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Python Basics

Setup Python

Look at the guide in here or follow bellow steps.

Install conda:

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm ~/miniconda3/miniconda.sh

After installing, initialize your newly-installed Miniconda.

~/miniconda3/bin/conda init bash

Setup your python:

conda create -n some_name python=3.10
conda activate some_name

You can put conda activate some_name in your ~/.bashrc to activate it when open a new terminal.

Remove your conda environment:

conda remove -n some_name --all

Remove Conda

To completely remove Miniconda from your Ubuntu system, including all associated configurations and files, follow these steps:

Jupyter Kernel

# This process installs a new Jupyter kernel named test with the display name "bird".
pip install ipykernel
sudo python -m ipykernel install --name test --display-name bird

# Location of the Installed Kernel
jupyter kernelspec list
# This command will display a list of all installed kernels along with their corresponding paths. 
#  test       /home/your_username/.local/share/jupyter/kernels/test

# Removing the Installed Kernel
jupyter kernelspec uninstall test

Deactivate Any Active Conda Environments

Ensure that no Conda environments are active by running:

conda deactivate

Remove the Miniconda Installation Directory

Delete the directory where Miniconda is installed. By default, this is ~/miniconda3. Use the following command, adjusting the path if necessary:

rm -rf ~/miniconda3/

Note: Replace ~/miniconda3/ with the correct path if you installed Miniconda elsewhere.

Remove hidden files and directories in your home directory that Conda uses:

rm -rf ~/.conda ~/.condarc ~/.continuum

These directories store Conda environments and settings.

Remove Conda Initialization from Shell Configuration

Conda adds initialization code to your shell's configuration file (e.g., .bashrc). To remove these lines:

  • Open the configuration file in a text editor:
nano ~/.bashrc
  • Scroll to the section managed by 'conda init', which looks like:
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/username/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/username/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/home/username/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/username/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

  • Delete this entire block.

  • Save the file and exit the editor (in nano, press CTRL+O to save and CTRL+X to exit).

  • Apply the changes by sourcing the file:

source ~/.bashrc

Check for and remove any remaining Conda-related cache files:

rm -rf ~/.cache/conda

Conda Commands Cheat Sheet

conda create -n some_name python=3.10 # Create a new Conda virtual env
conda activate some_name # Activate the Conda virtual env
conda remove -n some_name --all # Remove the Conda virtual env
conda install openblas-devel -c anaconda # Install a package from Conda
conda list | grep blas # Search for a package in the installed list (similar to `pip freeze | grep blas`)
echo $CONDA_PREFIX # Path of the currently active env (e.g., ~/miniconda3/envs/some_name)

Useful pip Commands

pip -U install package1 packag2 # -U: for update
pip uinstall package
pip-autoremove -y package1 package2  # Remove package completely. First install `pip install -y pip-autoremove`
pip freeze
pip list
pip check

Python Courses

From https://software-carpentry.org/lessons, below courses are offered. - Programming with Python - Plotting and Programming in Python

For more on software engineering side, you could also attend this course: - Intermediate Research Software Development with Python