SPEC Documentation Style Guide

Some interesting and applicable words from the Google Style Guide:

BE CONSISTENT.

If you’re editing code, take a few minutes to look at the code around you and determine its style. If they use spaces around all their arithmetic operators, you should too. If their comments have little boxes of hash marks around them, make your comments have little boxes of hash marks around them too.

The point of having style guidelines is to have a common vocabulary of coding so people can concentrate on what you’re saying rather than on how you’re saying it. We present global style rules here so people know the vocabulary, but local style is also important. If code you add to a file looks drastically different from the existing code around it, it throws readers out of their rhythm when they go to read it. Avoid this.

With these words in mind, this SPEC Documentation Style Guide documents the conventions set forth to use for SPEC macros at the APS.

The concept of docstrings

In-line source documentation resides inside comment blocks directly within the SPEC macro files. In analogy to the python language, we will refer to these documentation comments as docstrings. These docstrings are processed by the specdomain package for the Sphinx documentation creator to produce user or reference manual in a variety of formats (html, pdf, man-pages, text files, etc.)

The following section sets forth some formatting conventions for SPEC docstrings.

One-line docstrings

There are two distinct scenarios where one-line docstrings are appropriate or even necessary:

  1. Obvious cases (where one line is completely sufficient to describe the code).
  2. Descriptive comments, that are used to document code objects (variables, one-line rdef or def declarations, or `cdef definitions) which cannot contain extended docstrings.
Obvious cases:

Obvious cases are those where the macro or macro function definition is so clear that no elaborate explanation is necessary. For example, the following macro function definition can probably be documented in a one-liner:

def sind(x) '{
  """ Return the sine of x, where x is given in degrees."""

  return sin(x*PI/180)
}'

One-liners need to be enclosed in triple double-quotes (""") which are placed on the same line as the docstring. A single space between the opening quotes and the docstring is optional. A blank line after the docstring helps to visually separate it from the actual code.

Descriptive comments:
 

Descriptive comments are a new a construct which can be used to document items that cannot contain extended comments (triple-quoted strings) themselves, such as variable declarations, one-line def or rdef declarations, or cdef definitions. They appear either as comments in the same line after the declaration (in-line) or as a comment-only line immediately preceding the declaration (one-liner). Descriptive comments are marked by a preceding #:, which lets them appear like normal SPEC comments, but the colon triggers the parser to process the docstring:

global TTH            #: The scattering angle two-theta [float].

#: Clear the ccd shutter handler
rdef ccdset_shutter ''

def do_nothing() ''   #: This macro does not do anything.

Multi-line docstrings

Multi-line docstrings are surrounded by a pair of triple double-quotes ("""), which should be placed on a line by themselves. For macro definitions, the opening quotes should appear on the next line immediately below the macro definition. It is recommended to insert a blank line between the last paragraph in a multi-line docstring and its closing quotes, followed by another blank line before the next code item begins.

The entire docstring is indented the same as the quotes at its first line. Docstrings inside macro declarations should be indented from the definition statement by the same level as the code contained in the definition.

Multi-line docstrings consist of a summary line just like a one-line docstring, followed by a blank line and then a more elaborate description. The summary line will be used by the specdomain indexing and summary tools. It is therefore important to make the summary lines very clear and concise. They should always be written as complete sentences, starting with a capital letter and ending with a period.

Documentation of code objects

We will refer to certain types or components of the SPEC macro code as code objects. These may include:

  • Macro files
  • Macro definitions (def, rdef, cdef)
  • Variables (global, local, etc.)
  • Entire collections of macro files

Each type of these code objects requires certain information to be included in the documentation. The following sections should help to ensure that all the required information is included and will appear in a consistent format.

File headers

The macro file header docstring provides information about the macro file as a whole (in the python world, this might be called a module).

As with any docstring, the first item should be a concise summary line of what the macro file provides and which could be used in summary tables, indexes, etc.

This is followed by sections about the detailed functionality, setup and configuration instructions, file information, and so on. The full power of Sphinx and ReST markup is available at this level, so sections can be broken up in subsections and subsubsections, tables may be included as well as figures or mathematical formulas.

The following information should be included, and the below layout may aid in supplying a complete set of information. Note that this can always be changed to meet the particular requirements of individual macro files:

Description (top-level header):
A more elaborate description of the functionality provided in the macro file. Include any number of subsections and subsubsections.
Notes (top-level header):
Any additional notes or comments about the file or its usage.
Installation (top-level header):

Information on how to set up the macro functionality. This includes, if applicable, the following subsections (second level headers):

Configuration:
Prerequisites in the SPEC configuration. For example, the configuration of dedicated counters may be necessary in order to use the macros.
Setup:
The steps necessary to set up the macro functionality. For example, loading the macro file (qdo) and running the macro_init function.
Dependencies:
List all the dependencies on other macros, hardware, software, EPICS channels, etc.
Impact:
Describe the impact that the use of the macro may have. For example, list all the changes made to other cdef macro definitions by this macro file.
File Information (top-level header):

All the information about the macro file itself, like authors, license, version, etc.

It is recommended to build up this section as a definition list. The headings for each item are CAPITALIZED and end with a colon. The content under each of these items should be indented one level. This results in a more lightweight layout, and prevents cluttering the tables of content with too many subsections.

The following items should be included, preferably in this order:

  • AUTHOR(S):
  • CREATION DATE:
  • COPYRIGHT:
  • LICENSE:
  • VERSION:
  • CHANGE LOG:
  • TO DO:
  • KNOWN BUGS:

See the example below for more details on each of these items.

Example of a file header docstring

"""
Summary line: a concise sentence about what this macro file provides.

Description
===========
A more detailed description of the macro file and the functionality that the
library of macro definitions it contains provides.

Note(s)
=======
Any special notes about the macro file, its usage, or its history can go here.

Installation
============
Describe, as applicable, the installation procedure, necessary changes in the
SPEC configuration, dependencies, and impact on chained macro definitions
(``cdef``) or redefinitions (``rdef``). The sections below give hypothetical
examples of what the content may look like.

Configuration
-------------
For this macro to work, the SPEC configuration may need to be modified. The
following counters are required:

        ========  ============  ==============  =======================
        Counter   Mnemonic      Type            Description
        ========  ============  ==============  =======================
        mycount1  mcnt1         None            My first counter
        mycount2  mcnt2         Macro counter   My second counter
        ========  ============  ==============  =======================

Setup
-----
With the above configuration change, simply load the macro file
``template.mac`` and run :spec:def:`template_setup`::

        > qdo template.mac
        > template_setup

Dependencies
------------
This macro depends on the following macro files and macros:

* filter.mac

        - :spec:def:`filter_trans`
        - :spec:def:`filter_get_trans()`

* bpm.mac

        - :spec:def:`bpm_get_pos`

Impact
------
The following chained macro definitions are affected by template.mac:

* :spec:def:`user_precount`:  Adding :spec:def:`template_precount`
* :spec:def:`user_getcounts`: Adding :spec:def:`template_getcounts`
        to the end ``(0x20)``

File information
================

AUTHOR(S):

        * A.B. Sample (AS, asamp), asamp@aps.anl.gov, Argonne National Laboratory

CREATION DATE:

        YYYY-MM-DD

COPYRIGHT:

        .. automatically retrieve the current year:
        .. |current_year| date:: %Y

        Copyright (c) 2010-|current_year|, UChicago Argonne, LLC
        Operator of Argonne National Laboratory
        All Rights Reserved

        APS SPEC macros

LICENSE::

        OPEN SOURCE LICENSE

        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:

        1. Redistributions of source code must retain the above copyright notice,
                 this list of conditions and the following disclaimer.  Software changes,
                 modifications, or derivative works, should be noted with comments and
                 the author and organization's name.

        2. Redistributions in binary form must reproduce the above copyright notice,
                 this list of conditions and the following disclaimer in the documentation
                 and/or other materials provided with the distribution.

        3. Neither the names of UChicago Argonne, LLC or the Department of Energy
                 nor the names of its contributors may be used to endorse or promote
                 products derived from this software without specific prior written
                 permission.

        4. The software and the end-user documentation included with the
                 redistribution, if any, must include the following acknowledgment:

                 "This product includes software produced by UChicago Argonne, LLC
                 under Contract No. DE-AC02-06CH11357 with the Department of Energy."

        *****************************************************************************

        DISCLAIMER

        THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT WARRANTY OF ANY KIND.

        Neither the United States GOVERNMENT, nor the United States Department
        of Energy, NOR UChicago Argonne, LLC, nor any of their employees, makes
        any warranty, express or implied, or assumes any legal liability or
        responsibility for the accuracy, completeness, or usefulness of any
        information, data, apparatus, product, or process disclosed, or
        represents that its use would not infringe privately owned rights.

        *****************************************************************************

VERSION::

        $Revision: 1124 $
        $Date: 2012-10-01 13:08:46 -0500 (Mon, 01 Oct 2012) $
        $Author: jemian $
        $URL: https://subversion.xray.aps.anl.gov/bcdaext/specdomain/tags/src/v1.03/doc/style_guide.rst $

CHANGE LOG:

        YYYY-MM-DD (AS):

        - created first version of this macro.
        - tested on a dummy SPEC version not connected to a diffractometer.

        YYYY-MM-DD (AS):

        - added a new macro definition: :spec:def:`new_macro` to display the status.

TO DO:

        - List all the TODO items

KNOWN BUGS:

        - List all the known bugs and limitations

"""

Macro definition docstrings

The docstring for a macro or macro function definition should summarize its behavior and document its arguments, return value(s), side effects, and restrictions on when it can be called (all if applicable). A docstring should give enough information to write a call to the function without reading the function’s code. A docstring should describe the function’s calling syntax and its semantics, not its implementation.

Certain aspects of a macro definition should be documented in special sections, listed below. Since Sphinx does not generally allow for the presence of any types of formal headings inside the code object docstrings, the docstring should be build up as a ReST definition list (see example below). The section titles are all CAPITALIZED for improved visibility and end with a colon. The contents for each section are indented by two spaces with respect to the section title.

Sections

The following sections should be included in the macro docstring after the summary line, in the below order, if applicable:

DESCRIPTION:
A more elaborate description of the macro’s functionality.
USAGE:

The syntax for calling the macro. This should contain all possible variants of the macro call. Argument names are enclosed in angle brackets (<>) to indicate that they should be replaced by actual values in the macro call. Optional arguments are additionally enclosed in square brackets ([]). The actual USAGE syntax should appear as pre-formatted text, and each input line should start with a “>“-symbol to represent the SPEC command line prompt:

USAGE::

  > my_macro <pos1> [<pos2>]
  > <return_value> = my_function(<input_value>)
ARGUMENTS:

All the arguments to a function or macro call should be listed in the form of a ReST field list. The argument name is enclosed between colons (:), followed by the description, which can span several (indented) lines. It is useful to specify also the type of the argument in square brackets ([]).

If a macro call has both mandatory and optional arguments, list them in separate lists:

Required arguments:
  :pos1:    Target position for motor [float].

Optional arguments:
  :timeout: The wait-time before giving up on serial port communication in
    seconds [float].

Note that a number of python projects use a special kind of argument definition list which is processed by Sphinx to include more information, for example, the type of an argument. Other projects, however, actively discourage its use or prefer the above style for simplicity. The syntax is as follows:

:param str motor_name: name of motor to use.

This syntax is perfectly acceptable also for SPEC documentation, however it arguably results in harder to read in-line documentation and is often not rendered very neatly in the final Sphinx output. Use this at your own discretion.

EXAMPLE:

A short example, illustrating the usage of the macro. As in the case of the USAGE section, the syntax should appear as pre-formatted text, and each input line should start with the “>“-symbol to represent the SPEC command line prompt. Short explanation lines can be inserted as indented comment lines:

EXAMPLE::

  > set_temperatures 23.5 50.0
      # sets the two container temperatures to 23.5 and 50.0 degrees.
NOTE(S):
Additional notes on the macro usage.
SEE ALSO:

A list of other macros or documentation items to refer to for further information. If possible, these should be dynamically linked using the corresponding Sphinx specdomain roles:

SEE ALSO:
  * :spec:def:`my_other_macro`
  * http://spec.examples.com/example3.html

Using the definition list syntax, other sections may be included, as necessary or appropriate for the particular macro.

Example of a macro definition docstring

"""
Concise summary line.

USAGE::

        > my_move <motor> <position> [<sleep_time>]

ARGUMENTS:

        Required arguments:
                :motor:    The motor to be moved [str].
                :position: The position to move the motor to [float].

        Optional arguments:
                :sleep_time: Settling time after the move has finished [float].

EXAMPLE::

        > my_move del 23.2346 0.3
                        # move del to 23.2346 and wait for 0.3 seconds after move finishes.

NOTE:
        Indicate any side effects, restrictions or other usage notes here.

SEE ALSO:
        * :spec:def:`my_move2`
        * :spec:global:`MOVE_FLAG`
        * http://www.certif.com/spec_help/prdef.html

"""

This results in the following:

Concise summary line.

USAGE:

> my_move <motor> <position> [<sleep_time>]

ARGUMENTS:

Required arguments:
motor:The motor to be moved [str].
position:The position to move the motor to [float].
Optional arguments:
sleep_time:Settling time after the move has finished [float].

EXAMPLE:

> my_move del 23.2346 0.3
                # move del to 23.2346 and wait for 0.3 seconds after move finishes.
NOTE:
Indicate any side effects, restrictions or other usage notes here.
SEE ALSO:

One-line docstrings

As mentioned previously, one-line docstrings (also called descriptive comments) can be used to document code objects that cannot contain extended docstrings.

One-line docstrings begin with a capital letter and end with a period.

Variables

Docstrings for variables provide a short description of the variable. It is also recommended to specify the type of the variable in square brackets ([]). For example:

global TTH     #: The scattering angle two-theta [float].
local _ind     #: List index of the active reflection [int].

#: Associate array with orientation reflection HKL-indices & angles [float].
global ORIENTATION_REFLECTIONS

Macro definitions

One-line docstrings for macro definitions contain a short description of the purpose for the (re-)definition. For example:

#: Define the ccd shutter handler
rdef ccdset_shutter '_ccdset_shutter'

#: remove ccd_getcounts from user_getcounts
cdef("user_getcounts", "", "ccd_key", "delete")

Macro collection docstrings

As of now, there is no standard yet for documenting entire collections of macros, as, for example, those collected in particular directories of the SVN source code repository.

The documentation for such a collection should be in the form of normal ReST files (*.rst), residing in the same directory with the macro collection. There is no way of automatically including this information in the global documents yet, so it will need to be added manually somewhere in the documentation tree (at least in the global index.rst file or some other file that is included from the global scope).