Libraries¶

Overview:

Teaching: 5 min
Exercises: 10 min

Questions

How can I use software that other people have written?
How can I find out what that software does?

Objectives

Explain what software libraries are and why programmers create and use them.
Write programs that import and use libraries from Python’s standard library.
Find and read documentation for standard libraries interactively (in the interpreter) and online.

Why re-invent the wheel?¶

Until now we have made extensive use of Python's built-in libraries. But what if the functionality we want is not natively available? We must make use of libraries, which is where most of the power of a programming language lies:

A library is a collection of files (called modules) that contains functions for use by other programs.
May also contain data values (e.g. numerical constants) and other things.
Library’s contents are supposed to be related, but there’s no way to enforce that.
The Python standard library is an extensive suite of modules that comes with Python itself.
Many additional libraries are available from PyPI (the Python Package Index).
The Anaconda package also contains or can help install many useful scientific libraries

Libraries and modules

A library is a collection of modules, but the terms are often used interchangeably, especially since many libraries only consist of a single module, so don’t worry if you mix them.

Importing libraries¶

A program must import a library module before using it.

Use import to load a library module into a program’s memory.
Then refer to things from the module as module_name.thing_name.
Python uses . to mean “part of”.

We will illustrate how to do this with math, one of the modules in the standard library:

import math

print('pi is', math.pi)
print('cos(pi) is', math.cos(math.pi))

pi is 3.141592653589793
cos(pi) is -1.0

Notice that we have to refer to each item with the module’s name. math.cos(pi) won’t work, the reference to pi doesn’t somehow “inherit” the function’s reference to math.. We have to write math.cos(math.pi) referencing the math library for the constant math.pi and the function math.cos()

Help!

You can use help(module_name) to learn about the contents of a library module.
You can also use help(function_name) to get help on how to use an individual function.

In [2]:

help(math)

Help on module math:
NAME
    math
MODULE REFERENCE
    https://docs.python.org/3.7/library/math
    The following documentation is automatically generated from the Python
    source files.  It may be incomplete, incorrect or include features that
    are considered implementation detail and may vary between Python
    implementations.  When in doubt, consult the module reference at the
    location listed above.
DESCRIPTION
    This module is always available.  It provides access to the
    mathematical functions defined by the C standard.
FUNCTIONS
    acos(x, /)
        Return the arc cosine (measured in radians) of x.
    acosh(x, /)
        Return the inverse hyperbolic cosine of x.
    asin(x, /)
        Return the arc sine (measured in radians) of x.
    asinh(x, /)
        Return the inverse hyperbolic sine of x.
    atan(x, /)
        Return the arc tangent (measured in radians) of x.
    atan2(y, x, /)
        Return the arc tangent (measured in radians) of y/x.
        Unlike atan(y/x), the signs of both x and y are considered.
    atanh(x, /)
        Return the inverse hyperbolic tangent of x.
    ceil(x, /)
        Return the ceiling of x as an Integral.
        This is the smallest integer >= x.
    copysign(x, y, /)
        Return a float with the magnitude (absolute value) of x but the sign of y.
        On platforms that support signed zeros, copysign(1.0, -0.0)
        returns -1.0.
    cos(x, /)
        Return the cosine of x (measured in radians).
    cosh(x, /)
        Return the hyperbolic cosine of x.
    degrees(x, /)
        Convert angle x from radians to degrees.
    erf(x, /)
        Error function at x.
    erfc(x, /)
        Complementary error function at x.
    exp(x, /)
        Return e raised to the power of x.
    expm1(x, /)
        Return exp(x)-1.
        This function avoids the loss of precision involved in the direct evaluation of exp(x)-1 for small x.
    fabs(x, /)
        Return the absolute value of the float x.
    factorial(x, /)
        Find x!.
        Raise a ValueError if x is negative or non-integral.
    floor(x, /)
        Return the floor of x as an Integral.
        This is the largest integer <= x.
    fmod(x, y, /)
        Return fmod(x, y), according to platform C.
        x % y may differ.
    frexp(x, /)
        Return the mantissa and exponent of x, as pair (m, e).
        m is a float and e is an int, such that x = m * 2.**e.
        If x is 0, m and e are both 0.  Else 0.5 <= abs(m) < 1.0.
    fsum(seq, /)
        Return an accurate floating point sum of values in the iterable seq.
        Assumes IEEE-754 floating point arithmetic.
    gamma(x, /)
        Gamma function at x.
    gcd(x, y, /)
        greatest common divisor of x and y
    hypot(x, y, /)
        Return the Euclidean distance, sqrt(x*x + y*y).
    isclose(a, b, *, rel_tol=1e-09, abs_tol=0.0)
        Determine whether two floating point numbers are close in value.
          rel_tol
            maximum difference for being considered "close", relative to the
            magnitude of the input values
          abs_tol
            maximum difference for being considered "close", regardless of the
            magnitude of the input values
        Return True if a is close in value to b, and False otherwise.
        For the values to be considered close, the difference between them
        must be smaller than at least one of the tolerances.
        -inf, inf and NaN behave similarly to the IEEE 754 Standard.  That
        is, NaN is not close to anything, even itself.  inf and -inf are
        only close to themselves.
    isfinite(x, /)
        Return True if x is neither an infinity nor a NaN, and False otherwise.
    isinf(x, /)
        Return True if x is a positive or negative infinity, and False otherwise.
    isnan(x, /)
        Return True if x is a NaN (not a number), and False otherwise.
    ldexp(x, i, /)
        Return x * (2**i).
        This is essentially the inverse of frexp().
    lgamma(x, /)
        Natural logarithm of absolute value of Gamma function at x.
    log(...)
        log(x, [base=math.e])
        Return the logarithm of x to the given base.
        If the base not specified, returns the natural logarithm (base e) of x.
    log10(x, /)
        Return the base 10 logarithm of x.
    log1p(x, /)
        Return the natural logarithm of 1+x (base e).
        The result is computed in a way which is accurate for x near zero.
    log2(x, /)
        Return the base 2 logarithm of x.
    modf(x, /)
        Return the fractional and integer parts of x.
        Both results carry the sign of x and are floats.
    pow(x, y, /)
        Return x**y (x to the power of y).
    radians(x, /)
        Convert angle x from degrees to radians.
    remainder(x, y, /)
        Difference between x and the closest integer multiple of y.
        Return x - n*y where n*y is the closest integer multiple of y.
        In the case where x is exactly halfway between two multiples of
        y, the nearest even value of n is used. The result is always exact.
    sin(x, /)
        Return the sine of x (measured in radians).
    sinh(x, /)
        Return the hyperbolic sine of x.
    sqrt(x, /)
        Return the square root of x.
    tan(x, /)
        Return the tangent of x (measured in radians).
    tanh(x, /)
        Return the hyperbolic tangent of x.
    trunc(x, /)
        Truncates the Real x to the nearest Integral toward 0.
        Uses the __trunc__ magic method.
DATA
    e = 2.718281828459045
    inf = inf
    nan = nan
    pi = 3.141592653589793
    tau = 6.283185307179586
FILE
    /home/will/anaconda3/envs/JupyterKernels/lib/python3.7/lib-dynload/math.cpython-37m-x86_64-linux-gnu.so

help(math)

help(math)

Help on module math:
NAME
    math
MODULE REFERENCE
    https://docs.python.org/3.7/library/math
    The following documentation is automatically generated from the Python
    source files.  It may be incomplete, incorrect or include features that
    are considered implementation detail and may vary between Python
    implementations.  When in doubt, consult the module reference at the
    location listed above.
DESCRIPTION
    This module is always available.  It provides access to the
    mathematical functions defined by the C standard.
FUNCTIONS
    acos(x, /)
        Return the arc cosine (measured in radians) of x.
    acosh(x, /)
        Return the inverse hyperbolic cosine of x.
    asin(x, /)
        Return the arc sine (measured in radians) of x.
    asinh(x, /)
        Return the inverse hyperbolic sine of x.
    atan(x, /)
        Return the arc tangent (measured in radians) of x.
    atan2(y, x, /)
        Return the arc tangent (measured in radians) of y/x.
        Unlike atan(y/x), the signs of both x and y are considered.
    atanh(x, /)
        Return the inverse hyperbolic tangent of x.
    ceil(x, /)
        Return the ceiling of x as an Integral.
        This is the smallest integer >= x.
    copysign(x, y, /)
        Return a float with the magnitude (absolute value) of x but the sign of y.
        On platforms that support signed zeros, copysign(1.0, -0.0)
        returns -1.0.
    cos(x, /)
        Return the cosine of x (measured in radians).
    cosh(x, /)
        Return the hyperbolic cosine of x.
    degrees(x, /)
        Convert angle x from radians to degrees.
    erf(x, /)
        Error function at x.
    erfc(x, /)
        Complementary error function at x.
    exp(x, /)
        Return e raised to the power of x.
    expm1(x, /)
        Return exp(x)-1.
        This function avoids the loss of precision involved in the direct evaluation of exp(x)-1 for small x.
    fabs(x, /)
        Return the absolute value of the float x.
    factorial(x, /)
        Find x!.
        Raise a ValueError if x is negative or non-integral.
    floor(x, /)
        Return the floor of x as an Integral.
        This is the largest integer <= x.
    fmod(x, y, /)
        Return fmod(x, y), according to platform C.
        x % y may differ.
    frexp(x, /)
        Return the mantissa and exponent of x, as pair (m, e).
        m is a float and e is an int, such that x = m * 2.**e.
        If x is 0, m and e are both 0.  Else 0.5 <= abs(m) < 1.0.
    fsum(seq, /)
        Return an accurate floating point sum of values in the iterable seq.
        Assumes IEEE-754 floating point arithmetic.
    gamma(x, /)
        Gamma function at x.
    gcd(x, y, /)
        greatest common divisor of x and y
    hypot(x, y, /)
        Return the Euclidean distance, sqrt(x*x + y*y).
    isclose(a, b, *, rel_tol=1e-09, abs_tol=0.0)
        Determine whether two floating point numbers are close in value.
          rel_tol
            maximum difference for being considered "close", relative to the
            magnitude of the input values
          abs_tol
            maximum difference for being considered "close", regardless of the
            magnitude of the input values
        Return True if a is close in value to b, and False otherwise.
        For the values to be considered close, the difference between them
        must be smaller than at least one of the tolerances.
        -inf, inf and NaN behave similarly to the IEEE 754 Standard.  That
        is, NaN is not close to anything, even itself.  inf and -inf are
        only close to themselves.
    isfinite(x, /)
        Return True if x is neither an infinity nor a NaN, and False otherwise.
    isinf(x, /)
        Return True if x is a positive or negative infinity, and False otherwise.
    isnan(x, /)
        Return True if x is a NaN (not a number), and False otherwise.
    ldexp(x, i, /)
        Return x * (2**i).
        This is essentially the inverse of frexp().
    lgamma(x, /)
        Natural logarithm of absolute value of Gamma function at x.
    log(...)
        log(x, [base=math.e])
        Return the logarithm of x to the given base.
        If the base not specified, returns the natural logarithm (base e) of x.
    log10(x, /)
        Return the base 10 logarithm of x.
    log1p(x, /)
        Return the natural logarithm of 1+x (base e).
        The result is computed in a way which is accurate for x near zero.
    log2(x, /)
        Return the base 2 logarithm of x.
    modf(x, /)
        Return the fractional and integer parts of x.
        Both results carry the sign of x and are floats.
    pow(x, y, /)
        Return x**y (x to the power of y).
    radians(x, /)
        Convert angle x from degrees to radians.
    remainder(x, y, /)
        Difference between x and the closest integer multiple of y.
        Return x - n*y where n*y is the closest integer multiple of y.
        In the case where x is exactly halfway between two multiples of
        y, the nearest even value of n is used. The result is always exact.
    sin(x, /)
        Return the sine of x (measured in radians).
    sinh(x, /)
        Return the hyperbolic sine of x.
    sqrt(x, /)
        Return the square root of x.
    tan(x, /)
        Return the tangent of x (measured in radians).
    tanh(x, /)
        Return the hyperbolic tangent of x.
    trunc(x, /)
        Truncates the Real x to the nearest Integral toward 0.
        Uses the __trunc__ magic method.
DATA
    e = 2.718281828459045
    inf = inf
    nan = nan
    pi = 3.141592653589793
    tau = 6.283185307179586
FILE
    /home/will/anaconda3/envs/JupyterKernels/lib/python3.7/lib-dynload/math.cpython-37m-x86_64-linux-gnu.so

Import items from a module¶

Using the syntax from ... import ... you can load spcific items from a library module to shorten your programs. By doing this you can refer to what you imported without having to specify the library prefix:

from math import cos, pi

print('cos(pi) is', cos(pi))

cos(pi) is -1.0

Import under an alias¶

Another useful feature is to use an alias. If we do this we do need to reference the module but we can use an alias to refer to the module:

import math as m

print('cos(pi) is', m.cos(m.pi))

cos(pi) is -1.0

Exploring the Math Module

What function from the math module can you use to calculate a square root without using sqrt? Since the library contains this function, why does sqrt exist?

Solution

Locating the Right Module

You want to select a random character from a string:

In [5]:

bases = 'ACTTGCTTGAC'

Which standard library module could help you? Which function would you select from that module? Are there alternatives? Try to write a program that uses the function.

Solution

bases = 'ACTTGCTTGAC'

bases = 'ACTTGCTTGAC'

Which standard library module could help you? Which function would you select from that module? Are there alternatives? Try to write a program that uses the function.

Solution

Jigsaw Puzzle (Parson’s Problem) Programming Example

Rearrange the following statements so that a random DNA base is printed and its index in the string. Not all statements may be needed. Feel free to use/add intermediate variables.

bases="ACTTGCTTGAC"
import math
import random
___ = random.randrange(n_bases)
___ = len(bases)
print("random base ", bases[___], "base index", ___)

Solution

When Is Help Available?

When a colleague of yours types help(math), Python reports an error:

help(math)
NameError: name 'math' is not defined

What has your colleague forgotten to do?

Solution

Importing Specific Items

Fill in the blanks so that the program below prints 90.0.

____ math import ____, ____
angle = degrees(pi / 2)
print(angle)

Do you find this version easier to read than preceding ones? Why wouldn’t programmers always use this form of import?

Solution

Key Points:

Much of the power of a programming language is in its libraries.
A program must import a library module in order to use it.
Use help to learn about the contents of a library module.
Import specific items from a library to shorten programs.
Create an alias for a library when importing it to shorten programs.

Libraries¶

Overview:

Why re-invent the wheel?¶

Libraries and modules

Importing libraries¶

Help!

Import items from a module¶

Import under an alias¶

Exploring the Math Module

Locating the Right Module

Jigsaw Puzzle (Parson’s Problem) Programming Example

When Is Help Available?

Importing Specific Items

Key Points:

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