Geomstats v2.6.0

What's Changed

• fixing the typo in docs by @soma2000-lang in #1510
• compute log euclidean in closed form by @SaitejaUtpala in #1516
• Add trapz to backends by @luisfpereira in #1522
• Fix torch import in tests_backends by @luisfpereira in #1521
• Enhance notebook on cell shapes by analyzing with general elastic metric by @ninamiolane in #1526
• vectorization of connection.exp, addition of n_steps as argument in geodesic by @Jules-Deschamps in #1529
• Simple new pullbackdiffeo by @ymontmarin in #1514
• updates to riemannian metric by @Jules-Deschamps in #1535
• Add take to the backend by @luisfpereira in #1532
• Vectorize RiemannianMetric closest_neighbor_index by @luisfpereira in #1530
• SRV changes by @shubhamtalbar96 in #1525
• Use assertTrue and add assertAllEqual by @luisfpereira in #1539
• Simplify WrappedGaussianProcess by @luisfpereira in #1538
• Add pad to backend by @luisfpereira in #1541
• Graph space stratified by @annacalissano in #1488
• Initial docs reorganization by @luisfpereira in #1518
• gamma distributions by @Jules-Deschamps in #1523
• matrices.py: add 'full_matrices=False' to svd call by @ambellan in #1546
• Correct documentation rendering by @qbarthelemy in #1544
• Remove fixme and todo workflows by @luisfpereira in #1548
• Fix and simplify pytorch backend: array, einsum, from_numpy by @luisfpereira in #1550
• Correct documentation rendering, 2nd part by @qbarthelemy in #1549
• Incremetal Frechet Mean estimator for Non Positively Curved Maifolds by @SaitejaUtpala in #1533
• Function spaces implementation : starting with infinite dimensional spheres by @kiranvad in #1257
• Update Doc Website Index + Add Roadmap and Governance Pages by @ninamiolane in #1553
• Small edits to doc website by @ninamiolane in #1554
• Add Figure From Adele Myers' notebook to the main page by @ninamiolane in #1555
• Enhance governance's page by @ninamiolane in #1556
• Fix empty list array creation for torch by @luisfpereira in #1558
• Fix shape of HypersphereMetric and KendallShapeMetric by @ambellan in #1560
• Fix lint issues due to #1560 by @luisfpereira in #1562
• Add clean way of getting backend name by @luisfpereira in #1561
• WaldSpace without Geometry by @JonasLueg in #1455
• Fix functions to work with tensorflow by @luisfpereira in #1563
• Update backend name for more meaningful error messages by @luisfpereira in #1564
• Update roadmap by @ninamiolane in #1566
• Add hackathon page to website by @ninamiolane in #1567
• Improve dependency handling and CI installations by @luisfpereira in #1572
• Clean backend (only a bit) by @luisfpereira in #1570
• Add utils to download remote datasets by @luisfpereira in #1573
• Fix typo in notebooks tests by @luisfpereira in #1577
• Add tests for geodesic regression on Euclidean space (sanity check) and DiscreteCurves by @ninamiolane in #1576
• Fix: Frechet mean of discrete curves by computing in SRV space by @ninamiolane in #1579
• Start fixing inheritance in Product/NFold/Landmarks/Curves Spaces by @ninamiolane in #1581
• Refactor test_examples following test_notebooks strategy by @luisfpereira in #1582
• Real world application: optimization of traffic in Sao Paulo by @Jules-Deschamps in #1569
• Change location of test_examples and test together with notebooks by @luisfpereira in #1583
• Introductory Notebook for the Connection/RiemannianMetric Classes by @adelemyers99 in #1551
• Final Draft of Instructional Notebook for the Connection and RiemannianMetric Classes by @adelemyers99 in #1585
• Continue Refactoring of Landmarks inheriting from NFoldManifold and associated metrics and tests by @ninamiolane in #1590
• Start Refactoring of Discrete Curves by @ninamiolane in #1591
• unskip tests by @SaitejaUtpala in #1595
• Update hackathons.rst by @ninamiolane in #1594
• Simplify computations of the FrechetMean for the ElasticMetric by @ninamiolane in #1592
• Refactor Closed Curves by @ninamiolane in #1596
• Geometric median by @shubhamtalbar96 in #1565
• Use p for the rank of Grassmannian manifolds by @p16i in #1586
• Refactor backend and corresponding tests (part 1) by @luisfpereira in #1599
• Improve matching handling in graph space by @luisfpereira in #1584
• Refactor FrechetMean by @luisfpereira in #1601
• Sasaki metric by @ambellan in #1568
• Template for the issue tracker by @nanjekyejoannah in #1603
• TestData inheritance and automatic tests by @luisfpereira in #1517
• Add ability of using kwargs in test functions by @luisfpereira in #1609
• Fix bug in collecting test data by @luisfpereira in #1611
• The contributor guide by @nanjekyejoannah in #1597
• Make array_from_sparse more general by @luisfpereira in #1610
• Fix max version of scipy by @luisfpereira in #1619
• Add strategy to vectorize tests during data generation by @luisfpereira in #1613
• FIX: adding inject_radius constraint to enforce minimizing geodesics by @franciscoeacosta in #1621
• Add k_sampling_points as an attribute for spaces of curves by @ninamiolane in #1617
• ADD geodesic for elastic curves + FIX tests inheritance in RiemannianMetric, Connection, & ElasticMetric by @ninamiolane in #1622
• Update information geometry readme by @alebrigant in #1630
• added backend function gs.quantile by @wrongu in #1629
• Create multinomial distributions by @alebrigant in #1633
• Refactor discrete curves using FiberBundle and QuotientMetric by @alebrigant in #1632
• Fix vertical -> horizontal in docstring of discrete curves by @ninamiolane in #1635
• Fix test skipping by @luisfpereira in #1634
• Revert #1621 by @luisfpereira in #1636
• Correct documentation rendering, 3rd part by @qbarthelemy in #1641
• AAC for graph space by @luisfpereira in #1608
• Add ability to globally control default dtype by @luisfpereira in #1615
• Improve code and complete tests for geometric median by @qbarthelemy in #1642
• AAC: save last X by @annacalissano in #1648
• Fix use of "projection" in visualization example by @luisfpereira in #1649
• Update ubuntu version in workflows due to deprecation warning by @luisfpereira in #1650
• Make default_point_type a property by @luisfpereira in #1644
• Simplify super() by @luisfpereira in #1646
• Fix pullback metric for manifolds of dim 1 by @ninamiolane in #1653
• Improve MDM, adding weights and removing n_classes from parameters by @qbarthelemy in #1647
• Fix inheritance of GrassmanianCanonicallMetric, SpecialEuclidean and SpecialOrthogonal by @luisfpereira in #1652
• Remove redundant geomstats.tests by @luisfpereira in #1654
• Remove upper version limit on torch by @luisfpereira in #1661
• Fix expm due to changes in scipy.linalg.expm by @luisfpereira in #1660
• Remove greetings GitHub workflow that often fails by @ninamiolane in #1666
• Fix bug in the autodiff of pullback metric matrix by @ninamiolane in #1664
• Improve jacobian_and_hessian in autograd by @luisfpereira in #1667
• mixins for information geometry by @Jules-Deschamps in #1612
• Skip unit-tests that are failing too often (Stiefel, Gamma, Dirichlet) by @ninamiolane in #1672
• Rename: OpenSet's ambient_space -> embedding_space & SPDMetricXXX -> SPDXXXMetric by @ninamiolane in #1671
• Add curvature tensors - Follow-up from PR #1606 by @ninamiolane in #1668
• Second fundamental form + mean curvature vector of pull back metric by @ninamiolane in #1673
• Remove unnecessary use of metric as property and fix SpecialEuclideanMatrixCanonicalLeftMetric name by @luisfpereira in #1674
• Add hermitian matrices, follow-up from PR 1593 by @ninamiolane in #1675
• Consistency fix in visualization of Sphere/Circle by @ballerin in #1677
• Fix wrong scaling in NormalMetric by @alebrigant in #1676
• Fixes math renderings in notebook tutorials by @jubrau in #1679
• Change docstrings on random_point methods by @johnharveymath in #1688
• Vectorization of metric_matrix by @johnharveymath in #1693
• Remove CDTYPE = gs.get_default_cdtype() from complex manifolds by @YannCabanes in #1698
• ProductManifold and ProductRiemannianMetric by @johnharveymath in #1689
• Improve comments and error for random_tangent_vec by @jubrau in #1713
• Cherry pick changes from #1712 by @luisfpereira in #1719
• Make gs.random.rand consistent across backends for complex fields by @luisfpereira in #1721
• Add sectional curvature of univariate normal distributions + tests by @ninamiolane in #1723
• Add sectional curvature for the multinomials + missing tests by @ninamiolane in #1722
• Add HPD matrices by @YannCabanes in #1682
• Add Siegel by @YannCabanes in #1687
• Add statistical manifold of multivariate diagonal normal distributions by @antoinecollas in #1710
• Fix _pool_outputs_from_function in ProductManifold by @luisfpereira in #1728
• Fix complex manifold inheritance structure by @luisfpereira in #1732
• Update README.rst by @ninamiolane in #1735
• Fix Siegel log and exp errors for zero matrices by @YannCabanes in #1731
• Add conda install guidelines by @nguigs in #1733
• Add siegel sectional curvature by @YannCabanes in #1730
• "Outputs" of ihp hackathon by @luisfpereira in #1716
• Create multivariate normal distributions by @alebrigant in #1729
• Make submersion and tangent_submersion abstract in LevelSet by @luisfpereira in #1681
• Amend errors.check_point_shape by @johnharveymath in #1736
• Update backend random distributions to accept complex type by @luisfpereira in #1741
• Fix point shapes by @luisfpereira in #1739
• Add the positive reals manifold by @YannCabanes in #1701
• Update sr metric and create notebook and tests by @mortenapedersen in #1467
• Fix autograd value_and_grad to avoid duplicate computation of value by @luisfpereira in #1743
• Update gsod.rst with Case Study by @ninamiolane in #1744
• Update gsod.rst: Edits on case study by @ninamiolane in #1745
• Simplify univariate normal metric matrix by @tramy1258 in #1746
• Fix FisherRaoMetric inner product derivative matrix by @luisfpereira in #1747
• Fix learning algorithms to work with last sklearn version by @luisfpereira in #1754
• Add complex poincare disk by @YannCabanes in #1709
• Simplify PositiveRealsMetric by @luisfpereira in #1756
• Two different versions of the scalar product metric. by @johnharveymath in #1740
• Support product manifolds of matrices by @YannCabanes in #1737
• Correct scaling in ScalarProductMetric by @johnharveymath in #1763
• Reserve scale parameter to ScalarProductMetric by @johnharveymath in #1761
• Remove code duplication in ProductManifold and ProductManifoldMetric by @luisfpereira in #1762
• Add product hpd matrices and siegel disks by @YannCabanes in #1727
• Fix SiegelMetric for tf by @luisfpereira in #1766
• Remove unnecessary metric specification in ProductHPDMatricesAndSiegelDisks by @YannCabanes in #1765
• Remove scales product manifold by @luisfpereira in #1768
• Allow gs.stack to receive arrays of different dtypes in tf by @luisfpereira in #1769
• Extend product manifold to handle factors with different fields by @luisfpereira in #1770
• Fixes and improvements coming from test refactoring by @luisfpereira in #1771
• Address deep source issues by @luisfpereira in #1772
• Stop tf tests in CI by @luisfpereira in #1773
• Fix typos and dead link for issues. by @johmathe in #1776
• Update PULL_REQUEST_TEMPLATE.md by @johmathe in #1779
• Skip failing tests by @johmathe in #1781
• Remove tf from cov flags by @johmathe in #1782
• Keep sphinx at v 5.3.0 by @johmathe in #1784
• Remove tensorflow backend by @johmathe in #1778
• Fix bugs that arise for complex matrices by @sophiaas in #1787
• Fix graph space notebooks due to new release of networkx by @luisfpereira in #1789
• Add functions and associated tests for Binomial and Exponential Distributions by @tramy1258 in #1755
• Fix sqrtm for pytorch due to changes in scipy by @luisfpereira in #1790
• Follow-up PR #1787 by @ninamiolane in #1791
• Skip failing tests to clean CI by @ninamiolane in #1792
• Update setup.cfg by @johnharveymath in #1793
• Fix link to contributing guide. by @olivierverdier in #1795
• Refactor Product and NFold by @johnharveymath in #1774
• Fix complex output types by @luisfpereira in #1798
• Add product positive reals and complex poincare disks by @YannCabanes in #1764
• Add Poisson and geometric distributions and associated tests by @tramy1258 in #1785
• Fix align in SRVShapeBundle by @alebrigant in #1823
• Freeze black version due to breaking updates by @luisfpereira in #1827
• Correct NotImplementedError log by @monsij in #1799
• Fixes and improvements coming from test refactoring (part 2) by @luisfpereira in #1828
• Allow vectorization for Fisher Rao Metric by @tramy1258 in #1809
• Make SRVMetric on DiscreteCurves inherit from PullbackDiffeoMetric by @alebrigant in #1714
• feat(ci): add pip caching to CI by @SauravMaheshkar in #1839
• Fix bad squeezes in random_unit_tangent_vec by @tramy1258 in #1837
• Make torch.linspace accept array-like inputs by @tramy1258 in #1835
• Minor changes so Developer setup works by @HarrisonSantiago in #1840
• ElasticMetric inherits from PullbackDiffeoMetric by @Abdellaoui-Souhail in #1844
• Continue PR 1711 on discrete surfaces by @ninamiolane in #1815
• Added Discrete Surfaces with Elastic Metrics by @emmanuel-hartman in #1711
• Refactor metric to receive space (equip_with_metric behavior) by @luisfpereira in #1836
• Fixes and improvements coming from test refactoring (part 3) by @luisfpereira in #1848
• Dynamic programming algorithm for computing distances and geodesics for the SRV metric by @Abdellaoui-Souhail in #1847
• Numerical solvers for log, exp, geodesic, ... by @luisfpereira in #1845
• Elastic Riemannian metrics of order 2 on parameterized discrete surfaces by @ninamiolane in #1852
• Remove code duplication between numpy and autograd backends by @luisfpereira in #1853
• feat(build): switch to pyproject.toml for packaging by @SauravMaheshkar in #1842
• Unfreeze sphinx by @luisfpereira in #1856
• Unfreeze black by @luisfpereira in #1855
• Bump python 3.11 by @luisfpereira in #1854
• Refactor Stiefel by @luisfpereira in #1858
• Refactor information geometry by @luisfpereira in #1860
• Fix product metric by @Abdellaoui-Souhail in #1862
• Update connection to use solvers by @luisfpereira in #1864
• Update README.rst: Python 3.7 --> 3.11 by @ninamiolane in #1865
• Prepare release 2.6.0 by @luisfpereira in #1866
• Correct Zenodo link by @johnharveymath in #1869
• Unfreeze numpy and update code for scipy 1.11.0 by @luisfpereira in #1870
• Fix test_connection due to use of solvers by @luisfpereira in #1867

New Contributors

• @soma2000-lang made their first contribution in #1510
• @ymontmarin made their first contribution in #1514
• @shubhamtalbar96 made their first contribution in #1525
• @ambellan made their first contribution in #1546
• @kiranvad made their first contribution in #1257
• @JonasLueg made their first contribution in #1455
• @nanjekyejoannah made their first contribution in #1603
• @franciscoeacosta made their first contribution in #1621
• @wrongu made their first contribution in #1629
• @ballerin made their first contribution in #1677
• @jubrau made their first contribution in #1679
• @johnharveymath made their first contribution in #1688
• @antoinecollas made their first contribution in #1710
• @tramy1258 made their first contribution in #1746
• @olivierverdier made their first contribution in #1795
• @SauravMaheshkar made their first contribution in #1839
• @HarrisonSantiago made their first contribution in #1840
• @Abdellaoui-Souhail made their first contribution in #1844
• @emmanuel-hartman made their first contribution in #1711

Full Changelog: 2.5.0...2.6.0