gpvolve-v2 1.0.0__tar.gz

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gpvolve_v2-1.0.0/Cargo.toml

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+[workspace]
+members = ["crates/gpvolve-core"]
+resolver = "2"
+
+[workspace.package]
+version = "1.0.0"
+edition = "2021"
+rust-version = "1.75"
+license = "MIT"
+authors = ["Luis Perez"]

gpvolve_v2-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Luis Perez
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

gpvolve_v2-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: gpvolve-v2
+Version: 1.0.0
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Rust
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Dist: numpy>=2.0
+Requires-Dist: scipy>=1.13
+Requires-Dist: networkx>=3.6
+Requires-Dist: gpmap-v2>=1.0
+Requires-Dist: gpgraph-v2>=1.0
+Requires-Dist: tqdm>=4.67
+Requires-Dist: typing-extensions>=4.12
+Requires-Dist: pyarrow>=14 ; extra == 'parquet'
+Requires-Dist: matplotlib>=3.10 ; extra == 'plot'
+Requires-Dist: pyslim>=1.0 ; extra == 'sim'
+Requires-Dist: tskit>=0.5 ; extra == 'sim'
+Requires-Dist: streamlit>=1.56 ; extra == 'streamlit'
+Requires-Dist: matplotlib>=3.10 ; extra == 'streamlit'
+Provides-Extra: parquet
+Provides-Extra: plot
+Provides-Extra: sim
+Provides-Extra: streamlit
+License-File: LICENSE
+Summary: Markov-chain evolutionary dynamics on genotype-phenotype maps. Rust-accelerated.
+Keywords: genotype,phenotype,fitness-landscape,markov,evolution,transition-path-theory,fixation
+Author-email: Luis Perez <lperezmo@users.noreply.github.com>
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Homepage, https://github.com/lperezmo/gpvolve-v2
+Project-URL: Issues, https://github.com/lperezmo/gpvolve-v2/issues
+Project-URL: Repository, https://github.com/lperezmo/gpvolve-v2
+
+# gpvolve-v2
+
+[![CI](https://github.com/lperezmo/gpvolve-v2/actions/workflows/ci.yml/badge.svg)](https://github.com/lperezmo/gpvolve-v2/actions/workflows/ci.yml)
+[![Documentation](https://github.com/lperezmo/gpvolve-v2/actions/workflows/docs.yml/badge.svg)](https://lperezmo.github.io/gpvolve-v2/)
+[![PyPI](https://img.shields.io/pypi/v/gpvolve-v2.svg)](https://pypi.org/project/gpvolve-v2/)
+[![Python](https://img.shields.io/pypi/pyversions/gpvolve-v2.svg)](https://pypi.org/project/gpvolve-v2/)
+[![License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
+
+Markov-chain evolutionary dynamics on genotype-phenotype maps. Rust-accelerated.
+
+gpvolve-v2 lifts a [gpgraph-v2](https://github.com/lperezmo/gpgraph-v2) `GenotypePhenotypeGraph`
+into a Markov state model and analyzes evolutionary dynamics on top of it. Given a fitness
+function and a fixation model (SSWM, Moran, McCandlish, Bloom DMS, weak-mutation), it builds
+a row-stochastic transition matrix and computes stationary distributions, relaxation
+timescales, mean first passage times, transition path theory committors and reactive flux,
+dominant pathways, stochastic walker trajectories, PCCA+ metastable sets, and fitness peaks.
+
+This is a clean-break rewrite of [harmslab/gpvolve](https://github.com/harmslab/gpvolve)
+(dormant since 2020) with selective architectural inspiration from the
+[harmsm/gpvolve](https://github.com/harmsm/gpvolve) fork (dormant since 2022). Hot paths
+(transition matrix assembly and stochastic walker sampling) live in Rust via PyO3 + rayon;
+spectral analysis stays in scipy.
+
+## Why v2
+
+- **Drops the dormant `msmtools` dependency.** PCCA+ and TPT are reimplemented natively.
+- **Fast.** Transition matrix assembly and walker sampling run in Rust with rayon parallelism.
+- **Sound convergence.** Stochastic path sampling stops on a real criterion (effective sample
+  size + Gelman-Rubin R-hat), not a Euclidean distance heuristic.
+- **Typed.** Full type hints, `mypy --strict` in CI.
+- **Modern tooling.** `uv` + `maturin` + `pyproject.toml`. Releases via
+  `python-semantic-release`. OIDC-based PyPI publishing.
+- **Consumes the v2 family.** Hard deps on `gpmap-v2` and `gpgraph-v2`; speaks their locked
+  `SCHEMA.md` contracts.
+
+## Install
+
+```bash
+pip install gpvolve-v2
+```
+
+Or with uv:
+
+```bash
+uv add gpvolve-v2
+```
+
+Plotting support is optional. For matplotlib:
+
+```bash
+pip install "gpvolve-v2[plot]"
+```
+
+Optional simulation backends (SLiM, tskit):
+
+```bash
+pip install "gpvolve-v2[sim]"
+```
+
+Python 3.11+. Prebuilt wheels ship for Linux (x86_64, aarch64), macOS (x86_64, aarch64),
+and Windows (x64).
+
+## Status
+
+Pre-release. See `CHANGELOG.md` for progress and `docs/migration/from-v1.md` for the
+v1 to v2 API map.
+

gpvolve_v2-1.0.0/README.md

@@ -0,0 +1,66 @@
+# gpvolve-v2
+
+[![CI](https://github.com/lperezmo/gpvolve-v2/actions/workflows/ci.yml/badge.svg)](https://github.com/lperezmo/gpvolve-v2/actions/workflows/ci.yml)
+[![Documentation](https://github.com/lperezmo/gpvolve-v2/actions/workflows/docs.yml/badge.svg)](https://lperezmo.github.io/gpvolve-v2/)
+[![PyPI](https://img.shields.io/pypi/v/gpvolve-v2.svg)](https://pypi.org/project/gpvolve-v2/)
+[![Python](https://img.shields.io/pypi/pyversions/gpvolve-v2.svg)](https://pypi.org/project/gpvolve-v2/)
+[![License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
+
+Markov-chain evolutionary dynamics on genotype-phenotype maps. Rust-accelerated.
+
+gpvolve-v2 lifts a [gpgraph-v2](https://github.com/lperezmo/gpgraph-v2) `GenotypePhenotypeGraph`
+into a Markov state model and analyzes evolutionary dynamics on top of it. Given a fitness
+function and a fixation model (SSWM, Moran, McCandlish, Bloom DMS, weak-mutation), it builds
+a row-stochastic transition matrix and computes stationary distributions, relaxation
+timescales, mean first passage times, transition path theory committors and reactive flux,
+dominant pathways, stochastic walker trajectories, PCCA+ metastable sets, and fitness peaks.
+
+This is a clean-break rewrite of [harmslab/gpvolve](https://github.com/harmslab/gpvolve)
+(dormant since 2020) with selective architectural inspiration from the
+[harmsm/gpvolve](https://github.com/harmsm/gpvolve) fork (dormant since 2022). Hot paths
+(transition matrix assembly and stochastic walker sampling) live in Rust via PyO3 + rayon;
+spectral analysis stays in scipy.
+
+## Why v2
+
+- **Drops the dormant `msmtools` dependency.** PCCA+ and TPT are reimplemented natively.
+- **Fast.** Transition matrix assembly and walker sampling run in Rust with rayon parallelism.
+- **Sound convergence.** Stochastic path sampling stops on a real criterion (effective sample
+  size + Gelman-Rubin R-hat), not a Euclidean distance heuristic.
+- **Typed.** Full type hints, `mypy --strict` in CI.
+- **Modern tooling.** `uv` + `maturin` + `pyproject.toml`. Releases via
+  `python-semantic-release`. OIDC-based PyPI publishing.
+- **Consumes the v2 family.** Hard deps on `gpmap-v2` and `gpgraph-v2`; speaks their locked
+  `SCHEMA.md` contracts.
+
+## Install
+
+```bash
+pip install gpvolve-v2
+```
+
+Or with uv:
+
+```bash
+uv add gpvolve-v2
+```
+
+Plotting support is optional. For matplotlib:
+
+```bash
+pip install "gpvolve-v2[plot]"
+```
+
+Optional simulation backends (SLiM, tskit):
+
+```bash
+pip install "gpvolve-v2[sim]"
+```
+
+Python 3.11+. Prebuilt wheels ship for Linux (x86_64, aarch64), macOS (x86_64, aarch64),
+and Windows (x64).
+
+## Status
+
+Pre-release. See `CHANGELOG.md` for progress and `docs/migration/from-v1.md` for the
+v1 to v2 API map.

gpvolve_v2-1.0.0/crates/gpvolve-core/Cargo.toml

@@ -0,0 +1,25 @@
+[package]
+name = "gpvolve-core"
+version.workspace = true
+edition.workspace = true
+rust-version.workspace = true
+license.workspace = true
+authors.workspace = true
+description = "Rust hot-path primitives for gpvolve-v2 (transition matrix, walker sampling, committor solver)."
+
+[lib]
+name = "gpvolve_core"
+crate-type = ["cdylib", "rlib"]
+
+[dependencies]
+pyo3 = { version = "0.28", features = ["abi3-py311", "extension-module"] }
+numpy = "0.28"
+ndarray = "0.17"
+rayon = "1.11"
+rand = "0.9"
+rand_pcg = "0.9"
+rustc-hash = "2"
+
+[features]
+default = []
+extension-module = ["pyo3/extension-module"]

gpvolve_v2-1.0.0/crates/gpvolve-core/src/lib.rs

@@ -0,0 +1,19 @@
+//! gpvolve-core: Rust hot-path primitives for gpvolve-v2.
+//!
+//! Exposed as `gpvolve._rust` inside the Python package.
+//!
+//! Scope (locked with Luis 2026-05-16):
+//!   - Transition matrix COO assembly with vectorized fixation kernels.
+//!   - Stochastic path sampling with per-walker rng streams.
+//!   - Sparse iterative committor solver for large MSMs.
+//!
+//! Pure-Python paths remain authoritative; Rust kernels accelerate the hot
+//! loops once the Python implementation is feature-complete and tested.
+
+use pyo3::prelude::*;
+
+#[pymodule]
+fn _rust(m: &Bound<'_, PyModule>) -> PyResult<()> {
+    m.add("__version__", env!("CARGO_PKG_VERSION"))?;
+    Ok(())
+}