PyCharm IDE

fonsecareyna82 edited this page Jul 17, 2018 · 10 revisions

PyCharm IDE

Getting started

  • Download PyCharm's community version here. Install following the instructions for your platform.
  • Clone Scipion git repository in your machine: git clone
  • Create a new Scipion project (Choose "open" in the open project dialog and select your scipion directory).


There is a couple of commands that we need to run before starting PyCharm in order to be able to debug Scipion and use the "Attach to local process" option. A handy way is to generate PyCharm's command line launcher and modify it:

1a. Edit .bashrc file and include LD_LIBRARY_PATH= <our-scipion-home>/software/lib/

1b. Generate Pycharm's command line launcher

Click on Tools > Create command line launcher... and type the desired path to the script.

1c. Find PyCharm's command line launcher if already have one

$ which charm
  1. Open the init script as root
$ sudo vim /usr/local/bin/charm
  1. In the function def process_args(argv):, add the code in bold. Remember to replace <your-scipion-home> with the right path and save your changes:
elif arg == 'merge' and i == 0:
elif arg == 'debug':
    os.system("export LD_LIBRARY_PATH=<your-scipion-home>/software/lib/")
    os.system("echo 0 | sudo tee /proc/sys/kernel/yama/ptrace_scope")
elif arg == '-l' or arg == '--line':
  1. Start pycharm from your terminal with your new debug option - will prompt you to enter your password.
$ charm debug
[sudo] password for <your-user>:
  1. Happy debugging!
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