Guidelines for HTMD developers

Coding Style Tips

Note: some style is at variance with Python PIP recommendations.

  • Class names start with capital letters

  • Method names start with lower-case, then camelCase

  • Same for generic function, e.g. testMe()

  • Modules should be nouns

  • Methods and functions should be verbs

  • Make the main a test case, where possible.

  • Use namespaces instead of composite name, e.g. charmm.build() instead of charmmBuild() when possible

  • Try to keep single names when possible, so there is no need for camelCase

Using modules inside HTMD

Creating efficient code is different from generating scripts for personal use. As such, when developing code for HTMD, be as minimal as possible when importing modules. As examples, please do _not_ use any of these types of imports inside HTMD code:

import htmd
from htmd.ui import *

Furthermore, from from <module> import * should _never_ be used, as it pollutes the namespace and can shadow same-name functionalities. Try as much as possible to only import the function/class you specifically need instead of importing an entire module, unless one wants to use that module heavily on that implementation. Keep a simple htmd.modulename.submodulename structure. So file names if they are not meant to be modules (e.g. util.py) should be imported in the upper module namespace.

Do not pollute the module and submodule names. Changes to the modules structure requires consensus and approval, as well as documentation creation.

Using Docstrings and Doctests

See this template:

def home(dataDir=None, libDir=False):
    """Return the pathname of the HTMD root directory (or a data subdirectory).

    Parameters
    ----------
    dataDir : str
        If not None, return the path to a specific data directory
    libDir : bool
        If True, return path to the lib directory

    Returns
    -------
    dir : str
        The directory

    Example
    -------
    >>> htmd.home()                                 # doctest: +ELLIPSIS
    '.../htmd'
    >>> htmd.home(dataDir="dhfr")                   # doctest: +ELLIPSIS
    '.../data/dhfr'
    >>> os.path.join(htmd.home(dataDir="dhfr"),"dhfr.pdb")  # doctest: +ELLIPSIS
    '.../data/dhfr/dhfr.pdb'
    """

Docstrings can be test cases (as above). This is convenient because you have four things in one place:

  1. the test case

  2. the expected result

  3. an example

  4. the rest of the documentation

It’s sufficient to add this in the main:

if __name__ == "__main__":
    import doctest

    failure_count, _ = doctest.testmod()
    if failure_count != 0:
        raise Exception('Doctests failed')

The doctest: +ELLIPSIS comment on the docstring indicates that match with ... is flexible. Other possibly useful directives are SKIP and NORMALIZE_WHITESPACE.

One can also:

  • run tests placed in external files with doctest.testfile('doctest_in_help.rst')

  • test a different module with doctest.testmod(doctest_simple)