Hardening
Environments
An Environment is one runnable biopixi fixture: a pixi.toml that installs and
runs without biopixi present. The grade scores how portable the packaging is, from L0
out-of-profile to L4, which requires a container observed at a public registry rather than
inferred from the package count. It says nothing about whether the science inside is any good.
L4 3 fixtures
- mmseqs2 MMseqs2, for fast sequence clustering — the tool that makes leakage-safe benchmark splits practical. application/structure-qamodality/sequence
- phate PHATE, a diffusion-based embedding for visualizing continuous trajectory structure in single-cell data. method/spectral-geometryapplication/single-cellmodality/high-dim-tabular
- ripser-cpp The Ripser C++ command-line tool for fast Vietoris-Rips persistent homology, installed as a single Bioconda package. method/persistent-homologymodality/point-cloud
L3 14 fixtures
- ann-backends hnswlib and pynndescent together, pinning the approximate-nearest-neighbour backends that make kNN graphs reproducible. application/single-cellmodality/high-dim-tabular
- batch-integration harmonypy and scanorama together, supplying the batch-integration step ahead of geometry learning on multi-sample cohorts. application/single-cellmodality/high-dim-tabular
- biopython Biopython, the structure and sequence I/O layer most other fixtures in this corpus parse their inputs through. modality/molecular-structuremodality/sequence
- dionysus Dionysus, a persistent-homology library with support for vineyards and circular coordinates alongside ordinary persistence. method/persistent-homologymodality/point-cloud
- dockq DockQ, the reference interface-quality metric that the topological scorers in this corpus are trained and judged against. application/structure-qamodality/molecular-structure
- dssp DSSP, providing the mkdssp binary for secondary-structure assignment and solvent accessibility from a structure. application/structure-qamodality/molecular-structure
- gudhi GUDHI, the general-purpose computational topology library covering simplicial complexes, filtrations, and persistence. method/persistent-homologymodality/point-cloud
- persim persim, the scikit-tda component for comparing and vectorizing persistence diagrams once they have been computed. method/persistent-homology
- prody ProDy, supplying the elastic network models whose training-free normal-mode analysis anchors per-residue flexibility prediction. application/molecular-sciencesmodality/molecular-structure
- ripser-py The ripser.py Python bindings over the Ripser engine, for computing persistence diagrams inside a Python workflow. method/persistent-homologymodality/point-cloud
- scanpy Scanpy and AnnData, the single-cell data structures and preprocessing the TopoMetry workflows are written against. application/single-cellmodality/high-dim-tabular
- scvelo scVelo for RNA velocity, the velocity half of the cell-cycle replication, run downstream of the learned geometry. application/single-cellmodality/high-dim-tabular
- scvi scvi-tools, the deep generative single-cell embedding used as a learned-representation comparator. application/single-cellmodality/high-dim-tabular
- topometry TopoMetry 0.2.1.1 from conda-forge: a packaging fixture pinning the only build on the channel, four years behind the paper. method/spectral-geometryapplication/single-cellmodality/high-dim-tabular
L1 14 fixtures
- giotto-ph giotto-ph, a parallel Rips persistence backend, built from an in-repo recipe because it vendors its C++ engine as submodules. method/persistent-homologymodality/point-cloud
- kmapper KeplerMapper, a Python implementation of the Mapper algorithm for building nerve-graph summaries of a point cloud. method/mappermodality/point-cloud
- open-topodockq-featurizer The MIT clean-room reimplementation of TopoDockQ's interface featurizer, bit-exact against the bytecode it replaces. method/persistent-laplacianapplication/structure-qamodality/molecular-structure
- open-topoqa-featurizer The MIT clean-room TopoQA interface featurizer, reproduced from the paper because the upstream code carries no license. method/persistent-homologyapplication/structure-qamodality/molecular-structure
- open-topoqa-scorer The MIT clean-room ProteinGAT scorer that closes the open TopoQA vertical, with weights retrained rather than reused. method/topological-deep-learningapplication/structure-qamodality/molecular-structure
- petls Upstream PETLS, the compiled persistent-topological-Laplacian library, kept as a local oracle rather than a shippable dependency. method/persistent-laplacian
- petls-pytorch The Apache-2.0 pure-Python reimplementation of PETLS, and the redistributable persistent-Laplacian engine this corpus actually ships. method/persistent-laplacian
- phat PHAT, the C++ persistent-homology matrix-reduction backend, exposed through pybind11 and built from an in-repo recipe. method/persistent-homology
- pydowker The full two-parameter persistence stack: pyDowker over pyrivet over the RIVET console engine, built as a three-recipe chain. method/multiparameter-persistencemethod/persistent-homologymodality/point-cloud
- pyflagser pyflagser, for persistent homology of directed flag complexes, built from an in-repo recipe over a vendored C++ engine. method/persistent-homology
- r-tda The R TDA package, covering persistent homology, density clustering, and statistical inference on diagrams from R. method/persistent-homologymodality/point-cloud
- r-tdastats TDAstats, a lightweight R interface to Ripser with plotting and hypothesis testing on persistence diagrams. method/persistent-homologymodality/point-cloud
- scikit-tda The scikit-tda meta-package, pulling the Python TDA stack together behind one install. method/persistent-homologymethod/mappermodality/point-cloud
- topometry-1.1 TopoMetry 1.1.0, the release the eLife version of record describes, staged from an in-repo recipe that fixes two upstream defects. method/spectral-geometryapplication/single-cellmodality/high-dim-tabular
L0 3 fixtures
- giotto-tda giotto-tda, the scikit-learn-compatible TDA toolkit, and the corpus's deliberate out-of-profile L0 fixture. method/persistent-homologymethod/mappermodality/point-cloud
- hiponet The HiPoNet research codebase run from a pinned git clone, with a locked dependency closure but nothing installable to package. method/simplicial-learningmethod/topological-deep-learningapplication/single-cellmodality/high-dim-tabular
- topodockq The TopoDockQ scorer run from a pinned git clone; MIT-licensed but built around a Python 3.8 bytecode core with no source. method/persistent-laplacianmethod/topological-deep-learningapplication/structure-qamodality/molecular-structure