Developer Guide

Note

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

Coding styles in C++

Indentation should be done with tabs, while alignment should be done with spaces.

New lines should be as follows. Note that due to limitation of rST syntax, I used spaces instead of tabs.

// Use this
void test(int a, int b)
{
    if (!flag)
    {
        A();
        B();
    }
    else
    {
        C();
        D();
    }
}

// Not this
void test(int a, int b) {
    if (!flag) {
        A();
        B();
    } else {
        A();
        B();
    }
}

How to compile this documentation

To compile this documentation into HTML, type:

make html

For PDF, perform:

make latex
cd build/latex
pdflatex relion.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:`Zivanov_estimation_2020`.
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 :button:`buttons`, :joblist:`joblists`, :jobtype:`jobtypes` and :guitab:`guitabs`.
|RELION| prints RELION in smallscaps.
We also have |MotionCor2| and |CTFFIND4.1| defined.

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 [ZNS20]. A link to rST documentation. Note the underline. You can use LaTeX math \(\sum x_i^2\).

We have custom tags for buttons, joblists, jobtypes and guitabs. relion prints RELION in smallscaps. We also have motioncor2 and ctffind 4.1 defined.

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.)