Analysis essentials

This is the source material for the analysis essentials website, a series of lessons for helping high-energy physics analysts become more comfortable working with the shell, version control, and programming.

The lessons introduce the basics of the bash shell, the git version control system, and the Python programming language. They are developed for and taught during the Starterkit, and aim to teach students enough to be able to follow the experiment-specific lessons that are taught afterwards.

Contributions to the lessons are highly encouraged. Please see the contributing guide for details on how to participate.

Prerequisites

There are two options for running these lessons. Running locally should be prefered on Linux and macOS as it is faster and makes it easier to save you work. On Windows it is likely easier to use Binder however care is needed to prevent notebooks being lost when the server is shut down.

Local

This tutorial uses Python 3.7 and requires some packages. It is recommended to use Conda to install the correct packages.

To install Conda you will need to do the following:

• Install Conda according to the instructions here
• You can add source /my/path/for/miniconda/etc/profile.d/conda.sh to your .bashrc
• Add the channel:

conda config --add channels conda-forge

Now to use your first Conda environment:

• Create an environment with some packages already installed:

conda create -n my-analysis-env python=3.7 jupyterlab ipython matplotlib uproot numpy pandas scikit-learn scipy tensorflow xgboost hep_ml wget

• Activate your environment by doing: conda activate my-analysis-env
• You can install additional packages by doing: conda install package_name
• For the lessons to work fully you will also need to install a special helper package with pip:

pip install git+https://github.com/hsf-training/python-lesson.git

You will also need Jupyter to run the examples in this tutorial. Jupyter was already installed in the previous command and can be ran by following the instructions here. Note: You will need Python.

Binder

Click this button:

Usage

You should now be able to use the tutorial.

• First clone with git:

git clone https://github.com/hsf-training/analysis-essentials.git

• For more information on getting started with git please see the Analysis Essentials course

cd analysis-essentials
jupyter lab

This should open a Jupyter webpage with the current directory displayed. Navigate to one of the lessons to start the tutorial.

If you have any problems or questions, you can open an issue on this repository.

.. toctree::
    :maxdepth: 3
    :includehidden:
    :caption: Contents:

    python/README.md
    advanced-python/README.md
    shell/README.md
    shell-extras/README.md
    snakemake/README.md
    git/README.md
    CONTRIBUTING.md