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https://github.com/triqs/dft_tools
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Work on doc.
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@ -98,7 +98,7 @@ ALWAYS_DETAILED_SEC = NO
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# members were ordinary class members. Constructors, destructors and assignment
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# members were ordinary class members. Constructors, destructors and assignment
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# operators of the base classes will not be shown.
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# operators of the base classes will not be shown.
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INLINE_INHERITED_MEMB = NO
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INLINE_INHERITED_MEMB = YES
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# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
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# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
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# path before files name in the file list and in the header files. If set
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# path before files name in the file list and in the header files. If set
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@ -521,7 +521,7 @@ EXCLUDE_PATTERNS =
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# The symbol name can be a fully qualified name, a word, or if the wildcard * is used,
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# The symbol name can be a fully qualified name, a word, or if the wildcard * is used,
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# a substring. Examples: ANamespace, AClass, AClass::ANamespace, ANamespace::*Test
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# a substring. Examples: ANamespace, AClass, AClass::ANamespace, ANamespace::*Test
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EXCLUDE_SYMBOLS = *::*details::*, *impl*
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EXCLUDE_SYMBOLS = *::*details::*
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# The EXAMPLE_PATH tag can be used to specify one or more files or
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# The EXAMPLE_PATH tag can be used to specify one or more files or
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# directories that contain example code fragments that are included (see
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# directories that contain example code fragments that are included (see
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@ -1049,7 +1049,7 @@ INCLUDE_FILE_PATTERNS =
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# undefined via #undef or recursively expanded use the := operator
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# undefined via #undef or recursively expanded use the := operator
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# instead of the = operator.
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# instead of the = operator.
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PREDEFINED =
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PREDEFINED = TRIQS_DOXYGEN
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# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
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# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
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# this tag can be used to specify a list of macro names that should be expanded.
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# this tag can be used to specify a list of macro names that should be expanded.
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@ -1121,7 +1121,7 @@ PERL_PATH = /usr/bin/perl
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# fallback. It is recommended to install and use dot, since it yields more
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# fallback. It is recommended to install and use dot, since it yields more
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# powerful graphs.
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# powerful graphs.
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CLASS_DIAGRAMS = YES
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CLASS_DIAGRAMS = NO
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# You can define message sequence charts within doxygen comments using the \msc
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# You can define message sequence charts within doxygen comments using the \msc
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# command. Doxygen will then run the mscgen tool (see http://www.mcternan.me.uk/mscgen/) to
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# command. Doxygen will then run the mscgen tool (see http://www.mcternan.me.uk/mscgen/) to
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@ -1149,7 +1149,7 @@ HAVE_DOT = NO
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# indirect inheritance relations. Setting this tag to YES will force the
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# indirect inheritance relations. Setting this tag to YES will force the
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# the CLASS_DIAGRAMS tag to NO.
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# the CLASS_DIAGRAMS tag to NO.
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CLASS_GRAPH = YES
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CLASS_GRAPH = NO
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# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
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# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
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# will generate a graph for each documented class showing the direct and
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# will generate a graph for each documented class showing the direct and
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@ -21,14 +21,15 @@ import sys, os
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# General configuration
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# General configuration
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# ---------------------
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# ---------------------
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sys.path +=["@CMAKE_BINARY_DIR@/doc/breathe",
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sys.path +=[ #"@CMAKE_BINARY_DIR@/doc/breathe",
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"@CMAKE_BINARY_DIR@/doc/mpl","@CMAKE_BINARY_DIR@/doc/autocompile",
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"@CMAKE_BINARY_DIR@/doc/mpl","@CMAKE_BINARY_DIR@/doc/autocompile",
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"@CMAKE_BINARY_DIR@/doc/sandbox","@CMAKE_BINARY_DIR@/doc"]
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"@CMAKE_BINARY_DIR@/doc/sandbox","@CMAKE_BINARY_DIR@/doc"]
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# Add any Sphinx extension module names here, as strings. They can be extensions
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# Add any Sphinx extension module names here, as strings. They can be extensions
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# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
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# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
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#extensions = ['sphinx.ext.autodoc','sphinx.ext.pngmath']
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#extensions = ['sphinx.ext.autodoc','sphinx.ext.pngmath']
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extensions = ['sphinx.ext.autodoc','sphinx.ext.@SPHINX_MATH_GENERATOR@','breathe','doxylink']
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#extensions = ['sphinx.ext.autodoc','sphinx.ext.@SPHINX_MATH_GENERATOR@','breathe','sphinxcontrib.doxylink']
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extensions = ['sphinx.ext.autodoc','sphinx.ext.@SPHINX_MATH_GENERATOR@','sphinxcontrib.doxylink']
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# adding support for matplotlib plots
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# adding support for matplotlib plots
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extensions += [
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extensions += [
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@ -121,12 +122,12 @@ pygments_style = 'sphinx'
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# Options for breathe extension
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# Options for breathe extension
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# -----------------------------
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# -----------------------------
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breathe_projects = {
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#breathe_projects = {
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"mc_tools":"@CMAKE_CURRENT_BINARY_DIR@/xml/",
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# "mc_tools":"@CMAKE_CURRENT_BINARY_DIR@/xml/",
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"arrays":"@CMAKE_CURRENT_BINARY_DIR@/xml/",
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# "arrays":"@CMAKE_CURRENT_BINARY_DIR@/xml/",
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}
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# "doxy":"@CMAKE_CURRENT_BINARY_DIR@/xml/",
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# }
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breathe_default_project = "mc_tools"
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#breathe_default_project = "mc_tools"
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# Options for doxylink extension
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# Options for doxylink extension
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# -----------------------------
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# -----------------------------
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@ -7,15 +7,22 @@
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Installing required libraries on Mac OS X
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Installing required libraries on Mac OS X
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=========================================
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=========================================
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This installation guide has been tried on Mountain Lion. It may work for older
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This is an installation guide for Os X Mountain Lion.
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It may work for older
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versions of Mac OS X but previous versions of Mac OS X are not supported.
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versions of Mac OS X but previous versions of Mac OS X are not supported.
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NB: The installation of TRIQS under previous versions of OS X requires installing clang (via Xcode).
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NB: The installation of TRIQS under previous versions of OS X requires installing clang (via Xcode).
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(On Mountain Lion, clang (llvm) replaces gcc 4.2 as the default C++ compiler).
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(On Mountain Lion, clang (llvm) replaces gcc as the default C++ compiler).
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We strongly recommend the following installation procedure, which provides a clean way to set up all dependencies, so that all
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We strongly recommend the following installation procedure, which provides a clean way to set up all dependencies, so that all
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of them are compatible with each other. Only the installation via homebrew is supported for the Mac.
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of them are compatible with each other. Only the installation via homebrew is supported for the Mac.
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.. warning::
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Because brew evolve with time, there is no notion of distribution on Mac, like e.g. Ubuntu.
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So, while the procedure worked at some point, there can be no guarantee that it still does.
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Installation of the dependencies
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Installation of the dependencies
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--------------------------------
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--------------------------------
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@ -50,6 +57,8 @@ Installation of the dependencies
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pip install scipy
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pip install scipy
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pip install mpi4py
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pip install mpi4py
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pip install matplotlib
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pip install matplotlib
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pip install breathe
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pip install sphinxcontrib-doxylink
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pip install tornado
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pip install tornado
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pip install pyzmq
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pip install pyzmq
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pip install jinja2
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pip install jinja2
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@ -42,26 +42,25 @@ A recent compiler is therefore mandatory.
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Libraries
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Libraries
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---------
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---------
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================== ================ ================================================================================
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+------------------------+----------+------------------------------------------------------------------------+
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Library/tool Version Comment
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| Library/tool | Version | Comment |
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================== ================ ================================================================================
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+========================+==========+========================================================================+
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mpi openmpi Parallelism.
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| mpi | openmpi | Parallelism (1). |
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Since standard linux distributions (and macports on OS X)
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| fftw | >= 3.2 | Fourier transforms |
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now provides openmpi, even on laptops, we avoid the unnecessary complication
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| boost | >= 1.49 | C++ librairies |
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of maintaining a non-parallel version of TRIQS
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| hdf5 | >= 1.8.0 | File storage system. Important: the *serial* version must be installed |
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fftw >= 3.2 Fourier transforms
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| python | >= 2.6.5 | The Python interpreter |
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boost >= 1.49 C++ librairies
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| scipy | >= ? | Python mathematical library |
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hdf5 >= 1.8.0 File storage system. Important: the *serial* version must be installed
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| numpy | >= ? | Python scientific library |
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python >= 2.6.5 The Python interpreter
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| h5py | >= ? | Python interface to hdf5 library |
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scipy Python mathematical library
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| mpi4py | >= ? | Python MPI |
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numpy Python scientific library
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| sphinx | >= 1.0.1 | Python documentation tools (to compile documentation) |
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h5py Python interface to hdf5 library
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| cmake | >= 2.8.7 | CMake is used to control the software compilation process |
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mpi4py Python MPI
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| pyparsing | >= ? | Tool for sphinx (to compile documentation) |
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sphinx >= 1.0.1 Python documentation tools (to compile documentation)
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| sphinxcontrib-doxylink | >= ? | Tool for sphinx (to compile documentation) |
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cmake >= 2.8.7 CMake is used to control the software compilation process
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| matplotlib | >= 0.99 | Python 2D plotting library |
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pyparsing Tool for sphinx (to compile documentation)
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| cython | >=0.17 | A language that allows to write C extensions for the Python language |
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matplotlib >= 0.99 Python 2D plotting library
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+------------------------+----------+------------------------------------------------------------------------+
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cython >=0.17 A language that allows to write C extensions for the Python language
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================== ================ ================================================================================
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(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
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@ -2,6 +2,7 @@
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set_property(GLOBAL APPEND PROPERTY DOXYGEN_SOURCES
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set_property(GLOBAL APPEND PROPERTY DOXYGEN_SOURCES
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${TRIQS_SOURCE_DIR}/triqs/arrays/h5/simple_read_write.hpp
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${TRIQS_SOURCE_DIR}/triqs/arrays/h5/simple_read_write.hpp
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${TRIQS_SOURCE_DIR}/triqs/arrays/h5/array_stack.hpp
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${TRIQS_SOURCE_DIR}/triqs/arrays/h5/array_stack.hpp
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${TRIQS_SOURCE_DIR}/triqs/h5/group.hpp
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${TRIQS_SOURCE_DIR}/triqs/arrays/array.hpp
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${TRIQS_SOURCE_DIR}/triqs/arrays/array.hpp
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${TRIQS_SOURCE_DIR}/triqs/arrays/matrix.hpp
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${TRIQS_SOURCE_DIR}/triqs/arrays/matrix.hpp
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${TRIQS_SOURCE_DIR}/triqs/arrays/vector.hpp
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${TRIQS_SOURCE_DIR}/triqs/arrays/vector.hpp
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@ -18,10 +18,16 @@ Reference
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h5_rw
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h5_rw
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h5_stack
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h5_stack
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h5_proxy
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h5_complex
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h5_complex
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You can also get the :doxy:`full C++ documentation<triqs::arrays::h5>` for these classes and functions.
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You can also get the :doxy:`full C++ documentation<triqs::h5::group>` for these classes and functions.
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.. :
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Breathe Documentation
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*********************
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.. doxygenclass:: triqs::h5::group
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:project: doxy
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:members:
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@ -24,8 +24,17 @@ It is typically used to store a Monte-Carlo data series for later analysis.
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Reference
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Reference
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------------
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------------
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Here is the :doxy:`full C++ documentation<triqs::arrays::h5::array_stack>` for this class.
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Here is the :doxy:`full C++ documentation<triqs::arrays::array_stack>` for this class.
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.. :
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Breathe Documentation
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--------------------------
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.. doxygenclass:: triqs::arrays::array_stack
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:project: arrays
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:members:
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Tutorial
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Tutorial
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-----------
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-----------
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@ -73,10 +73,10 @@ Doxygen documentation
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The :doxy:`full C++ documentation<triqs::mc_tools::mc_generic>` is available here.
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The :doxy:`full C++ documentation<triqs::mc_tools::mc_generic>` is available here.
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.. :
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Breathe Documentation
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Breathe Documentation
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*********************
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*********************
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.. doxygenclass:: triqs::mc_tools::mc_generic
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.. doxygenclass:: triqs::mc_tools::mc_generic
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:project: doxy
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:project: mc_tools
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:members:
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:members:
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