Slicer == Simplextree not satisfied"
-    assert np.array_equal(truc1.representation(bandwidth=0.1, kernel="linear"), output)
-
-    st = [random_st(npts=50).collapse_edges(-2, ignore_warning=True) for _ in range(5)]
-    some_fited_pipeline = mma.FilteredComplex2MMA(**args).fit([st])
-    truc1 = some_fited_pipeline.transform([st])
-    truc2 = mma.FilteredComplex2MMA(**args).fit_transform(
-        [[mp.Slicer(truc) for truc in st]]
-    )
-    for a, b in zip(truc1, truc2):
-        assert np.array_equal(
-            a[0].representation(bandwidth=0.01, kernel="linear"),
-            b[0].representation(bandwidth=0.01, kernel="linear"),
-        ), "Slicer == Simplextree not satisfied"
-
-
-@pytest.mark.parametrize("n_jobs", [1, 2])
-@pytest.mark.parametrize("prune_degrees_above", [1, None])
-@pytest.mark.parametrize("expand_dim", [None, 2, 3])
-def test_pipeline2(prune_degrees_above, n_jobs, expand_dim):
-    args = locals()
-    st = random_st(max_dim=1)
-    st.collapse_edges(-2)
-    truc = mma.FilteredComplex2MMA(**args).fit_transform([[st]])[0]
-    box = st.filtration_bounds()
-    st_copy = st.copy()
-    # if prune_degrees_above is not None:
-    #     st_copy.prune_above_dimension(prune_degrees_above)
-    if expand_dim is not None:
-        st_copy.expansion(expand_dim)
-
-    output = mp.module_approximation(st_copy, box=box).representation(bandwidth=0.01)
-    assert np.array_equal(truc[0].representation(bandwidth=-0.01), output)

multipers/tests/test_point_clouds.py

@@ -1,49 +0,0 @@
-import numpy as np
-
-import multipers as mp
-import pytest
-import platform 
-np.random.seed(0)
-
-
-@pytest.mark.skipif(
-    platform.system() == "Windows",
-    reason="Detected windows. Pykeops is not compatible with windows yet. Skipping this ftm.",
-)
-def test_throw_test():
-    import multipers.ml.point_clouds as mmp
-    pts = np.array([[1, 1], [2, 2]], dtype=np.float32)
-    st = mmp.PointCloud2FilteredComplex(masses=[0.1]).fit_transform([pts])[0][0]
-    assert isinstance(st, mp.simplex_tree_multi.SimplexTreeMulti_type)
-    st = mmp.PointCloud2FilteredComplex(bandwidths=[-0.1], complex="alpha").fit_transform(
-        [pts]
-    )[0][0]
-    assert isinstance(st, mp.simplex_tree_multi.SimplexTreeMulti_type)
-
-    st = mmp.PointCloud2FilteredComplex(masses=[0.1], complex="alpha", output_type="slicer_novine").fit_transform(
-        [pts]
-    )[0][0]
-    assert isinstance(st, mp.slicer.Slicer_type)
-    assert st.is_vine is False
-
-    st = mmp.PointCloud2FilteredComplex(masses=[0.1], complex="alpha", output_type="slicer").fit_transform(
-        [pts]
-    )[0][0]
-    assert isinstance(st, mp.slicer.Slicer_type)
-    assert st.is_vine
-
-    st1, st2 = mmp.PointCloud2FilteredComplex(bandwidths=[0.1], masses=[0.1]).fit_transform(
-        [pts]
-    )[0]
-    assert isinstance(st1, mp.simplex_tree_multi.SimplexTreeMulti_type)
-    assert isinstance(st2, mp.simplex_tree_multi.SimplexTreeMulti_type)
-    ## ensures it doesn't throw
-    assert isinstance(
-        mp.module_approximation(st),
-        mp.multiparameter_module_approximation.PyModule_type,
-    )
-    assert mp.signed_measure(st, degree=None, invariant="euler")[0][0].ndim == 2
-    assert mp.signed_measure(st, degree=0, invariant="hilbert")[0][0].ndim == 2
-    assert mp.signed_measure(st, degree=0, invariant="rank")[0][0].ndim == 2
-    assert mp.signed_measure(st, degree=0, invariant="rank")[0][0].shape[1] == 4
-