Using Python¶

The Python REPL (Read Evaluate Print Loop)¶

Assuming you have Python installed on your system, you can launch the REPL using the python command in a terminal

(base) $ which python
~/miniconda3/bin/python
(base) $ conda activate pycourse
(pycourse) $ which python
~/miniconda3/envs/pycourse/bin/python

To launch the REPL:

(pycourse) $ python
Python 3.8.3 (default, Jul  2 2020, 16:21:59)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>

You can then enter commands in and hit Enter to run a command

>>> print("hello world!")
hello world!
>>> 1 + 1
2
>>>

You can exit using the exit() function

>>> exit()
(pycourse) $

Alternatively, press ctrl + d to exit from terminal (this sends an end of file signal).

ipython¶

A popular Python REPL with more features is packaged with ipython.

(pycourse) $ conda install ipython
(pycourse) $ ipython

Python 3.8.3 (default, Jul  2 2020, 16:21:59)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.18.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: 1 + 1
Out[1]: 2

In [2]:

Python Scripts¶

Python scripts are text files stored with a .py extension. You can run scripts from the command line

First, let’s create a simple Python script which just prints a string:

(pycourse) $ echo 'print("hello world!")' > hello.py

You will now have a file hello.py

(pycourse) $ cat hello.py
print("hello world!")

You can run the script by executing python hello.py

(pycourse) $ python hello.py
hello world!

Here’s a slightly more complex example.

(pycourse) $ cat script.py
"""
A simple python script
run from the terminal using
$ python script.py
"""

# printing will print to the terminal
print("hello world")

# you can do anything in your script
# define functions or classes
# import packages
# and so on...
def f(a, b):
    """
    returns the sum of a and b
    """
    return a + b

a = 1
b = 2
print(f"{a} + {b} = {f(a,b)}")

When we run the script:

(pycourse) $ python script.py
hello world
1 + 2 = 3

Jupyter Notebooks¶

Jupyter (Julia, Python, R) notebooks mix code with markdown (a language for basic text formatting) in your browser. This document is a Jupyter notebook, and the text is written in markdown.

Installing Jupyter¶

First, launch a terminal, and install notebooks in your base environment

(base) $ conda install -c conda-forge notebook

(-c conda-forge tells conda to install from the conda-forge channel).

Test your installation¶

After installation, you should see a jupyter command is now available.

(base) $ which jupyter
~/miniconda3/bin/jupyter

Install A Kernel for your environment¶

The next thing you need to do is install a kernel for your pycourse environment. This will allow you to run code in Jupyter notebooks using the same setup as you would if you activate pycourse.

First, activate your pycourse environment in a terminal

(base) $ conda activate pycourse
(pycourse) $

Next, install the ipykernel package using conda

(pycourse) $ conda install ipykernel -c conda-forge

Now, you run the installation

(pycourse) $ python -m ipykernel install --user --name pycourse --display-name "Python (pycourse)"

Finally, deactivate your pycourse environment

(pycourse) $ conda deactivate

Launch a Jupyter notebook server¶

Now, to launch a Jupyter notebook server, simply type

(base) $ jupyter notebook

You can launch the notebook server from any directory.

You can either create new notebooks, or launch existing notebooks.

Scientific Computing with Python

Using Python

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