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This guide illustrates how to set up the Doxygen config file to document C/C++, python, java, and Fortran code. See also https://doxygen.nl/manual/index.html.

Step-by-step guide

Prerequisites: You must have a working version of Doxygen installed on your system.

Navigate to the top-level directory of the code you want to document.
Use doxygen -g <config-file> to create a new config file. If you don't provide a name for config-file , Doxygen will generate a file named Doxyfile.
# Our files are located in /path/to/src/new_project cd new_project # in project folder, do doxygen -g <config-file> # replacing <config-file> with your chosen file name, or leaving it empty

In the configuration file, there are some general settings that need to be changed from their default values:

# ----------------------------------------------------
# GENERAL SETTINGS

# set the project name
PROJECT_NAME = "My New Project"

# ----------------------------------------------------
# SPECIFYING WHAT SHOULD BE DOCUMENTED

# to include files in subdirectories, we need to change the RECURSIVE tag from NO to YES
RECURSIVE = YES

# to map and generate documentation for all files, set EXTRACT_ALL from NO to YES
EXTRACT_ALL = YES

# to include private class members in the documentation, set EXTRACT_PRIVATE from NO to YES
EXTRACT_PRIVATE = YES

# to include static class members in the documentation, set EXTRACT_STATIC from NO to YES
EXTRACT_STATIC = YES

# ----------------------------------------------------
# BETTER OUTPUT DESIGN

# to improve readability of output, set HIDE_SCOPENAMES from NO to YES
HIDE_SCOPE_NAMES = YES

# ----------------------------------------------------
# INCLUDING SOURCE CODE IN DOCUMENTATION

# to cross-reference source files with the documentation, SOURCE_BROWSER needs to be set to YES
SOURCE_BROWSER = YES

# to be able to apply input filters to the source files later on, set
FILTER_SOURCE_FILES = YES

There are several options to further customize Doxygen. We will discuss some of them in the following.

including and excluding files

# assuming our project has the following structure:
# new_project
# |– Doxyfile
# |– python_files
# |  |– a_file.py
# |  |– another_file.py
# |  |– examples
# |     |– example1.py
# |     |  ...
# |     |– example100.py
# |– cpp_files
# |  |– headerfiles
# |  |  |– some_header.h
# |  |  |– another_header.h
# |  |– src
# |	 |	|– some_file.cpp
# |	 |	|– another_file.cpp
# |	 |– examples
# |		|– more_examples.cpp
# |– yet_another_folder

# include by folder: we want to ignore yet_another_folder
INPUT = python_files cpp_files

# exclude all example files
EXCLUDE_PATTERNS = */examples/*

# only include .py and .cpp files
FILE_PATTERNS = .py .cpp

language-specific settings: It is possible to optimize Doxygen for a specific programming language. If your project contains only of C/C++, python/java, or Fortran files, you can specify this in the settings.

# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
# only. Doxygen will then generate output that is more tailored for C. For
# instance, some of the names that are used will be different. The list of all
# members will be omitted, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_FOR_C  = NO

# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
# Python sources only. Doxygen will then generate output that is more tailored
# for that language. For instance, namespaces will be presented as packages,
# qualified scopes will look different, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_JAVA   = NO

# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
# sources. Doxygen will then generate output that is tailored for Fortran.
# The default value is: NO.
OPTIMIZE_FOR_FORTRAN   = NO

There are many ways to further customize Doxygen. The autogenerated config file includes detailed descriptions of every setting.

Step-by-step guide

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