Computational Techniques for Life Sciences

Python Glossary

additive color model: A way to represent colors as the sum of contributions from primary colors such as red, green, and blue.
argument: A value given to a function or program when it runs. The term is often used interchangeably (and inconsistently) with parameter.
assertion: An expression which is supposed to be true at a particular point in a program. Programmers typically put assertions in their code to check for errors; if the assertion fails (i.e., if the expression evaluates as false), the program halts and produces an error message. See also: invariant, precondition, postcondition.
assign: To give a value a name by associating a variable with it.
body: (of a function): the statements that are executed when a function runs.
call stack: A data structure inside a running program that keeps track of active function calls.
case-insensitive: Treating text as if upper and lower case characters of the same letter were the same. See also: case-sensitive.
case-sensitive: Treating text as if upper and lower case characters of the same letter are different. See also: case-insensitive.
comment: A remark in a program that is intended to help human readers understand what is going on, but is ignored by the computer. Comments in Python, R, and the Unix shell start with a # character and run to the end of the line; comments in SQL start with --, and other languages have other conventions.
compose: To apply one function to the result of another, such as f(g(x)).
conditional statement: A statement in a program that might or might not be executed depending on whether a test is true or false.
comma-separated values: (CSV) A common textual representation for tables in which the values in each row are separated by commas.
default value: A value to use for a parameter if nothing is specified explicitly.
defensive programming: The practice of writing programs that check their own operation to catch errors as early as possible.
delimiter: A character or characters used to separate individual values, such as the commas between columns in a CSV file.
docstring: Short for “documentation string”, this refers to textual documentation embedded in Python programs. Unlike comments, docstrings are preserved in the running program and can be examined in interactive sessions.
documentation: Human-language text written to explain what software does, how it works, or how to use it.
dotted notation: A two-part notation used in many programming languages in which thing.component refers to the component belonging to thing.
empty string: A character string containing no characters, often thought of as the “zero” of text.
encapsulation: The practice of hiding something’s implementation details so that the rest of a program can worry about what it does rather than how it does it.
floating-point number: A number containing a fractional part and an exponent. See also: integer.
for loop: A loop that is executed once for each value in some kind of set, list, or range. See also: while loop.
function: A group of instructions (i.e., lines of code) that transform some input arguments to some output.
function call: A use of a function in another piece of software.
immutable: Unchangeable. The value of immutable data cannot be altered after it has been created. See also: mutable.
import: To load a library into a program.
in-place operators: An operator such as += that provides a shorthand notation for the common case in which the variable being assigned to is also an operand on the right hand side of the assignment. For example, the statement x += 3 means the same thing as x = x + 3.
index: A subscript that specifies the location of a single value in a collection, such as a single pixel in an image.
inner loop: A loop that is inside another loop. See also: outer loop.
integer: A whole number, such as -12343. See also: floating-point number.
invariant: An expression whose value doesn’t change during the execution of a program, typically used in an assertion. See also: precondition, postcondition.
library: A family of code units (functions, classes, variables) that implement a set of related tasks.
loop variable: The variable that keeps track of the progress of the loop.
member: A variable contained within an object.
method: A function which is tied to a particular object. Each of an object’s methods typically implements one of the things it can do, or one of the questions it can answer.
object: A collection of conceptually related variables (members) and functions using those variables (methods).
outer loop: A loop that contains another loop. See also: inner loop.
parameter: A variable named in the function’s declaration that is used to hold a value passed into the call. The term is often used interchangeably (and inconsistently) with argument.
pipe: A connection from the output of one program to the input of another. When two or more programs are connected in this way, they are called a “pipeline”.
postcondition: A condition that a function (or other block of code) guarantees is true once it has finished running. Postconditions are often represented using assertions.
precondition: A condition that must be true in order for a function (or other block of code) to run correctly.
regression: To re-introduce a bug that was once fixed.
return statement: A statement that causes a function to stop executing and return a value to its caller immediately.
RGB: An additive model that represents colors as combinations of red, green, and blue. Each color’s value is typically in the range 0..255 (i.e., a one-byte integer).
sequence: A collection of information that is presented in a specific order. For example, in Python, a string is a sequence of characters, while a list is a sequence of any variable.
shape: An array’s dimensions, represented as a vector. For example, a 5×3 array’s shape is (5,3).
silent failure: Failing without producing any warning messages. Silent failures are hard to detect and debug.
slice: A regular subsequence of a larger sequence, such as the first five elements or every second element.
stack frame: A data structure that provides storage for a function’s local variables. Each time a function is called, a new stack frame is created and put on the top of the call stack. When the function returns, the stack frame is discarded.
standard input: A process’s default input stream. In interactive command-line applications, it is typically connected to the keyboard; in a pipe, it receives data from the standard output of the preceding process.
standard output: A process’s default output stream. In interactive command-line applications, data sent to standard output is displayed on the screen; in a pipe, it is passed to the standard input of the next process.
string: Short for “character string”, a sequence of zero or more characters.
syntax error: A programming error that occurs when statements are in an order or contain characters not expected by the programming language.
test oracle: A program, device, data set, or human being against which the results of a test can be compared.
test-driven development: The practice of writing unit tests before writing the code they test.
traceback: The sequence of function calls that led to an error.
tuple: An immutable sequence of values.
type: The classification of something in a program (for example, the contents of a variable) as a kind of number (e.g. floating-point, integer), string, or something else.
type of error: Indicates the nature of an error in a program. For example, in Python, an IOError to problems with file input/output. See also: syntax error.
while loop: A loop that keeps executing as long as some condition is true. See also: for loop.

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