PyCharm is one of the most popular integrated development environment (IDE) for Python projects. PyCharm features a full integration with git(hub) support, and contains a rich project-based editor, as well as integrated python and bash terminals to run your python code or applications.

Moreover, if you create a free account on the Pycharm website with your university email, you can make use of the PyCharm Pro version, which supports working with Jupyter notebooks from within the Pycharm IDE (which makes for a much better experience than using the browser as a notebook front-end).

To run PyCharm on a cluster execution node simply run:

$ pycharm

You will encounter a graphical dialog through which you can select the PyCharm version you like to use (the wrapper then submits a job to the cluster).

Assuming that you have followed the Python exercise, we could load the demo conda environment as an example. Here are steps to follow:

  1. Start a new project, go to PyCharm’s Settings -> Project -> Python Interpreter and select your demo conda environment (you may have to click on Show All).

  2. Close the settings and open a bash command shell using the Terminal button in the bottom of the main window. You could now check in the terminal whether the nibabel Python module we installed earlier is still available by running: $ python

  3. Alternatively, use the menu to open the file in the editor and then the Run menu to run or debug the example code. This should give the same results as before.