PyEBSDIndex is a community maintained project. We welcome contributions in the form of bug reports, documentation, code, feature requests, and more. The source code is hosted on GitHub. This guide provides some tips on how to build documentation and run tests when contributing.

Building and writing documentation#

We use Sphinx for documenting functionality. Install necessary dependencies to build the documentation:

pip install --editable .[doc]

Then, build the documentation from the doc directory:

cd doc
make html

The documentation’s HTML pages are built in the doc/build/html directory from files in the reStructuredText (reST) plaintext markup language. They should be accessible in the browser by typing file:///your/absolute/path/to/pyebsdindex/doc/build/html/index.html in the address bar.

Tips for writing Jupyter Notebooks that are meant to be converted to reST text files by nbsphinx:

  • Use _ = ax[0].imshow(...) to disable Matplotlib output if a Matplotlib command is the last line in a cell.

  • Refer to our reference with this general MD [pcopt.optimize()](../reference.rst#pyebsdindex.pcopt.optimize). Remember to add the parentheses () for functions and methods.

  • Refer to external references via standard MD like [Signal2D](

  • The Sphinx gallery thumbnail used for a notebook is set by adding the nbsphinx-thumbnail tag to a code cell with an image output. The notebook must be added to the gallery in the index.rst to be included in the documentation pages.

  • The PyData Sphinx theme displays the documentation in a light or dark theme, depending on the browser/OS setting. It is important to make sure the documentation is readable with both themes. This means displaying all figures with a white background for axes labels and ticks and figure titles etc. to be readable.

Running and writing tests#

Some functionality in PyEBSDIndex is tested via the pytest framework. The tests reside in the pyebsdindex/tests directory. Tests are short methods that call functions in PyEBSDIndex and compare resulting output values with known answers. Install necessary dependencies to run the tests:

pip install --editable .[tests]

Some useful fixtures, like a dynamically simulated Al pattern, are available in the file.

To run the tests:

pytest --cov --pyargs pyebsdindex

The --cov flag makes print a nice report in the terminal. For an even nicer presentation, you can use directly:

coverage html

Then, you can open the created htmlcov/index.html in the browser and inspect the coverage in more detail.

To run only a specific test function or class, .e.g the TestEBSDIndexer class:

pytest -k TestEBSDIndexer

This is useful when you only want to run a specific test and not the full test suite, e.g. when you’re creating or updating a test. But remember to run the full test suite before pushing!

Tips for writing tests of Numba decorated functions:

  • A Numba decorated function numba_func() is only covered if it is called in the test as numba_func.py_func().

  • Always test a Numba decorated function calling numba_func() directly, in addition to numba_func.py_func(), because the machine code function might give different results on different OS with the same Python code.

Continuous integration (CI)#

We use GitHub Actions to ensure that PyEBSDIndex can be installed on macOS and Linux (Ubuntu). After a successful installation of the package, the CI server runs the tests. Add “[skip ci]” to a commit message to skip this workflow on any commit to a pull request.