================== README: Challenges ================== 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_. .. _Readthedocs: http://challenges.readthedocs.io :State: beta :License: MIT :Author: Elmar Hinz :Repository: https://github.com/elmar-hinz/Python.Challenges :Documentation: http://challenges.readthedocs.io |badge| :Installation: https://pypi.org/project/challenges/ .. |badge| image:: https://readthedocs.org/projects/challenges/badge/?version=latest :target: http://challenges.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status Hello world =========== .. code-block:: python 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. .. hint:: See a more verbose example of HelloWorld and other examples. * HelloWorldChallenge_ * HelloWorldTest_ * HelloFastaChallenge_ * HelloFastaTest_ * HelloGraphChallenge_ * HelloGraphTest_ .. _HelloWorldChallenge: https://github.com/elmar-hinz/Python.Challenges/blob/master/HelloWorld/challenge.py .. _HelloWorldTest: https://github.com/elmar-hinz/Python.Challenges/blob/master/HelloWorld/test.py .. _HelloFastaChallenge: https://github.com/elmar-hinz/Python.Challenges/blob/master/HelloFasta/challenge.py .. _HelloFastaTest: https://github.com/elmar-hinz/Python.Challenges/blob/master/HelloFasta/test.py .. _HelloGraphChallenge: https://github.com/elmar-hinz/Python.Challenges/blob/master/HelloGraph/challenge.py .. _HelloGraphTest: https://github.com/elmar-hinz/Python.Challenges/blob/master/HelloGraph/test.py 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. .. code-block:: bash 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. .. hint:: The files `__init__.py` are empty. They help unittest tools like *nosetest* to locate the files. Challenge runner ================ .. important:: Always move into the base directory to use the **Challenge Runner**. List the available challenges ----------------------------- .. code-block:: bash prompt> challenge --list * Challenge1 * Challenge2 * ... Scaffolding a new challenge --------------------------- .. code-block:: bash prompt> challenge --scaffold Challenge3 You now find the files: .. code-block:: bash myChallenges/ Challenge3/__init__.py Challenge3/challenge.py Challenge3/test.py Check it's working by running the unit test case. .. code-block:: bash prompt> challenge --unittest Challenge3 .sss. ---------------------------------------------------------------------- Ran 5 tests in 0.006s OK (skipped=3) Run from the class file -------------------------------- This is the small sample directly coded into the challenge class. .. code-block:: bash prompt> challenge --klass Challenge1 [the result output goes here] .. hint:: You will automatically find the latest output in two files, independent from the input method you choose. .. code-block:: bash myChallenges/Challenge1/latest.txt myChallenges/latest.txt These files are just for convenience and are overwritten by the next run. Read sample from an input file ------------------------------ .. code-block:: bash 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. .. code-block:: bash prompt> challenge Challenge1 --file ~/Downloads/data.txt --write You will find the files: .. code-block:: bash myChallenges/Challenge1/sample.txt myChallenges/Challenge1/result.txt This files are stored until the next run with the `--write` flag. Help ---- To quickly see all available options. .. code-block:: bash challenge --help .. tip:: 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 .. tip:: 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. .. code-block:: bash 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 Naming conventions ================== The naming conventions follow the standards as defined by `PEP 8`_ **Style Guide for Python Code** .. _`PEP 8`: https://www.python.org/dev/peps/pep-0008/ 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. .. _Rosalind: http://rosalind.info .. tip:: 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 . Now you can use the directory name as name of the challenge. A trailing slash is discarded. The following two inputs are equivalent. .. code-block:: bash prompt> challenge -k ExampleProblem prompt> challenge -k ExampleProblem/ Installation ============ .. important:: 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`. .. code-block:: bash 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. .. code-block:: bash prompt> bin/challenge --scaffold MyChallenge Use to install --------------------------------- If you have a fully configured python 3 environment up and running you can install with pip3. .. code-block:: bash 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`. .. code-block:: bash prompt> challenge --version challenge 0.8.0 prompt> stepik --version stepik 0.8.0 prompt> rosalind --version rosalind 0.8.0