v2.2.1

TL;DR: Bug fixes and optimizations.

[Features]

• SimplexTreeMulti are now pickle-able (thanks @hschreiber).
• Backend synced with gudhi PR
• Improved representation strings of slicer/simplextrees

[Fixes]

• In some situations, reading scc files from mpfree or function_delaunay was not giving the good degree
• Removed an optimization of GudhiCohomology to allow for arbitrary module presentation (@hschreiber)
• Fixed bugs preventing enabling the inf-optimization in all (non-vineyard) cases for Matrix and GudhiCohomology backends (@hschreiber).

[Optimizations]

• !Unsafe simplextree conversions are now safer, and enabled by default. This requires gudhi>=3.8.
  This can yield a significant performance (>20x) boost when converting gudhi simplextree to multipers.
• Re-enabled the inf-optimization for persistence slices with non-appearing simplices (@hschreiber).

[Documentation]

• !Changed the host to GitHub to auto-build the website with a GitHub action.

v2.2.0

TL;DR: Cubical complexes, Gudhi backend for slicers, and some nice optimizations and fixes.

Features

• Fill from distance matrix; similar to fill_lowerstar, but with distance matrices for clique complexes
• proper is_slicer, is_mma
• Compute grids from module approximation, and signed measures
• Typing improvements
• compute_bounding_box of given object
• benchmark file to check the performance of different alternatives
• unsqueeze operation. stuff.grid_squeeze(...).unsqueeze() should be the identity.
• GudhiCohomology backend for slicers. It uses native gudhi persistence for 1-parameter persistence computations.
  In some situations, this backend yields significantly faster non-vine computations.
• Cubical complexes from numpy tensor, with its corresponding notebook in the documentation.
• more tests, and tests are skipped if dependencies are not met.
• Better compilation options management. When compiling from source, the options can be tuned in the _tempita_grid_gen.py file.

Possibly breaking changes

• ! default rips threshold is now set to max-min of distance matrix. Topology is trivial after this point.
• ! representative cycles improvements (@hschreiber )
• ! non-vine slicers as default values. This is meant to make computation faster for signed measures, at the expense of a copy for module approximation (with a warning)
• ! squeezed slicers are unsqueezed before being written to an scc file (to prevent loss of information)
• ! disabled clement slicer backend, as it wasn't really used. This will be re-enabled when zigzag computations are needed, and can still be enabled when compiling from sources.
• ! simplextree manual insertion behaviour changed a bit.
  • Previous behaviour: insert simplex at specific location without any checks
  • New behaviour: each inserted simplex is insered at the first possible time with respect of the filtration that is greater than the given insertion value (defaults at $-\infty$). Also see GUDHI/gudhi-devel#974. Multi-critical filtrations are not affected (there is no natural definition for it in that case).

Fixes

• Point cloud pipeline was ignoring some arguments in some cases
• multipers initialization should load more documentation/core modules by default
• MMA representation pipelines issues
• Some hacks to fix the torch rips-density signed measure function

Optimizations

• vineyard backend optimizations (@hschreiber)
• Changed scc parser from python to cpp code (@hschreiber ) IO operations now also release the gil

v2.1.0

TL;DR SimplexTrees and Slicer behave more consistently, and share pipelines, complex reductions are better handled, and a bunch of backend code was changed.

Note. This may break code related to pipelines, or minimal presentations.
A bunch of code changed, as well as the interface, so bug are expected; please fill an issue if you find one.
Also, I may have forgotten some changes.

[Possibly breaking changes]

• ! Aligned minimal presentation degrees with (geometric) dimension.
• ! grid_conversion was renamed to grid
• ! Made pipeline take care of FilteredComplex=Union[SimplexTree,Slicer] instead of SimplexTree only.
  Warning This renamed pipelines: e.g.,
  • PointCloud2SimplexTree -> PointCloud2FilteredComplex,
  • SimplexTree2MMA -> FilteredComplex2MMA,
  • SimplexTree2SignedMeasure->FilteredComplex2SignedMeasure.
• method name uniformization between SimplexTree and Slicer
• Some default values were changed

[Features]

• Pipelines should handle both SimplexTrees and Slicers
• Minimal presentations are now checked, to prevent unnecessary computations (and bugs)
• mpfree is now an optional dependency (i.e., every function can be executed without this backend); but we still recommend users to use it for faster computations.
• Multi-Filtration backend update (sync with GUDHI/gudhi-devel#976) -- Thanks @hschreiber !
• Cleaner tempita templates
• optimized some tests
• Added a differentiable weakenned version of the delaunay complex bifiltration
• MMA representation
  • Better interface for custom kernels
  • More default kernels (now "exponential", "gaussian", "linear") and their signed versions
  • Optimized the code for custom kernels
• Added kernels to convolutions, e.g., sinc.
• Build system was updated -- Thanks @hschreiber !
• Bunch of typing fixes and improvements
• minimal presentations can be computed on multiple degrees at once
• Barcode estimation from line slices of rank invariant
• interfaced the barcodes (in parallel / vineyard) of lines from slicers
• updated barcode slicing of MMA outputs
• optimized and fixed (rank and hilbert) signed barcodes computations

[Documentation]

• Updated with latest version
• Improved documentation of some functions, e.g., signed_measure
• Added a contribution page #19, and issue templates
• Documentation now refers to github pages, for easier modification
• Fixed latex not rendering #18

v2.0.5

TL;DR Mostly bugfixes. And some optimizations to (non-vine) rank signed measure computations.

[Features]

• Slicer dimension pruning (similar to simplextree)
• Some documentation improvements, and type hints for slicer
• __repr__ for slicer (to show the various options)

[Fixes]

• Invariant was sometimes not properly infered from other arguments
• Simplextree's copy was not complete
• Module Formatter doesn't default anymore to degrees 0,1 when degree is not given
• Consistence between simplextree and slicer methods
• Plot argument are now taken into account for rank signed measures
• data and grids modules are imported by default (small + frequently used)

[Optimizations]

• Persistence computations with the non-vine pipeline now ignore infinite simplices
• Automatic dimension pruning when computing low homological degrees
• Point cloud generation in higher dimensions

[Workflows]

• Faster workflow, available for external contribution (without exposing secrets)
• For windows builds : still needs some investigation

v2.0.4

TL;DR. This is mostly a bugfix release, with some QOL warnings.

[Features]

• mass_default should be available for any invariant / conditions
• Persistence Matrix update (fixing several bugs with non-simplicial filtrations, and some optimizations)
• more natural choices in signed measures
• Slicer checks to prevent unnecessary computations (and mpfree segfaults)
• Slicer that come from minimal presentation now store their original dimension (under slicer.minpres_degree)
• Some external libraries, e.g., mpfree can break due to a boost update; added a check to remove a cryptic error message

[Bug Fixes]

• Rank invariant wasn't properly recovered in some conditions
• slicers could not be pushed on exact grids
• several other issues related to signed measures computations

[Tests]

• signed measure matrix of tests, and checking different backends (vanilla gudhi, persistence matrices with different options, mpfree)
• checks results with mpfree reductions, when available

v2.0.3

[Features]

• Compatibility with numpy>=2, gudhi>=3.10
• Added some missing functions in the doc
• test representative cycles

[Bug fixes]

• Fixed some bug which prevented multipers.signed_measure to properly recover the autodiff from the input, depending on the simplextree/slicer type or if using mpfree.
• Fixed a bug in multipers.signed_measure which, in some conditions, made it ignore the mass_default argument.
• It is now not possible anymore to give a grid resolution to exact strategies.
• added missing dependencies tqdm and matplotlib

Note

Some refactoring has been made to the multipers.signed_measure engine, and this requires some more testing.
Feel free to open an issue if you find one.

v2.0.2

[Features]

• Representative cycles are given by simplices instead of their keys, i.e., better interface
• Updated some documentation: added point cloud experiment from ICML 2024 paper

[Fixes]

• Differentiation of rips-density like: better errors

v2.0.1

[Features]

• More template activated (more columns, more numpy types) for slicers, simplextrees, mma modules
• weaken a simplextree to a flag complex
• weakened delaunay bifiltration auto-differentiation

[Fixes]

• mma modules from multiple slicers were not properly splitted
• some files generated by external libraries were not properly cleaned

v2.0.0

TL;DR: Differentiability, more k-critical support, and bunch of refactorizations.

Note. Due to the large amount of code moved, this release may contain some bugs.

[Features]

• templated simplextrees (float/int/kcritical)
• templated slicers (float/int/kcritical/vineyard/backend matrix column)
• templated module approximations
• more support for kcritical filtrations
• hilbert, rank invariant for multicritical filtrations
• differentiable signed measures
• rank invariant using vineyard, or any slicer
• non-inplace squeeze of slicer/st
• differentiable helpers (e.g. grids computations, convolutions)
• matrix backend updates (Thanks Hannah Schreiber)
• improved external libraries handling
• doc website, with notebook updates inside (Thanks Inés García-Redondo). Required dependencies: sphinx + myst-nb + sphinx_rtd_theme
• MMA module now can now be constructed from any orientations, and allows for custom paths
• more test coverage

[Fixes]

• removed some unsafe hacks in cpp
• plot fixes, and more consistent between invariants.
• Some pipelines were broken, due to some renamings.

[Optimizations]

• less copies between cpp and python, and some variable are view-able from python
• (Slightly) faster io with scc files
• backend optimizations
• simplextree python simplifications : __iter__ (same as get_simplices), __contains__ (same as find,), __getitem__ (same as simplex_filtration)

v1.2.2

[Features]

• clean measures (useful for euler characteristic)
• slicer to simplextree
• new grid module (multipers.grids)
• slicers can now be coarsenned
• Added proper build dependencies

[optimizations]

• grids optimizations
• backend optimizations

[Fixes]

• installations from venv