Some High-level Tips for Python Projects

Below are tips on a few very high-level and commonly-encountered topics in Python software development.

Directory structure

Suppose the the probject is called ‘becool’. A largely standard directory structure looks like this:

becool/
  |-- archive/
  |-- config/
  |-- doc/
  |-- becool/
  |   |-- __init__.py
  |   |-- module_a.py
  |   |-- module_b.py
  |   |-- becooler/
  |   |   |-- __init__.py
  |   |   |-- module_c.py
  |   |   |-- module_d.py
  |-- tests/
  |   |-- __init__.py
  |   |-- test_module_a.py
  |   |-- test_module_b.py
  |   |-- becooler/
  |   |   |-- __init__.py
  |   |   |-- test_module_c.py
  |   |   |-- test_module_d.py
  |-- scripts/
  |-- README.md
  |-- setup.py

Some highlights:

  • The project name, ‘becool’, is also the name of the git repo. Inside this repo, the main content a Python package called ‘becool’. Hence the repo and the package are both named after the project. This is a common situation.

    Although nothing forbids you from having multiple packages in one project (e.g. having a behot parallel to becool), it’s usually a bad idea. The reason is that if becool and behot closely interact, then maybe they should be one single package. On the other hand, if they do not closely interact, then they are independently deployable, therefore it’s better to have them in separate projects (i.e. repos).

  • Maintain a clean project file structure, and do not be afraid to adjust or refactor. Some reference; some more.

  • The directory scripts should not contain __init__.py, but may contain files named like *_test.py or test_*.py for testing functions in the scripts.

    Ideally, content of scripts is mainly short launchers of functions in packages. For this reason, the scripts often do not need tests.

    This directory may also be called bin.

  • archive is for any code segments that you have deleted from the “main line” but for some reason still want to keep a visible copy for reference. Do not use a branch for this purpose.

The center of gravity of the repo is the Python library (or “package”) becool. Scripts are applications of this library, and should strive to be short. In the scripts, the package becool should be treated just like any third-party library. In particular, file-path hacks should be avoided.

If you execute the code in a Docker container like I do, all dependencies are taken care of by the definition of the Docker image. In that case, setup.py does not need to worry about installing dependencies.

Where to put tests?

There are mainly two approaches. The first is to have tests subdirectories within the package becool. Specifically, every directory (includeing the top level becool) contains a subdirectory named tests, which hosts tests for the modules (i.e. *.py files) in its parent directory. The second approach uses a tests directory separate from the package being tested. This is the approach shown in the digram above. Both approaches are used by major open source projects.

After some time using the first approach, I switched to the second. The switch is prompted by some confusing situations related to running tests against the package that has been “installed” into the system site-packages. I can think of two other reasons. First, conceptually, “tests” are not the package’s intrinsic functionalities. They are supporting the development of the package, just like “doc” is another supporting component. Second, in substantial projects, one may build some utilities to be used by the test code. In the first approach, the location of this testing infrastructure may become awkward.

Alternative structure with a src sub-directory

There are discussions about having a src directory. This post advocates top-level directories like src, docs, tests, and a main point for this structure is related to testing.

Without carefully reading the arguments, I have switched to use this structure. I can think of two advantages of this structure:

  1. The top-level directories, like src, docs, tests, are more logical and extensible because they are on the same level of abstraction. It feels better.

  2. If there are non-Python code, such as Python extensions in C++, this structure can easily grow with the complexity of the codebase. An experimental package of mine of mine is an example.

Naming and style

For the project and packages, single-word names (or two words without hyphen) are more desirable.

For functions and variables, multi-word, verboses names are fine.

Use ‘snake-case’ names; see examples.

Do study the PEP 8 style guide; pick and stick to a decent style.

I use yapf to format Python code. This frees the developer from thinking about good style, and help avoids arguments about style between developers. Usually I use the following command:

$ yapf -ir -vv --no-local-style ./

Documentation

Do write documentation to help yourself, if not others.

  • In-source documentation: make use of Python’s docstring mechanism; follow the Google style; example 1, example 2.
  • Stand-alone documentation files in source tree (but outside of source code files):
    • README.md in the top-level (project root) or second-level (package root) directories.
    • Doc files in doc directory under the project root directory.
    • Plain text files are perferred. Preferred formats are ‘plain text’ (txt), ‘mark-down’ (md), or ‘reStructuredText’ (rst) (if you intend to do extensive documentation and generate friendly HTML versions using Sphinx).
    • If you use Mac, a decent Markdown editor is MacDown.
    • To edit rst files with live preview, use the Atom editor (by Github) with a couple plug-ins.
    • If you use Sphinx, reStructuredText markup syntax can be used in in-source docstrings as well.
  • Outside of source tree: for documentation aimed at non-developers or users from other groups that require different levels of access control.

How to generate documentation using Sphinx

If you go to the length of writing Sphinx documentation, below is my work flow.

  1. Basically, let Sphinx take over the doc directory in the repo. In doc/, run

    sphinx-quickstart
    

    Make sure you make these particular choices:

    Separate source and build directories (y/n) [n]: y
    autodoc: automatically insert docstrings from modules (y/n) [n]: y
    imgmath: include math, rendered as PNG or SVG images (y/n) [n]: n
    mathjax: include math, rendered in the browser by MathJax (y/n) [n]: y
    viewcode: include links to the source code of documented Python objects (y/n) [n]: y
    Create Makefile? (y/n) [y]: y
    

    In doc/source/conf.py, make sure the extensions list contains at least these items:

    • sphinx.ext.autodoc
    • sphinx.ext.inheritance_diagram
    • sphinx.ext.mathjax
    • sphinx.ext.napoleon
    • sphinx.ext.todo
    • sphinx.ext.viewcode

    Also make sure html_theme is set to nature (unless you have another preference). After that, search for alabaster in conf.py, and comment out that block, because that block is needed for the default alabaster theme but could get in the way of other thems.

  2. Create *.rst files as needed in doc/source/. These stand-alone doc files along with doc in source code will be used to generate documentation.

  3. In doc, run make html to generate HTML documentation, which will be located in doc/build/html/. View the documentation in a web browser, starting with the file doc/build/html/index.html.

  4. git commit the files doc/Makefile, doc/source/conf.py, as well as the *.rst and other files you’ve created in doc/source. DO NOT git commit the generated material in doc/build.

Logging

Prefer logging to print in most cases.

  • The twelve factor app advocates treating log events as an event stream, always sending the stream to standard output, and leaving capture of the stream into files to the execution environment.

    For capturing logging into files, see my other post. A more complete example appears in another post.

  • In all modules that need to do logging, always have this, and only this, at the top of the module:

    import logging
    logger = logging.getLogger(__name__)
    

    then use logger.info() etc to create log messages.

    Do not create custom names for the logger. The __name__ mechanism will create a hierarchy of loggers following your package structure, e.g. with loggers named

    package1
    package1.module1
    package1.module1.submodule2
    

    Log messages will pass to higher levels in this hierarchy. Customizing the logger names will disrupt this useful message forwarding.

  • In the __init__.py file in the top-level directory of your Python package, include this:

    # Set default logging handler to avoid "No handler found" warnings.
    import logging
    logging.getLogger(__name__).addHandler(logging.NullHandler())
    

    Do not add any other handler in your package code.

  • Do not do any format, handler (e.g. using a file handler), log level, or other configuration in your package code. These belong in the launch scripts and should happen at exactly one place in a running program.

    I basically call something like the following function in the launch script. Usually level is the only argument I need to specify.

    import logging
    import os
    import time
    
    def config_logger(level=None, use_utc=True, datefmt=None, format=None, **kwargs):
      # 'level' is a string form of the logging levels: 'debug', 'info', 'warning', 'error', 'critical'.
    
      if level is None:
        level = os.environ.get('LOGLEVEL', 'info')
    
      if level not in [logging.DEBUG, logging.INFO, logging.WARNING, logging.ERROR, logging.CRITICAL]:
        level = getattr(logging, level.upper())
    
      if use_utc:
        logging.Formatter.converter = time.gmtime
        datefmt = datefmt or '%Y-%m-%d %H:%M:%SZ'
      else:
        logging.Formatter.converter = time.localtime
        datefmt = datefmt or '%Y-%m-%d %H:%M:%S'
    
      format = format or '[%(asctime)s; %(name)s, %(funcName)s, %(lineno)d; %(levelname)s]    %(message)s'
    
      logging.basicConfig(format=format, datefmt=datefmt, level=level, **kwargs)
    
  • Use the old-style string formatting (%), not the new-style string formatting (str.format). The following example should serve most of your fomatting needs:

    logger.info('Line %s (%s) has spent %.2f by hour %d', 'asd9123las', 'Huge Sale!', 28.97, 23) 
    

    See here for more about formatting.

Testing

Write tests, and adopt a testing framework. My recommendation is py.test.

You do not need to import pytest unless you explicitly use pytest in the code.

See Directory Structure above for where to put the test files.

(Lightly revised on December 21, 2018.)

Written on September 17, 2016