Documentation

Getting started

Note: the following instructions were created for Linux/MacOS computers. If you are using a Windows machine, please install WSL2 (Windows Subsystem For Linux). Instructions are be found here.

Install uv: "An extremely fast Python package manager".

curl -LsSf https://astral.sh/uv/install.sh | sh

Create venv

``` uv venv --python 3.12 # Create a virtual environment at .venv. source .venv/bin/activate #To activate the virtual environment: deactivate

uv venv 2nd_env --python 3.13 #create with a diff python version

rm -rf 2nd_env #to remove 2nd_env

```

Install python package deps

``` uv pip install --editable . # Install the package in editable mode uv pip install .[test] uv pip install .[learning] uv pip install .[model_optimisation] uv pip install -e ".[test,learning,model_optimisation]" # Install the package in editable mode

uv pip uninstall ready

```

Debugging

source .venv/bin/activate #To activate the virtual environment: export PYTHONPATH=. #$HOME/ready #$HOME/<ADD_REPO_PATH>

If you experience issues installing onnxsim

In our experience, this issue often comes up because either cmake or python3.12-dev aren't installed on your machine. To fix this issue, please first run sudo apt-get install cmake, then sudo apt-get install python3.12-dev. Afterwards, run either uv pip install .[model_optimisation] or uv pip install onnxsim.

Testing

``` python -m pytest -v -s tests/test_data_paths.py::test_mobious_dataset python -m pytest -v -s tests/test_data_paths.py::test_mobious_dataset_labels

TODO: Fix the following tests with data in the repo

python -m pytest -v -s tests/test_data_paths.py::test_txt python -m pytest -v -s tests/test_data_paths.py::test_png python -m pytest -v -s tests/test_data_paths.py::test_masks python -m pytest -v -s tests/test_data_paths.py::test_tif_with_matplotlib ```

Pre-commit

pre-commit run -a