Shell, Git & Plotting and Programming in Python

Max Planck Institute for Evolutionary Biology

Mar 18-26, 2024

10:00 - 18:00 CEST

Instructors: Carsten Fortmann-Grote, Nikoleta Glynatsi

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. Preferrence will be given to first year IMPRS students at MPI Evolutionary and partnering institutes. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: August Thienemann Strasse 2, 24306 Plön, Germany. Get directions with OpenStreetMap or Google Maps.

When: Mar 18-26, 2024. Add to your Google Calendar.

Requirements: We provide a standard PC with all required software installed.

Participants may bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email computing@evolbio.mpg.de for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Who can attend?: This workshop is primarily targeted at early career scientists and students (Master or PhD students, early PostDocs) at MPI for Evolutionary Biology or affiliated institutions within the IMPRS graduate school. Should the allocated 24 seats not fill up, individuals from other institutions may apply as well. This will be communicated in due time.


Topics

The Unix Shell

  1. Introducing the Shell: What is a command shell and why would I use one?
  2. Navigating Files and Directories: How can I move around on my computer? How can I see what files and directories I have? How can I specify the location of a file or directory on my computer?
  3. Working With Files and Directories: How can I create, copy, and delete files and directories? How can I edit files?
  4. Pipes and Filters: How can I combine existing commands to do new things?
  5. Loops: How can I perform the same actions on many different files?
  6. Shell Scripts: How can I save and re-use commands?
  7. Finding Things: How can I find files? How can I find things in files?

Version Control with Git

  1. Automated Version Control: What is version control and why should I use it?
  2. Setting Up Git: How do I get set up to use Git?
  3. Creating a Repository: Where does Git store information?
  4. Tracking Changes: How do I record changes in Git? How do I check the status of my version control repository? How do I record notes about what changes I made and why?
  5. Exploring History: How can I identify old versions of files? How do I review my changes? How can I recover old versions of files?
  6. Ignoring Things: How can I tell Git to ignore files I don’t want to track?
  7. Remotes in GitHub: How do I share my changes with others on the web?
  8. Collaborating: How can I use version control to collaborate with other people?
  9. Conflicts: What do I do when my changes conflict with someone else’s?
  10. Open Science: How can version control help me make my work more open?
  11. Licensing: What licensing information should I include with my work?
  12. Citation: How can I make my work easier to cite?
  13. Hosting: Where should I host my version control repositories?

Plotting and Programming with Python

  1. Running and Quitting: How can I run Python programs?
  2. Variables and Assignment: How can I store data in programs?
  3. Data Types and Type Conversion: What kinds of data do programs store? How can I convert one type to another?
  4. Built-in Functions and Help: How can I use built-in functions? How can I find out what they do? What kind of errors can occur in programs?
  5. Libraries: How can I use software that other people have written? How can I find out what that software does?
  6. Reading Tabular Data into DataFrames: How can I read tabular data?
  7. Pandas DataFrames: How can I do statistical analysis of tabular data?
  8. Plotting: How can I plot my data? How can I save my plot for publishing?
  9. Lists: How can I store multiple values?
  10. For Loops: How can I make a program do many things?
  11. Conditionals: How can programs do different things for different data?
  12. Looping Over Data Sets: How can I process many data sets with a single command?
  13. Writing Functions: How can I create my own functions?
  14. Variable Scope: How do function calls actually work? How can I determine where errors occurred?
  15. Programming Style: How can I make my programs more readable? How do most programmers format their code? How can programs check their own operation?

Registration

To register, please use our registrations page.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

The workshop schedule is here: https://github.com/mpievolbio-scicomp/2023-04-04-MPIEvolBio/wiki/Schedule#schedule.


Setup

To participate in a Software Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do tasks more quickly.

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
    3. On the page that says "Adjusting the name of the initial branch in new repositories", ensure that "Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
    4. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    5. Select "Use bundled OpenSSH".
    6. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    7. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    8. Ensure that "Use Windows' default console window" is selected and click on "Next".
    9. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    10. Ensure that "Git Credential Manager" is selected and click on "Next".
    11. Ensure that "Enable file system caching" is selected and click on "Next".
    12. Click on "Install".
    13. Click on "Finish" or "Next".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press Enter)
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press Enter, you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing Enter

This will provide you with both Git and Bash in the Git Bash program.

Video Tutorial

The default shell in some versions of macOS is Bash, and Bash is available in all versions, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash

If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".

Video Tutorial

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in a terminal and press the Enter key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

For macOS, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Video Tutorial

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Python

Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

We will teach Python using the Jupyter Notebook, a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

  1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
  3. Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
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  1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
  3. Install Python 3 by running the Anaconda Installer using all of the defaults for installation.

Video Tutorial

  1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. Download the Anaconda Installer with Python 3 for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  4. Type
    bash Anaconda3-
    and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
  5. Press Enter (or Return depending on your keyboard). You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.