Guidelines for Contribution

We would like to thank you and several others who have offered / are willing to contribute their code. We are more than happy to add your code to this project. Just as we strive to ensure that you get the best possible software from us, we ask that you do the same for others. We do NOT ask that your code be as efficient as possible. Instead, we have some simpler and easier requests. We have compiled a list of best practices below with links to additional information. If you are confused or need more help, please feel free to contact us.

Before you begin

  1. All functionality in pyUSID revolves around the Universal Spectroscopic and Imaging Data (USID) model and its implementation into HDF5 files. Data is read from HDF5 files, processed, and written back to it. Therefore, it will be much easier to understand the rationale for certain practices in pyUSID and pycroscopy once USID is understood.

  2. Please consider familiarizing yourself with the examples and documentation on functionality available in pyUSID so that you can use the available functionality to simplify your code in addition to avoiding the development of duplicate code.

If you have not yet begun developing your code, please note that it will be far easier to understand USID, pyUSID and use tools in pyUSID while developing the code rather than adapting pre-written code that has not used pyUSID to be compatible with pyUSID.

Structuring code

General guidelines

  • Encapsulate independent sections of your code into functions that can be used individually if required.

  • Ensure that your code (functions) is well documented (numpy format) - expected inputs and outputs, purpose of functions

  • Please avoid very short names for variables like i or k. This makes it challenging to follow code, find and fix bugs.

  • Ensure that your code works in python 2.7 and python 3.7

  • Please consider using packages that are easy to install on Windows, Mac, and Linux. It is quite likely that packages included within Anaconda (has a comprehensive list packages for science and data analysis + visualization) can handle most needs. If this is not possible, try to use packages that are easy to to install (pip install). If even this is not possible, try to use packages that at least have conda installers.

  • Follow best practices for PEP8 compatibility. The easiest way to ensure compatibility is to set it up in your code editor. PyCharm does this by default. So, as long as PyCharm does not raise many warning, your code is beautiful!

pyUSID-specific guidelines

  • Engineering / science-agnostic tools fit better into pyUSID while scientific functionality go into pycroscopy.

  • Please ensure that your code files fit into our package structure (io, processing, viz)

  • Once you decide where your code will sit, please use relative import statements instead of absolute / external paths. For example, if you are contributing code for a new submodule within, you will need to turn your import statements and code from something like:

    import pyUSID as usid
    my_dataset = usid.USIDataset(my_hdf5_dataset)


    from .hdf_utils import print_tree
    from .usi_data import USIDataset
    my_dataset = USIDataset(my_hdf5_dataset)

You can look at our code in our GitHub project to get an idea of how we organize, document, and submit our code.

Contributing code

We recommend that you follow the steps below. Again, if you are ever need help, please contact us:

  1. Learn git if you are not already familiar with it. See our compilation of tutorials and guides, especially this one.

  2. Create a fork of pyUSID - this creates a separate copy of the entire pyUSID repository under your user ID. For more information see instructions here.

  3. Once inside your own fork, you can either work directly off master or create a new branch.

  4. Add / modify code

  5. Commit your changes (equivalent to saving locally on your laptop). Do this regularly.

  6. Repeat steps 4-5.

  7. After you reach a certain milestone, push your commits to your remote branch. This synchronizes your changes with the GitHub website and is similar to the Dropbox website /service making note of changes in your documents. To avoid losing work due to problems with your computer, consider pushing commits once at least every day / every few days.

  8. Repeat steps 4-7 till you are ready to have your code added to the parent pyUSID repository. At this point, create a pull request. Someone on the development team will review your pull request. If any changes are req and then merge these changes to master.

Writing tests

Software can become complicated very quickly through a complex interconnected web of dependencies, etc. Adding or modifying code at one location may break some use case or code in a different location. Unit tests are short functions that test to see if functions / classes respond in the expected way given some known inputs. Unit tests are a good start for ensuring that you spend more time using code than fixing it. New functions / classes must be accompanied with unit tests.

Additionally, examples on how to use the new code must also be added so others are aware about how to use the code. Fortunately, it is rather straightforward to turn unit tests into examples.