gpmap-v2 1.0.0

Genotype-phenotype map container and simulators, Rust-accelerated.

gpmap-v2

A typed, Rust-accelerated container and simulator toolkit for genotype-phenotype maps.

gpmap-v2 is a clean-break rewrite of harmslab/gpmap. It exposes the same conceptual model (a GenotypePhenotypeMap backed by a pandas DataFrame) with a locked schema, vectorized hot paths, and a PyO3 Rust core for the operations that used to be inner Python loops.

Why

• Fast. String-encoded genotypes are replaced with packed uint8 matrices. The encoding step (genotypes_to_binary) runs rayon-parallel in Rust, delivering two orders of magnitude over the pure-Python v1 at L >= 16.
• Typed. Full type hints, mypy-checked, strict mode.
• Safe. Cartesian-product enumeration is size-guarded out of the box (SpaceTooLargeError). No more silent 10^26 allocations.
• Stable surface. The container and encoding_table schema are locked in SCHEMA.md for downstream consumers.
• Modern tooling. uv + maturin + pyproject.toml. Automated releases via python-semantic-release. OIDC-based PyPI publishing.

Install

pip install gpmap-v2

Or with uv:

uv add gpmap-v2

Python 3.10+. Prebuilt wheels ship for Linux (x86_64, aarch64), macOS (x86_64, aarch64), and Windows (x64).

Quick start

from gpmap import GenotypePhenotypeMap

gpm = GenotypePhenotypeMap(
    wildtype="AAA",
    genotypes=["AAA", "AAT", "ATA", "TAA", "ATT", "TAT", "TTA", "TTT"],
    phenotypes=[0.1, 0.2, 0.2, 0.6, 0.4, 0.6, 1.0, 1.1],
    stdeviations=[0.05] * 8,
)

gpm.genotypes        # np.ndarray of strings, shape (8,)
gpm.phenotypes       # np.ndarray[float64], shape (8,)
gpm.binary_packed    # np.ndarray[uint8], shape (8, 3) - the fast path
gpm.binary           # np.ndarray of '0'/'1' strings - back-compat accessor
gpm.n_mutations      # per-genotype Hamming weight
gpm.encoding_table   # pandas DataFrame per SCHEMA.md
gpm.data             # pandas DataFrame view for Jupyter

Simulating landscapes

from gpmap.simulate import NKSimulation, MountFujiSimulation
import numpy as np

sim = NKSimulation(
    wildtype="AAAA",
    mutations={i: ["A", "T"] for i in range(4)},
    K=2,
    rng=np.random.default_rng(0),
)
sim.phenotypes.shape  # (16,)

I/O round-trips

from gpmap import to_json, read_json, to_csv, read_csv

to_json(gpm, "map.json")
gpm2 = read_json("map.json")

to_csv(gpm, "map.csv")   # writes map.csv + map.csv.meta.json
gpm3 = read_csv("map.csv")

Public API surface

The full list of stable exports lives in gpmap.__all__. The ones downstream consumers depend on (notably epistasis-v2) are:

• GenotypePhenotypeMap, GenotypePhenotypeMap.from_dataframe
• get_encoding_table, genotypes_to_binary, genotypes_to_binary_packed
• upper_transform, lower_transform
• StandardDeviationMap, StandardErrorMap
• SpaceTooLargeError, SchemaError, UnknownLetterError
• read_csv, read_json, read_pickle, read_excel (and to_* counterparts)
• All simulators under gpmap.simulate

The load-bearing schema contract (column names, dtypes, invariants) is in SCHEMA.md. Breaking changes to that document bump the major version.

Development

git clone https://github.com/lperezmo/gpmap-v2
cd gpmap-v2
uv sync
uv run maturin develop --release
uv run pytest
uv run ruff check python/gpmap tests

A typical dev inner loop after editing Rust:

uv run maturin develop --release && uv run pytest

Consuming from another local project

gpmap-v2 is designed to be consumed as an editable dependency during co-development with sister packages (e.g. epistasis-v2). In the consumer's pyproject.toml:

[tool.uv.sources]
gpmap-v2 = { path = "/absolute/path/to/gpmap-v2", editable = true }

[project]
dependencies = ["gpmap-v2"]

Then uv sync or uv add gpmap-v2 in the consumer. Imports remain import gpmap.

Migration from v1 (harmslab/gpmap)

gpmap-v2 is not wire-compatible with v1. Key differences:

• Distribution name is gpmap-v2 on PyPI; import path is still gpmap.
• The encoding_table column genotype_index has been renamed to site_index to match its actual meaning. The old name is still readable via a deprecated alias.
• read_dataframe is now from_dataframe.
• binary_packed (uint8 2D) is exposed alongside the string-form binary. Prefer the packed form for any hot-path consumer.
• JSON files must carry "schema_version": "1". Legacy files are readable with a warning.
• upper_transform and lower_transform are now genuinely distinct (v1 had a copy-paste bug where they were identical).
• stats.unbiased_var honors the axis kwarg (v1 ignored it and hardcoded axis=1).
• simulate.random_mutation_set no longer mutates the module-level amino-acid list.
• simulate.MultiPeakMountFujiSimulation peak search has a retry cap; it raises instead of spinning forever on infeasible constraints.

See CHANGELOG.md for the full list.

Releases

Releases are driven by python-semantic-release on merge to main. Commit messages follow Conventional Commits:

• fix: ... -> patch
• feat: ... -> minor
• feat!: ... or BREAKING CHANGE: footer -> major

CHANGELOG.md, version bumps, Git tags, GitHub Releases, wheel builds, and PyPI uploads all happen automatically.

License

MIT. See LICENSE.