Software Carpentry at UCL: Bash, Git, and Python Workshop 30 Sep - 1 Oct 2026

DAY 1:

Staff

Instructors: Haroon Chughtai, David Pérez-Suárez (Ruaridh Gollifer, Stephen Thompson)
Helpers: Henry Crosswell, Mary Tziraki

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• David Perez-Suarez - Linux (Instructor)

• ---

• Sicheng Lyu - Windows
• Chenyu Li - Mac
• Jiaming Huang - Mac
• ZhaoXiang Ding - Windows
• Jochem Langen - Windows
• Yasmine Yao - Mac
• YULIN CHEN - Windows
• YIXU LI -Mac
• Victor Culverwell - Mac
• Yuxin Tian - Windows
• Chloe Hooper - Mac
• Weiyue Li - Mac
• Jalaj - Mac
• Maxim - Windows
• Amara Callender - Windows
• yueliang - mac
• Zhangjie Xu - Windows
• Zhuowei Zhu -windows
• Oliver Shattock - Mac
• Rafael PH - Windows
• Xinling Yao - Windows
• Ruoxi Li - windows
• Yiyuan Jia -Mac
• Xinyue Li -Mac
• Chloe Langford - mac
• Xindong Liu - Mac
• Lewis Watt - Windows
• Botao Zhang - Mac
• Bohao Fang -Mac
• Jack Wang - MacOS
• Yan Zhang-Windows
• Qi Dai - MacOS
• Dai Yichu - Windows
• Xiangnan Li - MacOS
• Xinran Li - Windows

DAY 2:

Staff

Instructors: Paul Smith, Kimberly Meechan (Will Graham, Tuomas Koskela)
Helpers: Henry Crosswell, Mary Tziraki

Sign In

Please also include whether you are using Windows/Mac/Linux

• Paul Smith - (Intel) Mac (Instructor)
• Xiangnan Li - MacOS
• Qi Dai - MacOS
• Chloe Hooper - MacOS
• Yulin Chen - Windows
• Dai Yichu - Windows
• Amara Callender - Windows
• chloe langford - mac

Anonymous Questions

If you have a questions during the session and don’t want to ask it publicly, you can write them here!

Feedback and Surveys

Pre-workshop survey

Post-workshop survey

Notes

Shell

• pwd : Print Working Directory. Displays the folder (directory) that your terminal is currently “looking at”. Everything you ask your terminal to do will be done from this folder, and any commands you ask give it will be interpreted as being “relative to” that directory.
• cd: Change Directory. Move your terminal from the current working directory (what pwd prints) to a new directory. You can give the name after the cd command to select the folder to move to. i.e., cd <folder_name>
  • cd without any arguments take you to the home directory
• ls : List contents. Displays all the files and folders inside the current working directory. Can take extra options using dashes (-).
  • ls -F : List contents, and also distinguish between files and folders using a trailing / after the names.
  • ls -a : List all files, even hidden files.
  • ls <folder_name>: List the contents of the given folder, rather than the current working directory.
• nano <filename>: Open nano, a text editor, to edit the given file (create the file if it does not exist already). When in nano, you can type text using the cursor.
  • Press CTRL + O (^O) to save. You will need to then press RETURN to confirm the name of the file to save.
  • Press CTRL + X (^X) to exit. If you have changed the file and haven’t saved, you’ll be prompted to save your changes before you exit.
• mv source destination: Move the file source to the destination.
  • BEWARE: this will overwrite the destination file if it already exists!!!
  • If the destination is a FOLDER, not a FILE, then the source file will be placed inside the destination folder.
  • mv my_file.txt my_folder/new_name.txt: Move my_file.txt into the my_folder directory, and change the file name to new_name.txt.
  • mv my_file.txt new_name.txt: Move my_file.txt into the current folder, and change the file name to new_name.txt. This is effectively “renaming” the file.
  • mv my_folder/my_file.txt .: Move my_file.txt out of my_folder and into the current working directory (. = current working directory). Note that the name is unchanged if the destination is a folder.
• cp source copy_destination: Copy a file to a new location. Similar to mv, except we get a copy rather than just move the file. It works almost identically to the mv command and the examples above, though some differences are below:
  • cp -r: The -r flag stands for “recursive”. If source is a folder, cp -r source destination will copy the entire source folder to the destination!
• rm filename: Delete (REMOVE) the filename.
  • DELETEING IS FOREVER!!!. Be careful - there is no recovery of files deleted in the terminal!
  • The related rmdir folder command will delete the folder, but only if it’s EMPTY.
  • rm has a -r flag, which stands for recursive. This will delete everything inside a folder. AGAIN, BE CAREFUL!!!
  • -i flag helps to prompt you a question to make sure you want to delete that directory.
• wc word count provides some metrics of text files. They are number of lines, words and characters of a file. With -l, -w, -c gives you the lines, words and characters respectively.
• cat shows the content of a file.
• head shows the top lines of a file, using -n X will restrict that to the first X lines.
• sort does what it does, sort the file alphabetically
  • -n sorts it numerically, i.e., 1, 2, 3, 10, 21,... rather than 1, 10, 2, 21, 3, ...
• > redirects the output of a command into a file: e.g., sort filename > new_filename will produce a new file with the same content than the original but with their lines sorted.
  • >> Using two symbols will append the output of the command to the content that may already exists on the output file.
• | pipes the output of a command into another command: e.g., sort -n lenghts.txt | head -n 1 will result on the first line of the output from sorting numerically the lengths.txt file.
  • pipes can be used multiple times to connect the output of many commands.

Git

Teams

User A / User B

• arc-teaching / dpshelio / https://github.com/arc-teaching/recipes/invitations
• .ShuShengDing / LewisW7
• .YasmineYao / benjaminwong058-source
• .leechenyu1 / Ju5t1ce / xindongliu768
• .
• .Tom Fraczek / Tom Fraczek / Tom Fraczek
• .Maxime0990 / RPH-ml
• .zhangbotao202301-spec / Rmapccw
• .
• .Weiyue0511 / fangjieshen2-sudo
• .ruoxili34-del / Cici0520-cici
• yuanbaoaw / ucfahz3
• . ch-UCL (A) / oliver-ucl-25 / jalajarora06032003 / https://github.com/ch-UCL/recipes/invitations
• .Hank03032004/ YulinChen3132
• https://github.com/Hank03032004/recipes/invitations
• acallender65 / chloelangford2 / https://github.com/acallender65/recipes/invitations
• .HarvestDark / yan306198-prog
• .77774523y / edanfortuna7777
• /
• LvnaticLunaC / fangbohao030225-afk
• denchidai/imyuxin

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Python

# Bash > Python
# Use glob to discover all our data files
filenames = glob("data/inflammation-*.csv")
filenames = sorted(filenames)
print(filenames)

for file in filenames:
    print("Currently at file:", file)
    
    # Load this dataset
    data = np.loadtxt(file, delimiter=",")
    
    # Do our analysis (create our plots)
    avg_inflam = np.mean(data, axis=0)
    min_inflam = np.min(data, axis=0)
    max_inflam = np.max(data, axis=0)
    
    # Create our plot for this dataset and save it!
    fig = plt.figure(figsize=(10, 3))
    avg_axes = fig.add_subplot(1, 3, 1)
    max_axes = fig.add_subplot(1, 3, 2)
    min_axes = fig.add_subplot(1, 3, 3)
    
    # Actually plot things on our figure
    avg_axes.plot(avg_inflam)
    avg_axes.set_ylabel("Average")
    
    max_axes.plot(max_inflam)
    max_axes.set_ylabel("Max")
    
    min_axes.plot(min_inflam)
    min_axes.set_ylabel("Min")
    
    # Tidy things up, save, and display
    max_axes.set_title(file)
    fig.tight_layout()
    
    # Generate a save file location from the current file name, by substituting
    # the .csv extension for .png
    png_file_name = file.split(".")[0] + ".png"
    png_file_name = "outputs/" + png_file_name.split("/")[1]
    fig.savefig(png_file_name)
    
    fig.show()

tags: workshop