1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
|
#######################################################################
#create Doxyfiles for html documentation
set(CF_OPENMS_BIN_PATH ${PROJECT_BINARY_DIR})
set(CF_OPENMS_SRC_PATH ${PROJECT_SOURCE_DIR})
find_package(Doxygen)
find_package(LATEX)
if (DOXYGEN_FOUND)
configure_file(${PROJECT_SOURCE_DIR}/doc/doxygen/Doxyfile.in ${PROJECT_BINARY_DIR}/doc/doxygen/Doxyfile)
configure_file(${PROJECT_SOURCE_DIR}/doc/doxygen/Doxyfile_dot.in ${PROJECT_BINARY_DIR}/doc/doxygen/Doxyfile_dot)
configure_file(${PROJECT_SOURCE_DIR}/doc/doxygen/Doxyfile_noclass.in ${PROJECT_BINARY_DIR}/doc/doxygen/Doxyfile_noclass)
configure_file(${PROJECT_SOURCE_DIR}/doc/doxygen/Doxyfile_xml.in ${PROJECT_BINARY_DIR}/doc/doxygen/Doxyfile_xml)
configure_file(${PROJECT_SOURCE_DIR}/doc/OpenMS_tutorial/Doxyfile.in ${PROJECT_BINARY_DIR}/doc/OpenMS_tutorial/Doxyfile)
configure_file(${PROJECT_SOURCE_DIR}/doc/TOPP_tutorial/Doxyfile.in ${PROJECT_BINARY_DIR}/doc/TOPP_tutorial/Doxyfile)
#######################################################################
#create refman files for PDF tutorials
configure_file(${PROJECT_SOURCE_DIR}/doc/OpenMS_tutorial/refman_overwrite.tex.in ${PROJECT_BINARY_DIR}/doc/OpenMS_tutorial/refman_overwrite.tex)
configure_file(${PROJECT_SOURCE_DIR}/doc/TOPP_tutorial/refman_overwrite.tex.in ${PROJECT_BINARY_DIR}/doc/TOPP_tutorial/refman_overwrite.tex)
#######################################################################
##doc_param_internal target
if(NOT MSVC)
set(_TOPPDOCUMENTER_EXECUTABLE "${PROJECT_BINARY_DIR}/doc/doxygen/parameters/TOPPDocumenter")
set(_DEFAULTPARAMHANDLERDOCUMENTER_EXECUTABLE "${PROJECT_BINARY_DIR}/doc/doxygen/parameters/DefaultParamHandlerDocumenter")
set(_BINARY_PATH "${PROJECT_BINARY_DIR}/bin")
else()
set(_TOPPDOCUMENTER_EXECUTABLE "${PROJECT_BINARY_DIR}/doc/doxygen/parameters/$(ConfigurationName)/TOPPDocumenter")
set(_DEFAULTPARAMHANDLERDOCUMENTER_EXECUTABLE "${PROJECT_BINARY_DIR}/doc/doxygen/parameters/$(ConfigurationName)/DefaultParamHandlerDocumenter")
set(_BINARY_PATH "${PROJECT_BINARY_DIR}/bin/$(ConfigurationName)")
endif()
file(TO_NATIVE_PATH "${_TOPPDOCUMENTER_EXECUTABLE}" TOPPDOCUMENTER_EXECUTABLE)
file(TO_NATIVE_PATH "${_DEFAULTPARAMHANDLERDOCUMENTER_EXECUTABLE}" DEFAULTPARAMHANDLERDOCUMENTER_EXECUTABLE)
file(TO_NATIVE_PATH "${_BINARY_PATH}" BINARY_PATH)
add_custom_target(doc_param_internal
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "Creating the algorithm parameter and TOPP parameter documentation"
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "Note: A functioning OpenMS/TOPP installation and a running X-server (Linux) is required for this step!"
COMMAND ${CMAKE_COMMAND} -E echo " Windows only: OpenMS and Open_GUI.dll's need to be in your PATH!"
COMMAND ${CMAKE_COMMAND} -E echo " If this step fails, use the target 'doc_minimal'."
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "Building OpenMS parameter docu:"
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E make_directory doc/doxygen/parameters/output/
COMMAND ${CMAKE_COMMAND} -E chdir doc/doxygen/parameters/ ${DEFAULTPARAMHANDLERDOCUMENTER_EXECUTABLE}
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "Building TOPP/UTILS docu:"
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E chdir doc/doxygen/parameters/ ${TOPPDOCUMENTER_EXECUTABLE} ${BINARY_PATH}
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMENT "Build the parameters documentation"
VERBATIM)
add_dependencies(doc_param_internal doc_progs)
#######################################################################
## doc target
add_custom_target(doc
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "Creating html documentation"
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E remove_directory doc/html
COMMAND ${CMAKE_COMMAND} -E chdir doc "${DOXYGEN_EXECUTABLE}" doxygen/Doxyfile
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/doc/index.html doc/index.html
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/doc/doxygen/common/style_ini.css doc/html/style_ini.css
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "The documentation has been successfully created."
COMMAND ${CMAKE_COMMAND} -E echo "You can now open 'doc/index.html' in a web browser."
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMENT "Build the doxygen documentation"
VERBATIM)
add_dependencies(doc doc_param_internal)
#######################################################################
## doc_internal target
add_custom_target(doc_xml
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "Creating XML documentation"
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E remove_directory doc/xml_output
COMMAND ${CMAKE_COMMAND} -E chdir doc doxygen doxygen/Doxyfile_xml
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "The XML documentation has been successfully created."
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMENT "Build the doxygen documentation"
VERBATIM)
#######################################################################
## doc_noclass target
add_custom_target(doc_noclass
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "Creating html documentation without class documentation"
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E remove_directory doc/html
COMMAND ${CMAKE_COMMAND} -E chdir doc doxygen doxygen/Doxyfile_noclass
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/doc/index.html doc/index.html
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/doc/doxygen/common/style_ini.css doc/html/style_ini.css
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "The documentation has been successfully created."
COMMAND ${CMAKE_COMMAND} -E echo "You can now open 'doc/index.html' in a web browser."
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMENT "Build the doxygen documentation"
VERBATIM)
add_dependencies(doc_noclass doc_param_internal)
#######################################################################
## doc_minimal target
add_custom_target(doc_minimal
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "Creating html documentation without class/TOPP/UTILS documentation"
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E remove_directory doc/html
COMMAND ${CMAKE_COMMAND} -E chdir doc doxygen doxygen/Doxyfile_noclass
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/doc/index.html doc/index.html
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/doc/doxygen/common/style_ini.css doc/html/style_ini.css
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "The documentation has been successfully created."
COMMAND ${CMAKE_COMMAND} -E echo "You can now open 'doc/index.html' in a web browser."
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMENT "Build the doxygen documentation"
VERBATIM)
if (DOXYGEN_DOT_FOUND OR DOXYGEN_DOT_EXECUTABLE)
#######################################################################
## doc_dot target
add_custom_target(doc_dot
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "Creating DOT html documentation"
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E remove_directory doc/html-dot
COMMAND ${CMAKE_COMMAND} -E chdir doc doxygen doxygen/Doxyfile_dot
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/doc/index.html doc/index.html
COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/doc/doxygen/common/style_ini.css doc/html/style_ini.css
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "The documentation has been successfully created."
COMMAND ${CMAKE_COMMAND} -E echo "You can now open 'doc/index.html' in a web browser."
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMENT "Build the doxygen documentation"
VERBATIM)
add_dependencies(doc_dot doc_param_internal)
else()
Message(STATUS "DOT not found. Disabling target 'doc_dot'!")
endif()
else()
Message(STATUS "Doxygen not found. Disabling all documentation targets!")
endif()
if (DOXYGEN_FOUND AND LATEX_COMPILER AND DVIPS_CONVERTER)
#######################################################################
# doc_tutorials target
set(DOC_TUTORIALS_ACTIVE TRUE)
set(DOXYGEN_START_BUGGY "1.6.3")
set(DOXYGEN_END_BUGGY "1.7.2")
EXEC_PROGRAM(${DOXYGEN_EXECUTABLE}
ARGS "--version"
OUTPUT_VARIABLE DOXYGEN_VERSION)
if (DOXYGEN_VERSION STRGREATER DOXYGEN_START_BUGGY AND DOXYGEN_VERSION STRLESS DOXYGEN_END_BUGGY )
MESSAGE(ERROR "Warning, DoxygenBug ( 1.6.? < vers. installed < 1.7.3 ) disguises generated tex inputfiles and files will not be recognized")
endif ()
add_custom_target(doc_tutorials
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "Creating OpenMS pdf tutorial"
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E remove_directory doc/OpenMS_tutorial/latex_output
COMMAND ${CMAKE_COMMAND} -E chdir doc/OpenMS_tutorial/ doxygen Doxyfile
COMMAND ${CMAKE_COMMAND} -E copy doc/OpenMS_tutorial/refman_overwrite.tex doc/OpenMS_tutorial/latex_output/refman.tex
COMMAND ${CMAKE_COMMAND} -E chdir doc/OpenMS_tutorial/latex_output/ pdflatex refman.tex
COMMAND ${CMAKE_COMMAND} -E chdir doc/OpenMS_tutorial/latex_output/ makeindex refman.idx
COMMAND ${CMAKE_COMMAND} -E chdir doc/OpenMS_tutorial/latex_output/ pdflatex refman.tex
COMMAND ${CMAKE_COMMAND} -E chdir doc/OpenMS_tutorial/latex_output/ pdflatex refman.tex
COMMAND ${CMAKE_COMMAND} -E copy doc/OpenMS_tutorial/latex_output/refman.pdf doc/OpenMS_tutorial.pdf
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "The OpenMS tutorial in PDF format has been successfully created:"
COMMAND ${CMAKE_COMMAND} -E echo "doc/OpenMS_tutorial.pdf"
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
COMMAND ${CMAKE_COMMAND} -E echo "Creating TOPP/TOPPView pdf tutorial"
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E remove_directory doc/TOPP_tutorial/latex_output
COMMAND ${CMAKE_COMMAND} -E chdir doc/TOPP_tutorial/ doxygen Doxyfile
COMMAND ${CMAKE_COMMAND} -E copy doc/TOPP_tutorial/refman_overwrite.tex doc/TOPP_tutorial/latex_output/refman.tex
COMMAND ${CMAKE_COMMAND} -E chdir doc/TOPP_tutorial/latex_output/ pdflatex refman.tex
COMMAND ${CMAKE_COMMAND} -E chdir doc/TOPP_tutorial/latex_output/ makeindex refman.idx
COMMAND ${CMAKE_COMMAND} -E chdir doc/TOPP_tutorial/latex_output/ pdflatex refman.tex
COMMAND ${CMAKE_COMMAND} -E chdir doc/TOPP_tutorial/latex_output/ pdflatex refman.tex
COMMAND ${CMAKE_COMMAND} -E copy doc/TOPP_tutorial/latex_output/refman.pdf doc/TOPP_tutorial.pdf
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMAND ${CMAKE_COMMAND} -E echo "The OpenMS tutorial in PDF format has been successfully created:"
COMMAND ${CMAKE_COMMAND} -E echo "doc/TOPP_tutorial.pdf"
COMMAND ${CMAKE_COMMAND} -E echo ""
COMMENT "Build the OpenMS/TOPP pdf tutorial"
VERBATIM)
else()
set(DOC_TUTORIALS_ACTIVE FALSE)
Message(STATUS "Doxygen or Latex missing. Disabling 'doc_tutorials' target!")
endif()
|
