Documentation

Why do you need documentation?

You want yourself to understand how code written some time ago works
You want others to understand how to (re-)use your code

For this you need to

Explain parts of your code with comments
Explain what to install and how to get started in your readme
Explain in-depth use of your code in a notebook

Comments

Comments are annotations you write directly in the code source.

They:

are written for users who deal with your source code
explain parts that are not intuitive from the code itself
do not replace readable or structured code
(in a specific structure) can be used to directly generate documentation for users.

When not to use comments

…to repeat in natural language what is written in your code

# Now we check if the age of a patient is greater than 18
if(agePatient > 18)

…to turn old code into zombie code (fine for troubleshooting, but do not leave it in!)

# Do not run this!!
# itDoesNotWork <- optimizeMulticoreDeepLearning(myProteins)
# if(itDoesNotWork == 1444){
#    connection <- connectToHPC(currentUser, password)
#}

…to replace version control, like git

# removed on August 5
# if() ...

#Now, it connects to the API with o-auth2, updated 05/05/2016
...

Comment lines: WHY over HOW

Comment lines are used to explain the purpose of some piece of code.

# Bug fix GH 20601
# If the data frame is too big, the number of unique index combination
# will cause int32 overflow on windows environments.
# We want to check and raise an error before this happens

num_rows = np.max([index_level.size for index_level in self.new_index_levels])
num_columns = self.removed_level.

Docstrings

Structured comments, associated to segments (rather than lines) of code, can be used to generate documentation for users* of your project.
These comments are called docstrings.
Docstrings are parsed as the first statement of a module (e.g. a function or class).
Docstrings allow you to provide documentation to a function, that is relevant to the user of that function.
Writing docstrings makes you generate your documentation as you are generating the code: efficiently, comprehensively!

Generating docstrings

In R you will need a separate package to deal with docstrings:

library(docstring)

multiply <- function(x,y){
#' @title Multiply two numbers
#' @description This function takes two
#' input numbers and multiplies
#' them. It returns the multiplied result.
#' @param x The first value
#' @param y The second value
#' @return The two arguments multiplied.

  return(x*y)
}

?multiply

Generating docstrings

In Python, docstrings are string literal comments following a function declaration:

def multiply(x,y):
  """
  Multiply two numbers
  
  This function takes two input numbers and multiplies them.
  It returns the multiplied result.

  Parameters
  ----------
  x : int or float
      the first value
  y : int or float
      the second value

  Returns
  -------
  int or float
      result of multiplication
  """
  return x*y

NB: a triple single quote (''') works, but PEP style prefers double quotes for docstrings.

A glimpse into code generation

Docstrings are formatted so that they can easily be turned into documentation of your package.

You will need additional tools:

http://www.doxygen.nl/ : C++ (and many more languages)
http://www.sphinx-doc.org/ : Python
https://roxygen2.r-lib.org/ : R

We will not do this today, but it is worth checking out if you want to release your code!

In the console, in RStudio, run the following command:

roxygen2::roxygenise()

The command above will create documentation files that can be visualized by calling help(your package)

Your turn (choose one!)

Comment lines

Do you have superfluous comments? Remove them!
- Remove your zombie code and version control-like comments +See if you can replace a ‘how’ comment for a ‘why’ comment (what is the purpose of this code? rather than this is how this code works)

Are there elements without comments that need them? Add them!
- Have you found yourself staring at a piece of code for too long without understanding it? Perhaps it needs more information!
- Try to comment on the thought behind the code rather than phrasing it in English.

Docstrings

Add a docstring to a function, preferably the last function you worked on (so it’s fresh in your memory).
Keep in mind: what does my user need to know when they are working with this function?