Installation

Docker

This is already included in the deps image and other images that use it as a base image.

Mac

1. To run python/src/dzi.py on mac, you need to install the following packages:

brew install python

2. Homebrew's python formula now points to Python 3 by default. Verify that python3 is installed by running:

python3 --version

3. Install vips for managing large images:

brew install vips

4. Now in order to install pyvips check if you have a python virtual env by running python3 -V, if not you can create one by running

python3 -m venv ~/pppython
source ~/pppython/bin/activate

# check the installed path
which python3
# Gives the absolute path to the python installattion in the virtual environment

5. Now you should by able to install all the relevant python modules by installing all modules in the requirement.txt file

pip3 install -r requirements.txt

#To test it you can run
python3 src/dzi.py /path/to/file.svs /path/to/images

6. In order for the nodejs server code to use python virtual environment that has been set up, you can do one of the following:

• a. set a serverconfig.python option that equals the absolute path to your .venv/bin/python3 installation
• b. call source path/to/.venv/bin/activate in the same shell or terminal tab/window before running a package script like npm run dev , npm run test:integration, etc.

7. Once Python development and testing are finished, execute the following command from the proteinpaint/python directory to deactivate the currently active virtual environment:

source .venv/bin/deactivate

This is important to keep the GitHub hook working.