sleap-roots 0.0.1a0

Analysis tools for SLEAP-based plant root phenotyping.

sleap-roots

Analysis tools for SLEAP-based plant root phenotyping.

Installation

pip install git+https://github.com/talmolab/sleap-roots.git@main

If you are using conda:

conda create -n sleap-roots python=3.8
conda activate sleap-roots
pip install git+https://github.com/talmolab/sleap-roots.git@main

Development

For development, first clone the repository:

git clone https://github.com/talmolab/sleap-roots && cd sleap-roots

Then, to create a new conda environment and install the package in editable mode:

conda env create -f environment.yml

This will create a conda environment called sleap-roots.

If you have an existing conda environment (such as where you installed SLEAP), you can just install in editable mode directly. First, activate your environment and then:

pip install -e ".[dev]"

Note: The [dev] makes sure that the development-only dependencies are also installed.

To start fresh, just delete the environment:

conda env remove -n sleap-roots

To run tests, first activate the environment:

conda activate sleap-roots

Then run pytest with:

pytest tests

To develop on M1 Macs, you'll need to manually install SLEAP first like this:

git clone https://github.com/talmolab/sleap && cd sleap
conda env create -f environment_m1.yml -n sleap-roots

Then, install this package in editable mode:

cd .. && git clone https://github.com/talmolab/sleap-roots
pip install -e ".[dev]"