.. index::
   single: python

.. _python:

Python
======

.. index::
   single: conda

.. _python_availability:

Anaconda3 Python is available in /usr/local/anaconda3/bin.

Conda
-----

You may install a conda environment in your home directory as described in the conda documentation:
https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html


.. tip::

    I recommend disabling the automatic base activation. Run the following at the command line::

        conda config --set auto_activate_base false

To list conda environments, run::

    conda env list

To activate a conda base environment, run::

    conda activate myenv

(replace <myenv> with your environment name)


packages
--------

Conda provides excellent documentation for installing packages:
    https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#using-pip-in-an-environment


To see a list of all packages installed in a specific environment, run::

    conda list -n myenv


Install a package from the 'defaults' channel::

    conda install -n myenv pip


Install a package from the 'conda-forge' channel::

    conda install -n myenv pip --channel conda-forge

.. Note::
    
    Read more about conda-forge here: https://conda-forge.org/docs/user/introduction/


.. _conda-sge:

Conda integration with Grid Engine (batch processing)
-----------------------------------------------------

By default, Grid Engine doesn't initialize conda environments from a user's .bashrc file. 

To initialize conda, add the following line to your qsub submit script::

    eval "$(/usr/local/anaconda3/bin/conda shell.bash hook)"
    conda activate <environment>

(replace <environment> with your env name)

.. index::
   single: jupyter


.. _jupyter:

Jupyter Notebook
----------------
You may run jupyter notebook/lab anywhere on the neuro cluster, and view it on your local desktop.

#. Log in via :ref:`SSH <sshclient>`, or :ref:`X2Go remote desktop session<nxclient>` 

#. If you logged in via X2Go, then open a terminal window

#. From your terminal on the neuro cluster, run 'jupyter notebook' with the '--no-browser' option::

        jupyter notebook --no-browser


   You will see output similar to the following::
   
        Copy/paste this URL into your browser when you connect for the first time,
        to login with a token:
        http://localhost:8780/?token=76e3a90efd4159sdfllfaa73e6f8sdf2b6dsdf3cddbc742f
   

#. On your Mac, open a terminal window, and use the ssh command to create a tunnel::

        ssh -L <port>:localhost:<port> <username>@<servername>neuro.berkeley.edu

   | where...
   | the port number was automatically assigned in step #2, shown after the word 'localhost:'. In this example, the port number is 8780.
   | username is your neuro cluster user name
   | servername is the neuro cluster server from in step #1 (where you ran the jupyter command).

   For example::

        ssh -L 8780:localhost:8780 user@nx1.neuro.berkeley.edu

#. Copy and paste the URL displayed above (in step #2) into your web browser's address bar on your desktop.