Florian Frantzen

Add a separate numpydoc validation step to the projects CI setup, similar to pyt-team/TopoNetX#318.

Add a separate numpydoc validation step to the projects CI setup, similar to pyt-team/TopoNetX#318.

`Dist2Cycle` never calls `Dist2CycleLayer`s

5

While `Dist2CycleLayer`s are [correctly constructed](https://github.com/pyt-team/TopoModelX/blob/e4a893fcb2e99c9868b1423c41bb4d90893f85bc/topomodelx/nn/simplicial/dist2cycle.py#L19) in `Dist2Cyle`, they are [never actually called](https://github.com/pyt-team/TopoModelX/blob/e4a893fcb2e99c9868b1423c41bb4d90893f85bc/topomodelx/nn/simplicial/dist2cycle.py#L55). - [ ] Correctly call layers in the `forward` method. - [ ] This should have been catched...

TopoModelX contains some scatter functions in `utils.scatter`, that -- according to the module docstring -- are adapted from `torch_scatter`. Is there a specific reason why we ship our own implementation?...

Use `Self` return type where applicable

1

The `Self` return type has been introduced in Python 3.11. It allows to express that the return type is of the current enclosed class while correctly considering subclasses. As usual,...

Use new `@deprecated` decorator

1

The `@deprecated` decorator has been proposed in PEP 702 and is part of Python 3.13. The huge benefit of the decorator is that it moves deprecations into the type system,...

First Implementation of a Simplex Trie

10

This implements a simplex trie as presented in [1] as backend data structure for the `SimplicialComplex` class. This is also used in gudhi's SC implementation. However, they do not expose...

Import Convention for TopoNetX

1

Since #215, classes and functions are only available with explicit imports, e.g.: ```python from toponetx.classes import SimplicialComplex from toponetx.transform import graph_to_clique_complex SC1 = SimplicialComplex() SC2 = graph_to_clique_complex(nx.erdos_renyi_graph(50, 0.3)) ``` Following...

After submission to JMLR, we should add a corresponding `CITATION.cff` file to the repository. GitHub uses this to help users cite this work. See [the documentation](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files), in particular the section...

SciPy and downstream packages (e.g., NetworkX) transition from sparse matrices to sparse arrays, featuring a more NumPy array-like interface. See for example the first note in `scipy.sparse`: https://docs.scipy.org/doc/scipy/reference/sparse.html. We should...