SPACES: Mnemonic for core values of good modeling software
Posted on Thu 10 May 2018 in Modeling
Mathematical models of scientific phenomena are essential in engineering. We use them to design experiments and select instruments based on estimates of the sensitivities of relationships between factors. We derive models from the experimental results and use them to develop more predictive models. Sometimes we can use models to reorganize experimental results to fit into the context of our understanding of the physical world, and sometimes this leads to the discovery of new factors and new relationships. When we are confident in our models ability to explain physical phenomena and describe relationships, we use them to predict. We can use predictive models to find solutions by optimizing our objectives. Good models are powerful, and they are the very essense of science.
Computers have revolutionalized the derivation and use of mathematical models to understand, describe, and predict our universe. We use code to interpret mathematics and science into a language that computers can use to perform calculations that would have taken us years to do by hand. But just like pencil and paper work there are ways to organize code best to accomplish your objectives. Good modeling software is based on a set core values.
SPACES is a mnemonic for the core values of good modeling software.
Good modeling software is simple. It doesn't do more or less than what it needs
to do. It doesn't create more problems than it solves. It isn't convoluted or
difficult to explain. It may contain complex algorithms, but the art and beauty
of good code is that it makes the complex elegant. Document your code well. Use
autodocumentation so that there isn't double documentation. Keep as much of the
documenation in the source code as possible. Make comments that explain the
intent of your code and read like a human being wrote them. Write comments to
FIXME frequently in your code as reminders of
changes you still need or want. Break up your documentation into sections based
on the target audience.
Always include a Quickstart Tutorial that is one page and has simple but realistic examples!
Include a detailed but simple user guide, a separate, more detailed theory guide, a comprehensive API, and a developer guide that explains things like how to build the documentation, how the CI is set up, how the server is configured, how to deploy the software, and what conventions were used. Be detailed. Consider adding a cookbook of examples, a gallery, tutorials, or HOWTO sections. Your API should be 100% covered.
It just has to be fast enough. Usually there is a trade off between speed and accuracy, so finding the balance is tricky. But in order to be useful, modeling software must not be slow. Efficiency where possible should always be a priority. Maybe not in the first draft, but in revisions inefficiency should be removed wherever it's found. Don't repeat yourself. However, don't create overly complicated code. Efficient code should still be simple. Strive for elegance.
It just has to be accurate enough. Understand your uncertainties. Regardless, modeling software that is inaccurate is useless. Make sure it works the way it's expected. Validate with publicly available data and publish your results in a notebook, like Jupyter, with the analysis code so others can run your calculations too. Check the bias:
- plot the distribution of the bias
- auto correlate against the output
- look for correlation versus time and location, by month and hour of the day, and by vertical and horizontal position
- cross correlate against the inputs
Calculate the mean bias difference (MBD) and root mean square difference (RMSD). All correlations should be random and bias should be uniformly distributed. Don't validate with your training data. Save a third of the data for validation.
Include high precision test data and use it in your unit tests.
Work together. Science is consensus. Others have already solved your problems. Others can find new problems. Use what is out there already. Don't reinvent the wheel. Ask for help. Get opinions. Listen. Consider alternatives. Collaborate.
Things change. Our understanding of the physical world changes. New technologies evolve. Build in the capacity for change in your modeling software. Anticipate that your code will need to adapt. Make it easy to maintain and update. Make it extensible to customization. Modularize. Break down your model into units that can be reused, so that intermediate values can be interrogated easily, and so contributions can be made at different entry points. Consider making your application a stack with a common object that is passed from unit to unit, and can be serialized and deserialized when needed. This will make it easier to save and load state, and to scale and parallelize. It will also make it easier to test.
Good modeling software isn't fragile. It should be bomb proof. Test it. Use a
unitest framework as well as some end-to-end tests. Strive for 100% coverage.
Set up a CI server to test on every push to the master branch and on pulls.
Don't use polynomial fits over 3rd order unless they are physical. Set limits
on arguments, and handle exceptions gracefully. Make sure that equations don't
blow up unexpectedly and return
Inf everywhere. Make sure that units
are explained in the documentation or user interface. Scale big numbers and
watch out for overflows. Watch for interger division. It's okay to follow the
practice of "easier to ask for forgiveness than permission" but errors have to
be handled eventually, and users deserve meaningful feedback. Just make sure it
always works as expected.
Put spaces in your code. Don't be terse. Follow the coding guidelines common for the codebase.