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Work on doc.

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Olivier Parcollet 2013-11-03 18:56:55 +01:00
parent e703b1e2b7
commit 0b7bfec32e
8 changed files with 72 additions and 47 deletions
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10
cmake/Doxyfile.in
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@ -98,7 +98,7 @@ ALWAYS_DETAILED_SEC = NO
# members were ordinary class members. Constructors, destructors and assignment # members were ordinary class members. Constructors, destructors and assignment
# operators of the base classes will not be shown. # operators of the base classes will not be shown.
INLINE_INHERITED_MEMB = NO INLINE_INHERITED_MEMB = YES
# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full # If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
# path before files name in the file list and in the header files. If set # path before files name in the file list and in the header files. If set
@ -521,7 +521,7 @@ EXCLUDE_PATTERNS =
# The symbol name can be a fully qualified name, a word, or if the wildcard * is used, # The symbol name can be a fully qualified name, a word, or if the wildcard * is used,
# a substring. Examples: ANamespace, AClass, AClass::ANamespace, ANamespace::*Test # a substring. Examples: ANamespace, AClass, AClass::ANamespace, ANamespace::*Test
EXCLUDE_SYMBOLS = *::*details::*, *impl* EXCLUDE_SYMBOLS = *::*details::*
# The EXAMPLE_PATH tag can be used to specify one or more files or # The EXAMPLE_PATH tag can be used to specify one or more files or
# directories that contain example code fragments that are included (see # directories that contain example code fragments that are included (see
@ -1049,7 +1049,7 @@ INCLUDE_FILE_PATTERNS =
# undefined via #undef or recursively expanded use the := operator # undefined via #undef or recursively expanded use the := operator
# instead of the = operator. # instead of the = operator.
PREDEFINED = PREDEFINED = TRIQS_DOXYGEN
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
# this tag can be used to specify a list of macro names that should be expanded. # this tag can be used to specify a list of macro names that should be expanded.
@ -1121,7 +1121,7 @@ PERL_PATH = /usr/bin/perl
# fallback. It is recommended to install and use dot, since it yields more # fallback. It is recommended to install and use dot, since it yields more
# powerful graphs. # powerful graphs.
CLASS_DIAGRAMS = YES CLASS_DIAGRAMS = NO
# You can define message sequence charts within doxygen comments using the \msc # You can define message sequence charts within doxygen comments using the \msc
# command. Doxygen will then run the mscgen tool (see http://www.mcternan.me.uk/mscgen/) to # command. Doxygen will then run the mscgen tool (see http://www.mcternan.me.uk/mscgen/) to
@ -1149,7 +1149,7 @@ HAVE_DOT = NO
# indirect inheritance relations. Setting this tag to YES will force the # indirect inheritance relations. Setting this tag to YES will force the
# the CLASS_DIAGRAMS tag to NO. # the CLASS_DIAGRAMS tag to NO.
CLASS_GRAPH = YES CLASS_GRAPH = NO
# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen # If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
# will generate a graph for each documented class showing the direct and # will generate a graph for each documented class showing the direct and

17
doc/conf.py.in
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@ -21,14 +21,15 @@ import sys, os
# General configuration # General configuration
# --------------------- # ---------------------
sys.path +=["@CMAKE_BINARY_DIR@/doc/breathe", sys.path +=[ #"@CMAKE_BINARY_DIR@/doc/breathe",
"@CMAKE_BINARY_DIR@/doc/mpl","@CMAKE_BINARY_DIR@/doc/autocompile", "@CMAKE_BINARY_DIR@/doc/mpl","@CMAKE_BINARY_DIR@/doc/autocompile",
"@CMAKE_BINARY_DIR@/doc/sandbox","@CMAKE_BINARY_DIR@/doc"] "@CMAKE_BINARY_DIR@/doc/sandbox","@CMAKE_BINARY_DIR@/doc"]
# Add any Sphinx extension module names here, as strings. They can be extensions # Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
#extensions = ['sphinx.ext.autodoc','sphinx.ext.pngmath'] #extensions = ['sphinx.ext.autodoc','sphinx.ext.pngmath']
extensions = ['sphinx.ext.autodoc','sphinx.ext.@SPHINX_MATH_GENERATOR@','breathe','doxylink'] #extensions = ['sphinx.ext.autodoc','sphinx.ext.@SPHINX_MATH_GENERATOR@','breathe','sphinxcontrib.doxylink']
extensions = ['sphinx.ext.autodoc','sphinx.ext.@SPHINX_MATH_GENERATOR@','sphinxcontrib.doxylink']
# adding support for matplotlib plots # adding support for matplotlib plots
extensions += [ extensions += [
@ -121,12 +122,12 @@ pygments_style = 'sphinx'
# Options for breathe extension # Options for breathe extension
# ----------------------------- # -----------------------------
breathe_projects = { #breathe_projects = {
"mc_tools":"@CMAKE_CURRENT_BINARY_DIR@/xml/", # "mc_tools":"@CMAKE_CURRENT_BINARY_DIR@/xml/",
"arrays":"@CMAKE_CURRENT_BINARY_DIR@/xml/", # "arrays":"@CMAKE_CURRENT_BINARY_DIR@/xml/",
} # "doxy":"@CMAKE_CURRENT_BINARY_DIR@/xml/",
# }
breathe_default_project = "mc_tools" #breathe_default_project = "mc_tools"
# Options for doxylink extension # Options for doxylink extension
# ----------------------------- # -----------------------------

13
doc/installation/osx_lion.rst
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@ -7,15 +7,22 @@
Installing required libraries on Mac OS X Installing required libraries on Mac OS X
========================================= =========================================
This installation guide has been tried on Mountain Lion. It may work for older This is an installation guide for Os X Mountain Lion.
It may work for older
versions of Mac OS X but previous versions of Mac OS X are not supported. versions of Mac OS X but previous versions of Mac OS X are not supported.
NB: The installation of TRIQS under previous versions of OS X requires installing clang (via Xcode). NB: The installation of TRIQS under previous versions of OS X requires installing clang (via Xcode).
(On Mountain Lion, clang (llvm) replaces gcc 4.2 as the default C++ compiler). (On Mountain Lion, clang (llvm) replaces gcc as the default C++ compiler).
We strongly recommend the following installation procedure, which provides a clean way to set up all dependencies, so that all We strongly recommend the following installation procedure, which provides a clean way to set up all dependencies, so that all
of them are compatible with each other. Only the installation via homebrew is supported for the Mac. of them are compatible with each other. Only the installation via homebrew is supported for the Mac.
.. warning::
Because brew evolve with time, there is no notion of distribution on Mac, like e.g. Ubuntu.
So, while the procedure worked at some point, there can be no guarantee that it still does.
Installation of the dependencies Installation of the dependencies
-------------------------------- --------------------------------
@ -50,6 +57,8 @@ Installation of the dependencies
pip install scipy pip install scipy
pip install mpi4py pip install mpi4py
pip install matplotlib pip install matplotlib
pip install breathe
pip install sphinxcontrib-doxylink
pip install tornado pip install tornado
pip install pyzmq pip install pyzmq
pip install jinja2 pip install jinja2

41
doc/installation/requirements.rst
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@ -42,26 +42,25 @@ A recent compiler is therefore mandatory.
Libraries Libraries
--------- ---------
================== ================ ================================================================================ +------------------------+----------+------------------------------------------------------------------------+
Library/tool Version Comment | Library/tool | Version | Comment |
================== ================ ================================================================================ +========================+==========+========================================================================+
mpi openmpi Parallelism. | mpi | openmpi | Parallelism (1). |
Since standard linux distributions (and macports on OS X) | fftw | >= 3.2 | Fourier transforms |
now provides openmpi, even on laptops, we avoid the unnecessary complication | boost | >= 1.49 | C++ librairies |
of maintaining a non-parallel version of TRIQS | hdf5 | >= 1.8.0 | File storage system. Important: the *serial* version must be installed |
fftw >= 3.2 Fourier transforms | python | >= 2.6.5 | The Python interpreter |
boost >= 1.49 C++ librairies | scipy | >= ? | Python mathematical library |
hdf5 >= 1.8.0 File storage system. Important: the *serial* version must be installed | numpy | >= ? | Python scientific library |
python >= 2.6.5 The Python interpreter | h5py | >= ? | Python interface to hdf5 library |
scipy Python mathematical library | mpi4py | >= ? | Python MPI |
numpy Python scientific library | sphinx | >= 1.0.1 | Python documentation tools (to compile documentation) |
h5py Python interface to hdf5 library | cmake | >= 2.8.7 | CMake is used to control the software compilation process |
mpi4py Python MPI | pyparsing | >= ? | Tool for sphinx (to compile documentation) |
sphinx >= 1.0.1 Python documentation tools (to compile documentation) | sphinxcontrib-doxylink | >= ? | Tool for sphinx (to compile documentation) |
cmake >= 2.8.7 CMake is used to control the software compilation process | matplotlib | >= 0.99 | Python 2D plotting library |
pyparsing Tool for sphinx (to compile documentation) | cython | >=0.17 | A language that allows to write C extensions for the Python language |
matplotlib >= 0.99 Python 2D plotting library +------------------------+----------+------------------------------------------------------------------------+
cython >=0.17 A language that allows to write C extensions for the Python language
================== ================ ================================================================================
(1) Since standard linux distributions (and macports on OS X) now provides openmpi, even on laptops, we avoid the unnecessary complication of maintaining a non-parallel version of TRIQS

1
doc/reference/c++/arrays/CMakeLists.txt
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@ -2,6 +2,7 @@
set_property(GLOBAL APPEND PROPERTY DOXYGEN_SOURCES set_property(GLOBAL APPEND PROPERTY DOXYGEN_SOURCES
${TRIQS_SOURCE_DIR}/triqs/arrays/h5/simple_read_write.hpp ${TRIQS_SOURCE_DIR}/triqs/arrays/h5/simple_read_write.hpp
${TRIQS_SOURCE_DIR}/triqs/arrays/h5/array_stack.hpp ${TRIQS_SOURCE_DIR}/triqs/arrays/h5/array_stack.hpp
${TRIQS_SOURCE_DIR}/triqs/h5/group.hpp
${TRIQS_SOURCE_DIR}/triqs/arrays/array.hpp ${TRIQS_SOURCE_DIR}/triqs/arrays/array.hpp
${TRIQS_SOURCE_DIR}/triqs/arrays/matrix.hpp ${TRIQS_SOURCE_DIR}/triqs/arrays/matrix.hpp
${TRIQS_SOURCE_DIR}/triqs/arrays/vector.hpp ${TRIQS_SOURCE_DIR}/triqs/arrays/vector.hpp

10
doc/reference/c++/arrays/H5.rst
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@ -18,10 +18,16 @@ Reference
h5_rw h5_rw
h5_stack h5_stack
h5_proxy
h5_complex h5_complex
You can also get the :doxy:`full C++ documentation<triqs::arrays::h5>` for these classes and functions. You can also get the :doxy:`full C++ documentation<triqs::h5::group>` for these classes and functions.
.. :
Breathe Documentation
*********************
.. doxygenclass:: triqs::h5::group
:project: doxy
:members:

11
doc/reference/c++/arrays/h5_stack.rst
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@ -24,7 +24,16 @@ It is typically used to store a Monte-Carlo data series for later analysis.
Reference Reference
------------ ------------
Here is the :doxy:`full C++ documentation<triqs::arrays::h5::array_stack>` for this class. Here is the :doxy:`full C++ documentation<triqs::arrays::array_stack>` for this class.
.. :
Breathe Documentation
--------------------------
.. doxygenclass:: triqs::arrays::array_stack
:project: arrays
:members:
Tutorial Tutorial

12
doc/reference/c++/mctools/reference.rst
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@ -73,10 +73,10 @@ Doxygen documentation
The :doxy:`full C++ documentation<triqs::mc_tools::mc_generic>` is available here. The :doxy:`full C++ documentation<triqs::mc_tools::mc_generic>` is available here.
.. :
Breathe Documentation Breathe Documentation
********************* *********************
.. doxygenclass:: triqs::mc_tools::mc_generic .. doxygenclass:: triqs::mc_tools::mc_generic
:project: doxy :project: mc_tools
:members: :members: