Developer Guide

Note

This page describes information for developers and code contributors. General users do not need information here.

How to compile this documentation

To compile this documentation into HTML, type:

make html

For PDF, perform:

make latex
cd build/latex
pdflatex MultishotTomo.tex # you might have to install several style files

If your system has latexmk, this can be done in one line:

make latexpdf

If above commands complain about missing Python packages, try:

python3 -m pip install --upgrade sphinx sphinxcontrib-bibtex

Coding styles in reStructuredText (rST)

For Å, α, β in the main text, just type as is using Unicode. Don’t use TeX commands.

To make git diff easier to understand, each sentense should use a new line.

A sentence.
Next sentence.

A new paragraph.
``Keyword``, *emphasis by italic* and **emphasis by bold** are marked like this.
You can cite a paper :cite:`Khavnekar2022.04.10.487763`.
A link to `rST documentation <https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html>`_.
Note the underline.
You can use LaTeX math :math:`\sum x_i^2`.

We have custom tags for :semmenu:`SerialEM menu item`, :semmenusel:` slected SerialEM menu item`, and :sembutton:`SerialEM green button`.
Custom tags will be updates as the documentation evolves.

This paragram is a bad example. Two sentences are in one line.

::

    A block quote for commands is an indented block following two
    colons and an empty line. Please use FOUR SPACES, not tabs for indentation.

-   When using a list, be careful about indentation.
    The second sentence must be aligned.
-   The second item in the list.

:Field list: suggested value

    (Explanation sentence 1.
    Note the indentation of this line!
    Also note the following blank line.)

:Another option without a value: \

    (Please put `\` at the end of the line to the field that should be left empty.)

The above example is rendered as:

A sentence. Next sentence.

A new paragraph. Keyword, emphasis by italic and emphasis by bold are marked like this. You can cite a paper [KWM+22]. A link to rST documentation. Note the underline. You can use LaTeX math \(\sum x_i^2\).

We have custom tags for SerialEM menu item, :semmenusel:` slected SerialEM menu item`, and SerialEM green button. Custom tags will be updates as the documentation evolves.

This paragram is a bad example. Two sentences are in one line.

A block quote for commands is an indented block following two
colons and an empty line. Please use FOUR SPACES, not tabs for indentation.

  • When using a list, be careful about indentation. The second sentence must be aligned.

  • The second item in the list.

Field list

suggested value

(Explanation sentence 1. Note the indentation of this line! Also note the blank lines.)

Another option without a value

(Please put \ at the end of the line to the field that should be left empty.)