PyCharm IDE

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 https://github.com/I2PC/scipion.git
• Create a new Scipion project (Choose "open" in the open project dialog and select your scipion directory).

Debugging

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= /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
/usr/local/bin/charm

2. Open the init script as root

$ sudo vim /usr/local/bin/charm

3. 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:
    args.append(arg)
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':
...

4. Start pycharm from your terminal with your new debug option - will prompt you to enter your password.

$ charm debug
[sudo] password for <your-user>:

5. Happy debugging!