trnsparse 0.1.1__tar.gz

trnsparse-0.1.1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - run: pip install -e ".[dev]"
+      - run: pytest tests/ -v -x --tb=short -m "not neuron"

trnsparse-0.1.1/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install build
+      - run: python -m build
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-pypi:
+    needs: build
+    runs-on: ubuntu-latest
+    # Only publish stable releases (v1.2.3), not pre-releases (v1.2.3-rc1)
+    if: ${{ !contains(github.event.release.tag_name, '-') }}
+    environment:
+      name: pypi
+      url: https://pypi.org/project/trnsparse/
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-testpypi:
+    needs: build
+    runs-on: ubuntu-latest
+    # Only publish pre-releases to TestPyPI
+    if: ${{ contains(github.event.release.tag_name, '-') }}
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/project/trnsparse/
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

trnsparse-0.1.1/.gitignore

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+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+dist/
+build/
+.eggs/
+*.egg
+.pytest_cache/
+.tox/
+.venv/
+venv/
+*.so
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+files.zip

trnsparse-0.1.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.1] — 2026-04-12
+
+### Added
+
+- mkdocs site with `index`, `installation`, `quickstart`, `api`, `architecture`, `aws_setup`
+- `infra/terraform/` for on-hardware CI instance provisioning
+- `scripts/run_neuron_tests.sh` and benchmark helpers
+- GitHub Actions `ci.yml` for CPU-only pytest matrix
+- `Issues` URL in pyproject.toml
+
+### Changed
+
+- Bumped `neuronxcc` floor from `>=2.15` to `>=2.24` to unify with the
+  rest of the trnsci suite. `torch-neuronx` floor bumped to `>=2.9`.
+
+## [0.1.0] — 2026-04-12
+
+### Added
+
+- Initial scaffold: CSRMatrix / COOMatrix, SpMV / SpMM, Schwarz screening
+- NKI dispatch with gather-matmul-scatter kernel stub
+- `examples/sparse_fock.py` — screened Fock build demo

trnsparse-0.1.1/CLAUDE.md

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+# trnsparse
+
+Sparse matrix operations for AWS Trainium via NKI.
+Part of the trnsci scientific computing suite.
+
+## What This Is
+
+A cuSPARSE-equivalent for Trainium. CSR/COO formats, SpMV, SpMM,
+and integral screening for sparse scientific computing.
+
+**Primary use case:** Schwarz-screened Fock builds for DF-MP2 quantum chemistry.
+At >3000 basis functions, >99% of shell quartets screen to zero.
+Storing and operating on the integral tensor in dense format wastes
+both memory and compute. trnsparse makes the sparsity explicit.
+
+## Architecture
+
+```
+trnsparse/
+├── trnsparse/
+│   ├── __init__.py
+│   ├── formats.py       # CSRMatrix, COOMatrix, conversions, from_dense
+│   ├── ops.py           # spmv, spmm, spmv_symmetric, add, scale, transpose
+│   ├── screening.py     # schwarz_bounds, screen_quartets, density_screen
+│   └── nki/
+│       ├── __init__.py
+│       └── dispatch.py  # Gather-matmul-scatter pattern for SpMM
+├── tests/
+│   ├── test_formats.py  # CSR/COO construction, roundtrips
+│   ├── test_ops.py      # SpMV, SpMM vs dense reference
+│   └── test_screening.py
+├── examples/
+│   └── sparse_fock.py   # Screened Fock build demo
+```
+
+## NKI SpMM Strategy
+
+SpMM on Trainium uses a gather-matmul-scatter pattern:
+1. **DMA engine**: gather non-zero column indices into dense SBUF tiles
+2. **Tensor Engine**: matmul the dense tile against B columns
+3. **DMA engine**: scatter results back to output rows
+
+This is the same pattern used in sparse attention. The efficiency depends
+on the nnz distribution per row — uniform nnz maps cleanly to fixed-size
+tiles; highly variable nnz needs row-bucketing.
+
+## Dependencies
+
+- `torch>=2.1`, `numpy>=1.24`
+- `neuronxcc` (optional)
+
+## Development
+
+```bash
+pip install -e ".[dev]"
+pytest tests/ -v
+python examples/sparse_fock.py --demo
+```

trnsparse-0.1.1/CODE_OF_CONDUCT.md

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+# Code of Conduct
+
+This project adopts the [Contributor Covenant](https://www.contributor-covenant.org/), version 2.1, as its code of conduct. The full text is available at:
+
+https://www.contributor-covenant.org/version/2/1/code_of_conduct/
+
+## Scope
+
+This Code applies within all project spaces — the GitHub repositories under the [trnsci](https://github.com/trnsci) organization, issue trackers, pull request discussions, and any public forums where an individual is representing the project or its community.
+
+## Reporting
+
+Concerns about behaviour in project spaces may be reported confidentially to:
+
+**3011922+scttfrdmn@users.noreply.github.com**
+
+All reports will be reviewed and investigated promptly and fairly. The project maintainers are obligated to respect the privacy and security of the reporter.
+
+## Enforcement
+
+Maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. It is licensed under CC BY 4.0.

trnsparse-0.1.1/CONTRIBUTING.md

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+# Contributing to trnsparse
+
+Thanks for your interest in contributing. This document covers the whole suite — the same guidelines apply to the umbrella and to each of the six sub-projects (`trnfft`, `trnblas`, `trnrand`, `trnsolver`, `trnsparse`, `trntensor`).
+
+## Where does my change belong?
+
+- **Scoped to a single library** — bug fix, new feature, added kernel in one sub-project → open a PR in that sub-project's repo.
+- **Cross-cutting** — integration examples, umbrella docs, CUDA-rosetta content, coordinated version bumps, shared tooling → open a PR against [trnsci/trnsci](https://github.com/trnsci/trnsci).
+
+If you aren't sure, open the PR where it's easiest and we'll move it.
+
+## Development setup
+
+```bash
+git clone git@github.com:trnsci/trnsci.git
+cd trnsci
+# Clone sibling sub-projects if you don't already have them:
+for p in trnfft trnblas trnrand trnsolver trnsparse trntensor; do
+  [ -d "$p" ] || git clone "git@github.com:trnsci/$p.git"
+done
+make install-dev
+make test-all
+```
+
+A single sub-project in isolation:
+
+```bash
+cd trnfft   # or any other
+pip install -e ".[dev]"
+pytest tests/ -v -m "not neuron"
+```
+
+## Tests
+
+- `pytest tests/ -v -m "not neuron"` — the CPU-only suite. Must pass on every PR.
+- `pytest tests/ -v -m neuron` — on-hardware suite, run from a machine with AWS credentials via `scripts/run_neuron_tests.sh`. Not part of standard CI.
+
+## Conventions
+
+- **License header** — new files get the Apache 2.0 notice and `Copyright 2026 Scott Friedman` where a notice is customary (long source files, not one-line configs).
+- **Python** — ≥ 3.10; `torch` ≥ 2.1; `numpy` ≥ 1.24.
+- **No emoji** in source, commits, or docs unless the feature is literally about emoji.
+- **Docstrings** only where they help a reader who doesn't have the context you had when writing. Don't restate the signature.
+- **No throwaway files** in the repo root — work-in-progress notes belong in PR descriptions or `docs/`.
+
+## Commit style
+
+Conventional-ish prefixes: `fix:`, `feat:`, `docs:`, `test:`, `bench:`, `chore:`, `refactor:`. Keep the subject line ≤ 72 characters. Longer context goes in the body.
+
+## Pull requests
+
+Before opening a PR:
+
+- [ ] `pytest tests/ -v -m "not neuron"` passes
+- [ ] If you changed public API or behaviour, `CHANGELOG.md` has an `[Unreleased]` entry
+- [ ] If you added a public symbol, the project's `docs/api.md` lists it
+- [ ] PR description says *what* changed and *why*, not just *what*
+
+## Issues
+
+Label each issue one of: `bug`, `feature`, `question`, `docs`, `infra`. Bugs include repro steps and expected-vs-actual output. Features describe the use case.
+
+## Code of conduct
+
+By participating, you agree to abide by the [Contributor Covenant v2.1](CODE_OF_CONDUCT.md). Report concerns to the contact listed there.
+
+## License
+
+Contributions are Apache 2.0, per the repository's [LICENSE](LICENSE). You attest you have the right to submit the code.

trnsparse-0.1.1/LICENSE

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trnsparse-0.1.1/PKG-INFO

@@ -0,0 +1,85 @@
+Metadata-Version: 2.4
+Name: trnsparse
+Version: 0.1.1
+Summary: Sparse matrix operations for AWS Trainium via NKI
+Author-email: Scott Friedman <3011922+scttfrdmn@users.noreply.github.com>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/trnsci/trnsparse
+Project-URL: Repository, https://github.com/trnsci/trnsparse
+Project-URL: Issues, https://github.com/trnsci/trnsparse/issues
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch>=2.1
+Requires-Dist: numpy>=1.24
+Provides-Extra: neuron
+Requires-Dist: neuronxcc>=2.24; extra == "neuron"
+Requires-Dist: torch-neuronx>=2.9; extra == "neuron"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-benchmark>=4.0; extra == "dev"
+Requires-Dist: scipy>=1.11; extra == "dev"
+Dynamic: license-file
+
+# trnsparse
+
+[![CI](https://github.com/trnsci/trnsparse/actions/workflows/ci.yml/badge.svg)](https://github.com/trnsci/trnsparse/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/trnsparse)](https://pypi.org/project/trnsparse/)
+[![Python](https://img.shields.io/pypi/pyversions/trnsparse)](https://pypi.org/project/trnsparse/)
+[![License](https://img.shields.io/github/license/trnsci/trnsparse)](LICENSE)
+[![Docs](https://img.shields.io/badge/docs-mkdocs-blue)](https://trnsci.github.io/trnsparse/)
+
+Sparse matrix operations for AWS Trainium via NKI.
+
+CSR/COO formats, SpMV, SpMM, and integral screening for sparse scientific computing on Trainium. Part of the trnsci scientific computing suite ([github.com/trnsci](https://github.com/trnsci)).
+
+## Install
+
+```bash
+pip install trnsparse
+```
+
+## Usage
+
+```python
+import torch
+import trnsparse
+
+# Dense → sparse
+A = torch.randn(100, 100)
+A[torch.abs(A) < 1.0] = 0.0
+csr = trnsparse.from_dense(A)
+
+# SpMV: y = A @ x
+y = trnsparse.spmv(csr, x, alpha=2.0)
+
+# SpMM: C = A @ B
+C = trnsparse.spmm(csr, B)
+
+# Integral screening
+Q = trnsparse.schwarz_bounds(diagonal_integrals)
+mask = trnsparse.screen_quartets(Q, threshold=1e-10)
+stats = trnsparse.sparsity_stats(Q)
+```
+
+## Operations
+
+| Operation | Description |
+|-----------|-------------|
+| `spmv` | Sparse × dense vector |
+| `spmm` | Sparse × dense matrix |
+| `spmv_symmetric` | Symmetric SpMV (half storage) |
+| `sparse_add` | C = αA + βB |
+| `sparse_scale` | B = αA |
+| `sparse_transpose` | A^T |
+| `schwarz_bounds` | Schwarz screening bounds |
+| `screen_quartets` | Shell quartet significance mask |
+| `density_screen` | Density-weighted screening |
+
+## License
+
+Apache 2.0 — Copyright 2026 Scott Friedman

trnsparse-0.1.1/README.md

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+# trnsparse
+
+[![CI](https://github.com/trnsci/trnsparse/actions/workflows/ci.yml/badge.svg)](https://github.com/trnsci/trnsparse/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/trnsparse)](https://pypi.org/project/trnsparse/)
+[![Python](https://img.shields.io/pypi/pyversions/trnsparse)](https://pypi.org/project/trnsparse/)
+[![License](https://img.shields.io/github/license/trnsci/trnsparse)](LICENSE)
+[![Docs](https://img.shields.io/badge/docs-mkdocs-blue)](https://trnsci.github.io/trnsparse/)
+
+Sparse matrix operations for AWS Trainium via NKI.
+
+CSR/COO formats, SpMV, SpMM, and integral screening for sparse scientific computing on Trainium. Part of the trnsci scientific computing suite ([github.com/trnsci](https://github.com/trnsci)).
+
+## Install
+
+```bash
+pip install trnsparse
+```
+
+## Usage
+
+```python
+import torch
+import trnsparse
+
+# Dense → sparse
+A = torch.randn(100, 100)
+A[torch.abs(A) < 1.0] = 0.0
+csr = trnsparse.from_dense(A)
+
+# SpMV: y = A @ x
+y = trnsparse.spmv(csr, x, alpha=2.0)
+
+# SpMM: C = A @ B
+C = trnsparse.spmm(csr, B)
+
+# Integral screening
+Q = trnsparse.schwarz_bounds(diagonal_integrals)
+mask = trnsparse.screen_quartets(Q, threshold=1e-10)
+stats = trnsparse.sparsity_stats(Q)
+```
+
+## Operations
+
+| Operation | Description |
+|-----------|-------------|
+| `spmv` | Sparse × dense vector |
+| `spmm` | Sparse × dense matrix |
+| `spmv_symmetric` | Symmetric SpMV (half storage) |
+| `sparse_add` | C = αA + βB |
+| `sparse_scale` | B = αA |
+| `sparse_transpose` | A^T |
+| `schwarz_bounds` | Schwarz screening bounds |
+| `screen_quartets` | Shell quartet significance mask |
+| `density_screen` | Density-weighted screening |
+
+## License
+
+Apache 2.0 — Copyright 2026 Scott Friedman

trnsparse-0.1.1/docs/api.md

@@ -0,0 +1,33 @@
+# API Reference
+
+## Formats
+
+- `CSRMatrix(indptr, indices, data, shape)` — compressed sparse row
+  - `.from_dense(dense, threshold=0)` — construct by thresholding a dense tensor
+  - `.to_dense()` — materialize back to a dense `torch.Tensor`
+  - `.transpose()` — transpose to CSR (via CSC)
+  - `.nnz`, `.shape`, `.dtype`, `.device`
+- `COOMatrix(rows, cols, vals, shape)` — coordinate format
+  - `.to_csr()` / `CSRMatrix.to_coo()` — roundtrip conversions
+
+## Ops
+
+- `spmv(A, x)` — sparse matrix × dense vector
+- `spmv_symmetric(A, x)` — for symmetric A; skips duplicate work
+- `spmm(A, B)` — sparse matrix × dense matrix (gather-matmul-scatter on NKI)
+- `sparse_add(A, B, alpha=1.0, beta=1.0)` — `α A + β B`
+- `sparse_scale(A, s)` — scalar multiply
+- `transpose(A)` — transpose of CSR / COO
+
+## Screening
+
+- `schwarz_bounds(shell_pair_integrals)` — Cauchy-Schwarz bounds $Q_{pq} = \sqrt{(pq|pq)}$
+- `screen_quartets(Q, threshold)` — keep only quartets with $Q_{pq}Q_{rs} > \text{threshold}$
+- `density_screen(Q, P, threshold)` — density-weighted screening
+- `sparsity_stats(mask)` — density, nnz, per-row nnz distribution
+
+## Dispatch
+
+- `set_backend("auto" | "pytorch" | "nki")` — select compute backend
+- `get_backend()` — current backend
+- `HAS_NKI` — module-level flag set at import time