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Developer setup

Setting up Python Virtual Environment (VE)

Using conda

conda create -n "pixlVE" python=3.11  pip -c conda-forge --yes
conda activate pixlVE
conda list -n pixlVE #to check installed packages
conda deactivate #to deactivate VE 
conda remove -n pixlVE --all #to remove pixlVE environment

Using python virtual environment venv

You require python3-venv to setup your venv. See further details here.

# Create path for venv
cd $HOME
mkdir pixlVE
cd pixlVE
# Create virtual environment
python3 -m venv pixlVE
source pixlVE/bin/activate

Docker requirements

Most modules require docker and docker-compose to be installed to run tests.

Installation of PIXL modules

You can install all PIXL Python modules by running the following commands from the PIXL/ directory:

python -m pip install -e "pixl_core/[dev]"
python -m pip install -e "pytest-pixl/[dev,test]"
python -m pip install -e "pixl_core/[test]"
python -m pip install -e "cli/[dev,test]"
python -m pip install -e "pixl_imaging/[dev,test]"
python -m pip install -e "pixl_dcmd/[dev,test]"
python -m pip install -e "pixl_export/[dev,test]"
python -m pip install -e "hasher/[dev,test]"

See each service's README for instructions for individual developing and testing instructions.

Testing

Module-level testing

Once you have installed each module, you can run the tests for a module using the pytest command, e.g.

cd pixl_core/
pytest

Alternatively, you can run most of the module-level tests from the root of the repo with:

pytest #to test all tests `testpaths` pytest.ini

The pytest.ini file in the root of the repo contains the configuration for running most of the module-level tests at once. However, pixl_dcmd and hasher have conftests.py files that clash, so only pixl_dcmd is included as a testpath in the top-level pytest.ini. You will therefore need to run tests for hasher from the hasher directory.

Enabling default Docker socket for testing pixl_core

We have tests in pixl_core for uploading DICOM to XNAT as an endpoint. These tests use xnat4tests to spin up a docker container running XNAT.

xnat4tests requires you to allow the Docker daemon to listen for Docker Engine API requests via the default socket. This is because xnat4tests set up the XNAT Container Service for launching other containers that run analysis pipelines.

If you are using Docker Desktop, you will need to enable Docker to listen on the default socket by going to Settings > Advanced and checking the box Allow the default Docker socket to be used.

If your are running Docker Engine on Linux, listening on this socket should be enabled by default.

Integration tests

There are also integration tests in PIXL/test/ directory that can be run using the PIXL/test/run-system-test.sh. See the integration test docs for more info.

Workflow

Before raising a PR, make sure to run all tests for each PIXL module and not just the component you have been working on as this will help us catch unintentional regressions without spending GH actions minutes.

Linting

For Python development we use ruff and mypy alongside pytest. There is support (sometimes through plugins) for these tools in most IDEs & editors.

We run pre-commit as part of the GitHub Actions CI. To install and run it locally, do:

python -m pip install pre-commit
pre-commit install

The pre-commit configuration can be found in .pre-commit-config.yml.

Environment variables

Running the pixl pipeline and the tests requires a set of environment variables to be set. The test/ directory contains a complete .env file that can be used to run the pipeline and tests locally. Either run any pixl commands from the test/ directory, or copy the test/.env file to the root of the repository.

Secrets

PIXL uses an Azure Keyvault to store authentication details for external services. We have a development keyvault for testing. Access to this keyvault is provided by a set of environment variables specified in test/.secrets.env.sample. To run the pipeline locally, you will need to copy this file to test/.secrets.env and fill out the necessary values, which can be found in the pixl-dev-secrets.env shared LastPass note.