@sjcrh/proteinpaint-python v2.118.0

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 ./.venv
source .venv/bin/activate

# check the installed path
which python3
# /abs/path/to/proteinpaint/python/.venv, only an example installation dir location 

5. Now you should by able to install pyvips

pip install blitzgsea matplotlib nibabel numpy
pip install pyvips

#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.