Python coding for beginners

Systems

• MacOS/Linux
  • Terminal
• Windows
  • WSL
  • Git Bash

Linux shell

• https://swcarpentry.github.io/shell-novice/
• COMMAND --help
• ls [OPTION] [PATTERN]
  • -F: showing /
  • -a: showing ../
  • -r: reverse
  • -R: recursive
  • [PATTERN]: *.ext, ? (any single character)
• pwd
• cd
  • w/o arguments: going back to home ~
  • ..
• TAB completion
• mkdir
  • -p: for multi-level folders
• nano (text editor)
  • Ctrl-o + Enter: save
  • Ctrl-x: exit
• mv SRC/ DEST/
• cp FILE_A FILE_B
• rm
  • -i: interactive mode
  • -r: for folders
• wc (word counts)
  • -l: lines
• >: print into
• sort
  • -n: numeric
  • -r: reverse
• head/tail
  • -n #: # of lines
• | (pipe)
• uniq
  • -c: unique counts of sequential lines
• cut
  • -d ,: delimiter
  • -f #: field #
• Shell scripts (.sh)
  • bash script.sh
  • #: comments
  • "$#": shorthand for argument #

Python

• https://swcarpentry.github.io/python-novice-inflammation/
• Installation took time.
  • Miniforge
• jupyter
  • Re-run
  • Mouse vs. Keyboard strokes
• conda env list
• Variables
  • Naming convention
• Data types
• type(): type of variable
• print()
• help()
  • https://stackoverflow.com/
• import numpy
  • loadtxt('*.csv', delimiter=',')
  • type
    • numpy.ndarray
    • float64 (larger than a float)
  • shape (rows, columns)
  • index
    • Python is a “zero-indexed” language.
    • Slicing
      • up to but not including the number after the colon
      • no final number means go to the end
  • mean(), std(), amin(), amax(), diff()
    • (..., axis=0) (0 by column, 1 by row)
• import matplotlib.pyplot as plt
  • create a graph –> show the graph (plt.show()) –> save figure (plt.savefig(FILE.EXT))
  • imshow
  • plot
  • fig = figure(figsize=(8,8)
  • ax = fig.add_subplot(nrows, ncols, index)
  • ax.set_xlabel(), ax.set_ylabel(), ax.set_xlim(), ax.set_ylim()
  • ax.grid('on')
  • fig.tight_layout()
• List []
  • mutable
  • nested list
  • heterogeneousness
  • append(), pop(), reverse() vs. reversed()
• Tuple ()
  • immutable
• Loops
  • for [VARIABLE] in [List]:
  • indentation
  • comments with instructions
  • import glob
    • glob.glob('PATTERN'): all matched filenames
    • sorted()
• Conditions
  • if (CONDITIONS):
  • elif (CONDI_A and CONDI_B):
  • else:
  • indentation
  • >, >=, <, <=, ==, !=
  • '''COMMENTS'''
• Functions
  • def FUNCTION(INPUTS):
    • return OUTPUTS
  • indentation
  • OUTPUTS = FUNCTION(INPUTS)
  • Scopes (local, global)

Git

• https://swcarpentry.github.io/git-novice/index.html
• Configuration
  • git config --global user.name "NAME"
  • git config --global user.email "EMAIL"
  • git config --global core.editor "nano -w"
  • git config --global init.defaultBranch main
• Local repository
  • git init
    • ls -a (.git/)
  • git status
  • git add FILE_or_DIR –> (staged) –> git commit -m "DESCRIPTION" –> (committed)
  • git log
    • “q”: leave log
    • -#: last # entries
    • --oneline
  • git diff
    • +(green): added
    • -(red): deleted
    • --staged: for staged
  • .gitignore
    • files/folders or patterns of files/folders to be ignored
  • Useful commands
    • touch FILE: create an empty file
    • cat FILE: print file content
• Remote repository
  • Github account
  • git remote add origin git@github.com:ACCOUNT/REPO_NAME.git
  • git remote -v
  • SSH key
    • ssh-keygen -t ed25519 -C "COMMENTS"
    • copy & paste the public key (~/.ssh/id_ed25519.pub) to Github/Settings/SSH and GPG keys/
    • ssh -T git@github.com (test connection)
  • git push origin main (or with -u option)