Install PhytKit¶
From PyPI¶
The quickest way to get PhytKit is the Python package, which also installs
the pk command. It needs Python 3.9 or newer, and has prebuilt wheels for
Linux, macOS and Windows:
From source¶
Building from source needs:
- Rust 1.88 or newer: install it from rustup.rs.
- For the Python package: Python 3.9 or newer.
Get the source with
git clone https://github.com/PlantSimulationLab/PhytKit.git. All commands
below run from the top folder of the source, the one with Cargo.toml in it.
The pk command¶
The first build downloads PhytKit's Rust dependencies and takes a few minutes. Later builds are quick.
To run pk from anywhere, install it onto your PATH:
The rest of these docs write pk. If you didn't install it, use
./target/release/pk instead.
The Python package¶
The Python package is built with maturin, which compiles the Rust code into a Python extension:
python3 -m venv .venv
.venv/bin/pip install maturin
VIRTUAL_ENV=$PWD/.venv .venv/bin/maturin develop --release -m crates/py/Cargo.toml
.venv/bin/python -c "import phytkit; print(phytkit.__version__)"
maturin develop installs into the virtual environment named by
VIRTUAL_ENV. Use any environment you like; the commands above make a new
one.
Using Conda
If a Conda environment is active, maturin may install into Conda instead
of your virtual environment, or refuse to choose. Run it with
env -u CONDA_PREFIX in front:
The package also installs a pk command into the environment, which behaves
like the Rust one.
Check it works¶
The first prints the FvCB model's parameters. The second fits the sample A–Ci curves and prints the result. Your first fit explains it.