hamon 0.1.0__tar.gz

hamon-0.1.0/LICENSE

@@ -0,0 +1,202 @@
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hamon-0.1.0/NOTICE

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+Hamon
+Copyright 2025 dek3rr
+
+This project is a spiritual successor to thrml (https://github.com/Extropic-AI/thrml).
+Portions of the block sampling, factor, and PGM infrastructure are derived from the
+original thrml library:
+
+    thrml
+    Copyright 2025 Extropic AI
+    Licensed under the Apache License, Version 2.0
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

hamon-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: hamon
+Version: 0.1.0
+Summary: JAX-native thermal sampling for discrete energy-based models
+Author: dek3rr
+Maintainer: dek3rr
+License-Expression: Apache-2.0
+Project-URL: Repository, https://github.com/dek3rr/hamon
+Project-URL: Documentation, https://dek3rr.github.io/hamon
+Project-URL: Issues, https://github.com/dek3rr/hamon/issues
+Project-URL: Changelog, https://github.com/dek3rr/hamon/blob/main/CHANGELOG.md
+Keywords: jax,mcmc,parallel-tempering,gibbs-sampling,energy-based-models,ising,probabilistic-graphical-models,sampling,gpu
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: equinox>=0.11.2
+Requires-Dist: jaxtyping>=0.2.23
+Provides-Extra: examples
+Requires-Dist: jupyter>=1.0; extra == "examples"
+Requires-Dist: matplotlib>=3.7.1; extra == "examples"
+Requires-Dist: networkx>=2.6.3; extra == "examples"
+Requires-Dist: dwave_networkx>=0.8.0; extra == "examples"
+Requires-Dist: scikit-learn>=1.7.0; extra == "examples"
+Provides-Extra: testing
+Requires-Dist: coverage>=7.6; extra == "testing"
+Requires-Dist: pytest>=8.3; extra == "testing"
+Requires-Dist: nbmake>=1.5; extra == "testing"
+Requires-Dist: networkx>=2.6.3; extra == "testing"
+Requires-Dist: optax>=0.2.4; extra == "testing"
+Requires-Dist: setuptools>=75.0; extra == "testing"
+Provides-Extra: development
+Requires-Dist: ruff>=0.15; extra == "development"
+Requires-Dist: pyright>=1.1.400; extra == "development"
+Requires-Dist: pytest-cov>=4.0; extra == "development"
+Requires-Dist: build>=1.0; extra == "development"
+Requires-Dist: twine>=6.0; extra == "development"
+Provides-Extra: docs
+Requires-Dist: hippogriffe>=0.2.0; extra == "docs"
+Requires-Dist: griffe>=1.7; extra == "docs"
+Requires-Dist: mkdocs>=1.6; extra == "docs"
+Requires-Dist: mkdocs-include-exclude-files>=0.1.0; extra == "docs"
+Requires-Dist: mkdocs-ipynb>=0.1.0; extra == "docs"
+Requires-Dist: mkdocs-material>=9.6; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.28; extra == "docs"
+Requires-Dist: pymdown-extensions>=10.14; extra == "docs"
+Dynamic: license-file
+
+<h1 align="center">Hamon</h1>
+
+<p align="center">
+JAX-native thermal sampling for discrete energy-based models.
+</p>
+
+<p align="center">
+<a href="https://pypi.org/project/hamon"><img src="https://img.shields.io/pypi/v/hamon" alt="PyPI"></a>
+<a href="https://pypi.org/project/hamon"><img src="https://img.shields.io/pypi/pyversions/hamon" alt="Python"></a>
+<a href="https://github.com/dek3rr/hamon/blob/main/LICENSE"><img src="https://img.shields.io/github/license/dek3rr/hamon" alt="License"></a>
+</p>
+
+---
+
+Hamon is a JAX library for sampling from discrete probabilistic graphical models.
+It provides GPU-accelerated block Gibbs sampling, non-reversible parallel tempering
+with adaptive schedule optimization, and tools for building and training Ising models,
+RBMs, and other discrete energy-based models.
+
+Built on [Extropic AI's thrml](https://github.com/Extropic-AI/thrml) foundation,
+Hamon diverges as an independent library with original algorithmic contributions
+and performance optimizations.
+
+## Why "Hamon"?
+
+In Japanese swordsmithing, the *hamon* (刃文, "blade pattern") is the visible
+wave that appears along the edge of a katana after differential hardening. The
+smith coats the blade in clay — thin along the cutting edge, thick along the
+spine — then heats the steel to critical temperature and quenches it in water.
+The edge cools fast into hard martensite; the spine cools slowly into tough
+pearlite. The boundary between these two phases is the hamon: a pattern born
+entirely from a thermal process, where controlled temperature gradients reveal
+structure hidden in disordered steel.
+
+The parallel to this library is direct. Hamon explores discrete energy
+landscapes by running chains at different temperatures and exchanging
+information across the thermal gradient. Structure emerges at the boundary
+between mixing regimes — hot chains explore freely, cold chains resolve fine
+detail, and the communication between them is what makes sampling work. The
+hamon on a blade is proof that a thermal process found the right boundary.
+The diagnostics in this library measure the same thing.
+
+## Installation
+
+```bash
+pip install hamon
+```
+
+For development:
+
+```bash
+git clone https://github.com/dek3rr/hamon.git
+cd hamon
+pip install -e ".[development,testing,examples]"
+```
+
+Requires Python ≥ 3.10 and a JAX installation ([GPU setup guide](https://jax.readthedocs.io/en/latest/installation.html)).
+
+## Quick example
+
+```python
+import jax
+import jax.numpy as jnp
+from hamon import SpinNode, Block, SamplingSchedule, sample_states
+from hamon.models import IsingEBM, IsingSamplingProgram, hinton_init
+
+nodes = [SpinNode() for _ in range(5)]
+edges = [(nodes[i], nodes[i + 1]) for i in range(4)]
+model = IsingEBM(nodes, edges, jnp.zeros(5), jnp.ones(4) * 0.5, jnp.array(1.0))
+
+free_blocks = [Block(nodes[::2]), Block(nodes[1::2])]
+program = IsingSamplingProgram(model, free_blocks, clamped_blocks=[])
+
+key = jax.random.key(0)
+k_init, k_samp = jax.random.split(key, 2)
+init_state = hinton_init(k_init, model, free_blocks, ())
+schedule = SamplingSchedule(n_warmup=100, n_samples=1000, steps_per_sample=2)
+
+samples = sample_states(k_samp, program, schedule, init_state, [], [Block(nodes)])
+```
+
+## Non-reversible parallel tempering
+
+Hamon implements adaptive NRPT based on
+[Syed et al. (2021)](https://arxiv.org/abs/1905.02939), with vectorized swaps
+that exploit the temperature-linearity of Ising energies:
+
+```python
+from hamon.nrpt import nrpt_adaptive
+
+def ebm_factory(betas):
+    return [IsingEBM(nodes, edges, biases, weights, jnp.array(float(b))) for b in betas]
+
+def program_factory(ebms):
+    return [IsingSamplingProgram(e, free_blocks, []) for e in ebms]
+
+states, _, stats = nrpt_adaptive(
+    jax.random.key(42),
+    ebm_factory,
+    program_factory,
+    init_states=[init_state] * 8,
+    clamp_state=[],
+    n_rounds=500,
+    gibbs_steps_per_round=5,
+    initial_betas=jnp.linspace(0.1, 2.0, 8),
+    n_tune=5,
+    rounds_per_tune=200,
+)
+
+print(f"Final Λ: {stats['round_trip_diagnostics']['Lambda']:.3f}")
+print(f"Round trip rate: {stats['round_trip_diagnostics']['tau_observed']:.4f}")
+```
+
+Key features of the NRPT implementation:
+
+- **Vectorized swaps**: 1 energy evaluation per chain (not 4 per pair), all
+  non-overlapping swaps execute simultaneously via permutation indexing
+- **Adaptive scheduling**: iteratively tunes β spacing to equalize rejection
+  rates, minimizing the global communication barrier Λ
+- **Round trip tracking**: monitors the index process per machine, estimates
+  Λ and predicted optimal rate τ̄ = 1/(2+2Λ)
+- **Chain count discovery**: iteratively probes to find the right number of
+  chains for a target acceptance rate
+
+## What makes Hamon fast
+
+**All chains run in one kernel.** Parallel tempering uses `jax.vmap` over chains
+instead of a Python loop. Compile time is constant regardless of chain count.
+
+**No redundant work in the sampler loop.** Global state is threaded through
+`lax.scan` as a carry. Block updates use targeted scatters instead of rebuilding
+the full state tensor each iteration.
+
+**Energy evaluation skips unnecessary work.** Pre-built `BlockSpec` objects are
+passed through directly — no reconstruction on every `energy()` call.
+
+**Accumulator dtypes are explicit.** The moment accumulator pins its dtype at
+construction, avoiding silent float64 promotion on GPU.
+
+## Citing Hamon
+
+If you use Hamon in your research, please cite:
+
+```bibtex
+@software{kerr2026hamon,
+    author       = {Kerr, Douglas E. Jr.},
+    title        = {Hamon: JAX-Native Thermal Sampling for Discrete Energy-Based Models},
+    year         = {2026},
+    url          = {https://github.com/dek3rr/hamon},
+    version      = {0.1.0},
+    license      = {Apache-2.0},
+}
+```
+
+Hamon's block sampling and PGM infrastructure is derived from
+[thrml](https://github.com/Extropic-AI/thrml) (v0.1.3) by
+[Extropic AI](https://extropic.ai), licensed under Apache 2.0.
+See [NOTICE](NOTICE) for full attribution. If you use the underlying
+block Gibbs framework, please also cite:
+
+```bibtex
+@misc{jelincic2025efficient,
+    title        = {An efficient probabilistic hardware architecture for diffusion-like models},
+    author       = {Andraž Jelinčič and Owen Lockwood and Akhil Garlapati and Guillaume Verdon and Trevor McCourt},
+    year         = {2025},
+    eprint       = {2510.23972},
+    archivePrefix= {arXiv},
+    primaryClass = {cs.LG},
+}
+```
+
+The non-reversible parallel tempering implementation is based on:
+
+> Syed, S., Bouchard-Côté, A., Deligiannidis, G., & Doucet, A. (2021).
+> Non-Reversible Parallel Tempering: a Scalable Highly Parallel MCMC Scheme.
+> [arXiv:1905.02939](https://arxiv.org/abs/1905.02939)
+
+## License
+
+Apache 2.0. See [LICENSE](LICENSE).

hamon-0.1.0/README.md

@@ -0,0 +1,180 @@
+<h1 align="center">Hamon</h1>
+
+<p align="center">
+JAX-native thermal sampling for discrete energy-based models.
+</p>
+
+<p align="center">
+<a href="https://pypi.org/project/hamon"><img src="https://img.shields.io/pypi/v/hamon" alt="PyPI"></a>
+<a href="https://pypi.org/project/hamon"><img src="https://img.shields.io/pypi/pyversions/hamon" alt="Python"></a>
+<a href="https://github.com/dek3rr/hamon/blob/main/LICENSE"><img src="https://img.shields.io/github/license/dek3rr/hamon" alt="License"></a>
+</p>
+
+---
+
+Hamon is a JAX library for sampling from discrete probabilistic graphical models.
+It provides GPU-accelerated block Gibbs sampling, non-reversible parallel tempering
+with adaptive schedule optimization, and tools for building and training Ising models,
+RBMs, and other discrete energy-based models.
+
+Built on [Extropic AI's thrml](https://github.com/Extropic-AI/thrml) foundation,
+Hamon diverges as an independent library with original algorithmic contributions
+and performance optimizations.
+
+## Why "Hamon"?
+
+In Japanese swordsmithing, the *hamon* (刃文, "blade pattern") is the visible
+wave that appears along the edge of a katana after differential hardening. The
+smith coats the blade in clay — thin along the cutting edge, thick along the
+spine — then heats the steel to critical temperature and quenches it in water.
+The edge cools fast into hard martensite; the spine cools slowly into tough
+pearlite. The boundary between these two phases is the hamon: a pattern born
+entirely from a thermal process, where controlled temperature gradients reveal
+structure hidden in disordered steel.
+
+The parallel to this library is direct. Hamon explores discrete energy
+landscapes by running chains at different temperatures and exchanging
+information across the thermal gradient. Structure emerges at the boundary
+between mixing regimes — hot chains explore freely, cold chains resolve fine
+detail, and the communication between them is what makes sampling work. The
+hamon on a blade is proof that a thermal process found the right boundary.
+The diagnostics in this library measure the same thing.
+
+## Installation
+
+```bash
+pip install hamon
+```
+
+For development:
+
+```bash
+git clone https://github.com/dek3rr/hamon.git
+cd hamon
+pip install -e ".[development,testing,examples]"
+```
+
+Requires Python ≥ 3.10 and a JAX installation ([GPU setup guide](https://jax.readthedocs.io/en/latest/installation.html)).
+
+## Quick example
+
+```python
+import jax
+import jax.numpy as jnp
+from hamon import SpinNode, Block, SamplingSchedule, sample_states
+from hamon.models import IsingEBM, IsingSamplingProgram, hinton_init
+
+nodes = [SpinNode() for _ in range(5)]
+edges = [(nodes[i], nodes[i + 1]) for i in range(4)]
+model = IsingEBM(nodes, edges, jnp.zeros(5), jnp.ones(4) * 0.5, jnp.array(1.0))
+
+free_blocks = [Block(nodes[::2]), Block(nodes[1::2])]
+program = IsingSamplingProgram(model, free_blocks, clamped_blocks=[])
+
+key = jax.random.key(0)
+k_init, k_samp = jax.random.split(key, 2)
+init_state = hinton_init(k_init, model, free_blocks, ())
+schedule = SamplingSchedule(n_warmup=100, n_samples=1000, steps_per_sample=2)
+
+samples = sample_states(k_samp, program, schedule, init_state, [], [Block(nodes)])
+```
+
+## Non-reversible parallel tempering
+
+Hamon implements adaptive NRPT based on
+[Syed et al. (2021)](https://arxiv.org/abs/1905.02939), with vectorized swaps
+that exploit the temperature-linearity of Ising energies:
+
+```python
+from hamon.nrpt import nrpt_adaptive
+
+def ebm_factory(betas):
+    return [IsingEBM(nodes, edges, biases, weights, jnp.array(float(b))) for b in betas]
+
+def program_factory(ebms):
+    return [IsingSamplingProgram(e, free_blocks, []) for e in ebms]
+
+states, _, stats = nrpt_adaptive(
+    jax.random.key(42),
+    ebm_factory,
+    program_factory,
+    init_states=[init_state] * 8,
+    clamp_state=[],
+    n_rounds=500,
+    gibbs_steps_per_round=5,
+    initial_betas=jnp.linspace(0.1, 2.0, 8),
+    n_tune=5,
+    rounds_per_tune=200,
+)
+
+print(f"Final Λ: {stats['round_trip_diagnostics']['Lambda']:.3f}")
+print(f"Round trip rate: {stats['round_trip_diagnostics']['tau_observed']:.4f}")
+```
+
+Key features of the NRPT implementation:
+
+- **Vectorized swaps**: 1 energy evaluation per chain (not 4 per pair), all
+  non-overlapping swaps execute simultaneously via permutation indexing
+- **Adaptive scheduling**: iteratively tunes β spacing to equalize rejection
+  rates, minimizing the global communication barrier Λ
+- **Round trip tracking**: monitors the index process per machine, estimates
+  Λ and predicted optimal rate τ̄ = 1/(2+2Λ)
+- **Chain count discovery**: iteratively probes to find the right number of
+  chains for a target acceptance rate
+
+## What makes Hamon fast
+
+**All chains run in one kernel.** Parallel tempering uses `jax.vmap` over chains
+instead of a Python loop. Compile time is constant regardless of chain count.
+
+**No redundant work in the sampler loop.** Global state is threaded through
+`lax.scan` as a carry. Block updates use targeted scatters instead of rebuilding
+the full state tensor each iteration.
+
+**Energy evaluation skips unnecessary work.** Pre-built `BlockSpec` objects are
+passed through directly — no reconstruction on every `energy()` call.
+
+**Accumulator dtypes are explicit.** The moment accumulator pins its dtype at
+construction, avoiding silent float64 promotion on GPU.
+
+## Citing Hamon
+
+If you use Hamon in your research, please cite:
+
+```bibtex
+@software{kerr2026hamon,
+    author       = {Kerr, Douglas E. Jr.},
+    title        = {Hamon: JAX-Native Thermal Sampling for Discrete Energy-Based Models},
+    year         = {2026},
+    url          = {https://github.com/dek3rr/hamon},
+    version      = {0.1.0},
+    license      = {Apache-2.0},
+}
+```
+
+Hamon's block sampling and PGM infrastructure is derived from
+[thrml](https://github.com/Extropic-AI/thrml) (v0.1.3) by
+[Extropic AI](https://extropic.ai), licensed under Apache 2.0.
+See [NOTICE](NOTICE) for full attribution. If you use the underlying
+block Gibbs framework, please also cite:
+
+```bibtex
+@misc{jelincic2025efficient,
+    title        = {An efficient probabilistic hardware architecture for diffusion-like models},
+    author       = {Andraž Jelinčič and Owen Lockwood and Akhil Garlapati and Guillaume Verdon and Trevor McCourt},
+    year         = {2025},
+    eprint       = {2510.23972},
+    archivePrefix= {arXiv},
+    primaryClass = {cs.LG},
+}
+```
+
+The non-reversible parallel tempering implementation is based on:
+
+> Syed, S., Bouchard-Côté, A., Deligiannidis, G., & Doucet, A. (2021).
+> Non-Reversible Parallel Tempering: a Scalable Highly Parallel MCMC Scheme.
+> [arXiv:1905.02939](https://arxiv.org/abs/1905.02939)
+
+## License
+
+Apache 2.0. See [LICENSE](LICENSE).