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‎.gitignore

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# build directory
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build/
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# vim temp files
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.*.sw*

‎CMakeLists.txt

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cmake_minimum_required(VERSION 2.8)
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project(chemkit-python)
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set(CMAKE_MODULE_PATH ${chemkit-python_SOURCE_DIR}/cmake)
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set(CMAKE_BUILD_TYPE Release)
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# find cython
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find_program(CYTHON cython REQUIRED)
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# find python interpreter
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find_package(PythonInterp REQUIRED)
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# source directory
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add_subdirectory(src)
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# testing
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enable_testing()
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add_subdirectory(tests)
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# uninstall target
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configure_file(
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"${CMAKE_MODULE_PATH}/cmake_uninstall.cmake.in"
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"${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake"
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IMMEDIATE @ONLY)
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add_custom_target(uninstall
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COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake)
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‎INSTALL

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=== Dependencies ==============================================================
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- Chemkit - http://www.chemkit.org
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- Cython - http://www.cython.org
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=== Compiling =================================================================
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From the chemkit-python directory (the same directory this file is in) run the
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following commands:
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mkdir build
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cd build
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cmake ..
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make
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=== Installation ==============================================================
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After successfully compiling chemkit run the following command to install the
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library (you may need root/administator privileges):
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make install

‎LICENSE

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Copyright (C) 2009-2011 Kyle Lutz
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions
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are met:
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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* Neither the name of the chemkit project nor the names of its
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contributors may be used to endorse or promote products derived
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from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎README

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chemkit-python - a python wrapper for the chemkit library
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=== Introduction ==============================================================
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chemkit-python provides a python interface to the chemkit library.
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For more information see the chemkit website: http://www.chemkit.org
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=== Installation and Usage ====================================================
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See the included INSTALL file for directions for compiling, installing, and
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using the chemkit-python library.
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=== License ===================================================================
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The chemkit-python library is licensed under the BSD license. See the included
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LICENSE file to view the full license text.
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‎cmake/FindEigen3.cmake

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# - Try to find Eigen3 lib
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#
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# This module supports requiring a minimum version, e.g. you can do
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# find_package(Eigen3 3.1.2)
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# to require version 3.1.2 or newer of Eigen3.
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#
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# Once done this will define
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#
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# EIGEN3_FOUND - system has eigen lib with correct version
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# EIGEN3_INCLUDE_DIR - the eigen include directory
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# EIGEN3_VERSION - eigen version
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# Copyright (c) 2006, 2007 Montel Laurent, <montel@kde.org>
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# Copyright (c) 2008, 2009 Gael Guennebaud, <g.gael@free.fr>
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# Copyright (c) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
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# Redistribution and use is allowed according to the terms of the 2-clause BSD license.
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if(NOT Eigen3_FIND_VERSION)
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if(NOT Eigen3_FIND_VERSION_MAJOR)
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set(Eigen3_FIND_VERSION_MAJOR 2)
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endif(NOT Eigen3_FIND_VERSION_MAJOR)
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if(NOT Eigen3_FIND_VERSION_MINOR)
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set(Eigen3_FIND_VERSION_MINOR 91)
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endif(NOT Eigen3_FIND_VERSION_MINOR)
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if(NOT Eigen3_FIND_VERSION_PATCH)
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set(Eigen3_FIND_VERSION_PATCH 0)
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endif(NOT Eigen3_FIND_VERSION_PATCH)
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set(Eigen3_FIND_VERSION "${Eigen3_FIND_VERSION_MAJOR}.${Eigen3_FIND_VERSION_MINOR}.${Eigen3_FIND_VERSION_PATCH}")
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endif(NOT Eigen3_FIND_VERSION)
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macro(_eigen3_check_version)
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file(READ "${EIGEN3_INCLUDE_DIR}/Eigen/src/Core/util/Macros.h" _eigen3_version_header)
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string(REGEX MATCH "define[ \t]+EIGEN_WORLD_VERSION[ \t]+([0-9]+)" _eigen3_world_version_match "${_eigen3_version_header}")
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set(EIGEN3_WORLD_VERSION "${CMAKE_MATCH_1}")
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string(REGEX MATCH "define[ \t]+EIGEN_MAJOR_VERSION[ \t]+([0-9]+)" _eigen3_major_version_match "${_eigen3_version_header}")
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set(EIGEN3_MAJOR_VERSION "${CMAKE_MATCH_1}")
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string(REGEX MATCH "define[ \t]+EIGEN_MINOR_VERSION[ \t]+([0-9]+)" _eigen3_minor_version_match "${_eigen3_version_header}")
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set(EIGEN3_MINOR_VERSION "${CMAKE_MATCH_1}")
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set(EIGEN3_VERSION ${EIGEN3_WORLD_VERSION}.${EIGEN3_MAJOR_VERSION}.${EIGEN3_MINOR_VERSION})
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if(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
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set(EIGEN3_VERSION_OK FALSE)
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else(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
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set(EIGEN3_VERSION_OK TRUE)
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endif(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
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if(NOT EIGEN3_VERSION_OK)
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message(STATUS "Eigen3 version ${EIGEN3_VERSION} found in ${EIGEN3_INCLUDE_DIR}, "
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"but at least version ${Eigen3_FIND_VERSION} is required")
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endif(NOT EIGEN3_VERSION_OK)
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endmacro(_eigen3_check_version)
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if (EIGEN3_INCLUDE_DIR)
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# in cache already
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_eigen3_check_version()
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set(EIGEN3_FOUND ${EIGEN3_VERSION_OK})
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else (EIGEN3_INCLUDE_DIR)
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find_path(EIGEN3_INCLUDE_DIR NAMES signature_of_eigen3_matrix_library
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PATHS
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${CMAKE_INSTALL_PREFIX}/include
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${KDE4_INCLUDE_DIR}
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PATH_SUFFIXES eigen3 eigen
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)
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if(EIGEN3_INCLUDE_DIR)
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_eigen3_check_version()
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endif(EIGEN3_INCLUDE_DIR)
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include(FindPackageHandleStandardArgs)
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find_package_handle_standard_args(Eigen3 DEFAULT_MSG EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
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mark_as_advanced(EIGEN3_INCLUDE_DIR)
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endif(EIGEN3_INCLUDE_DIR)
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‎cmake/cmake_uninstall.cmake.in

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if(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
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message(FATAL_ERROR "Cannot find install manifest: \"@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt\"")
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endif(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
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file(READ "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt" files)
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string(REGEX REPLACE "\n" ";" files "${files}")
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foreach(file ${files})
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message(STATUS "Uninstalling \"$ENV{DESTDIR}${file}\"")
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if(EXISTS "$ENV{DESTDIR}${file}")
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execute_process(
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COMMAND @CMAKE_COMMAND@ -E remove "$ENV{DESTDIR}${file}"
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OUTPUT_VARIABLE rm_out
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RESULT_VARIABLE rm_retval
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)
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if(NOT ${rm_retval} EQUAL 0)
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message(FATAL_ERROR "Problem when removing \"$ENV{DESTDIR}${file}\"")
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endif(NOT ${rm_retval} EQUAL 0)
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else(EXISTS "$ENV{DESTDIR}${file}")
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message(STATUS "File \"$ENV{DESTDIR}${file}\" does not exist.")
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endif(EXISTS "$ENV{DESTDIR}${file}")
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endforeach(file)

‎doc/.gitignore

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# build directory
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_build/
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‎doc/Makefile

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# Makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS =
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SPHINXBUILD = sphinx-build
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PAPER =
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BUILDDIR = _build
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# Internal variables.
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PAPEROPT_a4 = -D latex_paper_size=a4
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PAPEROPT_letter = -D latex_paper_size=letter
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ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
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.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
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help:
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@echo "Please use \`make <target>' where <target> is one of"
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@echo " html to make standalone HTML files"
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@echo " dirhtml to make HTML files named index.html in directories"
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@echo " singlehtml to make a single large HTML file"
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@echo " pickle to make pickle files"
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@echo " json to make JSON files"
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@echo " htmlhelp to make HTML files and a HTML help project"
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@echo " qthelp to make HTML files and a qthelp project"
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@echo " devhelp to make HTML files and a Devhelp project"
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@echo " epub to make an epub"
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@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
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@echo " latexpdf to make LaTeX files and run them through pdflatex"
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@echo " text to make text files"
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@echo " man to make manual pages"
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@echo " changes to make an overview of all changed/added/deprecated items"
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@echo " linkcheck to check all external links for integrity"
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@echo " doctest to run all doctests embedded in the documentation (if enabled)"
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clean:
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-rm -rf $(BUILDDIR)/*
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html:
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$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
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dirhtml:
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$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
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singlehtml:
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$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
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@echo
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@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
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pickle:
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$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
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@echo
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@echo "Build finished; now you can process the pickle files."
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json:
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$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
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@echo
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@echo "Build finished; now you can process the JSON files."
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htmlhelp:
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$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
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@echo
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@echo "Build finished; now you can run HTML Help Workshop with the" \
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".hhp project file in $(BUILDDIR)/htmlhelp."
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qthelp:
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$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
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@echo
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@echo "Build finished; now you can run "qcollectiongenerator" with the" \
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".qhcp project file in $(BUILDDIR)/qthelp, like this:"
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@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/chemkit.qhcp"
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@echo "To view the help file:"
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@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/chemkit.qhc"
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devhelp:
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$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
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@echo
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@echo "Build finished."
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@echo "To view the help file:"
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@echo "# mkdir -p $$HOME/.local/share/devhelp/chemkit"
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@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/chemkit"
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@echo "# devhelp"
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epub:
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$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
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@echo
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@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
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latex:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo
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@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
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@echo "Run \`make' in that directory to run these through (pdf)latex" \
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"(use \`make latexpdf' here to do that automatically)."
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latexpdf:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo "Running LaTeX files through pdflatex..."
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make -C $(BUILDDIR)/latex all-pdf
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@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
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text:
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$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
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@echo
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@echo "Build finished. The text files are in $(BUILDDIR)/text."
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man:
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$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
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@echo
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@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
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changes:
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$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
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@echo
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@echo "The overview file is in $(BUILDDIR)/changes."
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linkcheck:
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$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
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@echo
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@echo "Link check complete; look for any errors in the above output " \
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"or in $(BUILDDIR)/linkcheck/output.txt."
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doctest:
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$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
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@echo "Testing of doctests in the sources finished, look at the " \
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"results in $(BUILDDIR)/doctest/output.txt."

‎doc/_templates/layout.html

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{% extends "!layout.html" %}
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{% block footer %}
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{{ super() }}
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<script type="text/javascript">
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var _gaq = _gaq || [];
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_gaq.push(['_setAccount', 'UA-21520458-1']);
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_gaq.push(['_setDomainName', '.chemkit.org']);
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_gaq.push(['_trackPageview']);
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(function() {
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var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
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ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
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var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
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})();
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</script>
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{% endblock %}

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