ovarian follicle analysis pipeline
Project description
ovary-analysis
Image processing pipeline for ultrasound images of ovaries.
Installation
First, clone the repository
git clone git@git.bsse.ethz.ch:iber/ovary-analysis.git
Then, cd to the directory you cloned the repository into
cd ovary-analysis
Create a new python environment for the ovary-analysis package. If you are using anaconda, you can do the following
conda create -n ovary-analysis python=3.7
Activate your new environment
conda activate ovary-analysis
Install the ovary-analysis package with with. If you are just using the package, install using:
pip install .
If you want to install for development, use the pip editable mode:
pip install -e .
Developer tools
We use black and flake8 for formatting assistance. To install them, run the following from the repository directory
pip install -r requirements-dev.txt
Finally, install the pre-commit hooks.
pre-commit install
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