# Formatting Comments for Doxygen

The ROOT team has adopted Doxygen for generating the reference manual. Here you will find a number of conventions and tips for converting the existing source code to generate proper documentation.

## How to generate the doxygen documentation

Developers may generate the documentation by hand to see the results of the current changes before committing them to the repository. The automatic daily Jenkins procedures will generate the complete set of documentation.

$cd <root_sources>/documentation/doxygen$ make


The results are placed by default at ${HOME}/rootdoc/html. The file documentation/doxygen/Doxyfile can be edited to reduce the number of input files and thus reduce the time for generating the HTML pages. The property to be modified is INPUT = ../../<module> ## General Guidelines Classes and methods can be documented both in the .cxx and .h files. For the long descriptions of a class functionality and its methods we usually prefer the .cxx file. ### Class documentation The documentation for the class is in general located at the beginning of the .cxx file. The \class Doxygen command is mandatory otherwise Doxygen will not associate the comments to the proper class. The first sentence is a brief description of the class and will appear in all class listings. For an example see the TF2 class documentation: /** \class TF2 A 2-Dim function with parameters TF2 graphics function is via the TH1 drawing functions. Example of a function TF2 *f2 = new TF2("f2","sin(x)*sin(y)/(x*y)",0,5,0,5); f2->Draw(); \image html tf2_function2.png See TF1 class for the list of functions formats */ ### Method documentation Methods are documented just before the method/function is defined in the .cxx file. The use of \param[in] and \param[out] is encouraged to document the parameters of the method. The agreed formatting is as follows: //////////////////////////////////////////////////////////////////////////////// /// Compute distance from point px,py to a function /// /// \param[in] px x position /// \param[in] py y position /// /// Compute the closest distance of approach from point px,py to this function. /// The distance is computed in pixels units. Int_t TF2::DistancetoPrimitive(Int_t px, Int_t py) { ... } ### Free functions documentation Doxygen does not document default parameters of free functions if the only doxygen documentation provided for the function is in source files (as opposed to header files). To bypass this issue it is enough to provide a brief documentation for such functions in the header file. For example if the source file is:  //////////////////////////////////////////////////////////////////////////////// /// @param[in] numthreads Number of threads to use. If not specified or /// set to zero, the number of threads is automatically /// decided by the implementation. Any other value is /// used as a hint. /// /// ROOT must be built with the compilation flag imt=ON for this feature to be available. [...] void EnableImplicitMT(UInt_t numthreads) and the header file:  /// Enable ROOT's implicit multi-threading for all objects and methods that provide an internal /// parallelisation mechanism. void EnableImplicitMT(UInt_t numthreads = 0); Then a proper documentation with the default parameters is generated. ### Data Member documentation IMPORTANT: It is crucial to use "///<" and only "///<" to comment data members: this comment is correctly understood by genreflex/rootcling. The usage of other Doxygen constructs can interfere with the I/O subsystem!  Double_t fMymember ///< My Member Double_t fMyTransientMember ///<! My Member The usage of "//!" will still result in transiency of members but not in Doxygen documentation. ### Tutorials' documentation ROOT tutorials are also included in the ROOT documentation. The tutorials' macros headers should look like: \file \ingroup tutorial_hist \notebook Getting Contours From TH2D. #### Image produced by .x ContourList.C The contours values are drawn next to each contour. \macro_image #### Output produced by .x ContourList.C It shows that 6 contours and 12 graphs were found. \macro_output #### ContourList.C \macro_code \authors Josh de Bever, Olivier Couet This example shows that four new directives have been implemented: 1. \macro_image The images produced by this macro are shown. A caption can be added to document the pictures: \macro_image This is a picture 2. \macro_code The macro code is shown. A caption can be added: \macro_code This is code 3. \macro_output The output produced by this macro is shown. A caption can be added: \macro_output This the macro output 4. \notebook To generate the corresponding jupyter notebook. In case the tutorial does not generate any graphics output, the option -nodraw should be added. Note that the doxygen directive \authors or \author must be the last one of the macro header. ## Useful tips for common documentation artifacts A couple of useful online web tools for the conversion and formatting: ### Code blocks Simple code blocks are documented by indenting the code 4 spaces.  TEfficiency* pEff = 0; TFile* pFile = new TFile("myfile.root","recreate"); Longer code blocks can done with fenced lines consisting of 3 or more tilde (~) characters on a line. The end of the block should have the same number of tildes. Here is an example (note that tildes should start on first column!): ~~~{.cpp} TEfficiency* pEff = 0; TFile* pFile = new TFile("myfile.root","recreate"); //h_pass and h_total are valid and consistent histograms if(TEfficiency::CheckConsistency(h_pass,h_total)) { ... } ~~~ ### Macros and generated figures The keywords Begin_Macro and End_Macro are understood by the filter command to extract the code and produce the figure that will be inserted automatically in place. If in addition one wants to show the macro's code the parameter source should added to the Begin_Macro directive: Begin_Macro(source). The code enclosed by Begin_Macro and End_Macro can be plain C++ code: Begin_Macro { c = new TCanvas("c","c",0,0,300,300); TF2 *f2 = new TF2("f2","0.1+(1-(x-2)*(x-2))*(1-(y-2)*(y-2))",0.999,3.002,0.999,3.002); f2->SetContour(99); gStyle->SetPalette(kDeepSea); f2->Draw("surf2Z"); f2->SetTitle("kDeepSea"); } End_Macro or a file name containing the code to be executed: Begin_Macro(source) ../../../tutorials/graphs/multipalette.C End_Macro ### Images Images should be placed in in directory documentation/doxygen/images with the name <class>_<figurename>.png. They are referenced in the comments with the \image doxygen command: \image html tf2_function2.png ### Formulas In paragraph formulas can be added with \f$, for example \f$\frac{1}{1 - x}\f$. Column centered and multi-line formulas can be added with the commands \f[ ... \f] or \f{...}{ ...\f}. See the following examples:

\f[
\frac{1}{w_{new}} = \frac{1}{w_{1}} + \frac{1}{w_{2}}
\f]

\f{eqnarray*}{
w &=& \frac{\sigma L}{N_{gen} \epsilon_{trig}} \\
&-& \sigma ...\ cross\ section \\
&-& L ...\ luminosity \\
&-& N_{gen}\ ... number\ of\ generated\ events \\
&-& \epsilon_{trig}\ ...\ (known)\ trigger\ efficiency \\
\f}

### Tables

Markdown tables are very convening for tabulated documentation. See the following example:

/// Possible option values are:
///
/// option | description
/// -------|----------------------------------------
/// "SAME" | superimpose on top of existing picture
/// "L"    | connect all computed points with a straight line
/// "C"    | connect all computed points with a smooth curve
/// "FC"   | draw a fill area below a smooth curve
///

### Grouping classes in modules

You can group the classes according to the corresponding packages (e.g. math, hist, tree, etc...). In order to do this, you need to define first somewhere, as a code comment or in a separate page a group using the \defgroup tag. Example

/**
\defgroup Hist Histogram Library

The Histogram library is documented in the class TH1.

*/

Then one needs to add in the class description comments the \ingroup tag. For example in the class TH1, which is part of the Hist group one should add

/**
\class TH1
\ingroup Hist
....
*/

### Include additional documentation pages in HTML or Markdown format

One can add extra pages for the documentation in HTML or Markdown format (preferable) in the package/doc directory (e.g. hist/doc). These page could be used to provide a general documentation of the package. The pages should be included in a file with name as the package name and the .md or .html suffix (e.g. hist.md).
The file should contain, in addition to the package description, the Doxygen command \page [name] [title] which defines the internal page name (used to reference that page) and the page title.

For example

/**

\page HistPage The Histogram Library

This page provides a description of the Histogram library.

*/

Inside page you can reference to groups or other pages using the Doxygen commands \subpage [refname] ["text"] and \ref [refname] ["text"]. See as example the existing math/doc/Math.md file.