Install gpmap-v2¶

gpmap-v2 ships prebuilt wheels for Linux (x86_64, aarch64), macOS (x86_64, aarch64), and Windows (x64). Python 3.10 or newer is required.

Stable release¶

uvpip

uv add gpmap-v2

pip install gpmap-v2

The package installs the import path gpmap, regardless of the distribution name being gpmap-v2.

import gpmap
print(gpmap.__version__)

Why two names

The PyPI distribution is published as gpmap-v2 so it does not collide with the legacy gpmap package. The import path stays gpmap so downstream code that already wrote from gpmap import GenotypePhenotypeMap keeps working.

Optional extras¶

Extra	What it adds
`gpmap-v2[parquet]`	`pyarrow` for the optional parquet I/O codec
`gpmap-v2[dev]`	`pytest`, `pytest-benchmark`, `mypy`, `ruff`, `maturin`

Build from source¶

You need a Rust toolchain (stable, >= 1.70) and maturin. The recommended workflow uses uv:

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

After editing Rust under crates/:

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

Editable installs without the Rust extension

If maturin develop is skipped, the Python package still imports, but the encoding and enumeration hot paths fall back to a pure-Python implementation. You will see correct results, just measured in seconds instead of milliseconds for large maps.

Consuming from another local project¶

gpmap-v2 is designed to be consumed as an editable dependency during co-development with sister packages like epistasis-v2 and gpgraph-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.

Verify the install¶

from gpmap import GenotypePhenotypeMap

gpm = GenotypePhenotypeMap(
    wildtype="AA",
    genotypes=["AA", "AT", "TA", "TT"],
    phenotypes=[0.0, 0.5, 0.5, 1.0],
)
print(gpm.binary_packed)

If the import succeeds and binary_packed returns a 4x2 uint8 array, the Rust extension is wired in correctly.