petls-pytorch 1.0.0__tar.gz

petls_pytorch-1.0.0/LICENSE

@@ -0,0 +1,201 @@
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petls_pytorch-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: petls-pytorch
+Version: 1.0.0
+Summary: GPU-native Persistent Topological Laplacians in PyTorch
+Author-email: "Sumner K. Marston" <sumner@sylverity.com>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/Sylverity/petls-pytorch
+Project-URL: Repository, https://github.com/Sylverity/petls-pytorch
+Keywords: topological-data-analysis,persistent-laplacian,pytorch,gpu
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch>=2.0.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: scipy>=1.10.0
+Requires-Dist: gudhi>=3.10.0
+Requires-Dist: pyflagser>=0.0.1
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: matplotlib>=3.7.0
+Requires-Dist: tadasets>=0.2.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.4.0; extra == "dev"
+Requires-Dist: pytest-benchmark>=4.0.0; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Requires-Dist: mypy>=1.5.0; extra == "dev"
+Dynamic: license-file
+
+# PETLS-PyTorch
+
+A PyTorch-native implementation of persistent topological Laplacians, based on the
+public PETLS API, PETLS documentation, and the algorithms described in the
+**PETLS** paper.
+
+The goal of this project is to make PETLS-style computations easier to use in
+Python and PyTorch workflows, especially when downstream code already works with
+torch tensors or CUDA devices. The original C++/pybind11 PETLS implementation
+remains the reference for correctness.
+
+## Quick Start
+
+```python
+import petls_torch
+
+# Alpha complex from point cloud
+alpha = petls_torch.Alpha(points=[[0, 0], [1, 0], [0.5, 1]], max_dim=2)
+eigs = alpha.spectra(0, 0.0, 1.0)
+
+# Rips complex from distance matrix
+rips = petls_torch.Rips(distances=[[0, 1, 1], [1, 0, 1], [1, 1, 0]], max_dim=2)
+
+# Directed flag complex from .flag file
+dflag = petls_torch.dFlag("graph.flag", max_dim=3)
+
+# Sheaf Laplacian
+sst = petls_torch.sheaf_simplex_tree(st, extra_data, restriction)
+psl = petls_torch.PersistentSheafLaplacian(sst)
+```
+
+## Relationship to PETLS
+
+`petls_torch` is an independent PyTorch-native implementation of the PETLS
+methods and public API behavior, with attribution to the original PETLS paper
+and project. Correctness tests compare against the original implementation using
+shared inputs and the default tolerances used in this repository.
+
+This project is based on the public PETLS API, PETLS documentation, and the
+algorithms described in the PETLS paper. No source code from the original PETLS
+implementation is included in this repository.
+
+## API Coverage
+
+| Original PETLS API | PyTorch API | Status |
+|--------------------|-------------|--------|
+| `Complex` | `Complex` | Implemented |
+| `Alpha` | `Alpha` | Implemented |
+| `Rips` | `Rips` | Implemented |
+| `dFlag` | `dFlag` | Implemented |
+| `sheaf_simplex_tree` | `sheaf_simplex_tree` | Implemented |
+| `PersistentSheafLaplacian` | `PersistentSheafLaplacian` | Implemented |
+| `Profile`, `timer` | `Profile`, `Timer` | Implemented |
+| `summaries`, `plot_summary` | `summaries`, `plot_summary` | Implemented |
+| `up_Algorithms` enum | `up_Algorithms` enum | Implemented |
+| `eigvalsh_wrapper`, `sparse_wrapper`, `matrix_is_diagonal` | Same | Implemented |
+| `flipped` optimization | `flipped` + `get_L_top_dim_flipped` | Implemented |
+| `nonzero_spectra()` | `nonzero_spectra()` | Implemented |
+| `store_L()`, `store_spectra()`, `store_spectra_summary()` | Same | Implemented |
+| `time_to_csv()` | `time_to_csv()` | Implemented |
+
+## Benchmark Notes
+
+The benchmark results below are included to give a sense of current runtime
+behavior on one local machine. They should be read as preliminary measurements,
+not as a comprehensive performance study.
+
+The benchmark suite uses the same synthetic datasets, filtrations, and matrix
+sizes for both packages. The shared benchmark runner is parameterized with
+`--package petls` or `--package petls_torch`.
+
+### Hardware
+
+- CPU: Intel i7-14700K
+- GPU: NVIDIA RTX 4070 Ti 12GB
+- PyTorch 2.x with CUDA 12.x
+
+### Quick Preset
+
+Configuration: torus `n=500` plus sphere `n=300`, `max_dim=2`, 8 filtrations
+per dataset.
+
+| Package | Device | Total Time | Mean Trial | Mean Build | Mean Eigs |
+|---------|--------|-----------:|-----------:|-----------:|----------:|
+| `petls` | CPU | 8.29 s | 172.6 ms | 15.2 ms | 157.4 ms |
+| `petls_torch` | CPU | 1.82 s | 37.9 ms | 4.8 ms | 33.1 ms |
+| `petls_torch` | CUDA | 1.85 s | 38.5 ms | 4.7 ms | 33.8 ms |
+
+On this workload, the PyTorch implementation is about 4.5x faster than the
+reference PETLS run on the same CPU. The CUDA timing is similar to the CPU
+timing for this preset, which suggests that eigendecomposition and data sizes
+are still small enough that GPU overhead can offset part of the benefit.
+
+### Medium Workload
+
+Configuration: torus `n=500`, `max_dim=3`, 16 filtrations.
+
+| Package | Device | Total Time | Mean Trial | Max Matrix | Status |
+|---------|--------|-----------:|-----------:|-----------:|--------|
+| `petls` | CPU | > 300 s | unavailable | unavailable | Reached benchmark timeout |
+| `petls_torch` | CUDA | 8.80 s | 137.5 ms | 5990 x 5990 | Completed |
+
+For this larger dense-eigendecomposition workload, the PyTorch/CUDA path
+completed within the benchmark timeout. The PETLS CPU run reached the configured
+300-second timeout in this test configuration.
+
+### Operation Breakdown
+
+Quick preset timings:
+
+```text
+petls (CPU)          : build=15.2 ms  eigs=157.4 ms
+petls_torch (CPU)    : build=4.8 ms   eigs=33.1 ms
+petls_torch (CUDA)   : build=4.7 ms   eigs=33.8 ms
+```
+
+In these measurements, most time is spent in eigendecomposition. The PyTorch
+implementation benefits from PyTorch's dense linear algebra backends on CPU and
+from CUDA support on larger matrix workloads.
+
+## Running Benchmarks
+
+```bash
+# Original PETLS
+cd /path/to/workspace
+python -m benchmark_shared --preset quick --package petls --algorithm eigvalsh
+
+# PETLS-PyTorch on CUDA
+python -m benchmark_shared --preset quick --package petls_torch --algorithm eigvalsh --device cuda
+
+# PETLS-PyTorch on CPU
+python -m benchmark_shared --preset quick --package petls_torch --algorithm eigvalsh --device cpu
+
+# Custom single run
+python -m benchmark_shared \
+    --dataset torus --n_points 2000 --complex alpha --max_dim 3 \
+    --package petls_torch --algorithm eigvalsh
+```
+
+## Installation
+
+```bash
+pip install petls-pytorch
+```
+
+Dependencies:
+
+- `torch`
+- `numpy`
+- `scipy`
+- `gudhi`
+- `pyflagser`
+- `tadasets` for benchmarks
+
+## Test Suite
+
+```bash
+cd PETLS-PYTORCH
+pytest tests/ -v
+```
+
+The test suite covers core functionality, Rips complexes, alpha complexes,
+directed flag complexes, sheaf support, eigenvalue utilities, and I/O helpers.
+
+## Citation
+
+If you use `petls_torch` in research, please cite both this PyTorch
+implementation and the original PETLS paper.
+
+### PETLS-PyTorch
+
+```bibtex
+@software{marston2026petlstorch,
+  title        = {PETLS-PyTorch: A PyTorch-native implementation of persistent topological Laplacians},
+  author       = {Marston, Sumner K.},
+  year         = {2026},
+  publisher    = {Sylverity Research},
+  url          = {https://github.com/Sylverity/petls-pytorch}
+}
+```
+
+### Original PETLS paper
+
+```bibtex
+@misc{jones2025petlspersistenttopologicallaplacian,
+    title={PETLS: PErsistent Topological Laplacian Software},
+    author={Benjamin Jones and Guo-Wei Wei},
+    year={2025},
+    eprint={2508.11560},
+    archivePrefix={arXiv},
+    primaryClass={math.AT},
+    url={https://arxiv.org/abs/2508.11560},
+}
+```
+
+This project is an independent PyTorch-native implementation based on the
+public PETLS API, PETLS documentation, and the PETLS paper. No source code from
+the original PETLS implementation is included in this repository.
+
+- Original PETLS repository: https://github.com/bdjones13/PETLS
+- PETLS documentation: https://www.benjones-math.com/software/PETLS/
+- PETLS paper: https://arxiv.org/abs/2508.11560

petls_pytorch-1.0.0/README.md

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+# PETLS-PyTorch
+
+A PyTorch-native implementation of persistent topological Laplacians, based on the
+public PETLS API, PETLS documentation, and the algorithms described in the
+**PETLS** paper.
+
+The goal of this project is to make PETLS-style computations easier to use in
+Python and PyTorch workflows, especially when downstream code already works with
+torch tensors or CUDA devices. The original C++/pybind11 PETLS implementation
+remains the reference for correctness.
+
+## Quick Start
+
+```python
+import petls_torch
+
+# Alpha complex from point cloud
+alpha = petls_torch.Alpha(points=[[0, 0], [1, 0], [0.5, 1]], max_dim=2)
+eigs = alpha.spectra(0, 0.0, 1.0)
+
+# Rips complex from distance matrix
+rips = petls_torch.Rips(distances=[[0, 1, 1], [1, 0, 1], [1, 1, 0]], max_dim=2)
+
+# Directed flag complex from .flag file
+dflag = petls_torch.dFlag("graph.flag", max_dim=3)
+
+# Sheaf Laplacian
+sst = petls_torch.sheaf_simplex_tree(st, extra_data, restriction)
+psl = petls_torch.PersistentSheafLaplacian(sst)
+```
+
+## Relationship to PETLS
+
+`petls_torch` is an independent PyTorch-native implementation of the PETLS
+methods and public API behavior, with attribution to the original PETLS paper
+and project. Correctness tests compare against the original implementation using
+shared inputs and the default tolerances used in this repository.
+
+This project is based on the public PETLS API, PETLS documentation, and the
+algorithms described in the PETLS paper. No source code from the original PETLS
+implementation is included in this repository.
+
+## API Coverage
+
+| Original PETLS API | PyTorch API | Status |
+|--------------------|-------------|--------|
+| `Complex` | `Complex` | Implemented |
+| `Alpha` | `Alpha` | Implemented |
+| `Rips` | `Rips` | Implemented |
+| `dFlag` | `dFlag` | Implemented |
+| `sheaf_simplex_tree` | `sheaf_simplex_tree` | Implemented |
+| `PersistentSheafLaplacian` | `PersistentSheafLaplacian` | Implemented |
+| `Profile`, `timer` | `Profile`, `Timer` | Implemented |
+| `summaries`, `plot_summary` | `summaries`, `plot_summary` | Implemented |
+| `up_Algorithms` enum | `up_Algorithms` enum | Implemented |
+| `eigvalsh_wrapper`, `sparse_wrapper`, `matrix_is_diagonal` | Same | Implemented |
+| `flipped` optimization | `flipped` + `get_L_top_dim_flipped` | Implemented |
+| `nonzero_spectra()` | `nonzero_spectra()` | Implemented |
+| `store_L()`, `store_spectra()`, `store_spectra_summary()` | Same | Implemented |
+| `time_to_csv()` | `time_to_csv()` | Implemented |
+
+## Benchmark Notes
+
+The benchmark results below are included to give a sense of current runtime
+behavior on one local machine. They should be read as preliminary measurements,
+not as a comprehensive performance study.
+
+The benchmark suite uses the same synthetic datasets, filtrations, and matrix
+sizes for both packages. The shared benchmark runner is parameterized with
+`--package petls` or `--package petls_torch`.
+
+### Hardware
+
+- CPU: Intel i7-14700K
+- GPU: NVIDIA RTX 4070 Ti 12GB
+- PyTorch 2.x with CUDA 12.x
+
+### Quick Preset
+
+Configuration: torus `n=500` plus sphere `n=300`, `max_dim=2`, 8 filtrations
+per dataset.
+
+| Package | Device | Total Time | Mean Trial | Mean Build | Mean Eigs |
+|---------|--------|-----------:|-----------:|-----------:|----------:|
+| `petls` | CPU | 8.29 s | 172.6 ms | 15.2 ms | 157.4 ms |
+| `petls_torch` | CPU | 1.82 s | 37.9 ms | 4.8 ms | 33.1 ms |
+| `petls_torch` | CUDA | 1.85 s | 38.5 ms | 4.7 ms | 33.8 ms |
+
+On this workload, the PyTorch implementation is about 4.5x faster than the
+reference PETLS run on the same CPU. The CUDA timing is similar to the CPU
+timing for this preset, which suggests that eigendecomposition and data sizes
+are still small enough that GPU overhead can offset part of the benefit.
+
+### Medium Workload
+
+Configuration: torus `n=500`, `max_dim=3`, 16 filtrations.
+
+| Package | Device | Total Time | Mean Trial | Max Matrix | Status |
+|---------|--------|-----------:|-----------:|-----------:|--------|
+| `petls` | CPU | > 300 s | unavailable | unavailable | Reached benchmark timeout |
+| `petls_torch` | CUDA | 8.80 s | 137.5 ms | 5990 x 5990 | Completed |
+
+For this larger dense-eigendecomposition workload, the PyTorch/CUDA path
+completed within the benchmark timeout. The PETLS CPU run reached the configured
+300-second timeout in this test configuration.
+
+### Operation Breakdown
+
+Quick preset timings:
+
+```text
+petls (CPU)          : build=15.2 ms  eigs=157.4 ms
+petls_torch (CPU)    : build=4.8 ms   eigs=33.1 ms
+petls_torch (CUDA)   : build=4.7 ms   eigs=33.8 ms
+```
+
+In these measurements, most time is spent in eigendecomposition. The PyTorch
+implementation benefits from PyTorch's dense linear algebra backends on CPU and
+from CUDA support on larger matrix workloads.
+
+## Running Benchmarks
+
+```bash
+# Original PETLS
+cd /path/to/workspace
+python -m benchmark_shared --preset quick --package petls --algorithm eigvalsh
+
+# PETLS-PyTorch on CUDA
+python -m benchmark_shared --preset quick --package petls_torch --algorithm eigvalsh --device cuda
+
+# PETLS-PyTorch on CPU
+python -m benchmark_shared --preset quick --package petls_torch --algorithm eigvalsh --device cpu
+
+# Custom single run
+python -m benchmark_shared \
+    --dataset torus --n_points 2000 --complex alpha --max_dim 3 \
+    --package petls_torch --algorithm eigvalsh
+```
+
+## Installation
+
+```bash
+pip install petls-pytorch
+```
+
+Dependencies:
+
+- `torch`
+- `numpy`
+- `scipy`
+- `gudhi`
+- `pyflagser`
+- `tadasets` for benchmarks
+
+## Test Suite
+
+```bash
+cd PETLS-PYTORCH
+pytest tests/ -v
+```
+
+The test suite covers core functionality, Rips complexes, alpha complexes,
+directed flag complexes, sheaf support, eigenvalue utilities, and I/O helpers.
+
+## Citation
+
+If you use `petls_torch` in research, please cite both this PyTorch
+implementation and the original PETLS paper.
+
+### PETLS-PyTorch
+
+```bibtex
+@software{marston2026petlstorch,
+  title        = {PETLS-PyTorch: A PyTorch-native implementation of persistent topological Laplacians},
+  author       = {Marston, Sumner K.},
+  year         = {2026},
+  publisher    = {Sylverity Research},
+  url          = {https://github.com/Sylverity/petls-pytorch}
+}
+```
+
+### Original PETLS paper
+
+```bibtex
+@misc{jones2025petlspersistenttopologicallaplacian,
+    title={PETLS: PErsistent Topological Laplacian Software},
+    author={Benjamin Jones and Guo-Wei Wei},
+    year={2025},
+    eprint={2508.11560},
+    archivePrefix={arXiv},
+    primaryClass={math.AT},
+    url={https://arxiv.org/abs/2508.11560},
+}
+```
+
+This project is an independent PyTorch-native implementation based on the
+public PETLS API, PETLS documentation, and the PETLS paper. No source code from
+the original PETLS implementation is included in this repository.
+
+- Original PETLS repository: https://github.com/bdjones13/PETLS
+- PETLS documentation: https://www.benjones-math.com/software/PETLS/
+- PETLS paper: https://arxiv.org/abs/2508.11560