Tips and Tricks of the Trade

This guide is an ever growing list of issues or setups I personally encounter frequently enough to document here, but unfrequently enough that I forget them otherwise. Feel free to browse!

ZSH Installation

A Power Shell is a huge timesaver. It'll help you navigate through files a lot faster with nice autocomplete, amongst other features.

Quick Install

Install zsh from here
Install the theme here

Virtual Environments

If you want to work with a virtual env (which you absolutely should if you're not using a containerized solution), run these commands:

NEWENVNAME=tryiton
NEWENV_PYTHON_VERSION=python3.11

pip3 install virtualenv
virtualenv --python=$NEWENV_PYTHON_VERSION $NEWENVNAME
source $NEWENVNAME/bin/activate
...
python3 -m pip install ipykernel
python -m ipykernel install --user --name $NEWENVNAME --display-name "$NEWENVNAME"
...
deactivate

Jupyter and Virtual Envs

Sometimes the jupyter notebook kernel doesn't start where it should be (sys.executable returns the wrong python kernel). This is because our kernel list isn't updated properly. To do so, go to ~/.local/share/jupyter/kernels/{envname}/kernel.json and change the first parameter in the argv list to the python path in your specific kernel.

{
 "argv": [
  "path/to/kernel/python",
  "-m",
  "ipykernel_launcher",
  "-f",
  "{connection_file}"
 ],
 "display_name": "Python 3 (ipykernel)",
 "language": "python",
 "metadata": {
  "debugger": true
 }

SSH Keys

Guide for this.

Generate the SSH key you want to use with the following command:

$ ssh-keygen -t rsa -C "your_name@email_domain.com"

Make sure the key is cached by typing:

$ ssh-add -l

If no keys appear, then add the key by typing:

$ ssh-add ~/.ssh/id_rsa

To have all connections linked to the same id_rsa key, add this line of code to ~/.ssh/config:

Host *
    AddKeysToAgent yes
    PreferredAuthentications publickey
    IdentityFile ~/.ssh/id_rsa

Lastly, check that the connections work:

$ ssh -T git@github.com
Hi {user}! You've successfully authenticated, but GiHub does not provide shell access.
$ ssh -T git@gitlab.work.io
Welcome to GitLab, @{user}!

Viewing Jupyter Notebooks Locally from a Remote Machine

Jupyter notebook development is becoming the de-facto research environment. To work with Jupyter notebooks remotely, one must tunnel the output of jupyter to view it on a local browser. You can also use a reverse proxy, but I find this more troublesome.

ssh username@xx.xx.xx.xx -L 1234:localhost:1234

In the code above, data outgoing to port 1234 will be forwarded to localhost:1234 from the remote system. The L is used to specify the port to forward data to.

Once you're in the machine, start the jupyter notebook as such:

jupyter notebook --no-browser --port 1234

This will forward the output of the jupyter notebook to the port specified.

landmann / tips-and-tricks