challenges 1.4.0

Hello world

from challenges import Challenge

class AddChallenge(Challenge):

    sample = '''
        5, 6
    '''

    expect = '''
        11
    '''

    def build(self):
        self.model = self.line_to_integers(0)

    def calc(self):
        self.result = self.model[0] + self.model[1]

    def format(self):
        self.output = str(self.result)

The class to write lets you focus on the core algorithms of the challenge while keeping stuff like opening, reading and writing of files out of the way. You inherit several methods to set up the model or to format your result for writing.

While the class attribute sample just holds a minimal example of the input, the actual input is later injected by the Challenge Runner via the command line. In Bioinformatics this is often a large file of DNA.

Features

• listing available challenges

• scaffolding a new challenge directory with a challenge class and a unit test class

• executing the sample from the sample class attribute

• reading input files from the command line

• output formatted result on the command line

• writing sample.txt and matching result.txt into the challenges directory

• running the unit test case of a challenge

• reading lines with integers

• reading lines with floats

• reading lines with words

• reading fasta input

Directory layout

Lets call the base directory of your challenges project myChallenges/. Name it however you like.

myChallenges/
    Challenge1/__init__.py
    Challenge1/challenge.py
    Challenge1/test.py
    Challenge2/__init__.py
    Challenge2/challenge.py
    Challenge2/test.py
    ... more challenges ...

The names Challenge1 and Challenge2 are just placeholders for the names you choose during scaffolding.

Challenge runner

prompt> challenge --list
* Challenge1
* Challenge2
* ...

prompt> challenge --scaffold Challenge3

myChallenges/
    Challenge3/__init__.py
    Challenge3/challenge.py
    Challenge3/test.py

prompt> challenge --unittest Challenge3
.sss.
----------------------------------------------------------------------
Ran 5 tests in 0.006s

OK (skipped=3)

prompt> challenge --klass Challenge1
[the result output goes here]

prompt> challenge Challenge1 --file ~/Downloads/data.txt
[the result output goes here]

prompt> challenge Challenge1 --file ~/Downloads/data.txt --write

myChallenges/Challenge1/sample.txt
myChallenges/Challenge1/result.txt

challenge --help

Naming conventions

The naming conventions follow the standards as defined by PEP 8 Style Guide for Python Code

There are two deliberate exceptions:

1. Challenge module names are CamelCase:

   In contradiction to the style guide directories of the challenges are not all lowercase. Especially the first character must be uppercase. This is used to find and list the challenge directories between other modules. If the name of your challenge is ExampleProblem then this are the required names:

   directory:

   ExampleProblem/

   challenge file:

   ExampleProblem/challenge.py

   unittest file:

   ExampleProblem/test.py

   full qualified challenge class:

   ExampleProblem.challenge.ExampleProblemChallenge

   full qualified test class:

   ExampleProblem.test.ExampleProblemTest

   This is automatically wired up during scaffolding.

   Abbreviations or codes like on Rosalind may be all uppercase or camelcase, RSUB or Rsub.

2. Inherited class attributes and methods don’t have a leading underscore:

   The inherited functions and methods of the challenge are not a public API and the style guides recommends leading underscores. As inheritance is a core concept of the challenge class, this would lead to a hell of leading underscores. For this reason we don’t follow the style guide in this recommendation.

Installation

prompt> bin/challenge --unittest HelloWorld
...
----------------------------------------------------------------------
Ran 3 tests in 0.001s

OK

prompt> bin/challenge --scaffold MyChallenge

prompt> pip3 search challenges
prompt> pip3 install challenges

prompt> challenge --version
challenge 0.8.0

prompt> stepik --version
stepik 0.8.0

prompt> rosalind --version
rosalind 0.8.0