Library to assist programming, testing and execution of solutions for coding challenges like those on stepik.org orrosalind.info
Library to assist programming, testing and execution of solutions for coding challenges like those on stepik.org or rosalind.info.
Find the full documentation at Readthedocs.
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 + self.model 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.
- 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
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.
The files __init__.py are empty. They help unittest tools like nosetest to locate the files.
Always move into the base directory to use the Challenge Runner.
List the available challenges
prompt> challenge --list * Challenge1 * Challenge2 * ...
Scaffolding a new challenge
prompt> challenge --scaffold Challenge3
You now find the files:
myChallenges/ Challenge3/__init__.py Challenge3/challenge.py Challenge3/test.py
Check it’s working by running the unit test case.
prompt> challenge --unittest Challenge3 .sss. ---------------------------------------------------------------------- Ran 5 tests in 0.006s OK (skipped=3)
Run <sample> from the class file
This is the small sample directly coded into the challenge class.
prompt> challenge --klass Challenge1 [the result output goes here]
You will automatically find the latest output in two files, independent from the input method you choose.
These files are just for convenience and are overwritten by the next run.
Read sample from an input file
prompt> challenge Challenge1 --file ~/Downloads/data.txt [the result output goes here]
Storing data and results
Did you pass the challenge? Was the online grader content with the upload of latest.txt? Then you should store data and result.
prompt> challenge Challenge1 --file ~/Downloads/data.txt --write
You will find the files:
This files are stored until the next run with the –write flag.
To quickly see all available options.
For every double dashed option there is a single dashed one letter shortcut. Help lists them all.
prompt> challenge Challenge1 –scaffold prompt> challenge Challenge1 -s
You can palce the dashed options behind the name of the challenge. This makes it easy to exchange them. Practical usage may look like this.
prompt> challenge ExampleProblem -s prompt> challenge ExampleProblem -u prompt> challenge ExampleProblem -k prompt> challenge ExampleProblem -f ~/Downloads/data.txt prompt> challenge ExampleProblem -f ~/Downloads/data.txt -w
The naming conventions follow the standards as defined by PEP 8 Style Guide for Python Code
There are two deliberate exceptions:
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.
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.
One useful advantage of naming the directory just like your challenge is, that you can use the path expansion mechanism of the shell. Write the first characters of the directory name and hit <TAB>. Now you can use the directory name as name of the challenge. A trailing slash is discarded. The following two inputs are equivalent.
prompt> challenge -k ExampleProblem prompt> challenge -k ExampleProblem/
This software requires Python 3.
Clone from Github
You can clone (or download) the Challenges project directly from Github. In this case the scripts and paths are not configured globally. Either you configure it globally or you place your challenges immediately into the projects folder so that the paths are detected relatively.
Put your challenges immediately into the projects folder
This is the most simple setup to get started. After downloading change into the download folder an try to run the HelloWorld unit test. In this case the command is in the bin directory, you call it as bin/challenge.
prompt> bin/challenge --unittest HelloWorld ... ---------------------------------------------------------------------- Ran 3 tests in 0.001s OK
Now you are ready to create your challenge side-by-side with the HelloWorld challenge.
prompt> bin/challenge --scaffold MyChallenge
Use <pip> to install <challenges>
If you have a fully configured python 3 environment up and running you can install <challenges> with pip3.
prompt> pip3 search challenges prompt> pip3 install challenges
The library will be included into the python class path. The runner will be globally available as challenge, alternatively as stepik or rosalind.
prompt> challenge --version challenge 0.8.0 prompt> stepik --version stepik 0.8.0 prompt> rosalind --version rosalind 0.8.0
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