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Python Woes
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Caution
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This page is mostly unrelated to cookiecutter-chrisapp! You should be debugging your ChRIS plugin in a container. See our Developer’s Guide |
Virtual environments enable you to have different versions of the same package installed on the same system.
You need to specify a location for your environment (where packages are installed to). For example, ~/chrisenv
There are three popular solutions, just pick one and stick with it:
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Warning
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if you are working on a machine at the FNNDSC, you might encounter this bug. |
venv comes with Python 3, nothing extra to install.
# set up, run once
python -m venv ~/chrisenv
# activate, run each time you open a shell
source ~/chrisenv/bin/activate
# (optional) deactivate, run after you're done working
deactivateCreate a directory for your virtual environments e.g
mkdir ~/python_envs
Open your .bashrc file
vim ~/.bashrc
Add these two lines to your .bashrc file
export WORKON_HOME=~/python_envs source $(which virtualenvwrapper.sh | head -n 1)
Create a new Python3 virtual environment
mkvirtualenv --python=python3 chrisapp_env
To activate chrisapp_env
workon chrisapp_env
To deactivate chrisapp_env
deactivate
Conda is general-purpose, it is not specific to Python.
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Note
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anaconda users on macOS should use the conda environment tools directly instead. See this thread and the linked discussion on the anaconda mailing list. A working set of commands is noted here. |
pip changes the shebang (#!/bin/python) of scripts installed to the virtualenvironment.
When the virtualenvironment’s realpath is unusually long, it will not work.
E.g. the FNNDSC LDAP mount point causes the shebang to be #!/net/rc-fs-nfs/ifs/data/NoSync/FNNDSC-NR/neuro/labs/grantlab/users/my.name/my.virtualenvironment/bin/python.
The error will be:
-bash: /net/rc-fs-nfs/ifs/data/NoSync/FNNDSC-NR/neuro/labs/grantlab/users/.../bin/python: bad interpreter: No such file or directory