3. Running from PyCharm

This section describes how we can use OpenCMISS-Iron code from the PyCharm Integrated Development Environment (IDE).

3.1. Preliminaries

If you are a student or a researcher, follow the link below to determine if you are eligible to sign up for a free educational license to use the Professional Edition: link. This will give you access to features e.g. code profiling etc, remote debugging, interacting with dockers.

Alternatively, you can download the free Community Edition, which is the default option made available as part of the OpenCMISS-Iron Docker instructions.

3.2. For a Docker installation

3.2.1. Running PyCharm

The following Docker command can be used to start PyCharm.

PyCharm will automatically be downloaded and installed in the ~/work/PyCharm folder, which is a folder on the host machine that is mounted within the Docker container. This means that PyCharm will only need to be installed once and all settings will persist even after the Docker container is shutdown/restarted. The specific version of PyCharm that is downloaded can be specified in the oc/usr/bin/start-pycharm.sh script. By default, PyCharm 2020.2.3 is installed.

Important

If the commands for running docker outlined below give errors, please try the command again (or a few times).

3.2.1.1. Linux

Run the following command:

docker run \
    --rm \
    --name opencmiss-iron \
    -e DISPLAY=${DISPLAY} \
    -v /tmp/.X11-unix:/tmp/.X11-unix \
    -v ~/oc/opt:/home/jovyan/work \
    -v ~/oc/usr/local:/home/jovyan/.local \
    -v ~/oc/usr/cache:/home/jovyan/.cache \
    -v ~/oc/usr/config:/home/jovyan/.config \
    -v ~/oc/usr/java:/home/jovyan/.java \
    -v ~/oc/usr/etc/jupyter:/etc/jupyter \
    -v ~/oc/usr/bin/:/usr/local/bin \
    prasadbabarendagamage/opencmiss-iron:1.0-minimal-ssh start-pycharm.sh

Important

Ensure that there are no trailing spaces following the end of line backslash deliminators.

3.2.1.2. Mac

1. Follow the instructions in the FAQ Docker ‘Setup XQuartz X11 server on Mac’ Section.

2. Run the OpenCMISS-Iron Docker:

   docker run \
        --rm \
        --name opencmiss-iron \
        -e DISPLAY=$IP:0 \
        -v /tmp/.X11-unix:/tmp/.X11-unix \
        -v ~/oc/opt:/home/jovyan/work \
        -v ~/oc/usr/local:/home/jovyan/.local \
        -v ~/oc/usr/cache:/home/jovyan/.cache \
        -v ~/oc/usr/etc/jupyter:/etc/jupyter \
        -v ~/oc/usr/bin/:/usr/local/bin \
        -v ~/oc/usr/config:/home/jovyan/.config \
        -v ~/oc/usr/java:/home/jovyan/.java \
        prasadbabarendagamage/opencmiss-iron:1.0-minimal-ssh start-pycharm.sh
   

   Important

   Ensure that there are no trailing spaces following the end of line backslash deliminators.

3.2.1.3. Windows

1. Follow the instructions in the FAQ Docker ‘Setup VcXsrv X11 server on Windows’ Section.

   Important

   Ensure you have followed step 4 of the VcXsrv setup instructions. This step saves the IP address of your computer as an environmental variable in a PowerShell terminal. This specific step is required to be repeated each time you run PyCharm via docker.

2. Run PyCharm in the docker:

   docker run `
       --rm `
       --env DISPLAY=${env:IPAddress}:0.0 `
       --name opencmiss-iron `
       -it `
       -v c/Users/${env:UserName}/Documents/oc/opt:/home/jovyan/work `
       -v c/Users/${env:UserName}/Documents/oc/usr/local:/home/jovyan/.local `
       -v c/Users/${env:UserName}/Documents/oc/usr/cache:/home/jovyan/.cache `
       -v c/Users/${env:UserName}/Documents/oc/usr/etc/jupyter:/etc/jupyter `
       -v c/Users/${env:UserName}/Documents/oc/usr/bin/:/usr/local/bin/ `
       -v c/Users/${env:UserName}/Documents/oc/usr/config:/home/jovyan/.config `
       -v c/Users/${env:UserName}/Documents/oc/usr/java:/home/jovyan/.java `
       prasadbabarendagamage/opencmiss-iron:1.0-minimal-ssh start-pycharm.sh
   

   Important

   Ensure that there are no trailing spaces following the end-of-line tilda deliminators.

3.2.1.4. Configuring PyCharm

On the first run, you will need to configuring your python environment.

1. Create a new project folder and store it in the /home/jovyan/work/ folder.
2. In the interpreter section, select the existing system interpreter option and add the following path to the OpenCMISS-Iron python interpreter:

/opt/conda/bin/python

1. Create the project.

Since the PyCharm and its settings are stored in a folder that is mapped to your host machine, you will not need to repeat this setup next time you run the OpenCMISS-Iron Docker container.