Build and write documentation#

The documentation contains three categories of documents: examples, tutorials and the reference. The documentation strategy is based on the Diátaxis Framework. New documents should fit into one of these categories.

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

pip install --editable ".[doc]"

Note

The tutorials and examples require some small datasets to be downloaded via the orix.data module upon building the documentation. See the section on the data module for more details.

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/orix/doc/build/html/index.html in the address bar.

We can link to other documentation in reStructuredText files using Intersphinx. Which links are available from a package’s documentation can be obtained like so:

python -m sphinx.ext.intersphinx https://hyperspy.org/hyperspy-doc/current/objects.inv

We use Sphinx-Gallery to build the Examples. The examples are located in the top source directory examples/, and a new directory doc/examples/ is created when the docs are built.

We use nbsphinx for converting notebooks into tutorials. Code lines in notebooks should be formatted with black.

Writing tutorial notebooks#

Here are some tips for writing tutorial notebooks:

Notebooks (with the .ipynb file extension) are ignored by git (listed in the .gitignore file). The -f git flag must be added to git add -f notebook.ipynb in order to update an existing notebook or add a new one. Notebooks are ignored by git in general to avoid non-documentation changes to notebooks, like cell IDs, being pushed unnecessarily.
All notebooks should have a Markdown (MD) cell with this message at the top, “This notebook is part of the orix documentation https://orix.readthedocs.io. Links to the documentation won’t work from the notebook.”, and have "nbsphinx": "hidden" in the cell metadata so that the message is not visible when displayed in the documentation.
Use ax[0].imshow(...); to silence matplotlib output if a matplotlib command is the last line in a cell.
Refer to our API reference with this MD [Vector3d.zvector()](../reference/generated/orix.vector.Vector3d.zvector.rst). Remember to add the parentheses () if the reference points to a function or method.
Refer to to the examples section with [Examples section](../examples/index.rst).
Refer to sections in other tutorial notebooks using this MD [plotting](../tutorials/crystal_map.ipynb#Plotting).
Refer to external APIs via standard MD like [Lattice](https://www.diffpy.org/diffpy.structure/mod_lattice.html#diffpy.structure.lattice.Lattice).
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 relevant topic within the user guide to be included in the documentation pages.
The furo 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 for example displaying all figures with a white background for axes labels and ticks and figure titles etc. to be readable.
Whenever the documentation is built (locally or on the Read the Docs server), nbsphinx only runs the notebooks without any cell output stored. It is recommended that notebooks are stored without cell output, so that functionality within them are run and tested to ensure continued compatibility with code changes. Cell output should only be stored in notebooks which are too computationally intensive for the Read the Docs server to handle, which has a limit of 15 minutes and 3 GB of memory per documentation build.
We also use black to format notebooks cells. To run the black formatter on your notebook(s) locally please specify the notebook(s), ie. black my_notebook.ipynb or black *.ipynb, as black . will not format .ipynb files without explicit consent. To prevent black from automatically formatting regions of your code, please wrap these code blocks with the following:
```
# fmt: off
python_code_block = not_to_be_formatted
# fmt: on
```
Please see the black documentation for more details.

In general, we run all notebooks every time the documentation is built with Sphinx, to ensure that all notebooks are compatible with the current API at all times. This is important! For computationally expensive notebooks however, we store the cell outputs so the documentation doesn’t take too long to build, either by us locally or the Read The Docs GitHub action. To check that the notebooks with stored cell outputs are compatible with the current API, we run a scheduled GitHub Action every Monday morning which checks that the notebooks run OK and that they produce the same output now as when they were last executed. We use nbval for this.

The tutorial notebooks can be run interactively in the browser with the help of Binder. When creating a server from the orix source code, Binder installs the packages listed in the environment.yml configuration file, which must include all doc dependencies in setup.py necessary to run the notebooks.

Writing API reference#

Inherited attributes and methods are not listed in the API reference unless they are explicitly coded in the inheriting class.

A class’ set() method, if it has any, is excluded from the API reference. This is necessary because some plotting classes inheriting from Matplotlib’s Axes() class caused errors when the inherited set() method is to be included in the API reference by Sphinx (even though inherited methods are also explicitly excluded).

Mathematical notation#

We try to use a mathematical notation consistent throughout our documentation and internal (not user-facing) source code for naming variables. Rotation objects are denoted by uppercase letters and vector objects are denoted by lowercase letters.

Quaternion \(Q = (a, b, c, d)\)
Rotation axis \(\hat{\mathbf{n}}\)
Rotation angle \(\omega\)
Rotation \(R = (a, b, c, d)\)
Orientation \(O = (a, b, c, d)\)
Misorientation \(M = (a, b, c, d)\)
Symmetry operations:
- Set of operations \(S\)
- Single operation \(s = (a, b, c, d)\)
3D vector \(\mathbf{v} = (x, y, z)\)
Reciprocal or direct lattice vectors (Miller) with coordinate formats:
- “xyz”: \(\mathbf{m} = (x, y, z)\)
- “hkl” or “hkil”: \(\mathbf{g} = (h, k, l)\)
- “uvw” or “UVTW”: \(\mathbf{t} = [u, v, w]\)
Polar angles
- Azimuth \(\phi\)
- Polar \(\theta\)
Stereographic coordinates \((X, Y)\)