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https://pad.carpentries.org/2018-09-26-UCL

http://socrative.com/ RITS

PYTHON

setup: http://rits.github-pages.ucl.ac.uk/2018-09-26-UCL_software_carpentry/python/


def favorite_ice_cream():
    ice_creams = [
        "chocolate",
        "vanilla",
        "strawberry"
    ]
    print(ice_creams[3])

favorite_ice_cream()



def normalize_rectangle(rect):
    '''Normalizes a rectangle so that it is at the origin and 1.0 units long on its longest axis.'''
    assert len(rect) == 4, 'Rectangles must contain 4 coordinates'
    x0, y0, x1, y1 = rect
    assert x0 < x1, 'Invalid X coordinates'
    assert y0 < y1, 'Invalid Y coordinates'

    dx = x1 - x0
    dy = y1 - y0
    if dx > dy:
        scaled = float(dx) / dy
        upper_x, upper_y = 1.0, scaled
    else:
        scaled = float(dx) / dy
        upper_x, upper_y = scaled, 1.0

    assert 0 < upper_x <= 1.0, 'Calculated upper X coordinate invalid'
    assert 0 < upper_y <= 1.0, 'Calculated upper Y coordinate invalid'

    return (0, 0, upper_x, upper_y)



SHELL

Data: http://swcarpentry.github.io/shell-novice/data/data-shell.zip

pwd = print working directory
cd = change directory
  ~ = takes you to your home directory
      = (same if you don't put anything)
  /home/name/a/particular/path = takes you to a particular path
  ..  = it takes you to the directory above
ls = list files
  -F = shows a '/' after the directories
  -a = shows the "hidden" files
  -l  = long description of the files/directories
  -l *.pdb = shows only the files that end with ".pdb"
  -l ?ethane.pdb = shows what has only one letter before "ethane.pdb"
rm = remove files
  -r = (for recursive) remove a directory
cp = copy files
mv = move files
  mv thesis/drafts.txt .  = moves draft from thesis to here "."
wc = counts words
  -c = counts characters
  -c *.pdb = count characters for all the files ending with ".pdb"
  -w = counts words
  -l = counts lines
cat = displays or concatenate the file
less = displays the file
more = like less, but keeps the text on screen
sort = sort lines
  -n = sorts by numbers
head = shows the first few lines of a file
  -n 20 = shows the first 20 lines
tail = shows the last lines of a file
  -n 20 = shows the last 20 lines

|  = is a symbol to "pipe" the ouput of a command as input for the next one
> filname = ouputs will be saved into a filename
>> filename = ouputs will be appended into a filename


for variable in *.dat
do
ls $variable
done

Loops over all the files on *.dat, then list that particular file.


nano filename = Opens a file called filename with the nano text editor; ^ = Ctrl key.

To create a script you can write commands into a filename, where $1 is the first argument, $2 is the second, ...
e.g.,



grep = find text on files