Crash course in Jupyter and Python

  • Introduction to Jupyter

    • Using Markdown

    • Magic functions

    • REPL

    • Saving and exporting Jupyter notebooks

  • Python

    • Data types

    • Operators

    • Collections

    • Functions and methods

    • Control flow

    • Loops, comprehension

    • Packages and namespace

    • Coding style

    • Understanding error messages

    • Getting help

Class Repository

Course material will be posted here. Please make any personal modifications to a copy of the notebook to avoid merge conflicts.

https://github.com/cliburn/sta-663-2019.git

Introduction to Jupyter

  • Official Jupyter docs

  • User interface and kernels

  • Notebook, editor, terminal

  • Literate programming

  • Code and markdown cells

  • Menu and toolbar

  • Key bindings

  • Polyglot programming

In [1]:

%load_ext rpy2.ipython

In [2]:

import warnings
warnings.simplefilter('ignore', FutureWarning)

In [3]:

df = %R iris

In [4]:

df.head()

Out[4]:
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
0 5.1 3.5 1.4 0.2 setosa
1 4.9 3.0 1.4 0.2 setosa
2 4.7 3.2 1.3 0.2 setosa
3 4.6 3.1 1.5 0.2 setosa
4 5.0 3.6 1.4 0.2 setosa 
In [5]:

%%R -i df -o res

library(tidyverse)
res <- df %>% group_by(Species) %>% summarize_all(mean)

/usr/local/lib/python3.7/site-packages/rpy2/rinterface/__init__.py:146: RRuntimeWarning: ── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──

  warnings.warn(x, RRuntimeWarning)
/usr/local/lib/python3.7/site-packages/rpy2/rinterface/__init__.py:146: RRuntimeWarning: ✔ ggplot2 3.1.0     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.8
✔ tidyr   0.8.2     ✔ stringr 1.3.1
✔ readr   1.2.1     ✔ forcats 0.3.0

  warnings.warn(x, RRuntimeWarning)
/usr/local/lib/python3.7/site-packages/rpy2/rinterface/__init__.py:146: RRuntimeWarning: ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

  warnings.warn(x, RRuntimeWarning)

In [6]:

res

Out[6]:
R/rpy2 DataFrame (3 x 5)
Species Sepal.Length Sepal.Width Petal.Length Petal.Width
setosa 5.006000 3.428000 1.462000 0.246000
versicolor 5.936000 2.770000 4.260000 1.326000
virginica 6.588000 2.974000 5.552000 2.026000

Using Markdown

  • What is markdown?

  • Headers

  • Formatting text

  • Syntax-highlighted code

  • Lists

  • Hyperlinks and images

  • LaTeX

See Help | Markdown

Magic functions

In [7]:

%magic

REPL

  • Read, Eval, Print, Loop

  • Learn by experimentation

In [8]:

1 + 2

Out[8]:

3

Saving and exporting Jupyter notebooks

  • The File menu item

  • Save and Checkpoint

  • Exporting

  • Close and Halt

  • Cleaning up with the Running tab

In [ ]:

Introduction to Python

  • Official Python docs

  • Why Python?

  • General purpose language (web, databases, introductory programming classes)

  • Language for scientific computation (physics, engineering, statistics, ML, AI)

  • Human readable

  • Interpreted

  • Dynamic typing

  • Strong typing

  • Multi-paradigm

  • Implementations (CPython, PyPy, Jython, IronPython)

In [ ]:

Data types

  • boolean

  • int, double, complex

  • strings

  • None

In [9]:

True, False

Out[9]:

(True, False)

In [10]:

1, 2, 3

Out[10]:

(1, 2, 3)

In [11]:

import numpy as np

np.pi, np.e

Out[11]:

(3.141592653589793, 2.718281828459045)

In [12]:

3 + 4j

Out[12]:

(3+4j)

In [13]:

'hello, world'

Out[13]:

'hello, world'

In [14]:

"hell's bells"

Out[14]:

"hell's bells"

In [15]:

"""三轮车跑的快
上面坐个老太太
要五毛给一块
你说奇怪不奇怪"""

Out[15]:

'三轮车跑的快\n上面坐个老太太\n要五毛给一块\n你说奇怪不奇怪'

In [16]:

None

In [17]:

None is None

Out[17]:

True

Operators

  • mathematical

  • logical

  • bitwise

  • membership

  • identity

  • assignment and in-place operators

  • operator precedence

Arithmetic

In [18]:

2 ** 3

Out[18]:

8

In [19]:

11 / 3

Out[19]:

3.6666666666666665

In [20]:

11 // 3

Out[20]:

3

In [21]:

11 % 3

Out[21]:

2

Logical

In [22]:

True and False

Out[22]:

False

In [23]:

True or False

Out[23]:

True

In [24]:

not (True or False)

Out[24]:

False

Relational

In [25]:

2 == 2, 2 == 3, 2 != 3, 2 < 3, 2 <= 3, 2 > 3, 2 >= 3

Out[25]:

(True, False, True, True, True, False, False)

Bitwise

In [26]:

format(10, '04b')

Out[26]:

'1010'

In [27]:

format(7, '04b')

Out[27]:

'0111'

In [28]:

x = 10 & 7
x, format(x, '04b')

Out[28]:

(2, '0010')

In [29]:

x = 10 | 7
x, format(x, '04b')

Out[29]:

(15, '1111')

In [30]:

x = 10 ^ 7
x, format(x, '04b')

Out[30]:

(13, '1101')

Membership

In [31]:

'hell' in 'hello'

Out[31]:

True

In [32]:

3 in range(5), 7 in range(5)

Out[32]:

(True, False)

In [33]:

'a' in dict(zip('abc', range(3)))

Out[33]:

True

Identity

In [34]:

x = [2,3]
y = [2,3]
x == y, x is y

Out[34]:

(True, False)

In [35]:

id(x), id(y)

Out[35]:

(5142288200, 5142289032)

In [36]:

x = 'hello'
y = 'hello'

In [37]:

x == y, x is y

Out[37]:

(True, True)

In [38]:

id(x), id(y)

Out[38]:

(5142210240, 5142210240)

Assignment

In [39]:

x = 2

In [40]:

x = x + 2

In [41]:

x

Out[41]:

4

In [42]:

x *= 2

In [43]:

x

Out[43]:

8

Collections

Lists

In [44]:

xs = [1,2,3]
xs[0], xs[-1]

Out[44]:

(1, 3)

In [45]:

xs[1] = 9
xs

Out[45]:

[1, 9, 3]

Tuples

In [46]:

ys = (1,2,3)
ys[0], ys[-1]

Out[46]:

(1, 3)

In [47]:

try:
    ys[1] = 9
except TypeError as e:
    print(e)

'tuple' object does not support item assignment

Sets

In [48]:

zs = [1,1,2,2,2,3,3,3,3]

In [49]:

set(zs)

Out[49]:

{1, 2, 3}

Dictionaries

In [50]:

{'a': 0, 'b': 1, 'c': 2}

Out[50]:

{'a': 0, 'b': 1, 'c': 2}

In [51]:

dict(a=0, b=1, c=2)

Out[51]:

{'a': 0, 'b': 1, 'c': 2}

In [52]:

dict(zip('abc', range(3)))

Out[52]:

{'a': 0, 'b': 1, 'c': 2}

Functions and methods

  • Anatomy of a function

  • Docstrings

  • Class methods

In [53]:

list(range(10))

Out[53]:

[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]

In [54]:

[item for item in dir() if not item.startswith('_')]

Out[54]:

['In',
 'Out',
 'df',
 'exit',
 'get_ipython',
 'np',
 'quit',
 'res',
 'warnings',
 'x',
 'xs',
 'y',
 'ys',
 'zs']

In [55]:

def f(a, b):
    """Do something with a and b.

    Assume that the + and * operatores are defined for a and b.
    """

    return 2*a + 3*b

In [56]:

f(2, 3)

Out[56]:

13

In [57]:

f(3, 2)

Out[57]:

12

In [58]:

f(b=3, a=2)

Out[58]:

13

In [59]:

f(*(2,3))

Out[59]:

13

In [60]:

f(**dict(a=2, b=3))

Out[60]:

13

In [61]:

f('hello', 'world')

Out[61]:

'hellohelloworldworldworld'

In [62]:

f([1,2,3], ['a', 'b', 'c'])

Out[62]:

[1, 2, 3, 1, 2, 3, 'a', 'b', 'c', 'a', 'b', 'c', 'a', 'b', 'c']

Control flow

  • if and the ternary operator

  • Checking conditions - what evaluates as true/false?

  • if-elif-else

  • while

  • break, continue

  • pass

In [63]:

if 1 + 1 == 2:
    print("Phew!")

Phew!

In [64]:

'vegan' if 1 + 1  == 2 else 'carnivore'

Out[64]:

'vegan'

In [65]:

'vegan' if 1 + 1  == 3 else 'carnivore'

Out[65]:

'carnivore'

In [66]:

if 1+1 == 3:
    print("oops")
else:
    print("Phew!")

Phew!

In [67]:

for grade in [94, 79, 81, 57]:
    if grade > 90:
        print('A')
    elif grade > 80:
        print('B')
    elif grade > 70:
        print('C')
    else:
        print('Are you in the right class?')

A
C
B
Are you in the right class?

In [68]:

i = 10
while i > 0:
    print(i)
    i -= 1

10
9
8
7
6
5
4
3
2
1

In [69]:

for i in range(1, 10):
    if i % 2 == 0:
        continue
    print(i)

1
3
5
7
9

In [70]:

for i in range(1, 10):
    if i % 2 == 0:
        break
    print(i)

1

In [71]:

for i in range(1, 10):
    if i % 2 == 0:
        pass
    else:
        print(i)

1
3
5
7
9

Loops and comprehensions

  • for, range, enumerate

  • lazy and eager evaluation

  • list, set, dict comprehensions

  • generator expression

In [72]:

for i in range(1,5):
    print(i**2, end=',')

1,4,9,16,

In [73]:

for i, x in enumerate(range(1,5)):
    print(i, x**2)

0 1
1 4
2 9
3 16

In [74]:

for i, x in enumerate(range(1,5), start=10):
    print(i, x**2)

10 1
11 4
12 9
13 16

In [75]:

range(5)

Out[75]:

range(0, 5)

In [76]:

list(range(5))

Out[76]:

[0, 1, 2, 3, 4]

Comprehensions

In [77]:

[x**3 % 3 for x in range(10)]

Out[77]:

[0, 1, 2, 0, 1, 2, 0, 1, 2, 0]

In [78]:

{x**3 % 3 for x in range(10)}

Out[78]:

{0, 1, 2}

In [79]:

{k: v for k, v in enumerate('abcde')}

Out[79]:

{0: 'a', 1: 'b', 2: 'c', 3: 'd', 4: 'e'}

In [80]:

(x**3 for x in range(10))

Out[80]:

<generator object <genexpr> at 0x12edc1de0>

In [81]:

list(x**3 for x in range(10))

Out[81]:

[0, 1, 8, 27, 64, 125, 216, 343, 512, 729]

Packages and namespace

  • Modules (file)

  • Package (hierarchical modules)

  • Namespace and naming conflicts

  • Using import

  • Batteries included

In [82]:

%%file foo.py

def foo(x):
    return f"And FOO you too, {x}"

Overwriting foo.py

In [83]:

import foo

In [84]:

foo.foo("Winnie the Pooh")

Out[84]:

'And FOO you too, Winnie the Pooh'

In [85]:

from foo import foo

In [86]:

foo("Winnie the Pooh")

Out[86]:

'And FOO you too, Winnie the Pooh'

In [87]:

import numpy as np

In [88]:

np.random.randint(0, 10, (5,5))

Out[88]:

array([[1, 8, 6, 7, 0],
       [9, 5, 5, 6, 5],
       [0, 5, 1, 2, 6],
       [3, 3, 9, 8, 9],
       [8, 6, 5, 0, 8]])

Coding style

Understanding error messages

In [89]:

try:
    1 / 0
except ZeroDivisionError as e:
    print(e)

division by zero

Getting help

  • ?foo, foo?, help(foo)

  • Use a search engine

  • Use StackOverflow

  • Ask your TA

In [90]:

help(help)

Help on _Helper in module _sitebuiltins object:

class _Helper(builtins.object)
 |  Define the builtin 'help'.
 |
 |  This is a wrapper around pydoc.help that provides a helpful message
 |  when 'help' is typed at the Python interactive prompt.
 |
 |  Calling help() at the Python prompt starts an interactive help session.
 |  Calling help(thing) prints help for the python object 'thing'.
 |
 |  Methods defined here:
 |
 |  __call__(self, *args, **kwds)
 |      Call self as a function.
 |
 |  __repr__(self)
 |      Return repr(self).
 |
 |  ----------------------------------------------------------------------
 |  Data descriptors defined here:
 |
 |  __dict__
 |      dictionary for instance variables (if defined)
 |
 |  __weakref__
 |      list of weak references to the object (if defined)


In [ ]: