Windows Contributor Environment Setup

All contributor installation steps can be completed without administration access. To achieve this choose “Install for my user only” when prompted.

Overview

  • Install Python 3.7 (with Anaconda for example)
  • Install Poetry
  • Install git
  • Clone the PyMedPhys git repo
    • eg. git clone https://github.com/pymedphys/pymedphys.git
  • Run poetry install within the root of the repo
  • Run poetry run pre-commit install
  • Install pandoc

You’re good to go.

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More details

Install contributor system dependencies

Python

Download the latest Anaconda Python 3 version. When installing Anaconda make sure to install it for your user only, and tick the option “add to path”:

../../_images/add_anaconda_to_path.png

VSCode

Download and install VSCode. Make sure to tick the “Open with Code” boxes:

../../_images/open_with_code.png

Git and pandoc

Use the following links to install git and pandoc.

If you don’t have admin access make sure to install within your user account. When installing git it will ask you what default text editor to use. If you don’t know what vim is make sure to change the default setting from vim to VSCode (that was just installed).

Install poetry

To install Poetry run the following within a command prompt:

curl -sSL https://raw.githubusercontent.com/sdispater/poetry/master/get-poetry.py | python

What this does is detailed in the Install Poetry docs. You will need to close and reopen your command prompt after installing Poetry.

Install the development version of PyMedPhys and pre-commit

To download a copy of the PyMedPhys repository onto your machine run:

git clone https://github.com/pymedphys/pymedphys.git

Then change into the newly created directory by running:

cd pymedphys

Then install PyMedPhys and set up pre-commit by running:

poetry install
poetry run pre-commit install

Install a Jupyter Lab kernel for the development install

poetry run python -m ipykernel install --user --name pymedphys-master