Merge branch 'py3' into unstable

update unstable branch with python 3 compatibility and apps4triqs compatibility.

.clang-tidy

@@ -0,0 +1,2 @@
+Checks: '-*,modernize-*,cppcoreguidelines-*,-modernize-use-trailing-return-type'
+HeaderFilterRegex: 'triqs_dft_tools'

.dockerignore

@@ -1,2 +1,4 @@
+.travis.yml
 Dockerfile
 Jenkinsfile
+.git/objects/pack

.github/ISSUE_TEMPLATE/bug.md

@@ -32,7 +32,7 @@ Please provide the application version that you used.
 
 You can get this information from copy and pasting the output of
 ```bash
-python -c "from app4triqs.version import *; show_version(); show_git_hash();"
+python -c "from triqs_dft_tools.version import *; show_version(); show_git_hash();"
 ```
 from the command line. Also, please include the OS you are running and its version.
 

.gitignore

@@ -0,0 +1,2 @@
+compile_commands.json
+doc/cpp2rst_generated

.travis.yml

@@ -1,47 +1,34 @@
 
 language: cpp
 sudo: required
-dist: trusty
+dist: bionic
 
 compiler:
   - gcc
-    #  - clang
+  - clang
 
 before_install:
-  - sudo add-apt-repository 'deb http://apt.llvm.org/trusty/ llvm-toolchain-trusty-5.0 main' -y
-  - wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key|sudo apt-key add -
-  - sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
   - sudo apt-get update
-  - sudo apt-get install -y --allow-unauthenticated g++-7 clang-5.0
+  - sudo apt-get install -y --allow-unauthenticated libblas-dev libboost-all-dev libfftw3-dev libgfortran3 libhdf5-serial-dev libgmp-dev liblapack-dev libopenmpi-dev libclang-dev python-clang-6.0 python-dev python-h5py python-mako python-matplotlib python-mpi4py python-numpy python-scipy python-sphinx libjs-mathjax libnfft3-dev
-  - export LIBRARY_PATH=/usr/lib/llvm-5.0/lib:$LIBRARY_PATH
-  - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 60 --slave /usr/bin/g++ g++ /usr/bin/g++-7
-  - sudo update-alternatives --install /usr/bin/clang clang /usr/bin/clang-5.0 60 --slave /usr/bin/clang++ clang++ /usr/bin/clang++-5.0
-  - sudo apt-get install -y --allow-unauthenticated libboost-all-dev cmake git libgfortran3 gfortran openmpi-bin openmpi-common openmpi-doc libopenmpi-dev libblas-dev liblapack-dev libfftw3-dev libgmp-dev hdf5-tools libhdf5-serial-dev python-h5py python-dev python-numpy python-scipy python-jinja2 python-virtualenv python-matplotlib python-tornado python-zmq python-mpi4py python-mako clang-format-5.0 libclang-5.0-dev python-clang-5.0 python-sphinx libjs-mathjax valgrind libnfft3-dev
 
 install: true
 
 script:
-  # ===== Set up Cpp2Py
+  - export INSTALL_DIR=$HOME/root_install # We install outside the repository
-  - git clone https://github.com/triqs/cpp2py
-  - mkdir cpp2py/build && cd cpp2py/build
-  - git checkout master
-  - cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/${CXX} -DPYTHON_INTERPRETER=/usr/bin/python -DCMAKE_INSTALL_PREFIX=$TRAVIS_BUILD_DIR/root_install
-  - make -j8 install
-  - cd $TRAVIS_BUILD_DIR
-  - source root_install/share/cpp2pyvars.sh
   # ===== Set up TRIQS
-  - git clone https://github.com/TRIQS/triqs --branch $TRAVIS_BRANCH
-  - mkdir triqs/build && cd triqs/build
-  - cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/${CXX} -DBuild_Tests=OFF -DCMAKE_INSTALL_PREFIX=$TRAVIS_BUILD_DIR/root_install -DCMAKE_BUILD_TYPE=Debug
-  - make -j8 install
   - cd $TRAVIS_BUILD_DIR
-  - source root_install/share/triqsvars.sh
+  - git clone https://github.com/TRIQS/triqs --branch unstable
-  # ===== Set up dft_tools and Test using fsanitize=address
+  - mkdir triqs/build && cd triqs/build
+  - cmake .. -DBuild_Tests=OFF -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR
+  - make -j2 install
+  - source $INSTALL_DIR/share/triqsvars.sh
+  # ===== Set up triqs_dft_tools and test
+  - cd $TRAVIS_BUILD_DIR
   - mkdir build && cd build
-  - cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_COMPILER=/usr/bin/${CXX} -DCMAKE_CXX_FLAGS='-fsanitize=address -fno-omit-frame-pointer -fuse-ld=gold'
+  - cmake .. -DASAN=ON -DUBSAN=ON
-  - make -j8
+  - export UBSAN_SYMBOLIZER_PATH=$(which llvm-symbolizer)
-  - export ASAN_SYMBOLIZER_PATH=/usr/lib/llvm-5.0/bin/llvm-symbolizer
+  - export ASAN_SYMBOLIZER_PATH=$(which llvm-symbolizer)
+  - export UBSAN_OPTIONS=symbolize=1:print_stacktrace=1
   - export ASAN_OPTIONS=symbolize=1:detect_leaks=0
   - export CTEST_OUTPUT_ON_FAILURE=1
-  - if [ "$CXX" = g++ ]; then export LD_PRELOAD=/usr/lib/gcc/x86_64-linux-gnu/7/libasan.so; elif [ "$CXX" = clang++ ]; then export LD_PRELOAD=/usr/lib/llvm-5.0/lib/clang/5.0.1/lib/linux/libclang_rt.asan-x86_64.so; fi
+  - make -j2 && make test
-  - cd test && ctest

CMakeLists.txt

@@ -1,105 +1,164 @@
-# Start configuration
+# ##############################################################################
-cmake_minimum_required(VERSION 3.0.2 FATAL_ERROR)
+#
-project(triqs_dft_tools C CXX Fortran)
+# triqs_dft_tools - An example application using triqs and cpp2py
+#
+# Copyright (C) ...
+#
+# triqs_dft_tools is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# triqs_dft_tools is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with
+# triqs_dft_tools (in the file COPYING.txt in this directory). If not, see
+# <http://www.gnu.org/licenses/>.
+#
+# ##############################################################################
+
+cmake_minimum_required(VERSION 3.3.2 FATAL_ERROR)
+cmake_policy(VERSION 3.3.2)
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
 endif()
+if(POLICY CMP0077)
+  cmake_policy(SET CMP0077 NEW)
+endif()
+
+# ############
+# Define Project
+project(triqs_dft_tools VERSION 3.0.0 LANGUAGES C CXX Fortran)
+get_directory_property(IS_SUBPROJECT PARENT_DIRECTORY)
+
+# ############
+# Load TRIQS and CPP2PY
+find_package(TRIQS 3.0 REQUIRED)
+
+# Get the git hash & print status
+triqs_get_git_hash_of_source_dir(PROJECT_GIT_HASH)
+message(STATUS "${PROJECT_NAME} version : ${PROJECT_VERSION}")
+message(STATUS "${PROJECT_NAME} Git hash: ${PROJECT_GIT_HASH}")
+
+# Enforce Consistent Versioning
+if(NOT ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR} VERSION_EQUAL ${TRIQS_VERSION_MAJOR}.${TRIQS_VERSION_MINOR})
+  message(FATAL_ERROR "The ${PROJECT_NAME} version ${PROJECT_VERSION} is not compatible with TRIQS version ${TRIQS_VERSION}.")
+endif()
+
+# Default Install directory to TRIQS_ROOT if not given or invalid.
+if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT OR (NOT IS_ABSOLUTE ${CMAKE_INSTALL_PREFIX}))
+  message(STATUS "No install prefix given (or invalid). Defaulting to TRIQS_ROOT")
+  set(CMAKE_INSTALL_PREFIX ${TRIQS_ROOT} CACHE PATH "default install path" FORCE)
+  set(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT FALSE)
+endif()
+if(NOT IS_SUBPROJECT)
+  message(STATUS "-------- CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX} --------")
+endif()
+set(${PROJECT_NAME}_BINARY_DIR ${PROJECT_BINARY_DIR} CACHE STRING "Binary directory of the ${PROJECT_NAME} Project")
+
+
+# ############
+# Options
+
+# Make additional Find Modules available
+list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/share/cmake/Modules)
 
 # Default to Release build type
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE Release CACHE STRING "Type of build" FORCE)
 endif()
-message( STATUS "-------- BUILD-TYPE: ${CMAKE_BUILD_TYPE} --------")
+if(NOT IS_SUBPROJECT)
-
+  message(STATUS "-------- BUILD-TYPE: ${CMAKE_BUILD_TYPE} --------")
-# Use shared libraries
-set(BUILD_SHARED_LIBS ON)
-
-# Load TRIQS and Cpp2Py
-find_package(TRIQS 2.2 REQUIRED)
-find_package(Cpp2Py 1.6 REQUIRED)
-
-if (NOT ${TRIQS_WITH_PYTHON_SUPPORT})
- MESSAGE(FATAL_ERROR "dft_tools require Python support in TRIQS")
 endif()
 
-# Default Install directory to TRIQS_ROOT if not given. Checks an absolute name is given.
+# Python Support
-if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT OR (NOT IS_ABSOLUTE ${CMAKE_INSTALL_PREFIX}))
+option(PythonSupport "Build with Python support" ON)
-  message(STATUS " No install prefix given (or invalid). Defaulting to TRIQS_ROOT")
+if(PythonSupport AND NOT TRIQS_WITH_PYTHON_SUPPORT)
-  set(CMAKE_INSTALL_PREFIX ${TRIQS_ROOT} CACHE PATH "default install path" FORCE)
+  message(FATAL_ERROR "TRIQS was installed without Python support. Cannot build the Python Interface. Disable the build with -DPythonSupport=OFF")
 endif()
-message(STATUS "-------- CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX} -------------")
 
-# Define the dft_tools version numbers and get the git hash
+# Documentation
-set(DFT_TOOLS_VERSION_MAJOR 2)
+option(Build_Documentation "Build documentation" OFF)
-set(DFT_TOOLS_VERSION_MINOR 2)
-set(DFT_TOOLS_VERSION_PATCH 0)
-set(DFT_TOOLS_VERSION ${DFT_TOOLS_VERSION_MAJOR}.${DFT_TOOLS_VERSION_MINOR}.${DFT_TOOLS_VERSION_PATCH})
-triqs_get_git_hash_of_source_dir(DFT_TOOLS_GIT_HASH)
-message(STATUS "Dft_tools version : ${DFT_TOOLS_VERSION}")
-message(STATUS "Git hash: ${DFT_TOOLS_GIT_HASH}")
 
+# Testing
+option(Build_Tests "Build tests" ON)
+if(Build_Tests)
+  enable_testing()
+endif()
+
+# Export the list of compile-commands into compile_commands.json
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+# Global compiler options
+option(BUILD_SHARED_LIBS "Enable compilation of shared libraries" OFF)
+add_compile_options($<$<CONFIG:Debug>:-ggdb3>)
+
+# Create an Interface target for compiler warnings
+add_library(${PROJECT_NAME}_warnings INTERFACE)
+target_compile_options(${PROJECT_NAME}_warnings
+  INTERFACE
+    -Wall
+    -Wextra
+    -Wpedantic
+    -Wno-sign-compare
+    $<$<CXX_COMPILER_ID:GNU>:-Wshadow=local>
+    $<$<CXX_COMPILER_ID:GNU>:-Wno-attributes>
+    $<$<CXX_COMPILER_ID:Clang>:-Wshadow>
+    $<$<CXX_COMPILER_ID:Clang>:-Wno-gcc-compat>
+    $<$<CXX_COMPILER_ID:AppleClang>:-Wshadow>
+    $<$<CXX_COMPILER_ID:AppleClang>:-Wno-gcc-compat>
+)
+
+# #############
+# Build Project
+
+# Find / Build dependencies
+add_subdirectory(deps)
+
+# Build and install the library
+add_subdirectory(c++/${PROJECT_NAME})
+
+# add here stuff for the Fortran part in DFTTools
 add_subdirectory(fortran/dmftproj) 
 
-# Add the compiling options (-D... ) for C++
+# Tests
-message(STATUS "TRIQS : Adding compilation flags detected by the library (C++11/14, libc++, etc...) ")
+if(Build_Tests)
-
+  add_subdirectory(test)
-add_subdirectory(c++)
-add_subdirectory(python python/triqs_dft_tools)
-add_subdirectory(shells)
-
-#------------------------
-# tests
-#------------------------
-
-option(TEST_COVERAGE "Analyze the coverage of tests" OFF)
-
-# perform tests with coverage info
-if (${TEST_COVERAGE})
-  # we try to locate the coverage program
-  find_program(PYTHON_COVERAGE python-coverage)
-  find_program(PYTHON_COVERAGE coverage)
-  if(NOT PYTHON_COVERAGE)
-      message(FATAL_ERROR "Program coverage (or python-coverage) not found.\nEither set PYTHON_COVERAGE explicitly or disable TEST_COVERAGE!\nYou need to install the python package coverage, e.g. with\n  pip install coverage\nor with\n  apt install python-coverage")
-  endif()
-
-  message(STATUS "Setting up test coverage")
-  add_custom_target(coverage ${PYTHON_COVERAGE} combine --append .coverage plovasp/.coverage || true COMMAND ${PYTHON_COVERAGE} html COMMAND echo "Open ${CMAKE_BINARY_DIR}/test/htmlcov/index.html in browser!" WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/test)
 endif()
 
-enable_testing()
+# Python
-
+if(PythonSupport)
-option(Build_Tests "Build the tests of the library " ON)
+  add_subdirectory(python/${PROJECT_NAME})
-if (Build_Tests)
-  message(STATUS "-------- Preparing tests  -------------")
- add_subdirectory(test)
 endif()
 
-#------------------------
+# Docs
-# Documentation
+if(Build_Documentation)
-#------------------------
-option(Build_Documentation "Build documentation" OFF)
-if(${Build_Documentation})
-  if(NOT ${TRIQS_WITH_DOCUMENTATION})
-    message("Error: TRIQS library has not been compiled with its documentation")
-  endif()
   add_subdirectory(doc)
 endif()
 
-#--------------------------------------------------------
+# dfttols vasp interface bash scripts
-# Packaging
+add_subdirectory(bin)
-#--------------------------------------------------------
+
+# Additional configuration files
+add_subdirectory(share)
+
+# #############
+# Debian Package
+
 option(BUILD_DEBIAN_PACKAGE "Build a deb package" OFF)
-if(BUILD_DEBIAN_PACKAGE)
+if(BUILD_DEBIAN_PACKAGE AND NOT IS_SUBPROJECT)
   if(NOT CMAKE_INSTALL_PREFIX STREQUAL "/usr")
     message(FATAL_ERROR "CMAKE_INSTALL_PREFIX must be /usr for packaging")
   endif()
-  SET(CPACK_GENERATOR "DEB")
+  set(CPACK_PACKAGE_NAME ${PROJECT_NAME})
-  SET(CPACK_PACKAGE_VERSION ${DFT_TOOLS_VERSION})
+  set(CPACK_GENERATOR "DEB")
-  SET(CPACK_PACKAGE_CONTACT "https://github.com/TRIQS/dft_tools")
+  set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
-  EXECUTE_PROCESS(COMMAND dpkg --print-architecture OUTPUT_VARIABLE CMAKE_DEBIAN_PACKAGE_ARCHITECTURE OUTPUT_STRIP_TRAILING_WHITESPACE)
+  set(CPACK_PACKAGE_CONTACT "https://github.com/TRIQS/${PROJECT_NAME}")
-  SET(CPACK_DEBIAN_PACKAGE_DEPENDS "triqs (>= 2.2)")
+  execute_process(COMMAND dpkg --print-architecture OUTPUT_VARIABLE CMAKE_DEBIAN_PACKAGE_ARCHITECTURE OUTPUT_STRIP_TRAILING_WHITESPACE)
-  SET(CPACK_DEBIAN_PACKAGE_CONFLICTS "dft_tools")
+  set(CPACK_DEBIAN_PACKAGE_DEPENDS "triqs (>= 3.0)")
-  SET(CPACK_DEBIAN_PACKAGE_SHLIBDEPS ON)
+  set(CPACK_DEBIAN_PACKAGE_SHLIBDEPS ON)
-  SET(CPACK_DEBIAN_PACKAGE_GENERATE_SHLIBS ON)
+  set(CPACK_DEBIAN_PACKAGE_GENERATE_SHLIBS ON)
-  INCLUDE(CPack)
+  include(CPack)
 endif()

ChangeLog.md

@@ -0,0 +1 @@
+doc/ChangeLog.md

Dockerfile

@@ -1,12 +1,16 @@
 # See ../triqs/packaging for other options
-FROM flatironinstitute/triqs:master-ubuntu-clang
+FROM flatironinstitute/triqs:unstable-ubuntu-clang
+ARG APPNAME=triqs_dft_tools
 
-ARG APPNAME
+COPY requirements.txt /src/$APPNAME/requirements.txt
-COPY . $SRC/$APPNAME
+RUN pip3 install -r /src/$APPNAME/requirements.txt
+
+COPY --chown=build . $SRC/$APPNAME
 WORKDIR $BUILD/$APPNAME
 RUN chown build .
 USER build
 ARG BUILD_DOC=0
-RUN cmake $SRC/$APPNAME -DTRIQS_ROOT=${INSTALL} -DBuild_Documentation=${BUILD_DOC} && make -j2 && make test CTEST_OUTPUT_ON_FAILURE=1
+ARG BUILD_ID
+RUN cmake $SRC/$APPNAME -DTRIQS_ROOT=${INSTALL} -DBuild_Documentation=${BUILD_DOC} -DBuild_Deps=Always && make -j2 || make -j1 VERBOSE=1
 USER root
 RUN make install

Jenkinsfile

@@ -1,5 +1,6 @@
 def projectName = "dft_tools" /* set to app/repo name */
 
+def dockerName = projectName.toLowerCase();
 /* which platform to build documentation on */
 def documentationPlatform = "ubuntu-clang"
 /* depend on triqs upstream branch/project */
@@ -37,7 +38,12 @@ for (int i = 0; i < dockerPlatforms.size(); i++) {
         mv -f Dockerfile.jenkins Dockerfile
       """
       /* build and tag */
-      def img = docker.build("flatironinstitute/${projectName}:${env.BRANCH_NAME}-${env.STAGE_NAME}", "--build-arg APPNAME=${projectName} --build-arg BUILD_DOC=${platform==documentationPlatform} .")
+      def img = docker.build("flatironinstitute/${dockerName}:${env.BRANCH_NAME}-${env.STAGE_NAME}", "--build-arg APPNAME=${projectName} --build-arg BUILD_DOC=${platform==documentationPlatform} --build-arg BUILD_ID=${env.BUILD_TAG} .")
+      catchError(buildResult: 'UNSTABLE', stageResult: 'UNSTABLE') {
+        img.inside() {
+          sh "make -C \$BUILD/${projectName} test CTEST_OUTPUT_ON_FAILURE=1"
+        }
+      }
       if (!keepInstall) {
         sh "docker rmi --no-prune ${img.imageName()}"
       }
@@ -48,7 +54,7 @@ for (int i = 0; i < dockerPlatforms.size(); i++) {
 /****************** osx builds (on host) */
 def osxPlatforms = [
   ["gcc", ['CC=gcc-9', 'CXX=g++-9', 'FC=gfortran-9']],
-  ["clang", ['CC=$BREW/opt/llvm/bin/clang', 'CXX=$BREW/opt/llvm/bin/clang++', 'CXXFLAGS=-I$BREW/opt/llvm/include', 'LDFLAGS=-L$BREW/opt/llvm/lib', 'FC=gfortran-9']]
+  ["clang", ['CC=$BREW/opt/llvm/bin/clang', 'CXX=$BREW/opt/llvm/bin/clang++', 'FC=gfortran-9', 'CXXFLAGS=-I$BREW/opt/llvm/include', 'LDFLAGS=-L$BREW/opt/llvm/lib']]
 ]
 for (int i = 0; i < osxPlatforms.size(); i++) {
   def platformEnv = osxPlatforms[i]
@@ -58,29 +64,37 @@ for (int i = 0; i < osxPlatforms.size(); i++) {
       def srcDir = pwd()
       def tmpDir = pwd(tmp:true)
       def buildDir = "$tmpDir/build"
+      /* install real branches in a fixed predictable place so apps can find them */
       def installDir = keepInstall ? "${env.HOME}/install/${projectName}/${env.BRANCH_NAME}/${platform}" : "$tmpDir/install"
       def triqsDir = "${env.HOME}/install/triqs/${triqsBranch}/${platform}"
+      def venv = triqsDir
       dir(installDir) {
         deleteDir()
       }
 
       checkout scm
+
+      def hdf5 = "${env.BREW}/opt/hdf5@1.10"
       dir(buildDir) { withEnv(platformEnv[1].collect { it.replace('\$BREW', env.BREW) } + [
-        "PATH=$triqsDir/bin:${env.BREW}/bin:/usr/bin:/bin:/usr/sbin",
+	  "PATH=$venv/bin:${env.BREW}/bin:/usr/bin:/bin:/usr/sbin",
-        "CPLUS_INCLUDE_PATH=$triqsDir/include:${env.BREW}/include",
+	  "HDF5_ROOT=$hdf5",
-        "LIBRARY_PATH=$triqsDir/lib:${env.BREW}/lib",
+          "C_INCLUDE_PATH=$hdf5/include:${env.BREW}/include",
-        "CMAKE_PREFIX_PATH=$triqsDir/lib/cmake/triqs"]) {
+	  "CPLUS_INCLUDE_PATH=$venv/include:$hdf5/include:${env.BREW}/include",
+	  "LIBRARY_PATH=$venv/lib:$hdf5/lib:${env.BREW}/lib",
+          "LD_LIBRARY_PATH=$hdf5/lib",
+          "PYTHONPATH=$installDir/lib/python3.7/site-packages",
+	  "CMAKE_PREFIX_PATH=$venv/lib/cmake/triqs"]) {
         deleteDir()
         /* note: this is installing into the parent (triqs) venv (install dir), which is thus shared among apps and so not be completely safe */
-        sh "pip install -r $srcDir/requirements.txt"
+        sh "pip3 install -U -r $srcDir/requirements.txt"
-        sh "cmake $srcDir -DCMAKE_INSTALL_PREFIX=$installDir -DTRIQS_ROOT=$triqsDir"
+        sh "cmake $srcDir -DCMAKE_INSTALL_PREFIX=$installDir -DTRIQS_ROOT=$triqsDir -DBuild_Deps=Always"
-        sh "make -j3"
+        sh "make -j2"
-        try {
+        catchError(buildResult: 'UNSTABLE', stageResult: 'UNSTABLE') { try {
           sh "make test CTEST_OUTPUT_ON_FAILURE=1"
         } catch (exc) {
           archiveArtifacts(artifacts: 'Testing/Temporary/LastTest.log')
           throw exc
-        }
+        } }
         sh "make install"
       } }
     } }
@@ -95,15 +109,20 @@ try {
     stage("publish") { timeout(time: 5, unit: 'MINUTES') {
       def commit = sh(returnStdout: true, script: "git rev-parse HEAD").trim()
       def release = env.BRANCH_NAME == "master" || env.BRANCH_NAME == "unstable" || sh(returnStdout: true, script: "git describe --exact-match HEAD || true").trim()
-      def workDir = pwd()
+      def workDir = pwd(tmp:true)
       lock('triqs_publish') {
       /* Update documention on gh-pages branch */
       dir("$workDir/gh-pages") {
         def subdir = "${projectName}/${env.BRANCH_NAME}"
         git(url: "ssh://git@github.com/TRIQS/TRIQS.github.io.git", branch: "master", credentialsId: "ssh", changelog: false)
         sh "rm -rf ${subdir}"
-        docker.image("flatironinstitute/${projectName}:${env.BRANCH_NAME}-${documentationPlatform}").inside() {
+        docker.image("flatironinstitute/${dockerName}:${env.BRANCH_NAME}-${documentationPlatform}").inside() {
-          sh "cp -rp \$INSTALL/share/doc/triqs_${projectName} ${subdir}"
+          sh """#!/bin/bash -ex
+            base=\$INSTALL/share/doc
+            dir="${projectName}"
+            [[ -d \$base/triqs_\$dir ]] && dir=triqs_\$dir || [[ -d \$base/\$dir ]]
+            cp -rp \$base/\$dir ${subdir}
+          """
         }
         sh "git add -A ${subdir}"
         sh """

bin/CMakeLists.txt

@@ -1,9 +1,9 @@
 
-configure_file(plovasp.bash.in plovasp)
+configure_file(plovasp.in plovasp)
 install(FILES ${CMAKE_CURRENT_BINARY_DIR}/plovasp DESTINATION bin
         PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
 
-configure_file(vasp_dmft.bash.in vasp_dmft)
+configure_file(vasp_dmft.in vasp_dmft)
 install(FILES ${CMAKE_CURRENT_BINARY_DIR}/vasp_dmft DESTINATION bin
         PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
 

c++/plovasp/atm/.gitignore

@@ -1,5 +0,0 @@
-makefile
-Makefile
-*.so
-*.o
-*.pyc

c++/plovasp/atm/CMakeLists.txt

@@ -1,7 +0,0 @@
-add_library(atm_c dos_tetra3d.hpp dos_tetra3d.cpp argsort.hpp argsort.cpp)
-target_link_libraries(atm_c triqs)
-target_compile_options(atm_c PRIVATE -std=c++17)
-
-install(TARGETS atm_c DESTINATION lib)
-
-add_subdirectory(test)

c++/plovasp/atm/test/CMakeLists.txt

@@ -1,13 +0,0 @@
-enable_testing()
-
-FILE(GLOB TestList RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.cpp)
-FOREACH( TestName1  ${TestList} )
- STRING(REPLACE ".cpp" "" TestName ${TestName1})
- add_executable( ${TestName}  ${TestName}.cpp )
- target_link_libraries( ${TestName} atm_c triqs)
- triqs_set_rpath_for_target( ${TestName} )
- add_test(NAME ${TestName} COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${t})
-ENDFOREACH( TestName1  ${TestList} )
-
-
-

c++/triqs_dft_tools/CMakeLists.txt

@@ -0,0 +1,81 @@
+file(GLOB_RECURSE sources *.cpp)
+add_library(${PROJECT_NAME}_c ${sources})
+add_library(${PROJECT_NAME}::${PROJECT_NAME}_c ALIAS ${PROJECT_NAME}_c)
+
+# Link against triqs and enable warnings
+target_link_libraries(${PROJECT_NAME}_c PUBLIC triqs PRIVATE $<BUILD_INTERFACE:${PROJECT_NAME}_warnings>)
+
+# Configure target and compilation
+set_property(TARGET ${PROJECT_NAME}_c PROPERTY POSITION_INDEPENDENT_CODE ON)
+target_include_directories(${PROJECT_NAME}_c PUBLIC $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/c++>)
+target_include_directories(${PROJECT_NAME}_c SYSTEM INTERFACE $<INSTALL_INTERFACE:${CMAKE_INSTALL_PREFIX}/include>)
+target_compile_definitions(${PROJECT_NAME}_c PUBLIC
+				TRIQS_DFT_TOOLS_GIT_HASH=${PROJECT_GIT_HASH}
+				TRIQS_GIT_HASH=${TRIQS_GIT_HASH}
+				$<$<CONFIG:Debug>:TRIQS_DFT_TOOLS_DEBUG>
+				$<$<CONFIG:Debug>:TRIQS_DEBUG>
+				$<$<CONFIG:Debug>:TRIQS_ARRAYS_ENFORCE_BOUNDCHECK>
+			  )
+
+# Install library and headers
+install(TARGETS ${PROJECT_NAME}_c EXPORT ${PROJECT_NAME}-targets DESTINATION lib)
+install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} DESTINATION include FILES_MATCHING PATTERN "*.hpp" PATTERN "*.h")
+
+
+# ========= Static Analyzer Checks ==========
+
+option(ANALYZE_SOURCES OFF "Run static analyzer checks if found (clang-tidy, cppcheck)")
+if(ANALYZE_SOURCES)
+
+  # Locate static analyzer tools
+  find_program(CPPCHECK_EXECUTABLE NAMES "cppcheck" PATHS ENV PATH)
+  find_program(CLANG_TIDY_EXECUTABLE NAMES "clang-tidy" PATHS ENV PATH)
+
+  # Run clang-tidy if found
+  if(CLANG_TIDY_EXECUTABLE)
+    message(STATUS "clang-tidy found: ${CLANG_TIDY_EXECUTABLE}")
+    set_target_properties(${PROJECT_NAME}_c PROPERTIES CXX_CLANG_TIDY "${CLANG_TIDY_EXECUTABLE}")
+  else()
+    message(STATUS "clang-tidy not found in $PATH. Please consider installing clang-tidy for additional checks!")
+  endif()
+
+  # Run cppcheck if found
+  if(CPPCHECK_EXECUTABLE)
+    message(STATUS "cppcheck found: ${CPPCHECK_EXECUTABLE}")
+    add_custom_command(
+	TARGET ${PROJECT_NAME}_c
+	COMMAND ${CPPCHECK_EXECUTABLE}
+	  --enable=warning,style,performance,portability
+	  --std=c++17
+	  --template=gcc
+	  --verbose
+	  --force
+	  --quiet
+          ${sources}
+	WORKING_DIRECTORY
+	  ${CMAKE_CURRENT_SOURCE_DIR}
+    )
+  else()
+    message(STATUS "cppcheck not found in $PATH. Please consider installing cppcheck for additional checks!")
+  endif()
+
+endif()
+
+
+# ========= Dynamic Analyzer Checks ==========
+
+option(ASAN OFF "Compile library and executables with LLVM Address Sanitizer")
+option(UBSAN OFF "Compile library and executables with LLVM Undefined Behavior Sanitizer")
+
+if(ASAN)
+  if(NOT TARGET asan)
+    find_package(sanitizer REQUIRED "asan")
+  endif()
+  target_link_libraries(${PROJECT_NAME}_c PUBLIC $<BUILD_INTERFACE:asan>)
+endif()
+if(UBSAN)
+  if(NOT TARGET ubsan)
+    find_package(sanitizer REQUIRED "ubsan")
+  endif()
+  target_link_libraries(${PROJECT_NAME}_c PUBLIC $<BUILD_INTERFACE:ubsan>)
+endif()

c++/triqs_dft_tools/converters/vasp.hpp

@@ -0,0 +1,3 @@
+#pragma once
+#include "./vasp/argsort.hpp"
+#include "./vasp/dos_tetra3d.hpp"

c++/triqs_dft_tools/converters/vasp/dos_tetra3d.hpp

@@ -22,16 +22,14 @@
 
 #include <triqs/arrays.hpp>
 
-using triqs::arrays::array;
-using triqs::arrays::array_view;
 
 /// DOS of a band by analytical tetrahedron method
 ///
 ///   Returns corner weights for all tetrahedra for a given band and real energy.
-array<double, 2>
+triqs::arrays::array<double, 2>
-dos_tetra_weights_3d(array_view<double, 1> eigk, /// Band energies for each k-point
+dos_tetra_weights_3d(triqs::arrays::array_view<double, 1> eigk, /// Band energies for each k-point
                      double en, /// Energy at which DOS weights are to be calculated
-                     array_view<long, 2> itt /// Tetrahedra defined by k-point indices
+                     triqs::arrays::array_view<long, 2> itt /// Tetrahedra defined by k-point indices
 );
 //array<double, 2> 
 //dos_tetra_weights_3d(array<double, 1> eigk, /// Band energies for each k-point

c++/triqs_dft_tools/triqs_dft_tools.hpp

@@ -0,0 +1,3 @@
+#pragma once
+#include "./converters/vasp.hpp"
+

cmake/sitecustomize.py

@@ -1,8 +0,0 @@
-def application_pytriqs_import(name,*args,**kwargs):
-  if name.startswith('@package_name@'):
-    name = name[len('@package_name@')+1:]
-  return builtin_import(name,*args,**kwargs)
-
-import __builtin__
-__builtin__.__import__, builtin_import = application_pytriqs_import, __builtin__.__import__
-

deps/.gitignore

@@ -0,0 +1 @@
+*

deps/CMakeLists.txt

@@ -0,0 +1,66 @@
+include(external_dependency.cmake)
+
+# Add your dependencies with the function
+#
+#   external_dependency(name
+#       [VERSION <version-number>]
+#       [GIT_REPO <url>]
+#       [GIT_TAG <tag>]
+#       [BUILD_ALWAYS]
+#       [EXCLUDE_FROM_ALL]
+#   )
+#
+# Resolve the dependency using the following steps in order.
+# If a step was successful, skip the remaining ones.
+#
+#  1. Use find_package(name [<version-number>])
+#     to locate the package in the system.
+#     Skip this step if Build_Deps option is set.
+#  2. Try to find a directory containing the sources
+#     at ${PROJECT_SOURCE_DIR}/deps/name. If found
+#     build it as a cmake sub-project.
+#  3. If GIT_REPO is provided, git clone the sources,
+#     and build them as a cmake sub-project.
+#
+# Addtional options:
+#
+#  GIT_TAG - Use this keyword to specify the git-tag, branch or commit hash
+#
+#  BUILD_ALWAYS - If set, this dependency will always be built from source
+#                 and will never be searched in the system.
+#
+#  EXCLUDE_FROM_ALL - If set, targets of the dependency cmake subproject
+#                     will not be included in the ALL target of the project.
+#                     In particular the dependency will not be installed.
+
+if(NOT DEFINED Build_Deps)
+  set(Build_Deps "Never" CACHE STRING "Do we build dependencies from source? [Never/Always/IfNotFound]")
+else()
+  set(Build_Deps_Opts "Never" "Always" "IfNotFound")
+  if(NOT ${Build_Deps} IN_LIST Build_Deps_Opts)
+    message(FATAL_ERROR "Build_Deps option should be either 'Never', 'Always' or 'IfNotFound'")
+  endif()
+  set(Build_Deps ${Build_Deps} CACHE STRING "Do we build dependencies from source? [Never/Always/IfNotFound]")
+  if(NOT IS_SUBPROJECT AND NOT Build_Deps STREQUAL "Always" AND (ASAN OR UBSAN))
+    message(WARNING "For builds with llvm sanitizers (ASAN/UBSAN) it is recommended to use -DBuild_Deps=Always to avoid false positives.")
+  endif()
+endif()
+
+# -- Cpp2Py --
+if(PythonSupport OR Build_Documentation)
+  external_dependency(Cpp2Py
+    GIT_REPO https://github.com/TRIQS/cpp2py
+    VERSION 2.0
+    GIT_TAG master
+    BUILD_ALWAYS
+    EXCLUDE_FROM_ALL
+  )
+endif()
+
+# -- GTest --
+external_dependency(GTest
+  GIT_REPO https://github.com/google/googletest
+  GIT_TAG release-1.10.0
+  BUILD_ALWAYS
+  EXCLUDE_FROM_ALL
+)

deps/external_dependency.cmake

@@ -0,0 +1,70 @@
+###################################################################################
+#
+# TRIQS_DFT_TOOLS: a Toolbox for Research in Interacting Quantum Systems
+#
+# Copyright (C) 2020 Simons Foundation
+#    authors: N. Wentzell
+#
+# TRIQS_DFT_TOOLS is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# TRIQS_DFT_TOOLS is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License along with
+# TRIQS_DFT_TOOLS. If not, see <http://www.gnu.org/licenses/>.
+#
+###################################################################################
+
+function(external_dependency)
+  cmake_parse_arguments(ARG "EXCLUDE_FROM_ALL;BUILD_ALWAYS" "VERSION;GIT_REPO;GIT_TAG" "" ${ARGN})
+
+  # -- Was dependency already found?
+  get_property(${ARGV0}_FOUND GLOBAL PROPERTY ${ARGV0}_FOUND)
+  if(${ARGV0}_FOUND)
+    message(STATUS "Dependency ${ARGV0} was already resolved.")
+    return()
+  endif()
+
+  # -- Try to find package in system.
+  if(NOT ARG_BUILD_ALWAYS AND NOT Build_Deps STREQUAL "Always")
+    find_package(${ARGV0} ${ARG_VERSION} QUIET HINTS ${CMAKE_INSTALL_PREFIX})
+    if(${ARGV0}_FOUND)
+      message(STATUS "Found dependency ${ARGV0} in system ${${ARGV0}_ROOT}")
+      return()
+    elseif(Build_Deps STREQUAL "Never")
+      message(FATAL_ERROR "Could not find dependency ${ARGV0} in system. Please install the dependency manually or use -DBuild_Deps=IfNotFound during cmake configuration to automatically build all dependencies that are not found.")
+    endif()
+  endif()
+
+  # -- Build package from source
+  message(STATUS " =============== Configuring Dependency ${ARGV0} =============== ")
+  if(ARG_EXCLUDE_FROM_ALL)
+    set(subdir_opts EXCLUDE_FROM_ALL)
+    set(Build_Tests OFF)
+    set(Build_Documentation OFF)
+  endif()
+  if(IS_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${ARGV0})
+    message(STATUS "Found sources for dependency ${ARGV0} at ${CMAKE_CURRENT_SOURCE_DIR}/${ARGV0}")
+    add_subdirectory(${ARGV0} ${subdir_opts})
+  elseif(ARG_GIT_REPO)
+    set(bin_dir ${CMAKE_CURRENT_BINARY_DIR}/${ARGV0})
+    set(src_dir ${bin_dir}_src)
+    if(NOT IS_DIRECTORY ${src_dir})
+      if(ARG_GIT_TAG)
+	set(clone_opts --branch ${ARG_GIT_TAG} -c advice.detachedHead=false)
+      endif()
+      execute_process(COMMAND git clone ${ARG_GIT_REPO} --depth 1 ${clone_opts} ${src_dir})
+    endif()
+    add_subdirectory(${src_dir} ${bin_dir} ${subdir_opts})
+  else()
+    message(FATAL_ERROR "Could not find or build dependency ${ARGV0}")
+  endif()
+  message(STATUS " =============== End ${ARGV0} Configuration =============== ")
+  set_property(GLOBAL PROPERTY ${ARGV0}_FOUND TRUE)
+
+endfunction()

doc/CMakeLists.txt

@@ -1,23 +1,81 @@
-# generate the conf.py
+# Generate the sphinx config file
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in ${CMAKE_CURRENT_BINARY_DIR}/conf.py @ONLY)
 
+# -----------------------------------------------------------------------------
+# Create an optional target that allows us to regenerate the C++ doc with c++2rst
+# -----------------------------------------------------------------------------
+add_custom_target(${PROJECT_NAME}_docs_cpp2rst)
+include(${PROJECT_SOURCE_DIR}/share/cmake/extract_flags.cmake)
+extract_flags(${PROJECT_NAME}_c BUILD_INTERFACE)
+separate_arguments(${PROJECT_NAME}_c_CXXFLAGS)
+macro(generate_docs header_file)
+  add_custom_command(
+    TARGET ${PROJECT_NAME}_docs_cpp2rst
+    COMMAND rm -rf ${CMAKE_CURRENT_SOURCE_DIR}/cpp2rst_generated
+    COMMAND
+      PYTHONPATH=${CPP2PY_BINARY_DIR}:$ENV{PYTHONPATH}
+      PATH=${CPP2PY_BINARY_DIR}/bin:${CPP2PY_ROOT}/bin:$ENV{PATH}
+      c++2rst
+      ${header_file}
+      -N ${PROJECT_NAME}
+      --output_directory ${CMAKE_CURRENT_SOURCE_DIR}/cpp2rst_generated
+      -I${PROJECT_SOURCE_DIR}/c++
+      --cxxflags="${${PROJECT_NAME}_c_CXXFLAGS}"
+  )
+endmacro(generate_docs)
+
+generate_docs(${PROJECT_SOURCE_DIR}/c++/${PROJECT_NAME}/${PROJECT_NAME}.hpp)
+
+# --------------------------------------------------------
+# Build & Run the C++ doc examples and capture the output
+# --------------------------------------------------------
+
+add_custom_target(${PROJECT_NAME}_docs_example_output)
+file(GLOB_RECURSE ExampleList RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.cpp)
+foreach(example ${ExampleList})
+  get_filename_component(f ${example} NAME_WE)
+  get_filename_component(d ${example} DIRECTORY)
+  add_executable(${PROJECT_NAME}_doc_${f} EXCLUDE_FROM_ALL ${example})
+  set_property(TARGET ${PROJECT_NAME}_doc_${f} PROPERTY RUNTIME_OUTPUT_DIRECTORY ${d})
+  target_link_libraries(${PROJECT_NAME}_doc_${f} triqs)
+  add_custom_command(TARGET ${PROJECT_NAME}_doc_${f}
+   COMMAND ${PROJECT_NAME}_doc_${f} > ${CMAKE_CURRENT_SOURCE_DIR}/${d}/${f}.output 2>/dev/null
+   WORKING_DIRECTORY ${d}
+  )
+  add_dependencies(${PROJECT_NAME}_docs_example_output ${PROJECT_NAME}_doc_${f})
+endforeach()
+
 # ---------------------------------
 # Top Sphinx target
 # ---------------------------------
-# Sources
+if(NOT DEFINED SPHINXBUILD_EXECUTABLE)
-file(GLOB_RECURSE sources *.rst)
+  find_package(Sphinx)
+endif()
 
-# create documentation target
+# Sphinx has internal caching, always run it
-set(sphinx_top ${CMAKE_CURRENT_BINARY_DIR}/html/index.html)
+add_custom_target(${PROJECT_NAME}_docs_sphinx ALL)
-add_custom_command(OUTPUT ${sphinx_top} DEPENDS ${sources}
+add_custom_command(
-  		   COMMAND ${TRIQS_SPHINXBUILD_EXECUTABLE} -c . -j8 -b html ${CMAKE_CURRENT_SOURCE_DIR} html)
+  TARGET ${PROJECT_NAME}_docs_sphinx
-add_custom_target(doc_sphinx ALL DEPENDS ${sphinx_top} ${CMAKE_CURRENT_BINARY_DIR})
+  COMMAND PYTHONPATH=${PROJECT_BINARY_DIR}/python:$ENV{PYTHONPATH} ${SPHINXBUILD_EXECUTABLE} -c . -j8 -b html ${CMAKE_CURRENT_SOURCE_DIR} html
+)
+
+option(Sphinx_Only "When building the documentation, skip the Python Modules and the generation of C++ Api and example outputs" OFF)
+if(NOT Sphinx_Only)
+  # Autodoc usage requires the python modules to be built first
+  get_property(CPP2PY_MODULES_LIST GLOBAL PROPERTY CPP2PY_MODULES_LIST)
+  if(CPP2PY_MODULES_LIST)
+    add_dependencies(${PROJECT_NAME}_docs_sphinx ${CPP2PY_MODULES_LIST})
+  endif()
+
+  # Generation of C++ Api and Example Outputs
+  add_dependencies(${PROJECT_NAME}_docs_sphinx ${PROJECT_NAME}_docs_cpp2rst ${PROJECT_NAME}_docs_example_output)
+endif()
 
 # ---------------------------------
 # Install
 # ---------------------------------
-install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/ COMPONENT documentation DESTINATION share/doc/triqs_dft_tools
+install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/ COMPONENT documentation DESTINATION share/doc/${PROJECT_NAME}
- FILES_MATCHING
+  FILES_MATCHING
- REGEX "\\.(html|pdf|png|gif|jpg|js|xsl|css|py|txt|inv|bib|cfg)$"
+  REGEX "\\.(html|pdf|png|gif|jpg|svg|js|xsl|css|py|txt|inv|bib)$"
- PATTERN "_*"
+  PATTERN "_*"
- )
+)

doc/_templates/sideb.html

@@ -10,5 +10,5 @@
 </p>
 <hr>
 <p>
-<a href="https://github.com/triqs/dft_tools"> <img style="width: 200px; margin: 10px 0 0 5px" src='_static/logo_github.png' alt="Visit the project on GitHub"/> </a>
+<a href="https://github.com/triqs/triqs_dft_tools"> <img style="width: 200px; margin: 10px 0 0 5px" src='_static/logo_github.png' alt="Visit the project on GitHub"/> </a>
 </p>

doc/changelog.rst

@@ -3,6 +3,6 @@
 Changelog
 =========
 
-This document describes the main changes in DFTTools.
+This document describes the main changes in TRIQS_DFT_TOOLS.
 
 .. include:: ChangeLog.md

doc/conf.py.in

@@ -3,34 +3,36 @@
 # TRIQS documentation build configuration file
 
 import sys
-sys.path.insert(0, "@TRIQS_SPHINXEXT_PATH@/numpydoc")
+sys.path.insert(0, "@CMAKE_CURRENT_SOURCE_DIR@/sphinxext")
+sys.path.insert(0, "@CMAKE_CURRENT_SOURCE_DIR@/sphinxext/numpydoc")
 sys.path.insert(0, "@CMAKE_BINARY_DIR@/python")
 
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.mathjax',
               'sphinx.ext.intersphinx',
-              'matplotlib.sphinxext.plot_directive',
               'sphinx.ext.doctest',
               'sphinx.ext.todo',
               'sphinx.ext.viewcode',
               'sphinx.ext.autosummary',
-              'nbsphinx',
-              'numpydoc',
               'sphinx.ext.githubpages',
-              'IPython.sphinxext.ipython_console_highlighting'
+              'sphinx_autorun',
-              ]
+              'matplotlib.sphinxext.plot_directive',
+              'nbsphinx',
+              'IPython.sphinxext.ipython_console_highlighting',
+              'numpydoc']
 
 source_suffix = '.rst'
 
-project = u'TRIQS DFTTools'
+project = '@PROJECT_NAME@'
-copyright = u'2011-2019'
+version = '@PROJECT_VERSION@'
-version = '@DFT_TOOLS_VERSION@'
 
-mathjax_path = "@TRIQS_MATHJAX_PATH@/MathJax.js?config=default"
+copyright = '2011-2020'
-templates_path = ['@CMAKE_SOURCE_DIR@/doc/_templates']
+
+mathjax_path = "https://raw.githubusercontent.com/mathjax/MathJax/2.7.8/MathJax.js"
+templates_path = ['@CMAKE_CURRENT_SOURCE_DIR@/_templates']
 
 html_theme = 'triqs'
-html_theme_path = ['@TRIQS_THEMES_PATH@']
+html_theme_path = ['@CMAKE_CURRENT_SOURCE_DIR@/themes']
 html_show_sphinx = False
 html_context = {'header_title': 'dft tools',
                 'header_subtitle': 'connecting <a class="triqs" style="font-size: 12px" href="http://triqs.github.io/triqs">TRIQS</a> to DFT packages',
@@ -39,9 +41,9 @@ html_context = {'header_title': 'dft tools',
                                  ['Tutorials', 'tutorials'],
                                  ['Issues', 'issues'],
                                  ['About DFTTools', 'about']]}
-html_static_path = ['@CMAKE_SOURCE_DIR@/doc/_static']
+html_static_path = ['@CMAKE_CURRENT_SOURCE_DIR@/_static']
 html_sidebars = {'index': ['sideb.html', 'searchbox.html']}
 
-htmlhelp_basename = 'TRIQSDFTToolsdoc'
+htmlhelp_basename = '@PROJECT_NAME@doc'
 
-intersphinx_mapping = {'python': ('http://docs.python.org/2.7', None), 'triqslibs': ('http://triqs.github.io/triqs/latest', None), 'triqscthyb': ('https://triqs.github.io/cthyb/latest', None)}
+intersphinx_mapping = {'python': ('https://docs.python.org/3.8', None), 'triqslibs': ('https://triqs.github.io/triqs/latest', None), 'triqscthyb': ('https://triqs.github.io/cthyb/latest', None)}

doc/contents.rst

@@ -7,6 +7,7 @@ Table of contents
    index
    install
    documentation
+   tutorials
    issues
    changelog
    about

doc/guide/Sr2RuO4/calculate_dos_wannier_basis.py

@@ -1,4 +1,4 @@
-from triqs_dft_tools.converters.wien2k_converter import Wien2kConverter
+from triqs_dft_tools.converters.wien2k import Wien2kConverter
 from triqs_dft_tools import SumkDFTTools
 
 filename = 'Sr2RuO4'

doc/guide/analysis.rst

@@ -37,7 +37,7 @@ class::
 Note that all routines available in :class:`SumkDFT <dft.sumk_dft.SumkDFT>` are also available here.
 
 If required, we have to load and initialise the real-frequency self energy. Most conveniently,
-you have your self energy already stored as a real-frequency :class:`BlockGf <pytriqs.gf.BlockGf>` object
+you have your self energy already stored as a real-frequency :class:`BlockGf <triqs.gf.BlockGf>` object
 in a hdf5 file::
 
   with HDFArchive('case.h5', 'r') as ar:
@@ -45,10 +45,10 @@ in a hdf5 file::
 
 You may also have your self energy stored in text files. For this case the :ref:`TRIQS <triqslibs:welcome>` library offers
 the function :meth:`read_gf_from_txt`, which is able to load the data from text files of one Green function block
-into a real-frequency :class:`ReFreqGf <pytriqs.gf.ReFreqGf>` object. Loading each block separately and
+into a real-frequency :class:`ReFreqGf <triqs.gf.ReFreqGf>` object. Loading each block separately and
-building up a :class:´BlockGf <pytriqs.gf.BlockGf>´ is done with::
+building up a :class:´BlockGf <triqs.gf.BlockGf>´ is done with::
 
-  from pytriqs.gf.tools import *
+  from triqs.gf.tools import *
   # get block names
   n_list = [n for n,nl in SK.gf_struct_solver[0].iteritems()]
   # load sigma for each block - in this example sigma is composed of 1x1 blocks
@@ -128,7 +128,7 @@ Momentum resolved spectral function (with real-frequency self energy)
 
 Another quantity of interest is the momentum-resolved spectral function, which can directly be compared to ARPES
 experiments. First we have to execute `lapw1`, `lapw2 -almd` and :program:`dmftproj` with the `-band` 
-option and use the :meth:`convert_bands_input <dft.converters.wien2k_converter.Wien2kConverter.convert_bands_input>`
+option and use the :meth:`convert_bands_input <dft.converters.wien2k.Wien2kConverter.convert_bands_input>`
 routine, which converts the required files (for a more detailed description see :ref:`conversion`). The spectral function is then calculated by typing::
 
   SK.spaghettis(broadening=0.01,plot_shift=0.0,plot_range=None,ishell=None,save_to_file='Akw_')

doc/guide/blockstructure.rst

@@ -21,7 +21,7 @@ We can create a simple :class:`BlockStructure <dft.block_structure.BlockStructur
 
 This creates a block structure with one 3x3 block named *up*. Note that we have not created any Green's function yet; this is just the structure of those objects. If you want to create a Green's function with this structure, you can do (we will if with some content also)::
 
-    from pytriqs.gf import *
+    from triqs.gf import *
     GF_sumk = BS.create_gf(space='sumk', beta = 40, n_points = 1000)
     GF_sumk['up'][0,0] << iOmega_n - 2.0
     GF_sumk['up'][1,1] << iOmega_n + 0.5

doc/guide/conv_generalhk.rst

@@ -87,7 +87,7 @@ matrix of the imaginary part, and then move on to the next :math:`\mathbf{k}`-po
 
 The converter itself is used as::
 
-  from triqs_dft_tools.converters.hk_converter import *
+  from triqs_dft_tools.converters.hk import *
   Converter = HkConverter(filename = hkinputfile)
   Converter.convert_dft_input()
 

doc/guide/conv_vasp.rst

@@ -183,7 +183,7 @@ Running the VASP converter
 
 The actual conversion to a h5-file is performed with the orthonormalized projector functions readable by the :ref:`VaspConverter<refVASPconverter>` in the same fashion as with the other `DFTTools` converters::
 
-    from triqs_dft_tools.converters.vasp_converter import *
+    from triqs_dft_tools.converters.vasp import *
     Converter = VaspConverter(filename = 'vasp')
     Converter.convert_dft_input()
 

doc/guide/conv_wien2k.rst

@@ -94,9 +94,9 @@ directory name):
 
 Now we convert these files into an hdf5 file that can be used for the
 DMFT calculations. For this purpose we
-use the python module :class:`Wien2kConverter <dft.converters.wien2k_converter.Wien2kConverter>`. It is initialized as::
+use the python module :class:`Wien2kConverter <dft.converters.wien2k.Wien2kConverter>`. It is initialized as::
 
-  from triqs_dft_tools.converters.wien2k_converter import *
+  from triqs_dft_tools.converters.wien2k import *
   Converter = Wien2kConverter(filename = case)
 
 The only necessary parameter to this construction is the parameter `filename`.

doc/guide/dftdmft_singleshot.rst

@@ -80,8 +80,8 @@ for :emphasis:`use_dc_formula` are:
 
 At the end of the calculation, we can save the Green function and self energy into a file::
 
-    from pytriqs.archive import HDFArchive
+    from h5 import HDFArchive
-    import pytriqs.utility.mpi as mpi
+    import triqs.utility.mpi as mpi
     if mpi.is_master_node():
         ar = HDFArchive("YourDFTDMFTcalculation.h5",'w')
         ar["G"] = S.G_iw

doc/guide/transport.rst

@@ -52,13 +52,13 @@ real-frequency self energy.
   it is crucial to perform the analytic continuation in such a way that the real-frequency self energy
   is accurate around the Fermi energy as low-energy features strongly influence the final results.
 
-Besides the self energy the Wien2k files read by the transport converter (:meth:`convert_transport_input <dft.converters.wien2k_converter.Wien2kConverter.convert_transport_input>`) are:
+Besides the self energy the Wien2k files read by the transport converter (:meth:`convert_transport_input <dft.converters.wien2k.Wien2kConverter.convert_transport_input>`) are:
    * :file:`.struct`: The lattice constants specified in the struct file are used to calculate the unit cell volume.
    * :file:`.outputs`: In this file the k-point symmetries are given.
    * :file:`.oubwin`: Contains the indices of the bands within the projected subspace (written by :program:`dmftproj`) for each k-point.
    * :file:`.pmat`: This file is the output of the Wien2k optics package and contains the velocity (momentum) matrix elements between all bands in the desired energy
      window for each k-point. How to use the optics package is described below.
-   * :file:`.h5`: The hdf5 archive has to be present and should contain the dft_input subgroup. Otherwise :meth:`convert_dft_input <dft.converters.wien2k_converter.Wien2kConverter.convert_dft_input>` needs to be called before :meth:`convert_transport_input <dft.converters.wien2k_converter.Wien2kConverter.convert_transport_input>`.
+   * :file:`.h5`: The hdf5 archive has to be present and should contain the dft_input subgroup. Otherwise :meth:`convert_dft_input <dft.converters.wien2k.Wien2kConverter.convert_dft_input>` needs to be called before :meth:`convert_transport_input <dft.converters.wien2k.Wien2kConverter.convert_transport_input>`.
 
 
 Wien2k optics package
@@ -84,7 +84,7 @@ Using the transport code
 
 First we have to read the Wien2k files and store the relevant information in the hdf5 archive::
 
-    from triqs_dft_tools.converters.wien2k_converter import *
+    from triqs_dft_tools.converters.wien2k import *
     from triqs_dft_tools.sumk_dft_tools import *
 
     Converter = Wien2kConverter(filename='case', repacking=True)
@@ -92,7 +92,7 @@ First we have to read the Wien2k files and store the relevant information in the
 
     SK = SumkDFTTools(hdf_file='case.h5', use_dft_blocks=True)
 
-The converter :meth:`convert_transport_input <dft.converters.wien2k_converter.Wien2kConverter.convert_transport_input>`
+The converter :meth:`convert_transport_input <dft.converters.wien2k.Wien2kConverter.convert_transport_input>`
 reads the required data of the Wien2k output and stores it in the `dft_transp_input` subgroup of your hdf file. 
 Additionally we need to read and set the self energy, the chemical potential and the double counting::
 

doc/install.rst

@@ -37,34 +37,41 @@ Compiling DFTTools from source
 Prerequisites
 -------------
 
-#. The :ref:`TRIQS <triqslibs:welcome>` toolbox. 
+#. The :ref:`TRIQS <triqslibs:welcome>` library, see :ref:`TRIQS installation instruction <triqslibs:installation>`.
-
+   In the following, we assume that TRIQS is installed in the directory ``path_to_triqs``.
 #. Likely, you will also need at least one impurity solver, e.g. the :ref:`CTHYB solver <triqscthyb:welcome>`.
 
-Installation steps 
+Installation steps
 ------------------
 
-#. Download the source code by cloning the ``TRIQS/dft_tools`` repository from GitHub::
+#. Download the source code of the latest stable version by cloning the ``TRIQS/dft_tools`` repository from GitHub::
- 
+
-     $ git clone https://github.com/TRIQS/dft_tools.git dft_tools.src
+     $ git clone https://github.com/TRIQS/dft_tools dft_tools.src
- 
+
+#. Make sure that all additional dependencies are installed on your system and available in your environment.
+   Alternatively build the dependencies from source instead with::
+
+     $ (cd deps && ./download.sh)
+
+   In this case they will be installed together with your application.
+
 #. Create and move to a new directory where you will compile the code::
- 
+
      $ mkdir dft_tools.build && cd dft_tools.build
- 
+
 #. Ensure that your shell contains the TRIQS environment variables by sourcing the ``triqsvars.sh`` file from your TRIQS installation::
 
      $ source path_to_triqs/share/triqsvarsh.sh
-     
+
 #. In the build directory call cmake, including any additional custom CMake options, see below::
 
      $ cmake ../dft_tools.src
- 
+
-#. Compile the code, run the tests and install the application:: 
+#. Compile the code, run the tests and install the application::
- 
+
-     $ make 
+     $ make
-     $ make test 
+     $ make test
-     $ make install 
+     $ make install
 
 
 Installation steps for the use with WIEN2K version 14.2 and older
@@ -114,37 +121,41 @@ Finally, you will have to change the calls to :program:`python_with_DMFT` to
 your :program:`python` installation in the Wien2k :file:`path_to_Wien2k/run*` files.
 
  
-Version compatibility 
+Version compatibility
 ---------------------
- 
+
-Be careful that the version of the TRIQS library and of the :program:`DFTTools` must be
+Keep in mind that the version of ``dft_tools`` must be compatible with your TRIQS library version,
-compatible (more information on the :ref:`TRIQS website <triqslibs:welcome>`. 
+see :ref:`TRIQS website <triqslibs:versions>`.
-If you want to use a version of the :program:`DFTTools` that is not the latest one, go
+In particular the Major and Minor Version numbers have to be the same.
-into the directory with the sources and look at all available versions:: 
+To use a particular version, go into the directory with the sources, and look at all available versions::
- 
+
-     $ cd src && git tag 
+     $ cd dft_tools.src && git tag
- 
+
-Checkout the version of the code that you want, for instance:: 
+Checkout the version of the code that you want::
- 
+
-     $ git co 2.1 
+     $ git checkout 2.1.0
- 
+
-Then follow the steps 2 to 5 described above to compile the code. 
+and follow steps 2 to 4 above to compile the code.
 
 Custom CMake options
 --------------------
 
-Functionality of ``dft_tools`` can be tweaked using extra compile-time options passed to CMake::
+The compilation of ``dft_tools`` can be configured using CMake-options::
 
-    cmake -DOPTION1=value1 -DOPTION2=value2 ... ../dft_tools.src
+    cmake ../dft_tools.src -DOPTION1=value1 -DOPTION2=value2 ...
 
-+---------------------------------------------------------------+-----------------------------------------------+
++-----------------------------------------------------------------+-----------------------------------------------+
-| Options                                                       | Syntax                                        |
+| Options                                                         | Syntax                                        |
-+===============================================================+===============================================+
++=================================================================+===============================================+
-| Disable testing (not recommended)                             | -DBuild_Tests=OFF                             |
+| Specify an installation path other than path_to_triqs           | -DCMAKE_INSTALL_PREFIX=path_to_dft_tools|
-+---------------------------------------------------------------+-----------------------------------------------+
++-----------------------------------------------------------------+-----------------------------------------------+
-| Build the documentation locally                               | -DBuild_Documentation=ON                      |
+| Build in Debugging Mode                                         | -DCMAKE_BUILD_TYPE=Debug                      |
-+---------------------------------------------------------------+-----------------------------------------------+
++-----------------------------------------------------------------+-----------------------------------------------+
-| Check test coverage when testing                              | -DTEST_COVERAGE=ON                            |
+| Disable testing (not recommended)                               | -DBuild_Tests=OFF                             |
-| (run ``make coverage`` to show the results; requires the      |                                               |
++-----------------------------------------------------------------+-----------------------------------------------+
-| python ``coverage`` package)                                  |                                               |
+| Build the documentation                                         | -DBuild_Documentation=ON                      |
-+---------------------------------------------------------------+-----------------------------------------------+
++-----------------------------------------------------------------+-----------------------------------------------+
+| Check test coverage when testing                                | -DTEST_COVERAGE=ON                            |
+| (run ``make coverage`` to show the results; requires the        |                                               |
+| python ``coverage`` package)                                    |                                               |
++-----------------------------------------------------------------+-----------------------------------------------+

doc/issues.rst

@@ -1,13 +1,14 @@
+.. _issues:
 
 Reporting issues
 ================
 
 Please report all problems and bugs directly at the github issue page
-`<https://github.com/TRIQS/dft_tools/issues>`_.  In order to make it easier
+`<https://github.com/TRIQS/dft_tools/issues>`_.  In order to make it easier for us
-for us to solve the issue please follow these guidelines:
+to solve the issue please follow these guidelines:
 
 #. In all cases specify which version of the application you are using. You can
-   find the version number in the file :file:`README.txt` at the root of the
+   find the version number in the file :file:`CMakeLists.txt` at the root of the
    application sources.
 
 #. If you have a problem during the installation, give us information about

doc/reference/converters.rst

@@ -5,20 +5,20 @@ Converters
 
 Wien2k Converter
 ----------------
-.. autoclass:: triqs_dft_tools.converters.wien2k_converter.Wien2kConverter
+.. autoclass:: triqs_dft_tools.converters.wien2k.Wien2kConverter
    :members:
    :special-members:
    :show-inheritance:
 
 H(k) Converter
 --------------
-.. autoclass:: triqs_dft_tools.converters.hk_converter.HkConverter
+.. autoclass:: triqs_dft_tools.converters.hk.HkConverter
    :members:
    :special-members:
 
 Wannier90 Converter
 -------------------
-.. autoclass:: triqs_dft_tools.converters.wannier90_converter.Wannier90Converter
+.. autoclass:: triqs_dft_tools.converters.wannier90.Wannier90Converter
    :members:
    :special-members:
 
@@ -53,7 +53,7 @@ PLOVASP reference, the classes / functions are sorted the way the converter uses
 VASP Converter
 -------------------
 .. _refVASPconverter:
-.. autoclass:: triqs_dft_tools.converters.vasp_converter.VaspConverter
+.. autoclass:: triqs_dft_tools.converters.vasp.VaspConverter
    :members:
    :special-members:
 

doc/sphinxext/numpydoc/apigen.py

@@ -0,0 +1,427 @@
+"""Attempt to generate templates for module reference with Sphinx
+
+XXX - we exclude extension modules
+
+To include extension modules, first identify them as valid in the
+``_uri2path`` method, then handle them in the ``_parse_module`` script.
+
+We get functions and classes by parsing the text of .py files.
+Alternatively we could import the modules for discovery, and we'd have
+to do that for extension modules.  This would involve changing the
+``_parse_module`` method to work via import and introspection, and
+might involve changing ``discover_modules`` (which determines which
+files are modules, and therefore which module URIs will be passed to
+``_parse_module``).
+
+NOTE: this is a modified version of a script originally shipped with the
+PyMVPA project, which we've adapted for NIPY use.  PyMVPA is an MIT-licensed
+project."""
+
+# Stdlib imports
+import os
+import re
+
+# Functions and classes
+class ApiDocWriter:
+    ''' Class for automatic detection and parsing of API docs
+    to Sphinx-parsable reST format'''
+
+    # only separating first two levels
+    rst_section_levels = ['*', '=', '-', '~', '^']
+
+    def __init__(self,
+                 package_name,
+                 rst_extension='.rst',
+                 package_skip_patterns=None,
+                 module_skip_patterns=None,
+                 ):
+        ''' Initialize package for parsing
+
+        Parameters
+        ----------
+        package_name : string
+            Name of the top-level package.  *package_name* must be the
+            name of an importable package
+        rst_extension : string, optional
+            Extension for reST files, default '.rst'
+        package_skip_patterns : None or sequence of {strings, regexps}
+            Sequence of strings giving URIs of packages to be excluded
+            Operates on the package path, starting at (including) the
+            first dot in the package path, after *package_name* - so,
+            if *package_name* is ``sphinx``, then ``sphinx.util`` will
+            result in ``.util`` being passed for earching by these
+            regexps.  If is None, gives default. Default is:
+            ['\.tests$']
+        module_skip_patterns : None or sequence
+            Sequence of strings giving URIs of modules to be excluded
+            Operates on the module name including preceding URI path,
+            back to the first dot after *package_name*.  For example
+            ``sphinx.util.console`` results in the string to search of
+            ``.util.console``
+            If is None, gives default. Default is:
+            ['\.setup$', '\._']
+        '''
+        if package_skip_patterns is None:
+            package_skip_patterns = ['\\.tests$']
+        if module_skip_patterns is None:
+            module_skip_patterns = ['\\.setup$', '\\._']
+        self.package_name = package_name
+        self.rst_extension = rst_extension
+        self.package_skip_patterns = package_skip_patterns
+        self.module_skip_patterns = module_skip_patterns
+
+    def get_package_name(self):
+        return self._package_name
+
+    def set_package_name(self, package_name):
+        ''' Set package_name
+
+        >>> docwriter = ApiDocWriter('sphinx')
+        >>> import sphinx
+        >>> docwriter.root_path == sphinx.__path__[0]
+        True
+        >>> docwriter.package_name = 'docutils'
+        >>> import docutils
+        >>> docwriter.root_path == docutils.__path__[0]
+        True
+        '''
+        # It's also possible to imagine caching the module parsing here
+        self._package_name = package_name
+        self.root_module = __import__(package_name)
+        self.root_path = self.root_module.__path__[0]
+        self.written_modules = None
+
+    package_name = property(get_package_name, set_package_name, None,
+                            'get/set package_name')
+
+    def _get_object_name(self, line):
+        ''' Get second token in line
+        >>> docwriter = ApiDocWriter('sphinx')
+        >>> docwriter._get_object_name("  def func():  ")
+        'func'
+        >>> docwriter._get_object_name("  class Klass:  ")
+        'Klass'
+        >>> docwriter._get_object_name("  class Klass:  ")
+        'Klass'
+        '''
+        name = line.split()[1].split('(')[0].strip()
+        # in case we have classes which are not derived from object
+        # ie. old style classes
+        return name.rstrip(':')
+
+    def _uri2path(self, uri):
+        ''' Convert uri to absolute filepath
+
+        Parameters
+        ----------
+        uri : string
+            URI of python module to return path for
+
+        Returns
+        -------
+        path : None or string
+            Returns None if there is no valid path for this URI
+            Otherwise returns absolute file system path for URI
+
+        Examples
+        --------
+        >>> docwriter = ApiDocWriter('sphinx')
+        >>> import sphinx
+        >>> modpath = sphinx.__path__[0]
+        >>> res = docwriter._uri2path('sphinx.builder')
+        >>> res == os.path.join(modpath, 'builder.py')
+        True
+        >>> res = docwriter._uri2path('sphinx')
+        >>> res == os.path.join(modpath, '__init__.py')
+        True
+        >>> docwriter._uri2path('sphinx.does_not_exist')
+
+        '''
+        if uri == self.package_name:
+            return os.path.join(self.root_path, '__init__.py')
+        path = uri.replace('.', os.path.sep)
+        path = path.replace(self.package_name + os.path.sep, '')
+        path = os.path.join(self.root_path, path)
+        # XXX maybe check for extensions as well?
+        if os.path.exists(path + '.py'): # file
+            path += '.py'
+        elif os.path.exists(os.path.join(path, '__init__.py')):
+            path = os.path.join(path, '__init__.py')
+        else:
+            return None
+        return path
+
+    def _path2uri(self, dirpath):
+        ''' Convert directory path to uri '''
+        relpath = dirpath.replace(self.root_path, self.package_name)
+        if relpath.startswith(os.path.sep):
+            relpath = relpath[1:]
+        return relpath.replace(os.path.sep, '.')
+
+    def _parse_module(self, uri):
+        ''' Parse module defined in *uri* '''
+        filename = self._uri2path(uri)
+        if filename is None:
+            # nothing that we could handle here.
+            return ([],[])
+        f = open(filename, 'rt')
+        functions, classes = self._parse_lines(f)
+        f.close()
+        return functions, classes
+    
+    def _parse_lines(self, linesource):
+        ''' Parse lines of text for functions and classes '''
+        functions = []
+        classes = []
+        for line in linesource:
+            if line.startswith('def ') and line.count('('):
+                # exclude private stuff
+                name = self._get_object_name(line)
+                if not name.startswith('_'):
+                    functions.append(name)
+            elif line.startswith('class '):
+                # exclude private stuff
+                name = self._get_object_name(line)
+                if not name.startswith('_'):
+                    classes.append(name)
+            else:
+                pass
+        functions.sort()
+        classes.sort()
+        return functions, classes
+
+    def generate_api_doc(self, uri):
+        '''Make autodoc documentation template string for a module
+
+        Parameters
+        ----------
+        uri : string
+            python location of module - e.g 'sphinx.builder'
+
+        Returns
+        -------
+        S : string
+            Contents of API doc
+        '''
+        # get the names of all classes and functions
+        functions, classes = self._parse_module(uri)
+        if not len(functions) and not len(classes):
+            print('WARNING: Empty -',uri)  # dbg
+            return ''
+
+        # Make a shorter version of the uri that omits the package name for
+        # titles 
+        uri_short = re.sub(r'^%s\.' % self.package_name,'',uri)
+        
+        ad = '.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n'
+
+        chap_title = uri_short
+        ad += (chap_title+'\n'+ self.rst_section_levels[1] * len(chap_title)
+               + '\n\n')
+
+        # Set the chapter title to read 'module' for all modules except for the
+        # main packages
+        if '.' in uri:
+            title = 'Module: :mod:`' + uri_short + '`'
+        else:
+            title = ':mod:`' + uri_short + '`'
+        ad += title + '\n' + self.rst_section_levels[2] * len(title)
+
+        if len(classes):
+            ad += '\nInheritance diagram for ``%s``:\n\n' % uri
+            ad += '.. inheritance-diagram:: %s \n' % uri
+            ad += '   :parts: 3\n'
+
+        ad += '\n.. automodule:: ' + uri + '\n'
+        ad += '\n.. currentmodule:: ' + uri + '\n'
+        multi_class = len(classes) > 1
+        multi_fx = len(functions) > 1
+        if multi_class:
+            ad += '\n' + 'Classes' + '\n' + \
+                  self.rst_section_levels[2] * 7 + '\n'
+        elif len(classes) and multi_fx:
+            ad += '\n' + 'Class' + '\n' + \
+                  self.rst_section_levels[2] * 5 + '\n'
+        for c in classes:
+            ad += '\n:class:`' + c + '`\n' \
+                  + self.rst_section_levels[multi_class + 2 ] * \
+                  (len(c)+9) + '\n\n'
+            ad += '\n.. autoclass:: ' + c + '\n'
+            # must NOT exclude from index to keep cross-refs working
+            ad += '  :members:\n' \
+                  '  :undoc-members:\n' \
+                  '  :show-inheritance:\n' \
+                  '  :inherited-members:\n' \
+                  '\n' \
+                  '  .. automethod:: __init__\n'
+        if multi_fx:
+            ad += '\n' + 'Functions' + '\n' + \
+                  self.rst_section_levels[2] * 9 + '\n\n'
+        elif len(functions) and multi_class:
+            ad += '\n' + 'Function' + '\n' + \
+                  self.rst_section_levels[2] * 8 + '\n\n'
+        for f in functions:
+            # must NOT exclude from index to keep cross-refs working
+            ad += '\n.. autofunction:: ' + uri + '.' + f + '\n\n'
+        return ad
+
+    def _survives_exclude(self, matchstr, match_type):
+        ''' Returns True if *matchstr* does not match patterns
+
+        ``self.package_name`` removed from front of string if present
+
+        Examples
+        --------
+        >>> dw = ApiDocWriter('sphinx')
+        >>> dw._survives_exclude('sphinx.okpkg', 'package')
+        True
+        >>> dw.package_skip_patterns.append('^\\.badpkg$')
+        >>> dw._survives_exclude('sphinx.badpkg', 'package')
+        False
+        >>> dw._survives_exclude('sphinx.badpkg', 'module')
+        True
+        >>> dw._survives_exclude('sphinx.badmod', 'module')
+        True
+        >>> dw.module_skip_patterns.append('^\\.badmod$')
+        >>> dw._survives_exclude('sphinx.badmod', 'module')
+        False
+        '''
+        if match_type == 'module':
+            patterns = self.module_skip_patterns
+        elif match_type == 'package':
+            patterns = self.package_skip_patterns
+        else:
+            raise ValueError('Cannot interpret match type "%s"' 
+                             % match_type)
+        # Match to URI without package name
+        L = len(self.package_name)
+        if matchstr[:L] == self.package_name:
+            matchstr = matchstr[L:]
+        for pat in patterns:
+            try:
+                pat.search
+            except AttributeError:
+                pat = re.compile(pat)
+            if pat.search(matchstr):
+                return False
+        return True
+
+    def discover_modules(self):
+        ''' Return module sequence discovered from ``self.package_name`` 
+
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        mods : sequence
+            Sequence of module names within ``self.package_name``
+
+        Examples
+        --------
+        >>> dw = ApiDocWriter('sphinx')
+        >>> mods = dw.discover_modules()
+        >>> 'sphinx.util' in mods
+        True
+        >>> dw.package_skip_patterns.append('\.util$')
+        >>> 'sphinx.util' in dw.discover_modules()
+        False
+        >>> 
+        '''
+        modules = [self.package_name]
+        # raw directory parsing
+        for dirpath, dirnames, filenames in os.walk(self.root_path):
+            # Check directory names for packages
+            root_uri = self._path2uri(os.path.join(self.root_path,
+                                                   dirpath))
+            for dirname in dirnames[:]: # copy list - we modify inplace
+                package_uri = '.'.join((root_uri, dirname))
+                if (self._uri2path(package_uri) and
+                    self._survives_exclude(package_uri, 'package')):
+                    modules.append(package_uri)
+                else:
+                    dirnames.remove(dirname)
+            # Check filenames for modules
+            for filename in filenames:
+                module_name = filename[:-3]
+                module_uri = '.'.join((root_uri, module_name))
+                if (self._uri2path(module_uri) and
+                    self._survives_exclude(module_uri, 'module')):
+                    modules.append(module_uri)
+        return sorted(modules)
+    
+    def write_modules_api(self, modules,outdir):
+        # write the list
+        written_modules = []
+        for m in modules:
+            api_str = self.generate_api_doc(m)
+            if not api_str:
+                continue
+            # write out to file
+            outfile = os.path.join(outdir,
+                                   m + self.rst_extension)
+            fileobj = open(outfile, 'wt')
+            fileobj.write(api_str)
+            fileobj.close()
+            written_modules.append(m)
+        self.written_modules = written_modules
+
+    def write_api_docs(self, outdir):
+        """Generate API reST files.
+
+        Parameters
+        ----------
+        outdir : string
+            Directory name in which to store files
+            We create automatic filenames for each module
+            
+        Returns
+        -------
+        None
+
+        Notes
+        -----
+        Sets self.written_modules to list of written modules
+        """
+        if not os.path.exists(outdir):
+            os.mkdir(outdir)
+        # compose list of modules
+        modules = self.discover_modules()
+        self.write_modules_api(modules,outdir)
+        
+    def write_index(self, outdir, froot='gen', relative_to=None):
+        """Make a reST API index file from written files
+
+        Parameters
+        ----------
+        path : string
+            Filename to write index to
+        outdir : string
+            Directory to which to write generated index file
+        froot : string, optional
+            root (filename without extension) of filename to write to
+            Defaults to 'gen'.  We add ``self.rst_extension``.
+        relative_to : string
+            path to which written filenames are relative.  This
+            component of the written file path will be removed from
+            outdir, in the generated index.  Default is None, meaning,
+            leave path as it is.
+        """
+        if self.written_modules is None:
+            raise ValueError('No modules written')
+        # Get full filename path
+        path = os.path.join(outdir, froot+self.rst_extension)
+        # Path written into index is relative to rootpath
+        if relative_to is not None:
+            relpath = outdir.replace(relative_to + os.path.sep, '')
+        else:
+            relpath = outdir
+        idx = open(path,'wt')
+        w = idx.write
+        w('.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n')
+        w('.. toctree::\n\n')
+        for f in self.written_modules:
+            w('   %s\n' % os.path.join(relpath,f))
+        idx.close()

doc/sphinxext/numpydoc/docscrape.py

@@ -0,0 +1,497 @@
+"""Extract reference documentation from the NumPy source tree.
+
+"""
+
+import inspect
+import textwrap
+import re
+import pydoc
+from io import StringIO
+from warnings import warn
+4
+class Reader:
+    """A line-based string reader.
+
+    """
+    def __init__(self, data):
+        """
+        Parameters
+        ----------
+        data : str
+           String with lines separated by '\n'.
+
+        """
+        if isinstance(data,list):
+            self._str = data
+        else:
+            self._str = data.split('\n') # store string as list of lines
+
+        self.reset()
+
+    def __getitem__(self, n):
+        return self._str[n]
+
+    def reset(self):
+        self._l = 0 # current line nr
+
+    def read(self):
+        if not self.eof():
+            out = self[self._l]
+            self._l += 1
+            return out
+        else:
+            return ''
+
+    def seek_next_non_empty_line(self):
+        for l in self[self._l:]:
+            if l.strip():
+                break
+            else:
+                self._l += 1
+
+    def eof(self):
+        return self._l >= len(self._str)
+
+    def read_to_condition(self, condition_func):
+        start = self._l
+        for line in self[start:]:
+            if condition_func(line):
+                return self[start:self._l]
+            self._l += 1
+            if self.eof():
+                return self[start:self._l+1]
+        return []
+
+    def read_to_next_empty_line(self):
+        self.seek_next_non_empty_line()
+        def is_empty(line):
+            return not line.strip()
+        return self.read_to_condition(is_empty)
+
+    def read_to_next_unindented_line(self):
+        def is_unindented(line):
+            return (line.strip() and (len(line.lstrip()) == len(line)))
+        return self.read_to_condition(is_unindented)
+
+    def peek(self,n=0):
+        if self._l + n < len(self._str):
+            return self[self._l + n]
+        else:
+            return ''
+
+    def is_empty(self):
+        return not ''.join(self._str).strip()
+
+
+class NumpyDocString:
+    def __init__(self,docstring):
+        docstring = textwrap.dedent(docstring).split('\n')
+
+        self._doc = Reader(docstring)
+        self._parsed_data = {
+            'Signature': '',
+            'Summary': [''],
+            'Extended Summary': [],
+            'Parameters': [],
+            'Returns': [],
+            'Raises': [],
+            'Warns': [],
+            'Other Parameters': [],
+            'Attributes': [],
+            'Methods': [],
+            'See Also': [],
+            'Notes': [],
+            'Warnings': [],
+            'References': '',
+            'Examples': '',
+            'index': {}
+            }
+
+        self._parse()
+
+    def __getitem__(self,key):
+        return self._parsed_data[key]
+
+    def __setitem__(self,key,val):
+        if key not in self._parsed_data:
+            warn("Unknown section %s" % key)
+        else:
+            self._parsed_data[key] = val
+
+    def _is_at_section(self):
+        self._doc.seek_next_non_empty_line()
+
+        if self._doc.eof():
+            return False
+
+        l1 = self._doc.peek().strip()  # e.g. Parameters
+
+        if l1.startswith('.. index::'):
+            return True
+
+        l2 = self._doc.peek(1).strip() #    ---------- or ==========
+        return l2.startswith('-'*len(l1)) or l2.startswith('='*len(l1))
+
+    def _strip(self,doc):
+        i = 0
+        j = 0
+        for i,line in enumerate(doc):
+            if line.strip(): break
+
+        for j,line in enumerate(doc[::-1]):
+            if line.strip(): break
+
+        return doc[i:len(doc)-j]
+
+    def _read_to_next_section(self):
+        section = self._doc.read_to_next_empty_line()
+
+        while not self._is_at_section() and not self._doc.eof():
+            if not self._doc.peek(-1).strip(): # previous line was empty
+                section += ['']
+
+            section += self._doc.read_to_next_empty_line()
+
+        return section
+
+    def _read_sections(self):
+        while not self._doc.eof():
+            data = self._read_to_next_section()
+            name = data[0].strip()
+
+            if name.startswith('..'): # index section
+                yield name, data[1:]
+            elif len(data) < 2:
+                yield StopIteration
+            else:
+                yield name, self._strip(data[2:])
+
+    def _parse_param_list(self,content):
+        r = Reader(content)
+        params = []
+        while not r.eof():
+            header = r.read().strip()
+            if ' : ' in header:
+                arg_name, arg_type = header.split(' : ')[:2]
+            else:
+                arg_name, arg_type = header, ''
+
+            desc = r.read_to_next_unindented_line()
+            desc = dedent_lines(desc)
+
+            params.append((arg_name,arg_type,desc))
+
+        return params
+
+    
+    _name_rgx = re.compile(r"^\s*(:(?P<role>\w+):`(?P<name>[a-zA-Z0-9_.-]+)`|"
+                           r" (?P<name2>[a-zA-Z0-9_.-]+))\s*", re.X)
+    def _parse_see_also(self, content):
+        """
+        func_name : Descriptive text
+            continued text
+        another_func_name : Descriptive text
+        func_name1, func_name2, :meth:`func_name`, func_name3
+
+        """
+        items = []
+
+        def parse_item_name(text):
+            """Match ':role:`name`' or 'name'"""
+            m = self._name_rgx.match(text)
+            if m:
+                g = m.groups()
+                if g[1] is None:
+                    return g[3], None
+                else:
+                    return g[2], g[1]
+            raise ValueError("%s is not a item name" % text)
+
+        def push_item(name, rest):
+            if not name:
+                return
+            name, role = parse_item_name(name)
+            items.append((name, list(rest), role))
+            del rest[:]
+
+        current_func = None
+        rest = []
+        
+        for line in content:
+            if not line.strip(): continue
+
+            m = self._name_rgx.match(line)
+            if m and line[m.end():].strip().startswith(':'):
+                push_item(current_func, rest)
+                current_func, line = line[:m.end()], line[m.end():]
+                rest = [line.split(':', 1)[1].strip()]
+                if not rest[0]:
+                    rest = []
+            elif not line.startswith(' '):
+                push_item(current_func, rest)
+                current_func = None
+                if ',' in line:
+                    for func in line.split(','):
+                        push_item(func, [])
+                elif line.strip():
+                    current_func = line
+            elif current_func is not None:
+                rest.append(line.strip())
+        push_item(current_func, rest)
+        return items
+
+    def _parse_index(self, section, content):
+        """
+        .. index: default
+           :refguide: something, else, and more
+
+        """
+        def strip_each_in(lst):
+            return [s.strip() for s in lst]
+
+        out = {}
+        section = section.split('::')
+        if len(section) > 1:
+            out['default'] = strip_each_in(section[1].split(','))[0]
+        for line in content:
+            line = line.split(':')
+            if len(line) > 2:
+                out[line[1]] = strip_each_in(line[2].split(','))
+        return out
+    
+    def _parse_summary(self):
+        """Grab signature (if given) and summary"""
+        if self._is_at_section():
+            return
+
+        summary = self._doc.read_to_next_empty_line()
+        summary_str = " ".join([s.strip() for s in summary]).strip()
+        if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str):
+            self['Signature'] = summary_str
+            if not self._is_at_section():
+                self['Summary'] = self._doc.read_to_next_empty_line()
+        else:
+            self['Summary'] = summary
+
+        if not self._is_at_section():
+            self['Extended Summary'] = self._read_to_next_section()
+    
+    def _parse(self):
+        self._doc.reset()
+        self._parse_summary()
+
+        for (section,content) in self._read_sections():
+            if not section.startswith('..'):
+                section = ' '.join([s.capitalize() for s in section.split(' ')])
+            if section in ('Parameters', 'Attributes', 'Methods',
+                           'Returns', 'Raises', 'Warns'):
+                self[section] = self._parse_param_list(content)
+            elif section.startswith('.. index::'):
+                self['index'] = self._parse_index(section, content)
+            elif section == 'See Also':
+                self['See Also'] = self._parse_see_also(content)
+            else:
+                self[section] = content
+
+    # string conversion routines
+
+    def _str_header(self, name, symbol='-'):
+        return [name, len(name)*symbol]
+
+    def _str_indent(self, doc, indent=4):
+        out = []
+        for line in doc:
+            out += [' '*indent + line]
+        return out
+
+    def _str_signature(self):
+        if self['Signature']:
+            return [self['Signature'].replace('*','\*')] + ['']
+        else:
+            return ['']
+
+    def _str_summary(self):
+        if self['Summary']:
+            return self['Summary'] + ['']
+        else:
+            return []
+
+    def _str_extended_summary(self):
+        if self['Extended Summary']:
+            return self['Extended Summary'] + ['']
+        else:
+            return []
+
+    def _str_param_list(self, name):
+        out = []
+        if self[name]:
+            out += self._str_header(name)
+            for param,param_type,desc in self[name]:
+                out += ['%s : %s' % (param, param_type)]
+                out += self._str_indent(desc)
+            out += ['']
+        return out
+
+    def _str_section(self, name):
+        out = []
+        if self[name]:
+            out += self._str_header(name)
+            out += self[name]
+            out += ['']
+        return out
+
+    def _str_see_also(self, func_role):
+        if not self['See Also']: return []
+        out = []
+        out += self._str_header("See Also")
+        last_had_desc = True
+        for func, desc, role in self['See Also']:
+            if role:
+                link = ':%s:`%s`' % (role, func)
+            elif func_role:
+                link = ':%s:`%s`' % (func_role, func)
+            else:
+                link = "`%s`_" % func
+            if desc or last_had_desc:
+                out += ['']
+                out += [link]
+            else:
+                out[-1] += ", %s" % link
+            if desc:
+                out += self._str_indent([' '.join(desc)])
+                last_had_desc = True
+            else:
+                last_had_desc = False
+        out += ['']
+        return out
+
+    def _str_index(self):
+        idx = self['index']
+        out = []
+        out += ['.. index:: %s' % idx.get('default','')]
+        for section, references in idx.items():
+            if section == 'default':
+                continue
+            out += ['   :%s: %s' % (section, ', '.join(references))]
+        return out
+
+    def __str__(self, func_role=''):
+        out = []
+        out += self._str_signature()
+        out += self._str_summary()
+        out += self._str_extended_summary()
+        for param_list in ('Parameters','Returns','Raises'):
+            out += self._str_param_list(param_list)
+        out += self._str_section('Warnings')
+        out += self._str_see_also(func_role)
+        for s in ('Notes','References','Examples'):
+            out += self._str_section(s)
+        out += self._str_index()
+        return '\n'.join(out)
+
+
+def indent(str,indent=4):
+    indent_str = ' '*indent
+    if str is None:
+        return indent_str
+    lines = str.split('\n')
+    return '\n'.join(indent_str + l for l in lines)
+
+def dedent_lines(lines):
+    """Deindent a list of lines maximally"""
+    return textwrap.dedent("\n".join(lines)).split("\n")
+
+def header(text, style='-'):
+    return text + '\n' + style*len(text) + '\n'
+
+
+class FunctionDoc(NumpyDocString):
+    def __init__(self, func, role='func', doc=None):
+        self._f = func
+        self._role = role # e.g. "func" or "meth"
+        if doc is None:
+            doc = inspect.getdoc(func) or ''
+        try:
+            NumpyDocString.__init__(self, doc)
+        except ValueError as e:
+            print('*'*78)
+            print("ERROR: '%s' while parsing `%s`" % (e, self._f))
+            print('*'*78)
+            #print "Docstring follows:"
+            #print doclines
+            #print '='*78
+
+        if not self['Signature']:
+            func, func_name = self.get_func()
+            try:
+                # try to read signature
+                argspec = inspect.getargspec(func)
+                argspec = inspect.formatargspec(*argspec)
+                argspec = argspec.replace('*','\*')
+                signature = '%s%s' % (func_name, argspec)
+            except TypeError as e:
+                signature = '%s()' % func_name
+            self['Signature'] = signature
+
+    def get_func(self):
+        func_name = getattr(self._f, '__name__', self.__class__.__name__)
+        if inspect.isclass(self._f):
+            func = getattr(self._f, '__call__', self._f.__init__)
+        else:
+            func = self._f
+        return func, func_name
+            
+    def __str__(self):
+        out = ''
+
+        func, func_name = self.get_func()
+        signature = self['Signature'].replace('*', '\*')
+
+        roles = {'func': 'function',
+                 'meth': 'method'}
+
+        if self._role:
+            if self._role not in roles:
+                print("Warning: invalid role %s" % self._role)
+            out += '.. %s:: %s\n    \n\n' % (roles.get(self._role,''),
+                                             func_name)
+
+        out += super(FunctionDoc, self).__str__(func_role=self._role)
+        return out
+
+
+class ClassDoc(NumpyDocString):
+    def __init__(self,cls,modulename='',func_doc=FunctionDoc,doc=None):
+        if not inspect.isclass(cls):
+            raise ValueError("Initialise using a class. Got %r" % cls)
+        self._cls = cls
+
+        if modulename and not modulename.endswith('.'):
+            modulename += '.'
+        self._mod = modulename
+        self._name = cls.__name__
+        self._func_doc = func_doc
+
+        if doc is None:
+            doc = pydoc.getdoc(cls)
+
+        NumpyDocString.__init__(self, doc)
+
+    @property
+    def methods(self):
+        return [name for name,func in inspect.getmembers(self._cls)
+                if not name.startswith('_') and callable(func)]
+
+    def __str__(self):
+        out = ''
+        out += super(ClassDoc, self).__str__()
+        out += "\n\n"
+
+        #for m in self.methods:
+        #    print "Parsing `%s`" % m
+        #    out += str(self._func_doc(getattr(self._cls,m), 'meth')) + '\n\n'
+        #    out += '.. index::\n   single: %s; %s\n\n' % (self._name, m)
+
+        return out
+
+

doc/sphinxext/numpydoc/docscrape_sphinx.py

@@ -0,0 +1,136 @@
+import re, inspect, textwrap, pydoc
+from docscrape import NumpyDocString, FunctionDoc, ClassDoc
+
+class SphinxDocString(NumpyDocString):
+    # string conversion routines
+    def _str_header(self, name, symbol='`'):
+        return ['.. rubric:: ' + name, '']
+
+    def _str_field_list(self, name):
+        return [':' + name + ':']
+
+    def _str_indent(self, doc, indent=4):
+        out = []
+        for line in doc:
+            out += [' '*indent + line]
+        return out
+
+    def _str_signature(self):
+        return ['']
+        if self['Signature']:
+            return ['``%s``' % self['Signature']] + ['']
+        else:
+            return ['']
+
+    def _str_summary(self):
+        return self['Summary'] + ['']
+
+    def _str_extended_summary(self):
+        return self['Extended Summary'] + ['']
+
+    def _str_param_list(self, name):
+        out = []
+        if self[name]:
+            out += self._str_field_list(name)
+            out += ['']
+            for param,param_type,desc in self[name]:
+                out += self._str_indent(['**%s** : %s' % (param.strip(),
+                                                          param_type)])
+                out += ['']
+                out += self._str_indent(desc,8)
+                out += ['']
+        return out
+
+    def _str_section(self, name):
+        out = []
+        if self[name]:
+            out += self._str_header(name)
+            out += ['']
+            content = textwrap.dedent("\n".join(self[name])).split("\n")
+            out += content
+            out += ['']
+        return out
+
+    def _str_see_also(self, func_role):
+        out = []
+        if self['See Also']:
+            see_also = super(SphinxDocString, self)._str_see_also(func_role)
+            out = ['.. seealso::', '']
+            out += self._str_indent(see_also[2:])
+        return out
+
+    def _str_warnings(self):
+        out = []
+        if self['Warnings']:
+            out = ['.. warning::', '']
+            out += self._str_indent(self['Warnings'])
+        return out
+
+    def _str_index(self):
+        idx = self['index']
+        out = []
+        if len(idx) == 0:
+            return out
+
+        out += ['.. index:: %s' % idx.get('default','')]
+        for section, references in idx.items():
+            if section == 'default':
+                continue
+            elif section == 'refguide':
+                out += ['   single: %s' % (', '.join(references))]
+            else:
+                out += ['   %s: %s' % (section, ','.join(references))]
+        return out
+
+    def _str_references(self):
+        out = []
+        if self['References']:
+            out += self._str_header('References')
+            if isinstance(self['References'], str):
+                self['References'] = [self['References']]
+            out.extend(self['References'])
+            out += ['']
+        return out
+
+    def __str__(self, indent=0, func_role="obj"):
+        out = []
+        out += self._str_signature()
+        out += self._str_index() + ['']
+        out += self._str_summary()
+        out += self._str_extended_summary()
+        for param_list in ('Parameters', 'Attributes', 'Methods',
+                           'Returns','Raises'):
+            out += self._str_param_list(param_list)
+        out += self._str_warnings()
+        out += self._str_see_also(func_role)
+        out += self._str_section('Notes')
+        out += self._str_references()
+        out += self._str_section('Examples')
+        out = self._str_indent(out,indent)
+        return '\n'.join(out)
+
+class SphinxFunctionDoc(SphinxDocString, FunctionDoc):
+    pass
+
+class SphinxClassDoc(SphinxDocString, ClassDoc):
+    pass
+
+def get_doc_object(obj, what=None, doc=None):
+    if what is None:
+        if inspect.isclass(obj):
+            what = 'class'
+        elif inspect.ismodule(obj):
+            what = 'module'
+        elif callable(obj):
+            what = 'function'
+        else:
+            what = 'object'
+    if what == 'class':
+        return SphinxClassDoc(obj, '', func_doc=SphinxFunctionDoc, doc=doc)
+    elif what in ('function', 'method'):
+        return SphinxFunctionDoc(obj, '', doc=doc)
+    else:
+        if doc is None:
+            doc = pydoc.getdoc(obj)
+        return SphinxDocString(doc)
+

doc/sphinxext/numpydoc/inheritance_diagram.py

@@ -0,0 +1,407 @@
+"""
+Defines a docutils directive for inserting inheritance diagrams.
+
+Provide the directive with one or more classes or modules (separated
+by whitespace).  For modules, all of the classes in that module will
+be used.
+
+Example::
+
+   Given the following classes:
+
+   class A: pass
+   class B(A): pass
+   class C(A): pass
+   class D(B, C): pass
+   class E(B): pass
+
+   .. inheritance-diagram: D E
+
+   Produces a graph like the following:
+
+               A
+              / \
+             B   C
+            / \ /
+           E   D
+
+The graph is inserted as a PNG+image map into HTML and a PDF in
+LaTeX.
+"""
+
+import inspect
+import os
+import re
+import subprocess
+try:
+    from hashlib import md5
+except ImportError:
+    from md5 import md5
+
+from docutils.nodes import Body, Element
+from docutils.parsers.rst import directives
+from sphinx.roles import xfileref_role
+
+def my_import(name):
+    """Module importer - taken from the python documentation.
+
+    This function allows importing names with dots in them."""
+    
+    mod = __import__(name)
+    components = name.split('.')
+    for comp in components[1:]:
+        mod = getattr(mod, comp)
+    return mod
+
+class DotException(Exception):
+    pass
+
+class InheritanceGraph:
+    """
+    Given a list of classes, determines the set of classes that
+    they inherit from all the way to the root "object", and then
+    is able to generate a graphviz dot graph from them.
+    """
+    def __init__(self, class_names, show_builtins=False):
+        """
+        *class_names* is a list of child classes to show bases from.
+
+        If *show_builtins* is True, then Python builtins will be shown
+        in the graph.
+        """
+        self.class_names = class_names
+        self.classes = self._import_classes(class_names)
+        self.all_classes = self._all_classes(self.classes)
+        if len(self.all_classes) == 0:
+            raise ValueError("No classes found for inheritance diagram")
+        self.show_builtins = show_builtins
+
+    py_sig_re = re.compile(r'''^([\w.]*\.)?    # class names
+                           (\w+)  \s* $        # optionally arguments
+                           ''', re.VERBOSE)
+
+    def _import_class_or_module(self, name):
+        """
+        Import a class using its fully-qualified *name*.
+        """
+        try:
+            path, base = self.py_sig_re.match(name).groups()
+        except:
+            raise ValueError(
+                "Invalid class or module '%s' specified for inheritance diagram" % name)
+        fullname = (path or '') + base
+        path = (path and path.rstrip('.'))
+        if not path:
+            path = base
+        try:
+            module = __import__(path, None, None, [])
+            # We must do an import of the fully qualified name.  Otherwise if a
+            # subpackage 'a.b' is requested where 'import a' does NOT provide
+            # 'a.b' automatically, then 'a.b' will not be found below.  This
+            # second call will force the equivalent of 'import a.b' to happen
+            # after the top-level import above.
+            my_import(fullname)
+            
+        except ImportError:
+            raise ValueError(
+                "Could not import class or module '%s' specified for inheritance diagram" % name)
+
+        try:
+            todoc = module
+            for comp in fullname.split('.')[1:]:
+                todoc = getattr(todoc, comp)
+        except AttributeError:
+            raise ValueError(
+                "Could not find class or module '%s' specified for inheritance diagram" % name)
+
+        # If a class, just return it
+        if inspect.isclass(todoc):
+            return [todoc]
+        elif inspect.ismodule(todoc):
+            classes = []
+            for cls in list(todoc.__dict__.values()):
+                if inspect.isclass(cls) and cls.__module__ == todoc.__name__:
+                    classes.append(cls)
+            return classes
+        raise ValueError(
+            "'%s' does not resolve to a class or module" % name)
+
+    def _import_classes(self, class_names):
+        """
+        Import a list of classes.
+        """
+        classes = []
+        for name in class_names:
+            classes.extend(self._import_class_or_module(name))
+        return classes
+
+    def _all_classes(self, classes):
+        """
+        Return a list of all classes that are ancestors of *classes*.
+        """
+        all_classes = {}
+
+        def recurse(cls):
+            all_classes[cls] = None
+            for c in cls.__bases__:
+                if c not in all_classes:
+                    recurse(c)
+
+        for cls in classes:
+            recurse(cls)
+
+        return list(all_classes.keys())
+
+    def class_name(self, cls, parts=0):
+        """
+        Given a class object, return a fully-qualified name.  This
+        works for things I've tested in matplotlib so far, but may not
+        be completely general.
+        """
+        module = cls.__module__
+        if module == '__builtin__':
+            fullname = cls.__name__
+        else:
+            fullname = "%s.%s" % (module, cls.__name__)
+        if parts == 0:
+            return fullname
+        name_parts = fullname.split('.')
+        return '.'.join(name_parts[-parts:])
+
+    def get_all_class_names(self):
+        """
+        Get all of the class names involved in the graph.
+        """
+        return [self.class_name(x) for x in self.all_classes]
+
+    # These are the default options for graphviz
+    default_graph_options = {
+        "rankdir": "LR",
+        "size": '"8.0, 12.0"'
+        }
+    default_node_options = {
+        "shape": "box",
+        "fontsize": 10,
+        "height": 0.25,
+        "fontname": "Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",
+        "style": '"setlinewidth(0.5)"'
+        }
+    default_edge_options = {
+        "arrowsize": 0.5,
+        "style": '"setlinewidth(0.5)"'
+        }
+
+    def _format_node_options(self, options):
+        return ','.join(["%s=%s" % x for x in list(options.items())])
+    def _format_graph_options(self, options):
+        return ''.join(["%s=%s;\n" % x for x in list(options.items())])
+
+    def generate_dot(self, fd, name, parts=0, urls={},
+                     graph_options={}, node_options={},
+                     edge_options={}):
+        """
+        Generate a graphviz dot graph from the classes that
+        were passed in to __init__.
+
+        *fd* is a Python file-like object to write to.
+
+        *name* is the name of the graph
+
+        *urls* is a dictionary mapping class names to http urls
+
+        *graph_options*, *node_options*, *edge_options* are
+        dictionaries containing key/value pairs to pass on as graphviz
+        properties.
+        """
+        g_options = self.default_graph_options.copy()
+        g_options.update(graph_options)
+        n_options = self.default_node_options.copy()
+        n_options.update(node_options)
+        e_options = self.default_edge_options.copy()
+        e_options.update(edge_options)
+
+        fd.write('digraph %s {\n' % name)
+        fd.write(self._format_graph_options(g_options))
+
+        for cls in self.all_classes:
+            if not self.show_builtins and cls in list(__builtins__.values()):
+                continue
+
+            name = self.class_name(cls, parts)
+
+            # Write the node
+            this_node_options = n_options.copy()
+            url = urls.get(self.class_name(cls))
+            if url is not None:
+                this_node_options['URL'] = '"%s"' % url
+            fd.write('  "%s" [%s];\n' %
+                     (name, self._format_node_options(this_node_options)))
+
+            # Write the edges
+            for base in cls.__bases__:
+                if not self.show_builtins and base in list(__builtins__.values()):
+                    continue
+
+                base_name = self.class_name(base, parts)
+                fd.write('  "%s" -> "%s" [%s];\n' %
+                         (base_name, name,
+                          self._format_node_options(e_options)))
+        fd.write('}\n')
+
+    def run_dot(self, args, name, parts=0, urls={},
+                graph_options={}, node_options={}, edge_options={}):
+        """
+        Run graphviz 'dot' over this graph, returning whatever 'dot'
+        writes to stdout.
+
+        *args* will be passed along as commandline arguments.
+
+        *name* is the name of the graph
+
+        *urls* is a dictionary mapping class names to http urls
+
+        Raises DotException for any of the many os and
+        installation-related errors that may occur.
+        """
+        try:
+            dot = subprocess.Popen(['dot'] + list(args),
+                                   stdin=subprocess.PIPE, stdout=subprocess.PIPE,
+                                   close_fds=True)
+        except OSError:
+            raise DotException("Could not execute 'dot'.  Are you sure you have 'graphviz' installed?")
+        except ValueError:
+            raise DotException("'dot' called with invalid arguments")
+        except:
+            raise DotException("Unexpected error calling 'dot'")
+
+        self.generate_dot(dot.stdin, name, parts, urls, graph_options,
+                          node_options, edge_options)
+        dot.stdin.close()
+        result = dot.stdout.read()
+        returncode = dot.wait()
+        if returncode != 0:
+            raise DotException("'dot' returned the errorcode %d" % returncode)
+        return result
+
+class inheritance_diagram(Body, Element):
+    """
+    A docutils node to use as a placeholder for the inheritance
+    diagram.
+    """
+    pass
+
+def inheritance_diagram_directive(name, arguments, options, content, lineno,
+                                  content_offset, block_text, state,
+                                  state_machine):
+    """
+    Run when the inheritance_diagram directive is first encountered.
+    """
+    node = inheritance_diagram()
+
+    class_names = arguments
+
+    # Create a graph starting with the list of classes
+    graph = InheritanceGraph(class_names)
+
+    # Create xref nodes for each target of the graph's image map and
+    # add them to the doc tree so that Sphinx can resolve the
+    # references to real URLs later.  These nodes will eventually be
+    # removed from the doctree after we're done with them.
+    for name in graph.get_all_class_names():
+        refnodes, x = xfileref_role(
+            'class', ':class:`%s`' % name, name, 0, state)
+        node.extend(refnodes)
+    # Store the graph object so we can use it to generate the
+    # dot file later
+    node['graph'] = graph
+    # Store the original content for use as a hash
+    node['parts'] = options.get('parts', 0)
+    node['content'] = " ".join(class_names)
+    return [node]
+
+def get_graph_hash(node):
+    return md5(node['content'] + str(node['parts'])).hexdigest()[-10:]
+
+def html_output_graph(self, node):
+    """
+    Output the graph for HTML.  This will insert a PNG with clickable
+    image map.
+    """
+    graph = node['graph']
+    parts = node['parts']
+
+    graph_hash = get_graph_hash(node)
+    name = "inheritance%s" % graph_hash
+    path = '_images'
+    dest_path = os.path.join(setup.app.builder.outdir, path)
+    if not os.path.exists(dest_path):
+        os.makedirs(dest_path)
+    png_path = os.path.join(dest_path, name + ".png")
+    path = setup.app.builder.imgpath
+
+    # Create a mapping from fully-qualified class names to URLs.
+    urls = {}
+    for child in node:
+        if child.get('refuri') is not None:
+            urls[child['reftitle']] = child.get('refuri')
+        elif child.get('refid') is not None:
+            urls[child['reftitle']] = '#' + child.get('refid')
+
+    # These arguments to dot will save a PNG file to disk and write
+    # an HTML image map to stdout.
+    image_map = graph.run_dot(['-Tpng', '-o%s' % png_path, '-Tcmapx'],
+                              name, parts, urls)
+    return ('<img src="%s/%s.png" usemap="#%s" class="inheritance"/>%s' %
+            (path, name, name, image_map))
+
+def latex_output_graph(self, node):
+    """
+    Output the graph for LaTeX.  This will insert a PDF.
+    """
+    graph = node['graph']
+    parts = node['parts']
+
+    graph_hash = get_graph_hash(node)
+    name = "inheritance%s" % graph_hash
+    dest_path = os.path.abspath(os.path.join(setup.app.builder.outdir, '_images'))
+    if not os.path.exists(dest_path):
+        os.makedirs(dest_path)
+    pdf_path = os.path.abspath(os.path.join(dest_path, name + ".pdf"))
+
+    graph.run_dot(['-Tpdf', '-o%s' % pdf_path],
+                  name, parts, graph_options={'size': '"6.0,6.0"'})
+    return '\n\\includegraphics{%s}\n\n' % pdf_path
+
+def visit_inheritance_diagram(inner_func):
+    """
+    This is just a wrapper around html/latex_output_graph to make it
+    easier to handle errors and insert warnings.
+    """
+    def visitor(self, node):
+        try:
+            content = inner_func(self, node)
+        except DotException as e:
+            # Insert the exception as a warning in the document
+            warning = self.document.reporter.warning(str(e), line=node.line)
+            warning.parent = node
+            node.children = [warning]
+        else:
+            source = self.document.attributes['source']
+            self.body.append(content)
+            node.children = []
+    return visitor
+
+def do_nothing(self, node):
+    pass
+
+def setup(app):
+    setup.app = app
+    setup.confdir = app.confdir
+
+    app.add_node(
+        inheritance_diagram,
+        latex=(visit_inheritance_diagram(latex_output_graph), do_nothing),
+        html=(visit_inheritance_diagram(html_output_graph), do_nothing))
+    app.add_directive(
+        'inheritance-diagram', inheritance_diagram_directive,
+        False, (1, 100, 0), parts = directives.nonnegative_int)

doc/sphinxext/numpydoc/ipython_console_highlighting.py

@@ -0,0 +1,114 @@
+"""reST directive for syntax-highlighting ipython interactive sessions.
+
+XXX - See what improvements can be made based on the new (as of Sept 2009)
+'pycon' lexer for the python console.  At the very least it will give better
+highlighted tracebacks.
+"""
+
+#-----------------------------------------------------------------------------
+# Needed modules
+
+# Standard library
+import re
+
+# Third party
+from pygments.lexer import Lexer, do_insertions
+from pygments.lexers.agile import (PythonConsoleLexer, PythonLexer, 
+                                   PythonTracebackLexer)
+from pygments.token import Comment, Generic
+
+from sphinx import highlighting
+
+#-----------------------------------------------------------------------------
+# Global constants
+line_re = re.compile('.*?\n')
+
+#-----------------------------------------------------------------------------
+# Code begins - classes and functions
+
+class IPythonConsoleLexer(Lexer):
+    """
+    For IPython console output or doctests, such as:
+
+    .. sourcecode:: ipython
+
+      In [1]: a = 'foo'
+
+      In [2]: a
+      Out[2]: 'foo'
+
+      In [3]: print a
+      foo
+
+      In [4]: 1 / 0
+
+    Notes:
+
+      - Tracebacks are not currently supported.
+
+      - It assumes the default IPython prompts, not customized ones.
+    """
+    
+    name = 'IPython console session'
+    aliases = ['ipython']
+    mimetypes = ['text/x-ipython-console']
+    input_prompt = re.compile("(In \[[0-9]+\]: )|(   \.\.\.+:)")
+    output_prompt = re.compile("(Out\[[0-9]+\]: )|(   \.\.\.+:)")
+    continue_prompt = re.compile("   \.\.\.+:")
+    tb_start = re.compile("\-+")
+
+    def get_tokens_unprocessed(self, text):
+        pylexer = PythonLexer(**self.options)
+        tblexer = PythonTracebackLexer(**self.options)
+
+        curcode = ''
+        insertions = []
+        for match in line_re.finditer(text):
+            line = match.group()
+            input_prompt = self.input_prompt.match(line)
+            continue_prompt = self.continue_prompt.match(line.rstrip())
+            output_prompt = self.output_prompt.match(line)
+            if line.startswith("#"):
+                insertions.append((len(curcode),
+                                   [(0, Comment, line)]))
+            elif input_prompt is not None:
+                insertions.append((len(curcode),
+                                   [(0, Generic.Prompt, input_prompt.group())]))
+                curcode += line[input_prompt.end():]
+            elif continue_prompt is not None:
+                insertions.append((len(curcode),
+                                   [(0, Generic.Prompt, continue_prompt.group())]))
+                curcode += line[continue_prompt.end():]
+            elif output_prompt is not None:
+                # Use the 'error' token for output.  We should probably make
+                # our own token, but error is typicaly in a bright color like
+                # red, so it works fine for our output prompts.
+                insertions.append((len(curcode),
+                                   [(0, Generic.Error, output_prompt.group())]))
+                curcode += line[output_prompt.end():]
+            else:
+                if curcode:
+                    for item in do_insertions(insertions,
+                                              pylexer.get_tokens_unprocessed(curcode)):
+                        yield item
+                        curcode = ''
+                        insertions = []
+                yield match.start(), Generic.Output, line
+        if curcode:
+            for item in do_insertions(insertions,
+                                      pylexer.get_tokens_unprocessed(curcode)):
+                yield item
+
+
+def setup(app):
+    """Setup as a sphinx extension."""
+
+    # This is only a lexer, so adding it below to pygments appears sufficient.
+    # But if somebody knows that the right API usage should be to do that via
+    # sphinx, by all means fix it here.  At least having this setup.py
+    # suppresses the sphinx warning we'd get without it.
+    pass
+
+#-----------------------------------------------------------------------------
+# Register the extension as a valid pygments lexer
+highlighting.lexers['ipython'] = IPythonConsoleLexer()

doc/sphinxext/numpydoc/numpydoc.py

@@ -0,0 +1,116 @@
+"""
+========
+numpydoc
+========
+
+Sphinx extension that handles docstrings in the Numpy standard format. [1]
+
+It will:
+
+- Convert Parameters etc. sections to field lists.
+- Convert See Also section to a See also entry.
+- Renumber references.
+- Extract the signature from the docstring, if it can't be determined otherwise.
+
+.. [1] http://projects.scipy.org/scipy/numpy/wiki/CodingStyleGuidelines#docstring-standard
+
+"""
+
+import os, re, pydoc
+from docscrape_sphinx import get_doc_object, SphinxDocString
+import inspect
+
+def mangle_docstrings(app, what, name, obj, options, lines,
+                      reference_offset=[0]):
+    if what == 'module':
+        # Strip top title
+        title_re = re.compile(r'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*',
+                              re.I|re.S)
+        lines[:] = title_re.sub('', "\n".join(lines)).split("\n")
+    else:
+        doc = get_doc_object(obj, what, "\n".join(lines))
+        lines[:] = str(doc).split("\n")
+
+    if app.config.numpydoc_edit_link and hasattr(obj, '__name__') and \
+           obj.__name__:
+        if hasattr(obj, '__module__'):
+            v = dict(full_name="%s.%s" % (obj.__module__, obj.__name__))
+        else:
+            v = dict(full_name=obj.__name__)
+        lines += ['', '.. htmlonly::', '']
+        lines += ['    %s' % x for x in
+                  (app.config.numpydoc_edit_link % v).split("\n")]
+
+    # replace reference numbers so that there are no duplicates
+    references = []
+    for l in lines:
+        l = l.strip()
+        if l.startswith('.. ['):
+            try:
+                references.append(int(l[len('.. ['):l.index(']')]))
+            except ValueError:
+                print("WARNING: invalid reference in %s docstring" % name)
+
+    # Start renaming from the biggest number, otherwise we may
+    # overwrite references.
+    references.sort()
+    if references:
+        for i, line in enumerate(lines):
+            for r in references:
+                new_r = reference_offset[0] + r
+                lines[i] = lines[i].replace('[%d]_' % r,
+                                            '[%d]_' % new_r)
+                lines[i] = lines[i].replace('.. [%d]' % r,
+                                            '.. [%d]' % new_r)
+
+    reference_offset[0] += len(references)
+
+def mangle_signature(app, what, name, obj, options, sig, retann):
+    # Do not try to inspect classes that don't define `__init__`
+    if (inspect.isclass(obj) and
+        'initializes x; see ' in pydoc.getdoc(obj.__init__)):
+        return '', ''
+
+    if not (callable(obj) or hasattr(obj, '__argspec_is_invalid_')): return
+    if not hasattr(obj, '__doc__'): return
+
+    doc = SphinxDocString(pydoc.getdoc(obj))
+    if doc['Signature']:
+        sig = re.sub("^[^(]*", "", doc['Signature'])
+        return sig, ''
+
+def initialize(app):
+    try:
+        app.connect('autodoc-process-signature', mangle_signature)
+    except:
+        monkeypatch_sphinx_ext_autodoc()
+
+def setup(app, get_doc_object_=get_doc_object):
+    global get_doc_object
+    get_doc_object = get_doc_object_
+    
+    app.connect('autodoc-process-docstring', mangle_docstrings)
+    app.connect('builder-inited', initialize)
+    app.add_config_value('numpydoc_edit_link', None, True)
+
+#------------------------------------------------------------------------------
+# Monkeypatch sphinx.ext.autodoc to accept argspecless autodocs (Sphinx < 0.5)
+#------------------------------------------------------------------------------
+
+def monkeypatch_sphinx_ext_autodoc():
+    global _original_format_signature
+    import sphinx.ext.autodoc
+
+    if sphinx.ext.autodoc.format_signature is our_format_signature:
+        return
+
+    print("[numpydoc] Monkeypatching sphinx.ext.autodoc ...")
+    _original_format_signature = sphinx.ext.autodoc.format_signature
+    sphinx.ext.autodoc.format_signature = our_format_signature
+
+def our_format_signature(what, obj):
+    r = mangle_signature(None, what, None, obj, None, None, None)
+    if r is not None:
+        return r[0]
+    else:
+        return _original_format_signature(what, obj)

doc/sphinxext/numpydoc/plot_directive.py

@@ -0,0 +1,773 @@
+"""
+A directive for including a matplotlib plot in a Sphinx document.
+
+By default, in HTML output, `plot` will include a .png file with a
+link to a high-res .png and .pdf.  In LaTeX output, it will include a
+.pdf.
+
+The source code for the plot may be included in one of three ways:
+
+  1. **A path to a source file** as the argument to the directive::
+
+       .. plot:: path/to/plot.py
+
+     When a path to a source file is given, the content of the
+     directive may optionally contain a caption for the plot::
+
+       .. plot:: path/to/plot.py
+
+          This is the caption for the plot
+
+     Additionally, one my specify the name of a function to call (with
+     no arguments) immediately after importing the module::
+
+       .. plot:: path/to/plot.py plot_function1
+
+  2. Included as **inline content** to the directive::
+
+       .. plot::
+
+          import matplotlib.pyplot as plt
+          import matplotlib.image as mpimg
+          import numpy as np
+          img = mpimg.imread('_static/stinkbug.png')
+          imgplot = plt.imshow(img)
+
+  3. Using **doctest** syntax::
+
+       .. plot::
+          A plotting example:
+          >>> import matplotlib.pyplot as plt
+          >>> plt.plot([1,2,3], [4,5,6])
+
+Options
+-------
+
+The ``plot`` directive supports the following options:
+
+    format : {'python', 'doctest'}
+        Specify the format of the input
+
+    include-source : bool
+        Whether to display the source code. The default can be changed
+        using the `plot_include_source` variable in conf.py
+
+    encoding : str
+        If this source file is in a non-UTF8 or non-ASCII encoding,
+        the encoding must be specified using the `:encoding:` option.
+        The encoding will not be inferred using the ``-*- coding -*-``
+        metacomment.
+
+    context : bool
+        If provided, the code will be run in the context of all
+        previous plot directives for which the `:context:` option was
+        specified.  This only applies to inline code plot directives,
+        not those run from files.
+
+    nofigs : bool
+        If specified, the code block will be run, but no figures will
+        be inserted.  This is usually useful with the ``:context:``
+        option.
+
+Additionally, this directive supports all of the options of the
+`image` directive, except for `target` (since plot will add its own
+target).  These include `alt`, `height`, `width`, `scale`, `align` and
+`class`.
+
+Configuration options
+---------------------
+
+The plot directive has the following configuration options:
+
+    plot_include_source
+        Default value for the include-source option
+
+    plot_pre_code
+        Code that should be executed before each plot.
+
+    plot_basedir
+        Base directory, to which ``plot::`` file names are relative
+        to.  (If None or empty, file names are relative to the
+        directoly where the file containing the directive is.)
+
+    plot_formats
+        File formats to generate. List of tuples or strings::
+
+            [(suffix, dpi), suffix, ...]
+
+        that determine the file format and the DPI. For entries whose
+        DPI was omitted, sensible defaults are chosen.
+
+    plot_html_show_formats
+        Whether to show links to the files in HTML.
+
+    plot_rcparams
+        A dictionary containing any non-standard rcParams that should
+        be applied before each plot.
+
+"""
+
+import sys, os, glob, shutil, imp, warnings, io, re, textwrap, \
+       traceback, exceptions
+
+from docutils.parsers.rst import directives
+from docutils import nodes
+from docutils.parsers.rst.directives.images import Image
+align = Image.align
+import sphinx
+
+sphinx_version = sphinx.__version__.split(".")
+# The split is necessary for sphinx beta versions where the string is
+# '6b1'
+sphinx_version = tuple([int(re.split('[a-z]', x)[0])
+                        for x in sphinx_version[:2]])
+
+try:
+    # Sphinx depends on either Jinja or Jinja2
+    import jinja2
+    def format_template(template, **kw):
+        return jinja2.Template(template).render(**kw)
+except ImportError:
+    import jinja
+    def format_template(template, **kw):
+        return jinja.from_string(template, **kw)
+
+import matplotlib
+import matplotlib.cbook as cbook
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+from matplotlib import _pylab_helpers
+
+__version__ = 2
+
+#------------------------------------------------------------------------------
+# Relative pathnames
+#------------------------------------------------------------------------------
+
+# os.path.relpath is new in Python 2.6
+try:
+    from os.path import relpath
+except ImportError:
+    # Copied from Python 2.7
+    if 'posix' in sys.builtin_module_names:
+        def relpath(path, start=os.path.curdir):
+            """Return a relative version of a path"""
+            from os.path import sep, curdir, join, abspath, commonprefix, \
+                 pardir
+
+            if not path:
+                raise ValueError("no path specified")
+
+            start_list = abspath(start).split(sep)
+            path_list = abspath(path).split(sep)
+
+            # Work out how much of the filepath is shared by start and path.
+            i = len(commonprefix([start_list, path_list]))
+
+            rel_list = [pardir] * (len(start_list)-i) + path_list[i:]
+            if not rel_list:
+                return curdir
+            return join(*rel_list)
+    elif 'nt' in sys.builtin_module_names:
+        def relpath(path, start=os.path.curdir):
+            """Return a relative version of a path"""
+            from os.path import sep, curdir, join, abspath, commonprefix, \
+                 pardir, splitunc
+
+            if not path:
+                raise ValueError("no path specified")
+            start_list = abspath(start).split(sep)
+            path_list = abspath(path).split(sep)
+            if start_list[0].lower() != path_list[0].lower():
+                unc_path, rest = splitunc(path)
+                unc_start, rest = splitunc(start)
+                if bool(unc_path) ^ bool(unc_start):
+                    raise ValueError("Cannot mix UNC and non-UNC paths (%s and %s)"
+                                                                        % (path, start))
+                else:
+                    raise ValueError("path is on drive %s, start on drive %s"
+                                                        % (path_list[0], start_list[0]))
+            # Work out how much of the filepath is shared by start and path.
+            for i in range(min(len(start_list), len(path_list))):
+                if start_list[i].lower() != path_list[i].lower():
+                    break
+            else:
+                i += 1
+
+            rel_list = [pardir] * (len(start_list)-i) + path_list[i:]
+            if not rel_list:
+                return curdir
+            return join(*rel_list)
+    else:
+        raise RuntimeError("Unsupported platform (no relpath available!)")
+
+#------------------------------------------------------------------------------
+# Registration hook
+#------------------------------------------------------------------------------
+
+def plot_directive(name, arguments, options, content, lineno,
+                   content_offset, block_text, state, state_machine):
+    return run(arguments, content, options, state_machine, state, lineno)
+plot_directive.__doc__ = __doc__
+
+def _option_boolean(arg):
+    if not arg or not arg.strip():
+        # no argument given, assume used as a flag
+        return True
+    elif arg.strip().lower() in ('no', '0', 'false'):
+        return False
+    elif arg.strip().lower() in ('yes', '1', 'true'):
+        return True
+    else:
+        raise ValueError('"%s" unknown boolean' % arg)
+
+def _option_format(arg):
+    return directives.choice(arg, ('python', 'doctest'))
+
+def _option_align(arg):
+    return directives.choice(arg, ("top", "middle", "bottom", "left", "center",
+                                   "right"))
+
+def mark_plot_labels(app, document):
+    """
+    To make plots referenceable, we need to move the reference from
+    the "htmlonly" (or "latexonly") node to the actual figure node
+    itself.
+    """
+    for name, explicit in document.nametypes.items():
+        if not explicit:
+            continue
+        labelid = document.nameids[name]
+        if labelid is None:
+            continue
+        node = document.ids[labelid]
+        if node.tagname in ('html_only', 'latex_only'):
+            for n in node:
+                if n.tagname == 'figure':
+                    sectname = name
+                    for c in n:
+                        if c.tagname == 'caption':
+                            sectname = c.astext()
+                            break
+
+                    node['ids'].remove(labelid)
+                    node['names'].remove(name)
+                    n['ids'].append(labelid)
+                    n['names'].append(name)
+                    document.settings.env.labels[name] = \
+                        document.settings.env.docname, labelid, sectname
+                    break
+
+def setup(app):
+    setup.app = app
+    setup.config = app.config
+    setup.confdir = app.confdir
+
+    options = {'alt': directives.unchanged,
+               'height': directives.length_or_unitless,
+               'width': directives.length_or_percentage_or_unitless,
+               'scale': directives.nonnegative_int,
+               'align': _option_align,
+               'class': directives.class_option,
+               'include-source': _option_boolean,
+               'format': _option_format,
+               'context': directives.flag,
+               'nofigs': directives.flag,
+               'encoding': directives.encoding
+               }
+
+    app.add_directive('plot', plot_directive, True, (0, 2, False), **options)
+    app.add_config_value('plot_pre_code', None, True)
+    app.add_config_value('plot_include_source', False, True)
+    app.add_config_value('plot_formats', ['png', 'hires.png', 'pdf'], True)
+    app.add_config_value('plot_basedir', None, True)
+    app.add_config_value('plot_html_show_formats', True, True)
+    app.add_config_value('plot_rcparams', {}, True)
+
+    app.connect('doctree-read', mark_plot_labels)
+
+#------------------------------------------------------------------------------
+# Doctest handling
+#------------------------------------------------------------------------------
+
+def contains_doctest(text):
+    try:
+        # check if it's valid Python as-is
+        compile(text, '<string>', 'exec')
+        return False
+    except SyntaxError:
+        pass
+    r = re.compile(r'^\s*>>>', re.M)
+    m = r.search(text)
+    return bool(m)
+
+def unescape_doctest(text):
+    """
+    Extract code from a piece of text, which contains either Python code
+    or doctests.
+
+    """
+    if not contains_doctest(text):
+        return text
+
+    code = ""
+    for line in text.split("\n"):
+        m = re.match(r'^\s*(>>>|\.\.\.) (.*)$', line)
+        if m:
+            code += m.group(2) + "\n"
+        elif line.strip():
+            code += "# " + line.strip() + "\n"
+        else:
+            code += "\n"
+    return code
+
+def split_code_at_show(text):
+    """
+    Split code at plt.show()
+
+    """
+
+    parts = []
+    is_doctest = contains_doctest(text)
+
+    part = []
+    for line in text.split("\n"):
+        if (not is_doctest and line.strip() == 'plt.show()') or \
+               (is_doctest and line.strip() == '>>> plt.show()'):
+            part.append(line)
+            parts.append("\n".join(part))
+            part = []
+        else:
+            part.append(line)
+    if "\n".join(part).strip():
+        parts.append("\n".join(part))
+    return parts
+
+#------------------------------------------------------------------------------
+# Template
+#------------------------------------------------------------------------------
+
+
+TEMPLATE = """
+{{ source_code }}
+
+{{ only_html }}
+
+   {% if source_link or (html_show_formats and not multi_image) %}
+   (
+   {%- if source_link -%}
+   `Source code <{{ source_link }}>`__
+   {%- endif -%}
+   {%- if html_show_formats and not multi_image -%}
+     {%- for img in images -%}
+       {%- for fmt in img.formats -%}
+         {%- if source_link or not loop.first -%}, {% endif -%}
+         `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__
+       {%- endfor -%}
+     {%- endfor -%}
+   {%- endif -%}
+   )
+   {% endif %}
+
+   {% for img in images %}
+   .. figure:: {{ build_dir }}/{{ img.basename }}.png
+      {%- for option in options %}
+      {{ option }}
+      {% endfor %}
+
+      {% if html_show_formats and multi_image -%}
+        (
+        {%- for fmt in img.formats -%}
+        {%- if not loop.first -%}, {% endif -%}
+        `{{ fmt }} <{{ dest_dir }}/{{ img.basename }}.{{ fmt }}>`__
+        {%- endfor -%}
+        )
+      {%- endif -%}
+
+      {{ caption }}
+   {% endfor %}
+
+{{ only_latex }}
+
+   {% for img in images %}
+   .. image:: {{ build_dir }}/{{ img.basename }}.pdf
+   {% endfor %}
+
+"""
+
+exception_template = """
+.. htmlonly::
+
+   [`source code <%(linkdir)s/%(basename)s.py>`__]
+
+Exception occurred rendering plot.
+
+"""
+
+# the context of the plot for all directives specified with the
+# :context: option
+plot_context = dict()
+
+class ImageFile:
+    def __init__(self, basename, dirname):
+        self.basename = basename
+        self.dirname = dirname
+        self.formats = []
+
+    def filename(self, format):
+        return os.path.join(self.dirname, "%s.%s" % (self.basename, format))
+
+    def filenames(self):
+        return [self.filename(fmt) for fmt in self.formats]
+
+def out_of_date(original, derived):
+    """
+    Returns True if derivative is out-of-date wrt original,
+    both of which are full file paths.
+    """
+    return (not os.path.exists(derived) or
+            (os.path.exists(original) and
+             os.stat(derived).st_mtime < os.stat(original).st_mtime))
+
+class PlotError(RuntimeError):
+    pass
+
+def run_code(code, code_path, ns=None, function_name=None):
+    """
+    Import a Python module from a path, and run the function given by
+    name, if function_name is not None.
+    """
+
+    # Change the working directory to the directory of the example, so
+    # it can get at its data files, if any.  Add its path to sys.path
+    # so it can import any helper modules sitting beside it.
+
+    pwd = os.getcwd()
+    old_sys_path = list(sys.path)
+    if code_path is not None:
+        dirname = os.path.abspath(os.path.dirname(code_path))
+        os.chdir(dirname)
+        sys.path.insert(0, dirname)
+
+    # Redirect stdout
+    stdout = sys.stdout
+    sys.stdout = io.StringIO()
+
+    # Reset sys.argv
+    old_sys_argv = sys.argv
+    sys.argv = [code_path]
+
+    try:
+        try:
+            code = unescape_doctest(code)
+            if ns is None:
+                ns = {}
+            if not ns:
+                if setup.config.plot_pre_code is None:
+                    exec("import numpy as np\nfrom matplotlib import pyplot as plt\n", ns)
+                else:
+                    exec(setup.config.plot_pre_code, ns)
+            if "__main__" in code:
+                exec("__name__ = '__main__'", ns)
+            exec(code, ns)
+            if function_name is not None:
+                exec(function_name + "()", ns)
+        except (Exception, SystemExit) as err:
+            raise PlotError(traceback.format_exc())
+    finally:
+        os.chdir(pwd)
+        sys.argv = old_sys_argv
+        sys.path[:] = old_sys_path
+        sys.stdout = stdout
+    return ns
+
+def clear_state(plot_rcparams):
+    plt.close('all')
+    matplotlib.rc_file_defaults()
+    matplotlib.rcParams.update(plot_rcparams)
+
+def render_figures(code, code_path, output_dir, output_base, context,
+                   function_name, config):
+    """
+    Run a pyplot script and save the low and high res PNGs and a PDF
+    in outdir.
+
+    Save the images under *output_dir* with file names derived from
+    *output_base*
+    """
+    # -- Parse format list
+    default_dpi = {'png': 80, 'hires.png': 200, 'pdf': 200}
+    formats = []
+    plot_formats = config.plot_formats
+    if isinstance(plot_formats, str):
+        plot_formats = eval(plot_formats)
+    for fmt in plot_formats:
+        if isinstance(fmt, str):
+            formats.append((fmt, default_dpi.get(fmt, 80)))
+        elif type(fmt) in (tuple, list) and len(fmt)==2:
+            formats.append((str(fmt[0]), int(fmt[1])))
+        else:
+            raise PlotError('invalid image format "%r" in plot_formats' % fmt)
+
+    # -- Try to determine if all images already exist
+
+    code_pieces = split_code_at_show(code)
+
+    # Look for single-figure output files first
+    # Look for single-figure output files first
+    all_exists = True
+    img = ImageFile(output_base, output_dir)
+    for format, dpi in formats:
+        if out_of_date(code_path, img.filename(format)):
+            all_exists = False
+            break
+        img.formats.append(format)
+
+    if all_exists:
+        return [(code, [img])]
+
+    # Then look for multi-figure output files
+    results = []
+    all_exists = True
+    for i, code_piece in enumerate(code_pieces):
+        images = []
+        for j in range(1000):
+            if len(code_pieces) > 1:
+                img = ImageFile('%s_%02d_%02d' % (output_base, i, j), output_dir)
+            else:
+                img = ImageFile('%s_%02d' % (output_base, j), output_dir)
+            for format, dpi in formats:
+                if out_of_date(code_path, img.filename(format)):
+                    all_exists = False
+                    break
+                img.formats.append(format)
+
+            # assume that if we have one, we have them all
+            if not all_exists:
+                all_exists = (j > 0)
+                break
+            images.append(img)
+        if not all_exists:
+            break
+        results.append((code_piece, images))
+
+    if all_exists:
+        return results
+
+    # We didn't find the files, so build them
+
+    results = []
+    if context:
+        ns = plot_context
+    else:
+        ns = {}
+
+    for i, code_piece in enumerate(code_pieces):
+        if not context:
+            clear_state(config.plot_rcparams)
+        run_code(code_piece, code_path, ns, function_name)
+
+        images = []
+        fig_managers = _pylab_helpers.Gcf.get_all_fig_managers()
+        for j, figman in enumerate(fig_managers):
+            if len(fig_managers) == 1 and len(code_pieces) == 1:
+                img = ImageFile(output_base, output_dir)
+            elif len(code_pieces) == 1:
+                img = ImageFile("%s_%02d" % (output_base, j), output_dir)
+            else:
+                img = ImageFile("%s_%02d_%02d" % (output_base, i, j),
+                                output_dir)
+            images.append(img)
+            for format, dpi in formats:
+                try:
+                    figman.canvas.figure.savefig(img.filename(format), dpi=dpi)
+                except Exception as err:
+                    raise PlotError(traceback.format_exc())
+                img.formats.append(format)
+
+        results.append((code_piece, images))
+
+    if not context:
+        clear_state(config.plot_rcparams)
+
+    return results
+
+def run(arguments, content, options, state_machine, state, lineno):
+    # The user may provide a filename *or* Python code content, but not both
+    if arguments and content:
+        raise RuntimeError("plot:: directive can't have both args and content")
+
+    document = state_machine.document
+    config = document.settings.env.config
+    nofigs = 'nofigs' in options
+
+    options.setdefault('include-source', config.plot_include_source)
+    context = 'context' in options
+
+    rst_file = document.attributes['source']
+    rst_dir = os.path.dirname(rst_file)
+
+    if len(arguments):
+        if not config.plot_basedir:
+            source_file_name = os.path.join(setup.app.builder.srcdir,
+                                            directives.uri(arguments[0]))
+        else:
+            source_file_name = os.path.join(setup.app.builder.srcdir, config.plot_basedir,
+                                            directives.uri(arguments[0]))
+
+        # If there is content, it will be passed as a caption.
+        caption = '\n'.join(content)
+
+        # If the optional function name is provided, use it
+        if len(arguments) == 2:
+            function_name = arguments[1]
+        else:
+            function_name = None
+
+        fd = open(source_file_name, 'r')
+        code = fd.read()
+        fd.close()
+        output_base = os.path.basename(source_file_name)
+    else:
+        source_file_name = rst_file
+        code = textwrap.dedent("\n".join(map(str, content)))
+        counter = document.attributes.get('_plot_counter', 0) + 1
+        document.attributes['_plot_counter'] = counter
+        base, ext = os.path.splitext(os.path.basename(source_file_name))
+        output_base = '%s-%d.py' % (base, counter)
+        function_name = None
+        caption = ''
+
+    base, source_ext = os.path.splitext(output_base)
+    if source_ext in ('.py', '.rst', '.txt'):
+        output_base = base
+    else:
+        source_ext = ''
+
+    # ensure that LaTeX includegraphics doesn't choke in foo.bar.pdf filenames
+    output_base = output_base.replace('.', '-')
+
+    # is it in doctest format?
+    is_doctest = contains_doctest(code)
+    if 'format' in options:
+        if options['format'] == 'python':
+            is_doctest = False
+        else:
+            is_doctest = True
+
+    # determine output directory name fragment
+    source_rel_name = relpath(source_file_name, setup.app.srcdir)
+    source_rel_dir = os.path.dirname(source_rel_name)
+    while source_rel_dir.startswith(os.path.sep):
+        source_rel_dir = source_rel_dir[1:]
+
+    # build_dir: where to place output files (temporarily)
+    build_dir = os.path.join(os.path.dirname(setup.app.doctreedir),
+                             'plot_directive',
+                             source_rel_dir)
+    # get rid of .. in paths, also changes pathsep
+    # see note in Python docs for warning about symbolic links on Windows.
+    # need to compare source and dest paths at end
+    build_dir = os.path.normpath(build_dir)
+
+    if not os.path.exists(build_dir):
+        os.makedirs(build_dir)
+
+    # output_dir: final location in the builder's directory
+    dest_dir = os.path.abspath(os.path.join(setup.app.builder.outdir,
+                                            source_rel_dir))
+    if not os.path.exists(dest_dir):
+        os.makedirs(dest_dir) # no problem here for me, but just use built-ins
+
+    # how to link to files from the RST file
+    dest_dir_link = os.path.join(relpath(setup.app.srcdir, rst_dir),
+                                 source_rel_dir).replace(os.path.sep, '/')
+    build_dir_link = relpath(build_dir, rst_dir).replace(os.path.sep, '/')
+    source_link = dest_dir_link + '/' + output_base + source_ext
+
+    # make figures
+    try:
+        results = render_figures(code, source_file_name, build_dir, output_base,
+                                 context, function_name, config)
+        errors = []
+    except PlotError as err:
+        reporter = state.memo.reporter
+        sm = reporter.system_message(
+            2, "Exception occurred in plotting %s\n from %s:\n%s" % (output_base,
+                                                source_file_name, err),
+            line=lineno)
+        results = [(code, [])]
+        errors = [sm]
+
+    # Properly indent the caption
+    caption = '\n'.join('      ' + line.strip()
+                        for line in caption.split('\n'))
+
+    # generate output restructuredtext
+    total_lines = []
+    for j, (code_piece, images) in enumerate(results):
+        if options['include-source']:
+            if is_doctest:
+                lines = ['']
+                lines += [row.rstrip() for row in code_piece.split('\n')]
+            else:
+                lines = ['.. code-block:: python', '']
+                lines += ['    %s' % row.rstrip()
+                          for row in code_piece.split('\n')]
+            source_code = "\n".join(lines)
+        else:
+            source_code = ""
+
+        if nofigs:
+            images = []
+
+        opts = [':%s: %s' % (key, val) for key, val in list(options.items())
+                if key in ('alt', 'height', 'width', 'scale', 'align', 'class')]
+
+        only_html = ".. only:: html"
+        only_latex = ".. only:: latex"
+
+        if j == 0:
+            src_link = source_link
+        else:
+            src_link = None
+
+        result = format_template(
+            TEMPLATE,
+            dest_dir=dest_dir_link,
+            build_dir=build_dir_link,
+            source_link=src_link,
+            multi_image=len(images) > 1,
+            only_html=only_html,
+            only_latex=only_latex,
+            options=opts,
+            images=images,
+            source_code=source_code,
+            html_show_formats=config.plot_html_show_formats,
+            caption=caption)
+
+        total_lines.extend(result.split("\n"))
+        total_lines.extend("\n")
+
+    if total_lines:
+        state_machine.insert_input(total_lines, source=source_file_name)
+
+    # copy image files to builder's output directory, if necessary
+    if not os.path.exists(dest_dir):
+        cbook.mkdirs(dest_dir)
+
+    for code_piece, images in results:
+        for img in images:
+            for fn in img.filenames():
+                destimg = os.path.join(dest_dir, os.path.basename(fn))
+                if fn != destimg:
+                    shutil.copyfile(fn, destimg)
+
+    # copy script (if necessary)
+    #if source_file_name == rst_file:
+    target_name = os.path.join(dest_dir, output_base + source_ext)
+    f = open(target_name, 'w')
+    f.write(unescape_doctest(code))
+    f.close()
+
+    return errors

doc/sphinxext/sphinx_autorun/__init__.py

@@ -0,0 +1,93 @@
+# -*- coding: utf-8 -*-
+"""
+sphinxcontirb.autorun
+~~~~~~~~~~~~~~~~~~~~~~
+
+Run the code and insert stdout after the code block.
+"""
+import os
+from subprocess import PIPE, Popen
+
+from docutils import nodes
+from docutils.parsers.rst import Directive, directives
+from sphinx.errors import SphinxError
+
+from sphinx_autorun import version
+
+__version__ = version.version
+
+
+class RunBlockError(SphinxError):
+    category = 'runblock error'
+
+
+class AutoRun(object):
+    here = os.path.abspath(__file__)
+    pycon = os.path.join(os.path.dirname(here), 'pycon.py')
+    config = {
+        'pycon': 'python ' + pycon,
+        'pycon_prefix_chars': 4,
+        'pycon_show_source': False,
+        'console': 'bash',
+        'console_prefix_chars': 1,
+    }
+
+    @classmethod
+    def builder_init(cls, app):
+        cls.config.update(app.builder.config.autorun_languages)
+
+
+class RunBlock(Directive):
+    has_content = True
+    required_arguments = 1
+    optional_arguments = 0
+    final_argument_whitespace = False
+    option_spec = {
+        'linenos': directives.flag,
+    }
+
+    def run(self):
+        config = AutoRun.config
+        language = self.arguments[0]
+
+        if language not in config:
+            raise RunBlockError('Unknown language %s' % language)
+
+        # Get configuration values for the language
+        args = config[language].split()
+        input_encoding = config.get(language+'_input_encoding', 'utf8')
+        output_encoding = config.get(language+'_output_encoding', 'utf8')
+        prefix_chars = config.get(language+'_prefix_chars', 0)
+        show_source = config.get(language+'_show_source', True)
+
+        # Build the code text
+        proc = Popen(args, bufsize=1, stdin=PIPE, stdout=PIPE, stderr=PIPE)
+        codelines = (line[prefix_chars:] for line in self.content)
+        code = u'\n'.join(codelines).encode(input_encoding)
+
+        # Run the code
+        stdout, stderr = proc.communicate(code)
+
+        # Process output
+        if stdout:
+            out = stdout.decode(output_encoding)
+        if stderr:
+            out = stderr.decode(output_encoding)
+
+        # Get the original code with prefixes
+        if show_source:
+            code = u'\n'.join(self.content)
+            code_out = u'\n'.join((code, out))
+        else:
+            code_out = out
+
+        literal = nodes.literal_block(code_out, code_out)
+        literal['language'] = language
+        literal['linenos'] = 'linenos' in self.options
+        return [literal]
+
+
+def setup(app):
+    app.add_directive('runblock', RunBlock)
+    app.connect('builder-inited', AutoRun.builder_init)
+    app.add_config_value('autorun_languages', AutoRun.config, 'env')

doc/sphinxext/sphinx_autorun/pycon.py

@@ -0,0 +1,31 @@
+import sys
+from code import InteractiveInterpreter
+
+
+def main():
+    """
+    Print lines of input along with output.
+    """
+    source_lines = (line.rstrip() for line in sys.stdin)
+    console = InteractiveInterpreter()
+    source = ''
+    try:
+        while True:
+            source = next(source_lines)
+            # Allow the user to ignore specific lines of output.
+            if not source.endswith('# ignore'):
+                print('>>>', source)
+            more = console.runsource(source)
+            while more:
+                next_line = next(source_lines)
+                print('...', next_line)
+                source += '\n' + next_line
+                more = console.runsource(source)
+    except StopIteration:
+        if more:
+            print('... ')
+            more = console.runsource(source + '\n')
+
+
+if __name__ == '__main__':
+    main()

doc/sphinxext/sphinx_autorun/version.py

@@ -0,0 +1,4 @@
+# coding: utf-8
+# file generated by setuptools_scm
+# don't change, don't track in version control
+version = '1.1.1'

doc/sphinxext/triqs_example/triqs_example.py

@@ -0,0 +1,123 @@
+import tempfile
+# -*- coding: utf-8 -*-
+# seems to be executed at the level of the conf.py
+# so we need to link the lib at that place...
+"""
+"""
+import os
+import codecs
+from os import path
+from subprocess import Popen,PIPE
+from docutils import nodes
+from docutils.parsers.rst import Directive
+from docutils.parsers.rst import directives
+from sphinx.errors import SphinxError
+
+class TriqsExampleError(SphinxError):
+    category = 'triqs_example error'
+
+class TriqsExampleRun:
+    #here = os.path.abspath(__file__)
+    #pycon = os.path.join(os.path.dirname(here),'pycon.py')
+    config = dict(
+    )
+    @classmethod
+    def builder_init(cls,app):
+        #cls.config.update(app.builder.config.autorun_languages)
+        #cls.config.update(app.builder.config.autocompile_opts)
+        pass 
+
+class TriqsExample(Directive):
+    has_content = True
+    required_arguments = 1
+    optional_arguments = 0
+    final_argument_whitespace = False
+    option_spec = {
+        'linenos': directives.flag,
+    }
+
+    def run(self):
+        document = self.state.document
+        filename = self.arguments[0]
+        if not document.settings.file_insertion_enabled:
+            return [document.reporter.warning('File insertion disabled',
+                                              line=self.lineno)]
+        env = document.settings.env
+        if filename.startswith('/') or filename.startswith(os.sep):
+            rel_fn = filename[1:]
+        else:
+            docdir = path.dirname(env.doc2path(env.docname, base=None))
+            rel_fn = path.normpath(path.join(docdir, filename))
+        try:
+            fn = path.join(env.srcdir, rel_fn)
+        except UnicodeDecodeError:
+            # the source directory is a bytestring with non-ASCII characters;
+            # let's try to encode the rel_fn in the file system encoding
+            rel_fn = rel_fn.encode(sys.getfilesystemencoding())
+            fn = path.join(env.srcdir, rel_fn)
+
+        encoding = self.options.get('encoding', env.config.source_encoding)
+        try:
+            f = codecs.open(fn, 'rU', encoding)
+            lines = f.readlines()
+            f.close()
+        except (IOError, OSError):
+            return [document.reporter.warning(
+                'Include file %r not found or reading it failed' % filename,
+                line=self.lineno)]
+        except UnicodeError:
+            return [document.reporter.warning(
+                'Encoding %r used for reading included file %r seems to '
+                'be wrong, try giving an :encoding: option' %
+                (encoding, filename))]
+
+        config = TriqsExampleRun.config
+
+        # Get configuration values for the language
+        input_encoding = 'utf8' #config.get(language+'_input_encoding','ascii')
+        output_encoding = 'utf8' #config.get(language+'_output_encoding','ascii')
+        show_source = True 
+
+        # Build the code text
+        code = ''.join(lines).strip()
+        filename_clean = filename.rsplit('.',1)[0]
+        if filename_clean.startswith('./') : filename_clean = filename_clean[2:]
+        #print "Running the example ....",filename_clean
+        #print "Root ?", env.doc2path(env.docname, base=None)
+
+        import subprocess as S
+        error = True
+        try : 
+            stdout =''
+            #resout = S.check_output("./example_bin/doc_%s"%(filename_clean) ,stderr=S.STDOUT,shell=True)
+            resout = S.check_output("./%s/doc_%s"%(docdir,filename_clean) ,stderr=S.STDOUT,shell=True)
+            if resout : 
+               stdout = '---------- Result is -------\n' + resout.strip()
+            error = False
+        except S.CalledProcessError as E : 
+            stdout ='---------- RunTime error -------\n'
+            stdout += E.output
+
+        # Process output 
+        if stdout:
+            stdout = stdout.decode(output_encoding,'ignore')
+            out = ''.join(stdout).decode(output_encoding)
+        else:
+            out = '' #.join(stderr).decode(output_encoding)
+        
+        # Get the original code with prefixes
+        code_out = '\n'.join((code,out))
+
+        if error : # report on console
+            print(" Error in processing ")
+            print(code_out) 
+
+        literal = nodes.literal_block(code_out,code_out)
+        literal['language'] = 'c' 
+        literal['linenos'] = 'linenos' in self.options
+        return [literal]
+
+def setup(app):
+    app.add_directive('triqs_example', TriqsExample)
+    app.connect('builder-inited',TriqsExampleRun.builder_init)
+

doc/themes/agogo/layout.html

@@ -0,0 +1,92 @@
+{#
+    agogo/layout.html
+    ~~~~~~~~~~~~~~~~~
+
+    Sphinx layout template for the agogo theme, originally written
+    by Andi Albrecht.
+
+    :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS.
+    :license: BSD, see LICENSE for details.
+#}
+{% extends "basic/layout.html" %}
+
+{% block header %}
+    <div class="header-wrapper">
+      <div class="header">
+        {%- if logo %}
+          <p class="logo"><a href="{{ pathto(theme_index) }}">
+            <img class="logo" src="{{ pathto('_static/' + logo, 1) }}" alt="Logo"/>
+          </a></p>
+        {%- endif %}
+        {%- block headertitle %}
+        <h1><a href="{{ pathto(theme_index) }}">{{ shorttitle|e }}</a></h1>
+        {%- endblock %}
+        <div class="rel">
+          <a href="http://ipht.cea.fr/triqs" title="TRIQS Home">HOME</a> |
+          {%- for rellink in rellinks %}
+          <a href="{{ pathto(rellink[0]) }}" title="{{ rellink[1]|striptags|e }}"
+             {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
+          {%- if not loop.last %}{{ reldelim2 }}{% endif %}
+          {%- endfor %}
+        </div>
+       </div>
+    </div>
+{% endblock %}
+
+{% block content %}
+    <div class="content-wrapper">
+      <div class="content">
+        <div class="document">
+          {%- block document %}
+            {{ super() }}
+          {%- endblock %}
+        </div>
+        <div class="sidebar">
+          {%- block sidebartoc %}
+          <h3>{{ _('Table Of Contents') }}</h3>
+          {{ toctree(maxdepth=3) }}
+          {%- endblock %}
+          {%- block sidebarsearch %}
+          <h3 style="margin-top: 1.5em;">{{ _('Search') }}</h3>
+          <form class="search" action="{{ pathto('search') }}" method="get">
+            <input type="text" name="q" size="18" />
+            <input type="submit" value="{{ _('Go') }}" />
+            <input type="hidden" name="check_keywords" value="yes" />
+            <input type="hidden" name="area" value="default" />
+          </form>
+          <p class="searchtip" style="font-size: 90%">
+            {{ _('Enter search terms or a module, class or function name.') }}
+          </p>
+          {%- endblock %}
+        </div>
+        <div class="clearer"></div>
+      </div>
+    </div>
+{% endblock %}
+
+{% block footer %}
+    <div class="footer-wrapper">
+      <div class="footer">
+        <div class="left">
+          {%- for rellink in rellinks %}
+          <a href="{{ pathto(rellink[0]) }}" title="{{ rellink[1]|striptags|e }}"
+             {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
+          {%- if not loop.last %}{{ reldelim2 }}{% endif %}
+          {%- endfor %}
+          {%- if show_source and has_source and sourcename %}
+            <br/>
+            <a href="{{ pathto('_sources/' + sourcename, true)|e }}"
+               rel="nofollow">{{ _('Show Source') }}</a>
+          {%- endif %}
+        </div>
+
+        <div class="right">
+          {{ super() }}
+        </div>
+        <div class="clearer"></div>
+      </div>
+    </div>
+{% endblock %}
+
+{% block relbar1 %}{% endblock %}
+{% block relbar2 %}{% endblock %}

doc/themes/agogo/static/agogo.css_t

@@ -0,0 +1,519 @@
+/*
+ * agogo.css_t
+ * ~~~~~~~~~~~
+ *
+ * Sphinx stylesheet -- agogo theme.
+ *
+ * :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+* {
+  margin: 0px;
+  padding: 0px;
+}
+
+body {
+  font-family: {{ theme_bodyfont }};
+  font-size: 100%; // TRIQS
+  line-height: 1.0em; // TRIQS
+  color: black;
+  background-color: {{ theme_bgcolor }};
+}
+
+
+/* Page layout */
+
+div.header, div.content, div.footer {
+  width: {{ theme_pagewidth }};
+  margin-left: auto;
+  margin-right: auto;
+}
+
+div.header-wrapper {
+  background: {{ theme_headerbg }};
+  border-bottom: 3px solid #2e3436;
+}
+
+
+/* Default body styles */
+a {
+  color: {{ theme_linkcolor }};
+}
+
+div.bodywrapper a, div.footer a {
+  text-decoration: none; // TRIQS
+}
+
+div.bodywrapper a:hover, div.footer a:hover {
+  text-decoration: underline; // TRIQS
+}
+
+.clearer {
+  clear: both;
+}
+
+.left {
+  float: left;
+}
+
+.right {
+  float: right;
+}
+
+.line-block {
+    display: block;
+    margin-top: 1em;
+    margin-bottom: 1em;
+}
+
+.line-block .line-block {
+    margin-top: 0;
+    margin-bottom: 0;
+    margin-left: 1.5em;
+}
+
+h1, h2, h3, h4 {
+  font-family: {{ theme_headerfont }};
+  font-weight: normal;
+  color: {{ theme_headercolor2 }};
+  margin-bottom: .8em;
+}
+
+h1 {
+  color: {{ theme_headercolor1 }};
+}
+
+h2 {
+  padding-bottom: .5em;
+  border-bottom: 1px solid {{ theme_headercolor2 }};
+}
+
+a.headerlink {
+  visibility: hidden;
+  color: #dddddd;
+  padding-left: .3em;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink {
+  visibility: visible;
+}
+
+img {
+  border: 0;
+}
+
+div.admonition {
+  margin-top: 10px;
+  margin-bottom: 10px;
+  padding: 2px 7px 1px 7px;
+  border-left: 0.2em solid black;
+}
+
+p.admonition-title {
+  margin: 0px 10px 5px 0px;
+  font-weight: bold;
+  color: red; // TRIQS
+}
+
+dt:target, .highlighted {
+  background-color: #fbe54e;
+}
+
+/* Header */
+
+div.header {
+  padding-top: 10px;
+  padding-bottom: 10px;
+}
+
+div.header h1 {
+  font-family: {{ theme_headerfont }};
+  font-weight: normal;
+  font-size: 180%;
+  letter-spacing: .08em;
+}
+
+div.header h1 a {
+  color: white;
+}
+
+div.header div.rel {
+  margin-top: -1em; // TRIQS
+}
+
+div.header div.rel a {
+  color: {{ theme_headerlinkcolor }};
+  letter-spacing: .1em;
+  text-transform: uppercase;
+}
+
+p.logo {
+    float: right;
+}
+
+img.logo {
+    border: 0;
+}
+
+
+/* Content */
+div.content-wrapper {
+  background-color: white;
+  padding-top: 20px;
+  padding-bottom: 20px;
+}
+
+div.document {
+  width: {{ theme_documentwidth }};
+  float: left;
+}
+
+div.body {
+  padding-right: 2em;
+  text-align: {{ theme_textalign }};
+}
+
+div.document ul {
+  margin: 1.5em;
+  list-style-type: square;
+}
+
+div.document dd {
+  margin-left: 1.2em;
+  margin-top: .4em;
+  margin-bottom: 1em;
+}
+
+div.document .section {
+  margin-top: 1.7em;
+}
+div.document .section:first-child {
+  margin-top: 0px;
+}
+
+div.document div.highlight {
+  line-height: 1.0em; // TRIQS
+  padding: 3px;
+  background-color: #eeeeec;
+  border-top: 2px solid #dddddd;
+  border-bottom: 2px solid #dddddd;
+  margin-top: .8em;
+  margin-bottom: .8em;
+}
+
+div.document h2 {
+  margin-top: .7em;
+}
+
+div.document p {
+  margin-bottom: .5em;
+}
+
+div.document li.toctree-l1 {
+  margin-bottom: 0em; // TRIQS
+}
+div.document li.toctree-l2 {
+  margin-bottom: 0em; // TRIQS
+}
+
+div.document .descname {
+  font-weight: bold;
+  color: blue; // TRIQS
+}
+
+div.document .docutils.literal {
+  background-color: #eeeeec;
+  padding: 1px;
+}
+
+div.document .docutils.xref.literal {
+  background-color: transparent;
+  padding: 0px;
+}
+
+div.document blockquote {
+  margin: 1em;
+}
+
+div.document ol {
+  margin: 1.5em;
+}
+
+
+/* Sidebar */
+
+div.sidebar {
+  width: {{ theme_sidebarwidth }};
+  float: right;
+  font-size: .9em;
+}
+
+div.sidebar a, div.header a {
+  text-decoration: none;
+}
+
+div.sidebar a:hover, div.header a:hover {
+  text-decoration: underline;
+}
+
+div.sidebar h3 {
+  color: #2e3436;
+  text-transform: uppercase;
+  font-size: 130%;
+  letter-spacing: .1em;
+}
+
+div.sidebar ul {
+  list-style-type: none;
+}
+
+div.sidebar li.toctree-l1 a {
+  display: block;
+  padding: 1px;
+  border: 1px solid #dddddd;
+  background-color: #eeeeec;
+  margin-bottom: .4em;
+  padding-left: 3px;
+  color: #2e3436;
+}
+
+div.sidebar li.toctree-l2 a {
+  background-color: transparent;
+  border: none;
+  margin-left: 1em;
+  border-bottom: 1px solid #dddddd;
+}
+
+div.sidebar li.toctree-l3 a {
+  background-color: transparent;
+  border: none;
+  margin-left: 2em;
+  border-bottom: 1px solid #dddddd;
+}
+
+div.sidebar li.toctree-l2:last-child a {
+  border-bottom: none;
+}
+
+div.sidebar li.toctree-l1.current a {
+  border-right: 5px solid {{ theme_headerlinkcolor }};
+}
+
+div.sidebar li.toctree-l1.current li.toctree-l2 a {
+  border-right: none;
+}
+
+
+/* Footer */
+
+div.footer-wrapper {
+  background: {{ theme_footerbg }};
+  border-top: 4px solid #babdb6;
+  padding-top: 10px;
+  padding-bottom: 10px;
+  min-height: 80px;
+}
+
+div.footer, div.footer a {
+  color: #888a85;
+}
+
+div.footer .right {
+  text-align: right;
+}
+
+div.footer .left {
+  text-transform: uppercase;
+}
+
+
+/* Styles copied from basic theme */
+
+/* -- search page ----------------------------------------------------------- */
+
+ul.search {
+    margin: 10px 0 0 20px;
+    padding: 0;
+}
+
+ul.search li {
+    padding: 5px 0 5px 20px;
+    background-image: url(file.png);
+    background-repeat: no-repeat;
+    background-position: 0 7px;
+}
+
+ul.search li a {
+    font-weight: bold;
+}
+
+ul.search li div.context {
+    color: #888;
+    margin: 2px 0 0 30px;
+    text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+    font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+    width: 100%;
+}
+
+table.contentstable td {
+    padding: 10px 10px 10px 0;
+}
+
+table.contentstable p.biglink {
+    line-height: 150%;
+    text-align: left;
+}
+
+a.biglink {
+    font-size: 1.3em;
+}
+
+span.linkdescr {
+    font-style: italic;
+    padding-top: 5px;
+    font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable td {
+    text-align: left;
+    vertical-align: top;
+}
+
+table.indextable dl, table.indextable dd {
+    margin-top: 0;
+    margin-bottom: 0;
+}
+
+table.indextable tr.pcap {
+    height: 10px;
+}
+
+table.indextable tr.cap {
+    margin-top: 10px;
+    background-color: #f2f2f2;
+}
+
+img.toggler {
+    margin-right: 3px;
+    margin-top: 3px;
+    cursor: pointer;
+}
+
+/* -- viewcode extension ---------------------------------------------------- */
+
+.viewcode-link {
+    float: right;
+}
+
+.viewcode-back {
+    float: right;
+    font-family:: {{ theme_bodyfont }};
+}
+
+div.viewcode-block:target {
+    margin: -1px -3px;
+    padding: 0 3px;
+    background-color: #f4debf;
+    border-top: 1px solid #ac9;
+    border-bottom: 1px solid #ac9;
+}
+
+/* -- added for TRIQS ------------------------------------------------------- */
+
+div.warning {
+    margin: 1em 0 1em 0;
+    border: 1px solid #86989B;
+    background-color: lightpink; //#f7f7f7;
+}
+
+div.note {
+    margin: 1em 0 1em 0;
+    border: 1px solid #86989B;
+    background-color: lightcyan; //#f7f7f7;
+}
+
+div.note p.admonition-title {
+    margin: 0px 10px 5px 0px;
+    font-weight: bold;
+    color : blue;
+}
+
+div.highlight-python { 
+    margin-top : 5px;
+    margin-bottom : 7px;
+    background-color: lightcyan; //#f4debf;
+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+    vertical-align: middle;
+}
+
+div.body div.math p {
+    text-align: center;
+}
+
+span.eqno {
+    float: right;
+}
+
+/* -- tables ---------------------------------------------------------------- */
+
+table.docutils {
+    border: 0;
+    border-collapse: collapse;
+}
+
+table.docutils head {
+   color : blue;
+}
+
+table.docutils td, table.docutils th {
+    padding: 1px 8px 1px 5px;
+    border-top: 0;
+    border-left: 0;
+    border-right: 0;
+    border-bottom: 1px solid #aaa;
+}
+
+table.field-list td, table.field-list th {
+    border: 0 !important;
+}
+
+table.footnote td, table.footnote th {
+    border: 0 !important;
+}
+
+th {
+    text-align: left;
+    padding-right: 5px;
+}
+
+table.citation {
+    border-left: solid 1px gray;
+    margin-left: 1px;
+}
+
+table.citation td {
+    border-bottom: none;
+}
+

doc/themes/agogo/theme.conf

@@ -0,0 +1,20 @@
+[theme]
+inherit = basic
+stylesheet = agogo.css
+pygments_style = tango
+
+[options]
+bodyfont = "Verdana", Arial, sans-serif
+headerfont = "Georgia", "Times New Roman", serif
+pagewidth = 80%
+documentwidth = 75%
+sidebarwidth = 22.5%
+bgcolor = #eeeeec
+headerbg = url(bgtop.png) top left repeat-x
+footerbg = url(bgfooter.png) top left repeat-x
+linkcolor = #ce5c00
+headercolor1 = #204a87
+headercolor2 = #3465a4
+headerlinkcolor = #fcaf3e
+textalign = justify
+index = index

doc/themes/triqs/layout.html

@@ -0,0 +1,52 @@
+{#
+    layout.html
+    ~~~~~~~~~~~
+
+    TRIQS layout template heavily based on the sphinxdoc theme.
+
+    :copyright: Copyright 2013 by the TRIQS team.
+    :copyright: Copyright 2007-2013 by the Sphinx team.
+    :license: BSD, see LICENSE for details.
+#}
+{%- extends "basic/layout.html" %}
+
+{# put the sidebar before the body #}
+{% block sidebar1 %}{{ sidebar() }}{% endblock %}
+{% block sidebar2 %}{% endblock %}
+
+{% block extrahead %}
+    <link href='https://fonts.googleapis.com/css?family=Open+Sans:300,400,700' rel='stylesheet' type='text/css'>
+    <script src="{{ pathto('_static/cufon-yui.js',1) }}" type="text/javascript"></script>
+    <script src="{{ pathto('_static/spaceman.cufonfonts.js',1) }}" type="text/javascript"></script>
+    <script type="text/javascript">
+      Cufon.replace('.triqs', { fontFamily: 'spaceman', hover: true }); 
+    </script>
+{{ super() }}
+{%- if not embedded %}
+    <style type="text/css">
+      table.right { float: right; margin-left: 20px; }
+      table.right td { border: 1px solid #ccc; }
+      {% if pagename == 'index' %}
+      .related { display: none; }
+      {% endif %}
+    </style>
+{%- endif %}
+{% endblock %}
+
+{% block rootrellink %}
+    <li><a href="{{ pathto('index') }}">Home</a> &raquo;</li>
+{% endblock %}
+
+{% block header %}
+<div class="pageheader">
+  <ul>
+    {% for header_link in header_links %}
+    <li><a href="{{ pathto(header_link[1]) }}">{{ header_link[0] }}</a></li>
+    {% endfor %}
+  </ul>
+  <div>
+    <h1 style="padding:0; margin: 10px 0 0 0;"><a class="triqs" href="{{ pathto('index') }}">{{ header_title }}</a></h1>
+    <span style="font-size: 14px; margin: 0px; padding: 0px;">{{ header_subtitle }}</span>
+  </div>
+</div>
+{% endblock %}

doc/themes/triqs/static/triqs.css

@@ -0,0 +1,449 @@
+/*
+ * sphinx13.css
+ * ~~~~~~~~~~~~
+ *
+ * Sphinx stylesheet -- sphinx13 theme.
+ *
+ * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+@import url("basic.css");
+
+/* -- page layout ----------------------------------------------------------- */
+
+body {
+    font-family: 'Open Sans', 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva',
+                 'Verdana', sans-serif;
+    font-size: 14px;
+    text-align: center;
+    background-image: url(bodybg.png);
+    color: black;
+    padding: 0;
+    border-right: 1px solid #0a507a;
+    border-left: 1px solid #0a507a;
+
+    margin: 0 auto;
+    min-width: 780px;
+    max-width: 1080px;
+}
+
+
+.red{
+ color: red
+}
+.blue{
+ color: blue
+}
+.green{
+ color: green
+}
+
+.param{
+ color: blue
+}
+
+a.triqs {
+  color: #073958;
+  text-decoration: none;
+}
+
+a.triqs:hover {
+  color: #0a527f;
+  text-decoration: none;
+}
+
+.pageheader {
+    background-color: #dcdcdc;
+    text-align: left;
+    padding: 10px 15px;
+    color: #073958;
+    border: none;
+}
+
+.pageheader ul {
+    float: right;
+    color: #073958;
+    list-style-type: none;
+    padding-left: 0;
+    margin-top: 22px;
+    margin-right: 10px;
+}
+
+.pageheader li {
+    float: left;
+    margin: 0 0 0 10px;
+}
+
+.pageheader li a {
+    padding: 8px 12px;
+    color: #073958;
+    text-shadow: none;
+}
+
+.pageheader li a:hover {
+    background-color: #f9f9f0;
+    color: #0a507a;
+    text-shadow: none;
+}
+
+div.document {
+    background-color: white;
+    text-align: left;
+}
+
+div.bodywrapper {
+    margin: 0 240px 0 0;
+    border-right: 1px solid #0a507a;
+}
+
+div.body {
+    margin: 0;
+    padding: 0.5em 20px 20px 20px;
+}
+
+div.related {
+    font-size: 1em;
+    color: white;
+}
+
+div.related ul {
+    background-image: url(relbg.png);
+    height: 1.9em;
+    border-top: 1px solid #002e50;
+    border-bottom: 1px solid #002e50;
+}
+
+div.related ul li {
+    margin: 0 5px 0 0;
+    padding: 0;
+    float: left;
+}
+
+div.related ul li.right {
+    float: right;
+    margin-right: 5px;
+}
+
+div.related ul li a {
+    margin: 0;
+    padding: 0 5px 0 5px;
+    line-height: 1.75em;
+    color: #f9f9f0;
+    text-shadow: 0px 0px 1px rgba(0, 0, 0, 0.5);
+}
+
+div.related ul li a:hover {
+    color: white;
+    /*text-decoration: underline;*/
+    text-shadow: 0px 0px 1px rgba(255, 255, 255, 0.5);
+}
+
+div.sphinxsidebarwrapper {
+    position: relative;
+    top: 0px;
+    padding: 0;
+}
+
+div.sphinxsidebar {
+    margin: 0;
+    padding: 0 15px 15px 0;
+    width: 210px;
+    float: right;
+    font-size: 1em;
+    text-align: left;
+}
+
+div.sphinxsidebar .logo {
+    font-size: 1.8em;
+    color: #0A507A;
+    font-weight: 300;
+    text-align: center;
+}
+
+div.sphinxsidebar .logo img {
+    vertical-align: middle;
+}
+
+div.sphinxsidebar input {
+    border: 1px solid #aaa;
+    font-family: 'Open Sans', 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva',
+                 'Verdana', sans-serif;
+    font-size: 1em;
+}
+
+div.sphinxsidebar h3 {
+    font-size: 1.5em;
+    border-top: 1px solid #0a507a;
+    margin-top: 1em;
+    margin-bottom: 0.5em;
+    padding-top: 0.5em;
+}
+
+div.sphinxsidebar h4 {
+    font-size: 1.2em;
+    margin-bottom: 0;
+}
+
+div.sphinxsidebar h3, div.sphinxsidebar h4 {
+    margin-right: -15px;
+    margin-left: -15px;
+    padding-right: 14px;
+    padding-left: 14px;
+    color: #333;
+    font-weight: 300;
+    /*text-shadow: 0px 0px 0.5px rgba(0, 0, 0, 0.4);*/
+}
+
+div.sphinxsidebarwrapper > h3:first-child {
+    margin-top: 0.5em;
+    border: none;
+}
+
+div.sphinxsidebar h3 a {
+    color: #333;
+}
+
+div.sphinxsidebar ul {
+    color: #444;
+    margin-top: 7px;
+    padding: 0;
+    line-height: 130%;
+}
+
+div.sphinxsidebar ul ul {
+    margin-left: 20px;
+    list-style-image: url(listitem.png);
+}
+
+div.footer {
+    background-image: url(footerbg.png);
+    color: #ccc;
+    text-shadow: 0 0 .2px rgba(255, 255, 255, 0.8);
+    padding: 3px 8px 3px 0;
+    clear: both;
+    font-size: 0.8em;
+    text-align: right;
+}
+
+/* no need to make a visible link to Sphinx on the Sphinx page */
+div.footer a {
+    color: #ccc;
+}
+
+/* -- body styles ----------------------------------------------------------- */
+
+p {    
+    margin: 0.8em 0 0.5em 0;
+}
+
+a {
+    color: #A2881D;
+    text-decoration: none;
+}
+
+a:hover {
+    color: #E1C13F;
+}
+
+div.body a {
+    text-decoration: underline;
+}
+
+h1 {
+    margin: 10px 0 0 0;
+    font-size: 2.4em;
+    color: #0A507A;
+    font-weight: 300;
+}
+
+h2 {
+    margin: 1.em 0 0.2em 0;
+    font-size: 1.5em;
+    font-weight: 300;
+    padding: 0;
+    color: #174967;
+}
+
+h3 {
+    margin: 1em 0 -0.3em 0;
+    font-size: 1.3em;
+    font-weight: 300;
+}
+
+div.body h1 a, div.body h2 a, div.body h3 a, div.body h4 a, div.body h5 a, div.body h6 a {
+    text-decoration: none;
+}
+
+div.body h1 a tt, div.body h2 a tt, div.body h3 a tt, div.body h4 a tt, div.body h5 a tt, div.body h6 a tt {
+    color: #0A507A !important;
+    font-size: inherit !important;
+}
+
+a.headerlink {
+    color: #0A507A !important;
+    font-size: 12px;
+    margin-left: 6px;
+    padding: 0 4px 0 4px;
+    text-decoration: none !important;
+    float: right;
+}
+
+a.headerlink:hover {
+    background-color: #ccc;
+    color: white!important;
+}
+
+cite, code, tt {
+    font-family: 'Consolas', 'DejaVu Sans Mono',
+                 'Bitstream Vera Sans Mono', monospace;
+    font-size: 14px;
+    letter-spacing: -0.02em;
+}
+
+tt {
+    background-color: #f2f2f2;
+    border: 1px solid #ddd;
+    border-radius: 2px;
+    color: #333;
+    padding: 1px;
+}
+
+tt.descname, tt.descclassname, tt.xref {
+    border: 0;
+}
+
+hr {
+    border: 1px solid #abc;
+    margin: 2em;
+}
+
+a tt {
+    border: 0;
+    color: #a2881d;
+}
+
+a tt:hover {
+    color: #e1c13f;
+}
+
+pre {
+    font-family: 'Consolas', 'DejaVu Sans Mono',
+                 'Bitstream Vera Sans Mono', monospace;
+    font-size: 13px;
+    letter-spacing: 0.015em;
+    line-height: 120%;
+    padding: 0.5em;
+    border: 1px solid #ccc;
+    border-radius: 2px;
+    background-color: #f8f8f8;
+}
+
+pre a {
+    color: inherit;
+    text-decoration: underline;
+}
+
+td.linenos pre {
+    padding: 0.5em 0;
+}
+
+div.quotebar {
+    background-color: #f8f8f8;
+    max-width: 250px;
+    float: right;
+    padding: 0px 7px;
+    border: 1px solid #ccc;
+    margin-left: 1em;
+}
+
+div.topic {
+    background-color: #f8f8f8;
+}
+
+table {
+    border-collapse: collapse;
+    margin: 0 -0.5em 0 -0.5em;
+}
+
+table td, table th {
+    padding: 0.2em 0.5em 0.2em 0.5em;
+}
+
+div.admonition, div.warning {
+    font-size: 0.9em;
+    margin: 1em 0 1em 0;
+    border: 1px solid #86989B;
+    border-radius: 2px;
+    background-color: #f7f7f7;
+    padding: 0;
+}
+
+div.admonition p, div.warning p {
+    margin: 0.5em 1em 0.5em 1em;
+    padding: 0;
+}
+
+div.admonition pre, div.warning pre {
+    margin: 0.4em 1em 0.4em 1em;
+}
+
+div.admonition p.admonition-title,
+div.warning p.admonition-title {
+    margin-top: 1em;
+    padding-top: 0.5em;
+    font-weight: bold;
+}
+
+div.warning {
+    border: 1px solid #940000;
+/*    background-color: #FFCCCF;*/
+}
+
+div.warning p.admonition-title {
+}
+
+div.admonition ul, div.admonition ol,
+div.warning ul, div.warning ol {
+    margin: 0.1em 0.5em 0.5em 3em;
+    padding: 0;
+}
+
+div.admonition .highlight, div.warning .highlight {
+    background-color: #f7f7f7;
+}
+
+.viewcode-back {
+    font-family: 'Open Sans', 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva',
+                 'Verdana', sans-serif;
+}
+
+div.viewcode-block:target {
+    background-color: #f4debf;
+    border-top: 1px solid #ac9;
+    border-bottom: 1px solid #ac9;
+}
+
+
+.my-code-block.std-ref {
+ color : red;
+}
+
+.cppbrief {
+ color: #C6792C;
+ font-style: oblique;
+}
+
+.cppsynopsis {
+ background-color: #E7EDF9;
+ /*font-family: 'Open Sans', 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva', 'Verdana', sans-serif;*/
+ /*font-family: monospace; */
+ font-family: Verdana, Arial, Lucida Console;
+ font-size=80%;
+ /*font-style: oblique;*/
+ /* white-space: pre;*/
+}
+
+
+

doc/themes/triqs/theme.conf

@@ -0,0 +1,4 @@
+[theme]
+inherit = basic
+stylesheet = triqs.css
+pygments_style = sphinx

doc/tutorials/ce-gamma-fscs_wien2k.rst

@@ -96,7 +96,7 @@ In order to run DFT+DMFT calculations within Hubbard-I we need the corresponding
 with the CT-QMC solver (see :ref:`singleshot`), however there are also some differences. First
 difference is that we import the Hubbard-I solver by::
 
-   from pytriqs.applications.impurity_solvers.hubbard_I.hubbard_solver import Solver
+   from triqs.applications.impurity_solvers.hubbard_I.hubbard_solver import Solver
 
 The Hubbard-I solver is very fast and we do not need to take into account the DFT block structure
 or use any approximation for the *U*-matrix. We load and convert the :program:`dmftproj` output

doc/tutorials/images_scripts/Ce-gamma.py

@@ -1,6 +1,6 @@
 from triqs_dft_tools.sumk_dft import *
-from triqs_dft_tools.converters.wien2k_converter import *
+from triqs_dft_tools.converters.wien2k import *
-from pytriqs.applications.impurity_solvers.hubbard_I.hubbard_solver import Solver
+from triqs.applications.impurity_solvers.hubbard_I.hubbard_solver import Solver
 
 import os
 dft_filename = os.getcwd().rpartition('/')[2]
@@ -111,7 +111,7 @@ for iteration_number in range(1,Loops+1):
         #Save essential SumkDFT data:
         SK.save(['chemical_potential','dc_imp','dc_energ','correnerg'])
         if (mpi.is_master_node()):
-            print 'DC after solver: ',SK.dc_imp[0]
+            print('DC after solver: ',SK.dc_imp[0])
 
         # print out occupancy matrix of Ce 4f
         mpi.report("Orbital densities of impurity Green function:")

doc/tutorials/images_scripts/Ce-gamma_DOS.py

@@ -1,6 +1,6 @@
 from triqs_dft_tools.sumk_dft_tools import *
-from triqs_dft_tools.converters.wien2k_converter import *
+from triqs_dft_tools.converters.wien2k import *
-from pytriqs.applications.impurity_solvers.hubbard_I.hubbard_solver import Solver
+from triqs.applications.impurity_solvers.hubbard_I.hubbard_solver import Solver
 
 # Creates the data directory, cd into it:
 #Prepare_Run_Directory(DirectoryName = "Ce-Gamma") 
@@ -31,7 +31,7 @@ SK.dc_imp = mpi.bcast(SK.dc_imp)
 SK.dc_energ = mpi.bcast(SK.dc_energ)
 
 if (mpi.is_master_node()):
-    print 'DC after reading SK: ',SK.dc_imp[0]
+    print('DC after reading SK: ',SK.dc_imp[0])
 
 N = SK.corr_shells[0]['dim']
 l = SK.corr_shells[0]['l']

doc/tutorials/images_scripts/NiO_local_lattice_GF.py

@@ -1,12 +1,12 @@
 from itertools import *
 import numpy as np
-import pytriqs.utility.mpi as mpi
+import triqs.utility.mpi as mpi
-from pytriqs.archive import *
+from h5 import *
-from pytriqs.gf import *
+from triqs.gf import *
 from triqs_dft_tools.sumk_dft import *
 from triqs_dft_tools.sumk_dft_tools import *
-from pytriqs.operators.util.hamiltonians import *
+from triqs.operators.util.hamiltonians import *
-from pytriqs.operators.util.U_matrix import *
+from triqs.operators.util.U_matrix import *
 from triqs_cthyb import *
 import warnings
 warnings.filterwarnings("ignore", category=FutureWarning)
@@ -39,7 +39,7 @@ if mpi.is_master_node():
     if not 'Iterations' in ar['DMFT_results']: ar['DMFT_results'].create_group('Iterations')
     if 'iteration_count' in ar['DMFT_results']: 
         iteration_offset = ar['DMFT_results']['iteration_count']+1
-        print('offset',iteration_offset)
+        print(('offset',iteration_offset))
         Sigma_iw = ar['DMFT_results']['Iterations']['Sigma_it'+str(iteration_offset-1)]
         SK.dc_imp = ar['DMFT_results']['Iterations']['dc_imp'+str(iteration_offset-1)]
         SK.dc_energ = ar['DMFT_results']['Iterations']['dc_energ'+str(iteration_offset-1)]
@@ -54,13 +54,13 @@ SK.chemical_potential = mpi.bcast(SK.chemical_potential)
 
 SK.put_Sigma(Sigma_imp = [Sigma_iw])
 
-ikarray = numpy.array(range(SK.n_k))
+ikarray = numpy.array(list(range(SK.n_k)))
 
 # set up the orbitally resolved local lattice greens function:
 n_orbs = SK.proj_mat_csc.shape[2]
 spn = SK.spin_block_names[SK.SO]
 mesh = Sigma_iw.mesh
-block_structure = [range(n_orbs) for sp in spn]
+block_structure = [list(range(n_orbs)) for sp in spn]
 gf_struct = [(spn[isp], block_structure[isp])
          for isp in range(SK.n_spin_blocks[SK.SO])]
 block_ind_list = [block for block, inner in gf_struct]

doc/tutorials/images_scripts/Sr2MgOsO6_SOC.py

@@ -1,11 +1,11 @@
 # Import the modules:
 from triqs_dft_tools.sumk_dft import *
-from pytriqs.gf import *
+from triqs.gf import *
-from pytriqs.archive import HDFArchive
+from h5 import HDFArchive
-from pytriqs.operators.util import *
+from triqs.operators.util import *
-from pytriqs.operators.util.U_matrix import *
+from triqs.operators.util.U_matrix import *
 from triqs_cthyb import *
-import pytriqs.utility.mpi as mpi
+import triqs.utility.mpi as mpi
 
 # Init the SumK class:
 filename = 'Sr2MgOsO6_SOC.h5'

doc/tutorials/images_scripts/Sr2MgOsO6_noSOC.py

@@ -1,14 +1,14 @@
 # Import the modules:
 from triqs_dft_tools.sumk_dft import *
-from pytriqs.gf import *
+from triqs.gf import *
-from pytriqs.archive import HDFArchive
+from h5 import HDFArchive
-from pytriqs.operators.util import *
+from triqs.operators.util import *
-from pytriqs.operators.util.U_matrix import *
+from triqs.operators.util.U_matrix import *
 from triqs_cthyb import *
-import pytriqs.utility.mpi as mpi
+import triqs.utility.mpi as mpi
 
 # Convert the input
-from triqs_dft_tools.converters.wien2k_converter import *
+from triqs_dft_tools.converters.wien2k import *
 Converter = Wien2kConverter(filename = "Sr2MgOsO6_noSOC")
 Converter.convert_dft_input()
 

doc/tutorials/images_scripts/converter.py

@@ -1,3 +1,3 @@
-from triqs_dft_tools.converters.vasp_converter import *
+from triqs_dft_tools.converters.vasp import *
 Converter = VaspConverter(filename = 'nio')
 Converter.convert_dft_input()

doc/tutorials/images_scripts/dft_dmft_cthyb.py

@@ -1,10 +1,10 @@
-import pytriqs.utility.mpi as mpi
+import triqs.utility.mpi as mpi
-from pytriqs.operators.util import *
+from triqs.operators.util import *
-from pytriqs.archive import HDFArchive
+from h5 import HDFArchive
 from triqs_cthyb import *
-from pytriqs.gf import *
+from triqs.gf import *
 from triqs_dft_tools.sumk_dft import *
-from triqs_dft_tools.converters.wien2k_converter import *
+from triqs_dft_tools.converters.wien2k import *
 
 dft_filename='SrVO3'
 beta = 40
@@ -49,7 +49,7 @@ p["fit_min_n"] = 30
 p["fit_max_n"] = 60
 
 # If conversion step was not done, we could do it here. Uncomment the lines it you want to do this.
-#from triqs_dft_tools.converters.wien2k_converter import *
+#from triqs_dft_tools.converters.wien2k import *
 #Converter = Wien2kConverter(filename=dft_filename, repacking=True)
 #Converter.convert_dft_input()
 #mpi.barrier()
@@ -76,7 +76,7 @@ spin_names = ["up","down"]
 orb_names = [i for i in range(n_orb)]
 
 # Use GF structure determined by DFT blocks
-gf_struct = [(block, indices) for block, indices in SK.gf_struct_solver[0].iteritems()]
+gf_struct = [(block, indices) for block, indices in SK.gf_struct_solver[0].items()]
 
 # Construct Solver
 S = Solver(beta=beta, gf_struct=gf_struct)
@@ -97,7 +97,7 @@ if previous_present:
   SK.set_dc(dc_imp,dc_energ)
 
 for iteration_number in range(1,loops+1):
-    if mpi.is_master_node(): print "Iteration = ", iteration_number
+    if mpi.is_master_node(): print("Iteration = ", iteration_number)
 
     SK.symm_deg_gf(S.Sigma_iw,orb=0)                        # symmetrise Sigma
     SK.set_Sigma([ S.Sigma_iw ])                            # set Sigma into the SumK class

doc/tutorials/images_scripts/maxent.py

@@ -1,5 +1,5 @@
-from pytriqs.gf import *
+from triqs.gf import *
-from pytriqs.archive import *
+from h5 import *
 from triqs_maxent import *
 
 filename = 'nio'
@@ -12,7 +12,7 @@ if 'iteration_count' in ar['DMFT_results']:
 
 tm = TauMaxEnt(cost_function='bryan', probability='normal')
 
-print(G_latt['up'][0,0])
+print((G_latt['up'][0,0]))
 t2g_orbs = [0,1,3]
 eg_orbs = [2,4]
 op_orbs = [5,6,7]
@@ -22,7 +22,7 @@ orbs = [t2g_orbs, eg_orbs, op_orbs]
 
 for orb in orbs:
 
-    print '\n'+str(orb[0])+'\n'
+    print('\n'+str(orb[0])+'\n')
 
     gf = 0*G_latt['up'][0,0]
     for iO in orb:
@@ -43,7 +43,7 @@ for orb in orbs:
 
 
     # you may be interested in the details of the line analyzer:
-    # from pytriqs.plot.mpl_interface import oplot
+    # from triqs.plot.mpl_interface import oplot
     #plt.figure(2)
     #result.analyzer_results['LineFitAnalyzer'].plot_linefit()
     #plt.savefig('ana'+str(orb[0])+'.pdf',fmt='pdf')

doc/tutorials/images_scripts/nio.py

@@ -1,13 +1,13 @@
 from itertools import *
 import numpy as np
-import pytriqs.utility.mpi as mpi
+import triqs.utility.mpi as mpi
-from pytriqs.archive import *
+from h5 import *
-from pytriqs.gf import *
+from triqs.gf import *
-import sys, pytriqs.version as triqs_version
+import sys, triqs.version as triqs_version
 from triqs_dft_tools.sumk_dft import *
 from triqs_dft_tools.sumk_dft_tools import *
-from pytriqs.operators.util.hamiltonians import *
+from triqs.operators.util.hamiltonians import *
-from pytriqs.operators.util.U_matrix import *
+from triqs.operators.util.U_matrix import *
 from triqs_cthyb import *
 import triqs_cthyb.version as cthyb_version
 import triqs_dft_tools.version as dft_tools_version
@@ -30,7 +30,7 @@ for i_sh in range(len(SK.deg_shells)):
     mpi.report('found {0:d} blocks of degenerate orbitals in shell {1:d}'.format(num_block_deg_orbs, i_sh))
     for iblock in range(num_block_deg_orbs):
         mpi.report('block {0:d} consists of orbitals:'.format(iblock))
-        for keys in SK.deg_shells[i_sh][iblock].keys():
+        for keys in list(SK.deg_shells[i_sh][iblock].keys()):
             mpi.report('  '+keys)
 
 # Setup CTQMC Solver

doc/tutorials/images_scripts/nio_csc.py

@@ -1,17 +1,17 @@
 from itertools import *
 import numpy as np
-import pytriqs.utility.mpi as mpi
+import triqs.utility.mpi as mpi
-from pytriqs.archive import *
+from h5 import *
-from pytriqs.gf import *
+from triqs.gf import *
-import sys, pytriqs.version as triqs_version
+import sys, triqs.version as triqs_version
 from triqs_dft_tools.sumk_dft import *
 from triqs_dft_tools.sumk_dft_tools import *
-from pytriqs.operators.util.hamiltonians import *
+from triqs.operators.util.hamiltonians import *
-from pytriqs.operators.util.U_matrix import *
+from triqs.operators.util.U_matrix import *
 from triqs_cthyb import *
 import triqs_cthyb.version as cthyb_version
 import triqs_dft_tools.version as dft_tools_version
-from triqs_dft_tools.converters.vasp_converter import *
+from triqs_dft_tools.converters.vasp import *
 
 
 import warnings
@@ -37,7 +37,7 @@ def dmft_cycle():
         mpi.report('found {0:d} blocks of degenerate orbitals in shell {1:d}'.format(num_block_deg_orbs, i_sh))
         for iblock in range(num_block_deg_orbs):
             mpi.report('block {0:d} consists of orbitals:'.format(iblock))
-            for keys in SK.deg_shells[i_sh][iblock].keys():
+            for keys in list(SK.deg_shells[i_sh][iblock].keys()):
                 mpi.report('  '+keys)
     
     # Setup CTQMC Solver
@@ -176,15 +176,15 @@ def dmft_cycle():
     
     
     if mpi.is_master_node():
-        print 'calculating mu...'
+        print('calculating mu...')
     SK.chemical_potential = SK.calc_mu( precision = 0.000001 )
     
     if mpi.is_master_node():
-        print 'calculating GAMMA'
+        print('calculating GAMMA')
     SK.calc_density_correction(dm_type='vasp')
     
     if mpi.is_master_node():
-        print 'calculating energy corrections'
+        print('calculating energy corrections')
     
     correnerg = 0.5 * (S.G_iw * S.Sigma_iw).total_density()
     

doc/tutorials/sr2mgoso6_nosoc.rst

@@ -57,9 +57,9 @@ At the end of the run you see the density matrix in Wannier space:
 As you can see, there are off-diagonal elements between the :math:`d_{x^2-y^2}` and the :math:`d_{xy}` orbital.
 
 We convert the output to the hdf5 archive, using 
-the python module :class:`Wien2kConverter <dft.converters.wien2k_converter.Wien2kConverter>`. A simple python script doing this is::
+the python module :class:`Wien2kConverter <dft.converters.wien2k.Wien2kConverter>`. A simple python script doing this is::
 
-  from triqs_dft_tools.converters.wien2k_converter import *
+  from triqs_dft_tools.converters.wien2k import *
   Converter = Wien2kConverter(filename = "Sr2MgOsO6_noSOC")
   Converter.convert_dft_input()
 
@@ -123,8 +123,8 @@ The interaction Hamiltonian
 
 We now set up the interaction Hamiltonian. Since we want to rotate the interaction matrix into the local basis, we are using the Slater convention for it:: 
 
-    from pytriqs.operators.util import *
+    from triqs.operators.util import *
-    from pytriqs.operators.util.U_matrix import *
+    from triqs.operators.util.U_matrix import *
 
     U = 2.0
     J = 0.2
@@ -141,7 +141,7 @@ Note that we needed to set up the interaction Hamiltonian for the full set of fi
 Now we have the interaction Hamiltonian for the solver, which we set up next::
 
     from triqs_cthyb import *
-    import pytriqs.utility.mpi as mpi
+    import triqs.utility.mpi as mpi
 
     beta = 40.0
     S = Solver(beta=beta, gf_struct=SK.block_structure.gf_struct_solver_list[0])

doc/tutorials/sr2mgoso6_soc.rst

@@ -58,9 +58,9 @@ At the end of the run you see the density matrix in Wannier space:
 As you can see, there are a lot of off-diagonal elements now, in particular also off-diagonal in spin space. This is just telling us that spin is not a good quantum number any more in the presence of SOC.
 
 We convert the output to the hdf5 archive, using 
-the python module :class:`Wien2kConverter <dft.converters.wien2k_converter.Wien2kConverter>`. A simple python script doing this is::
+the python module :class:`Wien2kConverter <dft.converters.wien2k.Wien2kConverter>`. A simple python script doing this is::
 
-  from triqs_dft_tools.converters.wien2k_converter import *
+  from triqs_dft_tools.converters.wien2k import *
   Converter = Wien2kConverter(filename = "Sr2MgOsO6_SOC")
   Converter.convert_dft_input()
 
@@ -119,8 +119,8 @@ The interaction Hamiltonian
 
 We now set up the interaction Hamiltonian. Since we want to rotate the interaction matrix into the local basis, we are using the Slater convention for it. We use *l=2* for *d* orbitals. Also, for SOC calculations, we need to inflate the resulting matrix to size 10x10:: 
 
-    from pytriqs.operators.util import *
+    from triqs.operators.util import *
-    from pytriqs.operators.util.U_matrix import *
+    from triqs.operators.util.U_matrix import *
 
     U = 2.0
     J = 0.2
@@ -139,7 +139,7 @@ Note that we needed to set up the interaction Hamiltonian first for the full set
 Now we have the interaction Hamiltonian for the solver, which we set up next::
 
     from triqs_cthyb import *
-    import pytriqs.utility.mpi as mpi
+    import triqs.utility.mpi as mpi
 
     beta = 40.0
     S = Solver(beta=beta, gf_struct=SK.block_structure.gf_struct_solver_list[0])

doc/tutorials/srvo3.rst

@@ -51,10 +51,10 @@ Then :program:`dmftproj` is executed in its default mode (i.e. without spin-pola
    dmftproj 
 
 This program produces the necessary files for the conversion to the hdf5 file structure. This is done using
-the python module :class:`Wien2kConverter <dft.converters.wien2k_converter.Wien2kConverter>`.
+the python module :class:`Wien2kConverter <dft.converters.wien2k.Wien2kConverter>`.
 A simple python script that initialises the converter is::
 
-  from triqs_dft_tools.converters.wien2k_converter import *
+  from triqs_dft_tools.converters.wien2k import *
   Converter = Wien2kConverter(filename = "SrVO3")
 
 After initializing the interface module, we can now convert the input
@@ -77,11 +77,11 @@ Loading modules
 First, we load the necessary modules::
 
   from triqs_dft_tools.sumk_dft import *
-  from pytriqs.gf import *
+  from triqs.gf import *
-  from pytriqs.archive import HDFArchive
+  from h5 import HDFArchive
-  from pytriqs.operators.util import *
+  from triqs.operators.util import *
   from triqs_cthyb import *
-  import pytriqs.utility.mpi as mpi
+  import triqs.utility.mpi as mpi
 
 The last two lines load the modules for the construction of the
 :ref:`CTHYB solver <triqscthyb:welcome>`.
@@ -271,7 +271,7 @@ and perform only one DMFT iteration. The resulting self energy can be tail fitte
     Sigma_iw_fit << tail_fit(S.Sigma_iw, fit_max_moment = 4, fit_min_n = 40, fit_max_n = 160)[0]
 
 Plot the self energy and adjust the tail fit parameters such that you obtain a
-proper fit. The :meth:`fit_tail function <pytriqs.gf.tools.tail_fit>` is part
+proper fit. The :meth:`fit_tail function <triqs.gf.tools.tail_fit>` is part
 of the :ref:`TRIQS <triqslibs:welcome>` library.
 
 For a self energy which is going to zero for :math:`i\omega \rightarrow 0` our suggestion is

doc/tutorials/svo_vasp/svo_notebook.ipynb

@@ -247,7 +247,7 @@
    ],
    "source": [
     "# import VASPconverter\n",
-    "from triqs_dft_tools.converters.vasp_converter import *\n",
+    "from triqs_dft_tools.converters.vasp import *\n",
     "\n",
     "\n",
     "# create Converter\n",
@@ -312,7 +312,7 @@
     "    mpi.report('found {0:d} blocks of degenerate orbitals in shell {1:d}'.format(num_block_deg_orbs, i_sh))\n",
     "    for iblock in range(num_block_deg_orbs):\n",
     "        mpi.report('block {0:d} consists of orbitals:'.format(iblock))\n",
-    "        for keys in SK.deg_shells[i_sh][iblock].keys():\n",
+    "        for keys in list(SK.deg_shells[i_sh][iblock].keys()):\n",
     "            mpi.report('  '+keys)"
    ]
   },
@@ -335,21 +335,20 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
+   "pygments_lexer": "ipython3"
-   "version": "2.7.15+"
   }
  },
  "nbformat": 4,

fortran/dmftproj/CMakeLists.txt

@@ -6,8 +6,7 @@ set(SOURCES modules.f dmftproj.f readcomline.f set_ang_trans.f setsym.f
 
 # The main target and what to link with...
 add_executable(dmftproj ${SOURCES})
-find_package(LAPACK)
+target_link_libraries(dmftproj triqs::blas_lapack)
-target_link_libraries(dmftproj ${LAPACK_LIBRARIES})
 
 # where to install
 install (TARGETS dmftproj DESTINATION bin)
@@ -17,7 +16,7 @@ SET(D ${CMAKE_CURRENT_SOURCE_DIR}/SRC_templates/)
 SET(WIEN_SRC_TEMPL_FILES ${D}/case.cf_f_mm2  ${D}/case.cf_p_cubic  ${D}/case.indmftpr ${D}/run_triqs ${D}/runsp_triqs)
 message(STATUS "-----------------------------------------------------------------------------")
 message(STATUS "                             ********  WARNING ******** ")
-message(STATUS "  Wien2k 14.2 and older : after installation of TRIQS, copy the files from ")
+message(STATUS "  Wien2k 14.2 and older : after installation of DFTTools, copy the files from ")
 message(STATUS "  ${CMAKE_INSTALL_PREFIX}/share/triqs/Wien2k_SRC_files/SRC_templates ")
 message(STATUS "  to your Wien2k installation WIENROOT/SRC_templates (Cf documentation).     ")
 message(STATUS "  For newer versions these files are already shipped with Wien2k. ")

python/CMakeLists.txt

@@ -1,19 +0,0 @@
-# where will the python end up in triqs?
-set(PYTHON_LIB_DEST ${CPP2PY_PYTHON_LIB_DEST_ROOT}/triqs_dft_tools)
-
-# site_customize for build
-set(package_name "triqs_dft_tools")
-
-# Create a temporary copy of the python modules so that we can run before installation with the test
-FILE(GLOB PYTHON_SOURCES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.py )
-foreach(f ${PYTHON_SOURCES})
- configure_file(${f} ${f} COPYONLY)
-endforeach()
-
-# add version file
-configure_file(version.py.in version.py @ONLY)
-
-# install files
-install(FILES ${PYTHON_SOURCES} ${CMAKE_CURRENT_BINARY_DIR}/version.py DESTINATION ${PYTHON_LIB_DEST})
-
-add_subdirectory(converters)

python/converters/.gitignore

@@ -1 +0,0 @@
-*.pyc

python/converters/CMakeLists.txt

@@ -1,10 +0,0 @@
-# Create a temporary copy of the python modules so that we can run before installation with the test
-FILE(GLOB PYTHON_SOURCES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.py)
-foreach(f ${PYTHON_SOURCES})
- configure_file(${f} ${f} COPYONLY)
-endforeach()
-
-# install files
-install(FILES ${PYTHON_SOURCES} DESTINATION ${PYTHON_LIB_DEST}/converters)
-
-add_subdirectory(plovasp)

python/converters/plovasp/CMakeLists.txt

@@ -1,19 +0,0 @@
-# === Build and install atm module 
-add_cpp2py_module(atm)
-target_link_libraries(atm atm_c triqs)
-target_compile_options(atm PRIVATE -std=c++17)
-target_include_directories(atm PRIVATE ${CMAKE_SOURCE_DIR}/c++)
-
-install(TARGETS atm DESTINATION ${PYTHON_LIB_DEST}/converters/plovasp)
-
-# === Copy Python files to current build directory and register for install
-set(PYTHON_SOURCES __init__.py  converter.py elstruct.py  inpconf.py  plotools.py  proj_group.py  proj_shell.py  sc_dmft.py  vaspio.py)
-foreach(f ${PYTHON_SOURCES})
- configure_file(${f} ${f} COPYONLY)
-endforeach()
-
-# install files
-install(FILES ${PYTHON_SOURCES} DESTINATION ${PYTHON_LIB_DEST}/converters/plovasp)
-
-# This we need in order for tests to work
-#add_custom_command(TARGET atm POST_BUILD COMMAND ln -fs ${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_PROJECT_NAME}/atm.so ${CMAKE_BINARY_DIR}/python/dft/converters/plovasp)

python/triqs_dft_tools/CMakeLists.txt

@@ -0,0 +1,25 @@
+# Configure the version
+configure_file(version.py.in version.py)
+
+# All Python files. Copy them in the build dir to have a complete package for the tests.
+file(GLOB_RECURSE python_sources RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.py)
+file(GLOB_RECURSE wrap_generators RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *_desc.py)
+list(REMOVE_ITEM python_sources "${wrap_generators}")
+foreach(file ${python_sources})
+  configure_file(${file} ${file} COPYONLY)
+endforeach()
+
+# Install python files to proper location
+set(PYTHON_LIB_DEST ${TRIQS_PYTHON_LIB_DEST_ROOT}/${PROJECT_NAME})
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/version.py DESTINATION ${PYTHON_LIB_DEST})
+install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} DESTINATION ${TRIQS_PYTHON_LIB_DEST_ROOT} FILES_MATCHING PATTERN "*.py" PATTERN "*_desc.py" EXCLUDE)
+
+# Build and install any python modules
+foreach(gen ${wrap_generators})
+  string(REPLACE "_desc.py" "" gen ${gen})
+  get_filename_component(module_name ${gen} NAME_WE)
+  get_filename_component(module_dir ${gen} DIRECTORY)
+  add_cpp2py_module(NAME ${module_name} DIRECTORY ${module_dir})
+  target_link_libraries(${module_name} ${PROJECT_NAME}_c triqs_py)
+  install(TARGETS ${module_name} DESTINATION ${PYTHON_LIB_DEST}/${module_dir})
+endforeach()

python/triqs_dft_tools/__init__.py

@@ -20,11 +20,11 @@
 #
 ##########################################################################
 
-from sumk_dft import SumkDFT
+from .sumk_dft import SumkDFT
-from symmetry import Symmetry
+from .symmetry import Symmetry
-from block_structure import BlockStructure
+from .block_structure import BlockStructure
-from sumk_dft_tools import SumkDFTTools
+from .sumk_dft_tools import SumkDFTTools
-from converters import *
+from .converters import *
 
 __all__ = ['SumkDFT', 'Symmetry', 'SumkDFTTools',
            'Wien2kConverter', 'HkConverter','BlockStructure']

python/triqs_dft_tools/block_structure.py

@@ -25,9 +25,9 @@
 
 import copy
 import numpy as np
-from pytriqs.gf import GfImFreq, BlockGf
+from triqs.gf import GfImFreq, BlockGf
 from ast import literal_eval
-import pytriqs.utility.mpi as mpi
+import triqs.utility.mpi as mpi
 from warnings import warn
 from collections import defaultdict
 
@@ -142,7 +142,7 @@ class BlockStructure(object):
         if self.gf_struct_solver is None:
             return None
         # we sort by block name in order to get a reproducible result
-        return [sorted([(k, v) for k, v in gfs.iteritems()], key=lambda x: x[0])
+        return [sorted([(k, v) for k, v in list(gfs.items())], key=lambda x: x[0])
                 for gfs in self.gf_struct_solver]
 
     @property
@@ -203,10 +203,10 @@ class BlockStructure(object):
         N_solver = len(np.unique(self.corr_to_inequiv))
         if self.gf_struct_solver is not None:
             assert N_solver == len(self.gf_struct_solver)
-        assert sorted(np.unique(self.corr_to_inequiv)) == range(N_solver),\
+        assert sorted(np.unique(self.corr_to_inequiv)) == list(range(N_solver)),\
             "an inequivalent shell is missing in corr_to_inequiv"
         return [self.corr_to_inequiv.index(icrsh)
-                for icrsh in range(N_solver)]
+                for icrsh in list(range(N_solver))]
 
     @inequiv_to_corr.setter
     def inequiv_to_corr(self, value):
@@ -222,7 +222,7 @@ class BlockStructure(object):
         ret = []
         for ish, icrsh in enumerate(self.inequiv_to_corr):
             d = defaultdict(list)
-            for block_solver, block_sumk in self.solver_to_sumk_block[ish].iteritems():
+            for block_solver, block_sumk in list(self.solver_to_sumk_block[ish].items()):
                 d[block_sumk].append(block_solver)
             ret.append(d)
         return ret
@@ -251,7 +251,7 @@ class BlockStructure(object):
         assert len(trans) == len(self.gf_struct_sumk),\
             "give one transformation per correlated shell"
 
-        for icrsh in range(len(trans)):
+        for icrsh in list(range(len(trans))):
             ish = self.corr_to_inequiv[icrsh]
             if trans[icrsh] is None:
                 trans[icrsh] = {block: np.eye(len(indices))
@@ -261,7 +261,7 @@ class BlockStructure(object):
                 trans[icrsh] = {block: copy.deepcopy(trans[icrsh])
                                 for block, indices in self.gf_struct_sumk[icrsh]}
 
-            assert trans[icrsh].keys() == self.gf_struct_sumk_dict[icrsh].keys(),\
+            assert list(trans[icrsh].keys()) == list(self.gf_struct_sumk_dict[icrsh].keys()),\
                 "wrong block names used in transformation (icrsh = {})".format(icrsh)
 
             for block in trans[icrsh]:
@@ -422,15 +422,15 @@ class BlockStructure(object):
             # create new solver_to_sumk
             so2su = {}
             so2su_block = {}
-            for blk, idxs in gf_struct.items():
+            for blk,idxs in list(gf_struct.items()):
                 for i in range(len(idxs)):
                     so2su[(blk, i)] = self.solver_to_sumk[ish][(blk, idxs[i])]
                     so2su_block[blk] = so2su[(blk, i)][0]
             self.solver_to_sumk[ish] = so2su
             self.solver_to_sumk_block[ish] = so2su_block
             # create new sumk_to_solver
-            for k, v in self.sumk_to_solver[ish].items():
+            for k,v in list(self.sumk_to_solver[ish].items()):
-                blk, ind = v
+                blk,ind=v
                 if blk in gf_struct and ind in gf_struct[blk]:
                     new_ind = gf_struct[blk].index(ind)
                     self.sumk_to_solver[ish][k] = (blk, new_ind)
@@ -443,8 +443,8 @@ class BlockStructure(object):
 
             # reindexing gf_struct so that it starts with 0
             for k in gf_struct:
-                gf_struct[k] = range(len(gf_struct[k]))
+                gf_struct[k]=list(range(len(gf_struct[k])))
-            self.gf_struct_solver[ish] = gf_struct
+            self.gf_struct_solver[ish]=gf_struct
 
     def adapt_deg_shells(self, gf_struct, ish=0):
         """ Adapts the deg_shells to a new gf_struct
@@ -453,7 +453,7 @@ class BlockStructure(object):
         if self.deg_shells is not None:
             for degsh in self.deg_shells[ish]:
                 if isinstance(degsh, dict):
-                    for key in degsh.keys():
+                    for key in list(degsh.keys()):
                         if not key in gf_struct:
                             del degsh[key]
                             continue
@@ -539,11 +539,11 @@ class BlockStructure(object):
         for icrsh in range(len(new_gf_struct_transformed)):
             ish = self.corr_to_inequiv[icrsh]
             gfs.append({})
-            for block in new_gf_struct_transformed[icrsh].keys():
+            for block in list(new_gf_struct_transformed[icrsh].keys()):
                 for ind in new_gf_struct_transformed[icrsh][block]:
-                    ind_sol = self.sumk_to_solver[ish][(block, ind)]
+                    ind_sol = self.sumk_to_solver[ish][(block,ind)]
                     if not ind_sol[0] in gfs[icrsh]:
-                        gfs[icrsh][ind_sol[0]] = []
+                        gfs[icrsh][ind_sol[0]]=[]
                     gfs[icrsh][ind_sol[0]].append(ind_sol[1])
         self.pick_gf_struct_solver(gfs)
 
@@ -579,7 +579,7 @@ class BlockStructure(object):
             so2su = {}
             su2so = {}
             so2su_block = {}
-            for frm, to in mapping[ish].iteritems():
+            for frm,to in list(mapping[ish].items()):
                 if not to[0] in gf_struct:
                     gf_struct[to[0]] = []
                 gf_struct[to[0]].append(to[1])
@@ -594,7 +594,7 @@ class BlockStructure(object):
                 else:
                     so2su_block[to[0]] =\
                         self.solver_to_sumk_block[ish][frm[0]]
-            for k in self.sumk_to_solver[ish].keys():
+            for k in list(self.sumk_to_solver[ish].keys()):
                 if not k in su2so:
                     su2so[k] = (None, None)
 
@@ -669,7 +669,7 @@ class BlockStructure(object):
             raise Exception(
                 "Argument space has to be either 'solver' or 'sumk'.")
 
-        names = gf_struct[ish].keys()
+        names = list(gf_struct[ish].keys())
         blocks = []
         for n in names:
             G = gf_function(indices=gf_struct[ish][n], **kwargs)
@@ -738,7 +738,7 @@ class BlockStructure(object):
             assert len(G) == len(gf_struct),\
                 "list of G does not have the correct length"
             if ish is None:
-                ishs = range(len(gf_struct))
+                ishs = list(range(len(gf_struct)))
             else:
                 ishs = [ish]
             for ish in ishs:
@@ -755,17 +755,17 @@ class BlockStructure(object):
             for block, gf in G:
                 assert block in gf_struct[ish],\
                     "block " + block + " not in struct (shell {})".format(ish)
-                assert list(gf.indices) == 2 * [map(str, gf_struct[ish][block])],\
+                assert list(gf.indices) == 2 * [list(map(str, gf_struct[ish][block]))],\
                     "block " + block + \
                     " has wrong indices (shell {})".format(ish)
         else:
             for block in gf_struct[ish]:
                 assert block in G,\
                     "block " + block + " not in G (shell {})".format(ish)
-            for block, gf in G.iteritems():
+            for block, gf in list(G.items()):
                 assert block in gf_struct[ish],\
                     "block " + block + " not in struct (shell {})".format(ish)
-                assert range(len(gf)) == 2 * [map(str, gf_struct[ish][block])],\
+                assert list(range(len(gf))) == 2 * [list(map(str, gf_struct[ish][block]))],\
                     "block " + block + \
                     " has wrong indices (shell {})".format(ish)
 
@@ -775,20 +775,20 @@ class BlockStructure(object):
 
         Parameters
         ----------
-        O : pytriqs.operators.Operator
+        O : triqs.operators.Operator
             Operator in sumk structure
 
         ish : int
             shell index on which the operator acts
         """
 
-        from pytriqs.operators import Operator, c, c_dag
+        from triqs.operators import Operator, c, c_dag
-        
+
         T = self.transformation[ish]
         sk2s = self.sumk_to_solver[ish]
-        
+
         O_out = Operator(0)
-        
+
         for monomial in O:
             coefficient = monomial[-1]
             new_monomial = Operator(1)
@@ -796,7 +796,7 @@ class BlockStructure(object):
             for single_operator in monomial[0]:
                 new_single_operator = Operator(0)
                 daggered = single_operator[0]
-                
+
                 blockname = single_operator[1][0]
                 i = single_operator[1][1]
                 for j in range(len(T[blockname])):
@@ -961,7 +961,7 @@ class BlockStructure(object):
         else:
             raise Exception('G is neither BlockGf nor dict.')
 
-        for block_to in gf_struct_to.keys():
+        for block_to in list(gf_struct_to.keys()):
             if isinstance(G, BlockGf):
                 G_out[block_to].zero()
             else:
@@ -989,7 +989,7 @@ class BlockStructure(object):
                                                     ish_to=ish_from,
                                                     show_warnings=False,  # else we get an endless loop
                                                     space_from=space_to, space_to=space_from, **kwargs)
-            for name, gf in (G_back if isinstance(G, BlockGf) else G_back.iteritems()):
+            for name, gf in (G_back if isinstance(G, BlockGf) else list(G_back.items())):
                 if isinstance(G, BlockGf):
                     maxdiff = np.max(np.abs(G_back[name].data - G[name].data),
                                      axis=0)
@@ -1033,7 +1033,7 @@ class BlockStructure(object):
             self.gf_struct_solver.append({})
             self.solver_to_sumk.append({})
             self.solver_to_sumk_block.append({})
-            for frm,to in self.sumk_to_solver[ish].iteritems():
+            for frm,to in list(self.sumk_to_solver[ish].items()):
                 if to[0] is not None:
                     self.gf_struct_solver[ish][frm[0]+'_'+str(frm[1])]=[0]
                     self.sumk_to_solver[ish][frm]=(frm[0]+'_'+str(frm[1]),0)
@@ -1061,7 +1061,7 @@ class BlockStructure(object):
             elif isinstance(one,dict):
                 if set(one.keys()) != set(two.keys()):
                     return False
-                for k in set(one.keys()).intersection(two.keys()):
+                for k in set(one.keys()).intersection(list(two.keys())):
                     if not compare(one[k],two[k]):
                         return False
                 return True
@@ -1096,7 +1096,7 @@ class BlockStructure(object):
             d = []
             for ish in range(len(mapping)):
                 d.append({})
-                for k,v in mapping[ish].iteritems():
+                for k,v in list(mapping[ish].items()):
                     d[ish][repr(k)] = repr(v)
             return d
 
@@ -1112,7 +1112,7 @@ class BlockStructure(object):
             d = []
             for ish in range(len(mapping)):
                 d.append({})
-                for k,v in mapping[ish].iteritems():
+                for k,v in list(mapping[ish].items()):
                     # literal_eval is a saje alternative to eval
                     d[ish][literal_eval(k)] = literal_eval(v)
             return d
@@ -1138,7 +1138,7 @@ class BlockStructure(object):
                 s+=' shell '+str(ish)+'\n'
                 def keyfun(el):
                     return '{}_{:05d}'.format(el[0],el[1])
-                keys = sorted(element[ish].keys(),key=keyfun)
+                keys = sorted(list(element[ish].keys()),key=keyfun)
                 for k in keys:
                     s+='  '+str(k)+str(element[ish][k])+'\n'
         s += "deg_shells\n"
@@ -1147,7 +1147,7 @@ class BlockStructure(object):
             for l in range(len(self.deg_shells[ish])):
                 s+='  equivalent group '+str(l)+'\n'
                 if isinstance(self.deg_shells[ish][l],dict):
-                    for key, val in self.deg_shells[ish][l].iteritems():
+                    for key, val in list(self.deg_shells[ish][l].items()):
                         s+='   '+key+('*' if val[1] else '')+':\n'
                         s+='    '+str(val[0]).replace('\n','\n    ')+'\n'
                 else:
@@ -1157,5 +1157,5 @@ class BlockStructure(object):
         s += str(self.transformation)
         return s
 
-from pytriqs.archive.hdf_archive_schemes import register_class
+from h5.formats import register_class
 register_class(BlockStructure)

python/triqs_dft_tools/clear_h5_output.py

@@ -3,13 +3,13 @@ import sys
 import subprocess
 
 if len(sys.argv) < 2:
-    print "Usage: python clear_h5_output.py archive"
+    print("Usage: python clear_h5_output.py archive")
     sys.exit()
 
-print """
+print("""
 This script is to remove any SumkDFT generated output from the h5 archive
 and to restore it to the original post-converter state.
-"""
+""")
 
 filename = sys.argv[1]
 A = h5py.File(filename)
@@ -21,6 +21,6 @@ A.close()
 # Repack to reclaim disk space
 retcode = subprocess.call(["h5repack", "-i%s" % filename, "-otemphgfrt.h5"])
 if retcode != 0:
-    print "h5repack failed!"
+    print("h5repack failed!")
 else:
     subprocess.call(["mv", "-f", "temphgfrt.h5", "%s" % filename])

python/triqs_dft_tools/converters/__init__.py

@@ -20,10 +20,10 @@
 #
 ##########################################################################
 
-from wien2k_converter import Wien2kConverter
+from .wien2k import Wien2kConverter
-from hk_converter import HkConverter
+from .hk import HkConverter
-from vasp_converter import VaspConverter
+from .vasp import VaspConverter
-from wannier90_converter import Wannier90Converter
+from .wannier90 import Wannier90Converter
 
 __all__ =['Wien2kConverter','HkConverter','Wannier90Converter','VaspConverter']
 

python/triqs_dft_tools/converters/converter_tools.py

@@ -19,7 +19,7 @@
 # TRIQS. If not, see <http://www.gnu.org/licenses/>.
 #
 ##########################################################################
-import pytriqs.utility.mpi as mpi
+import triqs.utility.mpi as mpi
 
 class ConverterTools:
 
@@ -46,12 +46,12 @@ class ConverterTools:
         import os.path
         import string
         if not(os.path.exists(filename)):
-            raise IOError, "File %s does not exist." % filename
+            raise IOError("File %s does not exist." % filename)
         for line in open(filename, 'r'):
-            for old, new in to_replace.iteritems():
+            for old, new in to_replace.items():
                 line = line.replace(old, new)
             for x in line.split():
-                yield string.atof(x)
+                yield float(x)
 
     def repack(self):
         """

python/triqs_dft_tools/converters/hk.py

@@ -22,10 +22,10 @@
 
 from types import *
 import numpy
-from pytriqs.archive import *
+from h5 import *
-import pytriqs.utility.mpi as mpi
+import triqs.utility.mpi as mpi
 from math import sqrt
-from converter_tools import *
+from .converter_tools import *
 
 
 class HkConverter(ConverterTools):
@@ -53,8 +53,7 @@ class HkConverter(ConverterTools):
 
         """
 
-        assert type(
+        assert isinstance(filename, str), "HkConverter: filename must be a filename."
-            filename) == StringType, "HkConverter: filename must be a filename."
         if hdf_filename is None:
             hdf_filename = filename + '.h5'
         self.hdf_file = hdf_filename
@@ -96,20 +95,20 @@ class HkConverter(ConverterTools):
             # the energy conversion factor is 1.0, we assume eV in files
             energy_unit = 1.0
             # read the number of k points
-            n_k = int(R.next())
+            n_k = int(next(R))
             k_dep_projection = 0
             SP = 0                                        # no spin-polarision
             SO = 0                                        # no spin-orbit
             # total charge below energy window is set to 0
             charge_below = 0.0
             # density required, for setting the chemical potential
-            density_required = R.next()
+            density_required = next(R)
             symm_op = 0                                   # No symmetry groups for the k-sum
 
             # the information on the non-correlated shells is needed for
             # defining dimension of matrices:
             # number of shells considered in the Wanniers
-            n_shells = int(R.next())
+            n_shells = int(next(R))
             # corresponds to index R in formulas
             # now read the information about the shells (atom, sort, l, dim):
             shell_entries = ['atom', 'sort', 'l', 'dim']
@@ -117,7 +116,7 @@ class HkConverter(ConverterTools):
                 shell_entries, R)} for ish in range(n_shells)]
 
             # number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
-            n_corr_shells = int(R.next())
+            n_corr_shells = int(next(R))
             # corresponds to index R in formulas
             # now read the information about the shells (atom, sort, l, dim, SO
             # flag, irep):
@@ -141,8 +140,8 @@ class HkConverter(ConverterTools):
             T = []
             for ish in range(n_inequiv_shells):
                 # number of representatives ("subsets"), e.g. t2g and eg
-                n_reps[ish] = int(R.next())
+                n_reps[ish] = int(next(R))
-                dim_reps[ish] = [int(R.next()) for i in range(
+                dim_reps[ish] = [int(next(R)) for i in range(
                     n_reps[ish])]   # dimensions of the subsets
 
                 # The transformation matrix:
@@ -201,7 +200,7 @@ class HkConverter(ConverterTools):
             if (weights_in_file):
                 # weights in the file
                 for ik in range(n_k):
-                    bz_weights[ik] = R.next()
+                    bz_weights[ik] = next(R)
 
             # if the sum over spins is in the weights, take it out again!!
             sm = sum(bz_weights)
@@ -222,7 +221,7 @@ class HkConverter(ConverterTools):
                             else:
                                 istart = 0
                             for j in range(istart, n_orb):
-                                hopping[ik, isp, i, j] = R.next()
+                                hopping[ik, isp, i, j] = next(R)
 
                         for i in range(n_orb):
                             if (only_upper_triangle):
@@ -230,7 +229,7 @@ class HkConverter(ConverterTools):
                             else:
                                 istart = 0
                             for j in range(istart, n_orb):
-                                hopping[ik, isp, i, j] += R.next() * 1j
+                                hopping[ik, isp, i, j] += next(R) * 1j
                                 if ((only_upper_triangle)and(i != j)):
                                     hopping[ik, isp, j, i] = hopping[
                                         ik, isp, i, j].conjugate()
@@ -243,8 +242,8 @@ class HkConverter(ConverterTools):
                             else:
                                 istart = 0
                             for j in range(istart, n_orb):
-                                hopping[ik, isp, i, j] = R.next()
+                                hopping[ik, isp, i, j] = next(R)
-                                hopping[ik, isp, i, j] += R.next() * 1j
+                                hopping[ik, isp, i, j] += next(R) * 1j
 
                                 if ((only_upper_triangle)and(i != j)):
                                     hopping[ik, isp, j, i] = hopping[

python/triqs_dft_tools/converters/plovasp/__init__.py

@@ -1,4 +1,3 @@
- 
 ################################################################################
 #
 # TRIQS: a Toolbox for Research in Interacting Quantum Systems

python/triqs_dft_tools/converters/plovasp/atm_desc.py

@@ -1,5 +1,5 @@
 # Generated automatically using the command :
-# c++2py.py -m atm -o atm --moduledoc "Analytical Tetrahedron Method for DOS" ../../../c++/plovasp/atm/dos_tetra3d.hpp
+# c++2py.py -m atm -o atm --moduledoc "Analytical Tetrahedron Method for DOS" ../../../../c++/triqs_dft_tools/converters/vasp/dos_tetra3d.hpp
 from cpp2py.wrap_generator import *
 
 # The module
@@ -8,11 +8,12 @@ module = module_(full_name = "atm", doc = "Analytical Tetrahedron Method for cal
 # All the triqs C++/Python modules
 
 # Add here all includes beyond what is automatically included by the triqs modules
-module.add_include("plovasp/atm/dos_tetra3d.hpp")
+module.add_include("triqs_dft_tools/converters/vasp/dos_tetra3d.hpp")
 
 # Add here anything to add in the C++ code at the start, e.g. namespace using
 module.add_preamble("""
 #include <triqs/cpp2py_converters/arrays.hpp>
+using namespace triqs::arrays;
 """)
 
 module.add_function ("array<double,2> dos_tetra_weights_3d (array_view<double,1> eigk, double en, array_view<long,2> itt)", doc = """DOS of a band by analytical tetrahedron method\n\n   Returns corner weights for all tetrahedra for a given band and real energy.""")

python/triqs_dft_tools/converters/plovasp/converter.py

@@ -36,10 +36,10 @@ r"""
     Usage: python converter.py <conf-file> [<path-to-vasp-calculation>]
 """
 import sys
-import vaspio
+from . import vaspio
-from inpconf import ConfigParameters
+from .inpconf import ConfigParameters
-from elstruct import ElectronicStructure
+from .elstruct import ElectronicStructure
-from plotools import generate_plo, output_as_text
+from .plotools import generate_plo, output_as_text
 
 def generate_and_output_as_text(conf_filename, vasp_dir):
     """

python/triqs_dft_tools/converters/plovasp/elstruct.py

@@ -92,7 +92,7 @@ class ElectronicStructure:
 #        removed completely.
 #        if not vasp_data.eigenval.eigs is None:
         if False:
-            print "eigvals from EIGENVAL"
+            print("eigvals from EIGENVAL")
             self.eigvals = vasp_data.eigenval.eigs
             self.ferw = vasp_data.eigenval.ferw.transpose((2, 0, 1))
 
@@ -102,7 +102,7 @@ class ElectronicStructure:
 # Check that the number of band is the same in PROJCAR and EIGENVAL
             assert nb_plo == self.nband, "PLOCAR is inconsistent with EIGENVAL (number of bands)"
         else:
-            print "eigvals from LOCPROJ"
+            print("eigvals from LOCPROJ")
             self.eigvals = vasp_data.plocar.eigs
             self.ferw = vasp_data.plocar.ferw.transpose((2, 0, 1))
             self.efermi = vasp_data.doscar.efermi
@@ -142,7 +142,7 @@ class ElectronicStructure:
 ## Construct a map to access coordinates by index
 #        self.structure['ion_index'] = []
 #        for isort, nq in enumerate(self.structure['nq_types']):
-#            for iq in xrange(nq):
+#            for iq in range(nq):
 #                self.structure['ion_index'].append((isort, iq))
 
 
@@ -154,7 +154,7 @@ class ElectronicStructure:
         nproj, ns, nk, nb = plo.shape
         ions = sorted(list(set([param['isite'] for param in self.proj_params])))
         nions = len(ions)
-        norb = nproj / nions
+        norb = nproj // nions
 
 # Spin factor
         sp_fac = 2.0 if ns == 1 and not self.nc_flag else 1.0
@@ -163,8 +163,8 @@ class ElectronicStructure:
         overlap = np.zeros((ns, nproj, nproj), dtype=np.float64)
 #        ov_min = np.ones((ns, nproj, nproj), dtype=np.float64) * 100.0
 #        ov_max = np.zeros((ns, nproj, nproj), dtype=np.float64)
-        for ispin in xrange(ns):
+        for ispin in range(ns):
-            for ik in xrange(nk):
+            for ik in range(nk):
                 kweight = self.kmesh['kweights'][ik]
                 occ = self.ferw[ispin, ik, :]
                 den_mat[ispin, :, :] += np.dot(plo[:, ispin, ik, :] * occ, plo[:, ispin, ik, :].T.conj()).real * kweight * sp_fac
@@ -174,12 +174,12 @@ class ElectronicStructure:
 #                ov_min = np.minimum(ov, ov_min)
 
 # Output only the site-diagonal parts of the matrices
-        print
+        print()
-        print "  Unorthonormalized density matrices and overlaps:"
+        print("  Unorthonormalized density matrices and overlaps:")
-        for ispin in xrange(ns):
+        for ispin in range(ns):
-            print "  Spin:", ispin + 1
+            print("  Spin:", ispin + 1)
             for io, ion in enumerate(ions):
-                print "  Site:", ion
+                print("  Site:", ion)
                 iorb_inds = [(ip, param['m']) for ip, param in enumerate(self.proj_params) if param['isite'] == ion]
                 norb = len(iorb_inds)
                 dm = np.zeros((norb, norb))
@@ -189,9 +189,9 @@ class ElectronicStructure:
                         dm[iorb, iorb2] = den_mat[ispin, ind, ind2]
                         ov[iorb, iorb2] = overlap[ispin, ind, ind2]
 
-                print "  Density matrix" + (12*norb - 12 + 2)*" " + "Overlap"
+                print("  Density matrix" + (12*norb - 12 + 2)*" " + "Overlap")
                 for drow, dov in zip(dm, ov):
                     out = ''.join(map("{0:12.7f}".format, drow))
                     out += "    "
                     out += ''.join(map("{0:12.7f}".format, dov))
-                    print out
+                    print(out)

python/triqs_dft_tools/converters/plovasp/inpconf.py

@@ -29,20 +29,20 @@ r"""
 
   Module for parsing and checking an input config-file.
 """
-import ConfigParser
+import configparser
 import numpy as np
 import re
 import sys
 import itertools as it
-import vaspio
+from . import vaspio
 
 def issue_warning(message):
     """
     Issues a warning.
     """
-    print
+    print()
-    print "  !!! WARNING !!!: " + message
+    print("  !!! WARNING !!!: " + message)
-    print
+    print()
 
 ################################################################################
 ################################################################################
@@ -73,7 +73,7 @@ class ConfigParameters:
 ################################################################################
     def __init__(self, input_filename, verbosity=1):
         self.verbosity = verbosity
-        self.cp = ConfigParser.SafeConfigParser()
+        self.cp = configparser.SafeConfigParser()
         self.cp.readfp(open(input_filename, 'r'))
 
         self.parameters = {}
@@ -89,7 +89,7 @@ class ConfigParameters:
             'corr': ('corr', self.parse_string_logical, True)}
 
         self.gr_required = {
-            'shells': ('shells', lambda s: map(int, s.split())),
+            'shells': ('shells', lambda s: list(map(int, s.split()))),
             'ewindow': ('ewindow', self.parse_energy_window)}
 
         self.gr_optional = {
@@ -142,7 +142,7 @@ class ConfigParameters:
         else:
 # Check if a set of indices is given
             try:
-                l_tmp = map(int, par_str.split())
+                l_tmp = list(map(int, par_str.split()))
                 l_tmp.sort()
 # Subtract 1 so that VASP indices (starting with 1) are converted
 # to Python indices (starting with 0)
@@ -160,7 +160,7 @@ class ConfigParameters:
                 ion_list = []
                 nion = 0
                 for cl in classes:
-                    ions = map(int, re.findall(patt2, cl))
+                    ions = list(map(int, re.findall(patt2, cl)))
                     ion_list.append([ion - 1 for ion in ions])
                     nion += len(ions)
 
@@ -218,7 +218,7 @@ class ConfigParameters:
         Energy window is given by two floats, with the first one being smaller
         than the second one.
         """
-        ftmp = map(float, par_str.split())
+        ftmp = list(map(float, par_str.split()))
         assert len(ftmp) == 2, "EWINDOW must be specified by exactly two floats"
         assert ftmp[0] < ftmp[1], "The first float in EWINDOW must be smaller than the second one"
         return tuple(ftmp)
@@ -233,7 +233,7 @@ class ConfigParameters:
         Band window is given by two ints, with the first one being smaller
         than the second one.
         """
-        ftmp = map(int, par_str.split())
+        ftmp = list(map(int, par_str.split()))
         assert len(ftmp) == 2, "BANDS must be specified by exactly two ints"
         assert ftmp[0] < ftmp[1], "The first int in BANDS must be smaller than the second one"
         return tuple(ftmp)
@@ -250,7 +250,7 @@ class ConfigParameters:
         """
         str_rows = par_str.split('\n')
         try:
-            rows = [map(float, s.split()) for s in str_rows]
+            rows = [list(map(float, s.split())) for s in str_rows]
         except ValueError:
             err_mess = "Cannot parse a matrix string:\n%s"%(par_str)
             raise ValueError(err_mess)
@@ -266,7 +266,7 @@ class ConfigParameters:
             mat = np.array(rows)
         else:
             err_mess = "Complex matrix must contain 2*M values:\n%s"%(par_str)
-            assert 2 * (nm / 2) == nm, err_mess
+            assert 2 * (nm // 2) == nm, err_mess
 
             tmp = np.array(rows, dtype=np.complex128)
             mat = tmp[:, 0::2] + 1.0j * tmp[:, 1::2]
@@ -339,11 +339,11 @@ class ConfigParameters:
         For required parameters `exception=True` must be set.
         """
         parsed = {}
-        for par in param_set.keys():
+        for par in list(param_set.keys()):
             key = param_set[par][0]
             try:
                 par_str = self.cp.get(section, par)
-            except (ConfigParser.NoOptionError, ConfigParser.NoSectionError):
+            except (configparser.NoOptionError, configparser.NoSectionError):
                 if exception:
                     message = "Required parameter '%s' not found in section [%s]"%(par, section)
                     raise Exception(message)
@@ -354,7 +354,7 @@ class ConfigParameters:
                     continue
 
             if self.verbosity > 0:
-                print "  %s = %s"%(par, par_str)
+                print("  %s = %s"%(par, par_str))
 
             parse_fun = param_set[par][1]
             parsed[key] = parse_fun(par_str)
@@ -376,27 +376,27 @@ class ConfigParameters:
         sections = self.cp.sections()
 
         sh_patt1 = re.compile('shell +.*', re.IGNORECASE)
-        sec_shells = filter(sh_patt1.match, sections)
+        sec_shells = list(filter(sh_patt1.match, sections))
 
         self.nshells = len(sec_shells)
         assert self.nshells > 0, "No projected shells found in the input file"
 
         if self.verbosity > 0:
-            print
+            print()
             if self.nshells > 1:
-                print "  Found %i projected shells"%(self.nshells)
+                print("  Found %i projected shells"%(self.nshells))
             else:
-                print "  Found 1 projected shell"
+                print("  Found 1 projected shell")
 
 # Get shell indices
         sh_patt2 = re.compile('shell +([0-9]*)$', re.IGNORECASE)
         try:
             get_ind = lambda s: int(sh_patt2.match(s).groups()[0])
-            sh_inds = map(get_ind, sec_shells)
+            sh_inds = list(map(get_ind, sec_shells))
         except (ValueError, AttributeError):
             raise ValueError("Failed to extract shell indices from a list: %s"%(sec_shells))
 
-        self.sh_sections = {ind: sec for ind, sec in it.izip(sh_inds, sec_shells)}
+        self.sh_sections = {ind: sec for ind, sec in zip(sh_inds, sec_shells)}
 
 # Check that all indices are unique
 # In principle redundant because the list of sections will contain only unique names
@@ -405,7 +405,7 @@ class ConfigParameters:
 # Ideally, indices should run from 1 to <nshells>
 # If it's not the case, issue a warning
         sh_inds.sort()
-        if sh_inds != range(1, len(sh_inds) + 1):
+        if sh_inds != list(range(1, len(sh_inds) + 1)):
             issue_warning("Shell indices are not uniform or not starting from 1. "
                "This might be an indication of a incorrect setup.")
 
@@ -418,8 +418,8 @@ class ConfigParameters:
             section = self.sh_sections[ind]
 
             if self.verbosity > 0:
-                print
+                print()
-                print "  Shell parameters:"
+                print("  Shell parameters:")
 # Shell required parameters
             parsed = self.parse_parameter_set(section, self.sh_required, exception=True)
             shell.update(parsed)
@@ -453,7 +453,7 @@ class ConfigParameters:
         sections = self.cp.sections()
 
         gr_patt = re.compile('group +(.*)', re.IGNORECASE)
-        sec_groups = filter(gr_patt.match, sections)
+        sec_groups = list(filter(gr_patt.match, sections))
 
         self.ngroups = len(sec_groups)
 
@@ -471,8 +471,8 @@ class ConfigParameters:
             group['index'] = gr_ind
 
             if self.verbosity > 0:
-                print
+                print()
-                print "  Group parameters:"
+                print("  Group parameters:")
 # Group required parameters
             parsed = self.parse_parameter_set(section, self.gr_required, exception=True)
             group.update(parsed)
@@ -514,18 +514,18 @@ class ConfigParameters:
             sh_gr_required = dict(self.gr_required)
             sh_gr_required.pop('shells')
             try:
-                for par in sh_gr_required.keys():
+                for par in list(sh_gr_required.keys()):
                     key = sh_gr_required[par][0]
                     value = self.shells[0].pop(key)
                     self.groups[0][key] = value
             except KeyError:
                 message = "One [Shell] section is specified but no explicit [Group] section is provided."
                 message += " In this case the [Shell] section must contain all required group information.\n"
-                message += "  Required parameters are: %s"%(sh_gr_required.keys())
+                message += "  Required parameters are: %s"%(list(sh_gr_required.keys()))
                 raise KeyError(message)
 
 # Do the same for optional group parameters, but do not raise an exception
-            for par in self.gr_optional.keys():
+            for par in list(self.gr_optional.keys()):
                 try:
                     key = self.gr_optional[par][0]
                     value = self.shells[0].pop(key)
@@ -562,7 +562,7 @@ class ConfigParameters:
 # remove them and issue a warning.
 #
 # First, required group parameters
-                for par in self.gr_required.keys():
+                for par in list(self.gr_required.keys()):
                     try:
                         key = self.gr_required[par][0]
                         value = shell.pop(key)
@@ -573,7 +573,7 @@ class ConfigParameters:
                         continue
 
 # Second, optional group parameters
-                for par in self.gr_optional.keys():
+                for par in list(self.gr_optional.keys()):
                     try:
                         key = self.gr_optional[par][0]
                         value = shell.pop(key)
@@ -591,7 +591,7 @@ class ConfigParameters:
         sh_refs_used.sort()
 
 # Check that all shells are referenced in the groups
-        assert sh_refs_used == range(self.nshells), "Some shells are not inside any of the groups"
+        assert sh_refs_used == list(range(self.nshells)), "Some shells are not inside any of the groups"
 
 
 ################################################################################
@@ -605,7 +605,7 @@ class ConfigParameters:
         """
         self.general = {}
         sections = self.cp.sections()
-        gen_section = filter(lambda s: s.lower() == 'general', sections)
+        gen_section = [s for s in sections if s.lower() == 'general']
 # If no [General] section is found parse a dummy section name to the parser
 # to reset parameters to their default values
         if len(gen_section) > 1:

python/triqs_dft_tools/converters/plovasp/plotools.py

@@ -55,9 +55,9 @@ r"""
 """
 import itertools as it
 import numpy as np
-from proj_group import ProjectorGroup
+from .proj_group import ProjectorGroup
-from proj_shell import ProjectorShell
+from .proj_shell import ProjectorShell
-from proj_shell import ComplementShell
+from .proj_shell import ComplementShell
 
 np.set_printoptions(suppress=True)
 
@@ -71,9 +71,9 @@ def issue_warning(message):
     """
     Issues a warning.
     """
-    print
+    print()
-    print "  !!! WARNING !!!: " + message
+    print("  !!! WARNING !!!: " + message)
-    print
+    print()
 
 ################################################################################
 # check_data_consistency()
@@ -129,18 +129,18 @@ def generate_plo(conf_pars, el_struct):
 # check if at least one shell is correlated
     assert np.any([shell['corr'] for shell in conf_pars.shells]), 'at least one shell has be CORR = True'
     nshell = len(conf_pars.shells)
-    print
+    print()
-    print "  Generating %i shell%s..."%(nshell, '' if nshell == 1 else 's')
+    print("  Generating %i shell%s..."%(nshell, '' if nshell == 1 else 's'))
     pshells = []
     for sh_par in conf_pars.shells:
         pshell = ProjectorShell(sh_par, proj_raw, el_struct.proj_params, el_struct.kmesh, el_struct.structure, el_struct.nc_flag)
-        print
+        print()
-        print "    Shell         : %s"%(pshell.user_index)
+        print("    Shell         : %s"%(pshell.user_index))
-        print "    Orbital l     : %i"%(pshell.lorb)
+        print("    Orbital l     : %i"%(pshell.lorb))
-        print "    Number of ions: %i"%(pshell.nion)
+        print("    Number of ions: %i"%(pshell.nion))
-        print "    Dimension     : %i"%(pshell.ndim)
+        print("    Dimension     : %i"%(pshell.ndim))
-        print "    Correlated    : %r"%(pshell.corr)
+        print("    Correlated    : %r"%(pshell.corr))
-        print "    Ion sort      : %r"%(pshell.ion_sort)
+        print("    Ion sort      : %r"%(pshell.ion_sort))
         pshells.append(pshell)
 
 
@@ -153,49 +153,49 @@ def generate_plo(conf_pars, el_struct):
         if conf_pars.general['hk']:
             pgroup.calc_hk(eigvals)
             #testout = 'hk.out.h5'
-            #from pytriqs.archive import HDFArchive
+            #from h5 import HDFArchive
             #with HDFArchive(testout, 'w') as h5test:
             #    h5test['hk'] = pgroup.hk
 # DEBUG output
-        print "Density matrix:"
+        print("Density matrix:")
         nimp = 0.0
         ov_all = []
         for ish in pgroup.ishells:
             if  not isinstance(pshells[pgroup.ishells[ish]],ComplementShell):
-                print "  Shell %i"%(ish + 1)
+                print("  Shell %i"%(ish + 1))
                 dm_all, ov_all_ = pshells[ish].density_matrix(el_struct)
                 ov_all.append(ov_all_[0])
                 spin_fac = 2 if dm_all.shape[0] == 1 else 1
-                for io in xrange(dm_all.shape[1]):
+                for io in range(dm_all.shape[1]):
-                    print "    Site %i"%(io + 1)
+                    print("    Site %i"%(io + 1))
                     dm = spin_fac * dm_all[:, io, : ,:].sum(0)
                     for row in dm:
-                        print ''.join(map("{0:14.7f}".format, row))
+                        print(''.join(map("{0:14.7f}".format, row)))
                     ndm = dm.trace()
                     if pshells[ish].corr:
                         nimp += ndm
-                    print "      trace: ", ndm
+                    print("      trace: ", ndm)
-        print
+        print()
-        print "  Impurity density:", nimp
+        print("  Impurity density:", nimp)
-        print
+        print()
-        print "Overlap:"
+        print("Overlap:")
         for io, ov in enumerate(ov_all):
-            print "  Site %i"%(io + 1)
+            print("  Site %i"%(io + 1))
-            print ov[0,...]
+            print(ov[0,...])
-        print
+        print()
-        print "Local Hamiltonian:"
+        print("Local Hamiltonian:")
         for ish in pgroup.ishells:
             if  not isinstance(pshells[pgroup.ishells[ish]],ComplementShell):
-                print "  Shell %i"%(ish + 1)
+                print("  Shell %i"%(ish + 1))
                 loc_ham = pshells[pgroup.ishells[ish]].local_hamiltonian(el_struct)
-                for io in xrange(loc_ham.shape[1]):
+                for io in range(loc_ham.shape[1]):
-                    print "    Site %i (real | complex part)"%(io + 1)
+                    print("    Site %i (real | complex part)"%(io + 1))
                     for row in loc_ham[:, io, :, :].sum(0):
-                        print ''.join(map("{0:14.7f}".format, row.real))+' |'+''.join(map("{0:14.7f}".format, row.imag))
+                        print(''.join(map("{0:14.7f}".format, row.real))+' |'+''.join(map("{0:14.7f}".format, row.imag)))
 # END DEBUG output
         if 'dosmesh' in conf_pars.general:
-            print
+            print()
-            print "Evaluating DOS..."
+            print("Evaluating DOS...")
             mesh_pars = conf_pars.general['dosmesh']
             if np.isnan(mesh_pars['emin']):
                 dos_emin = pgroup.emin
@@ -208,12 +208,12 @@ def generate_plo(conf_pars, el_struct):
             emesh = np.linspace(dos_emin, dos_emax, n_points)
             for ish in pgroup.ishells:
                 if  not isinstance(pshells[pgroup.ishells[ish]],ComplementShell) or True:
-                    print "  Shell %i"%(ish + 1)
+                    print("  Shell %i"%(ish + 1))
                     dos = pshells[pgroup.ishells[ish]].density_of_states(el_struct, emesh)
                     de = emesh[1] - emesh[0]
                     ntot = (dos[1:,...] + dos[:-1,...]).sum(0) / 2 * de
-                    print "    Total number of states:", ntot
+                    print("    Total number of states:", ntot)
-                    for io in xrange(dos.shape[2]):
+                    for io in range(dos.shape[2]):
                         np.savetxt('pdos_%i_%i.dat'%(ish,io), np.vstack((emesh.T, dos[:, 0, io, :].T)).T)
 
         pgroups.append(pgroup)
@@ -254,7 +254,7 @@ def kpoints_output(basename, el_struct):
         f.write("%i\n"%(nktot))
 # TODO: add the output of reciprocal lattice vectors
         f.write("# List of k-points with weights\n")
-        for ik in xrange(nktot):
+        for ik in range(nktot):
             kx, ky, kz = kmesh['kpoints'][ik, :]
             kwght = kmesh['kweights'][ik]
             f.write("%15.10f%15.10f%15.10f%20.10f\n"%(kx, ky, kz, kwght))
@@ -266,7 +266,7 @@ def kpoints_output(basename, el_struct):
             f.write("\n# Number of tetrahedra and volume: ntet, volt\n")
             f.write("%i %s\n"%(ntet, volt))
             f.write("# List of tetrahedra: imult, ik1, ..., ik4\n")
-            for it in xrange(ntet):
+            for it in range(ntet):
                 f.write('  '.join(map("{0:d}".format, *kmesh['itet'][it, :])) + '\n')
         except KeyError:
             pass
@@ -315,14 +315,14 @@ def ctrl_output(conf_pars, el_struct, ng):
 
     header = json.dumps(head_dict, indent=4, separators=(',', ': '))
 
-    print "  Storing ctrl-file..."
+    print("  Storing ctrl-file...")
     with open(ctrl_fname, 'wt') as f:
         f.write(header + "\n")
         f.write("#END OF HEADER\n")
 
         f.write("# k-points and weights\n")
         labels = ['kx', 'ky', 'kz', 'kweight']
-        out = "".join(map(lambda s: s.center(15), labels))
+        out = "".join([s.center(15) for s in labels])
         f.write("#" + out + "\n")
         for ik, kp in enumerate(el_struct.kmesh['kpoints']):
             tmp1 = "".join(map("{0:15.10f}".format, kp))
@@ -330,7 +330,7 @@ def ctrl_output(conf_pars, el_struct, ng):
             f.write(out + "\n")
         f.write("# k-points and weights cartesian\n")
         labels = ['kx', 'ky', 'kz']
-        out = "".join(map(lambda s: s.center(15), labels))
+        out = "".join([s.center(15) for s in labels])
         f.write("#" + out + "\n")
         for ik, kp in enumerate(el_struct.kmesh['kpoints_cart']):
             out = "".join(map("{0:15.10f}".format, kp))
@@ -381,7 +381,7 @@ def plo_output(conf_pars, el_struct, pshells, pgroups):
     """
     for ig, pgroup in enumerate(pgroups):
         plo_fname = conf_pars.general['basename'] + '.pg%i'%(ig + 1)
-        print "  Storing PLO-group file '%s'..."%(plo_fname)
+        print("  Storing PLO-group file '%s'..."%(plo_fname))
         head_dict = {}
 
 
@@ -394,7 +394,7 @@ def plo_output(conf_pars, el_struct, pshells, pgroups):
 
 # Number of electrons within the window
         head_dict['nelect'] = pgroup.nelect_window(el_struct)
-        print "  Density within window:", head_dict['nelect']
+        print("  Density within window:", head_dict['nelect'])
 
         head_shells = []
         for ish in pgroup.ishells:
@@ -430,13 +430,13 @@ def plo_output(conf_pars, el_struct, pshells, pgroups):
                 f.write("# Eigenvalues within the energy window: %s, %s\n"%(pgroup.emin, pgroup.emax))
 
             nk, nband, ns_band = el_struct.eigvals.shape
-            for isp in xrange(ns_band):
+            for isp in range(ns_band):
                 f.write("# is = %i\n"%(isp + 1))
-                for ik in xrange(nk):
+                for ik in range(nk):
                     ib1, ib2 = pgroup.ib_win[ik, isp, 0], pgroup.ib_win[ik, isp, 1]
 # Output band indices in Fortran convention!
                     f.write(" %i  %i\n"%(ib1 + 1, ib2 + 1))
-                    for ib in xrange(ib1, ib2 + 1):
+                    for ib in range(ib1, ib2 + 1):
                         eigv_ef = el_struct.eigvals[ik, ib, isp] - el_struct.efermi
                         f_weight = el_struct.ferw[isp, ik, ib]
                         f.write("%13.8f %12.7f\n"%(eigv_ef, f_weight))
@@ -449,15 +449,15 @@ def plo_output(conf_pars, el_struct, pshells, pgroups):
                 f.write("# Shell %i\n"%(ish))
 
                 nion, ns, nk, nlm, nb = shell.proj_win.shape
-                for isp in xrange(ns):
+                for isp in range(ns):
                     f.write("# is = %i\n"%(isp + 1))
-                    for ik in xrange(nk):
+                    for ik in range(nk):
                         f.write("# ik = %i\n"%(ik + 1))
-                        for ion in xrange(nion):
+                        for ion in range(nion):
-                            for ilm in xrange(nlm):
+                            for ilm in range(nlm):
                                 ib1, ib2 = pgroup.ib_win[ik, isp, 0], pgroup.ib_win[ik, isp, 1]
                                 ib_win = ib2 - ib1 + 1
-                                for ib in xrange(ib_win):
+                                for ib in range(ib_win):
                                     p = shell.proj_win[ion, isp, ik, ilm, ib]
                                     f.write("{0:16.10f}{1:16.10f}\n".format(p.real, p.imag))
                                 f.write("\n")
@@ -494,7 +494,7 @@ def hk_output(conf_pars, el_struct, pgroups):
     for ig, pgroup in enumerate(pgroups):
 
         hk_fname = conf_pars.general['basename'] + '.hk%i'%(ig + 1)
-        print "  Storing HK-group file '%s'..."%(hk_fname)
+        print("  Storing HK-group file '%s'..."%(hk_fname))
 
         head_shells = []
         for ish in pgroup.ishells:
@@ -528,13 +528,13 @@ def hk_output(conf_pars, el_struct, pgroups):
                 f.write('%i %i %i %i      # atom sort l dim\n'%(head['ion_list'][0],head['ion_sort'][0],head['lorb'],head['ndim']))
 
             norbs = pgroup.hk.shape[2]
-            for isp in xrange(ns_band):
+            for isp in range(ns_band):
-                for ik in xrange(nk):
+                for ik in range(nk):
-                    for io in xrange(norbs):
+                    for io in range(norbs):
-                        for iop in xrange(norbs):
+                        for iop in range(norbs):
                             f.write(" {0:14.10f}".format(pgroup.hk[isp,ik,io,iop].real))
                         f.write("\n")
-                    for io in xrange(norbs):
+                    for io in range(norbs):
-                        for iop in xrange(norbs):
+                        for iop in range(norbs):
                             f.write(" {0:14.10f}".format(pgroup.hk[isp,ik,io,iop].imag))
                         f.write("\n")

python/triqs_dft_tools/converters/plovasp/proj_group.py

@@ -30,7 +30,7 @@ r"""
     Storage and manipulation of projector groups.
 """
 import numpy as np
-from proj_shell import ComplementShell
+from .proj_shell import ComplementShell
 np.set_printoptions(suppress=True)
 
 ################################################################################
@@ -89,8 +89,8 @@ class ProjectorGroup:
             assert np.all( n_bands == n_bands[0,0] ), "At each band the same number of bands has to be selected for calculating the complement (to end up with an equal number of orbitals at each k-point)."
             if n_orbs == n_bands[0,0]:
                 self.complement = False
-                print "\nWARNING: The total number of orbitals in this group is  "
+                print("\nWARNING: The total number of orbitals in this group is  ")
-                print "equal to the number of bands. Setting COMPLEMENT to FALSE!\n"
+                print("equal to the number of bands. Setting COMPLEMENT to FALSE!\n")
 
 
 # Select projectors within the energy window
@@ -112,8 +112,8 @@ class ProjectorGroup:
         self.nelect = 0
         nk, ns_band, _ = self.ib_win.shape
         rspin = 2.0 if ns_band == 1 else 1.0
-        for isp in xrange(ns_band):
+        for isp in range(ns_band):
-            for ik in xrange(nk):
+            for ik in range(nk):
                 ib1 = self.ib_win[ik, isp, 0]
                 ib2 = self.ib_win[ik, isp, 1]+1
                 occ = el_struct.ferw[isp, ik, ib1:ib2]
@@ -154,8 +154,8 @@ class ProjectorGroup:
         _, ns, nk, _, _ = self.shells[0].proj_win.shape
         p_mat = np.zeros((ndim, self.nb_max), dtype=np.complex128)
 # Note that 'ns' and 'nk' are the same for all shells
-        for isp in xrange(ns):
+        for isp in range(ns):
-            for ik in xrange(nk):
+            for ik in range(nk):
                 nb = self.ib_win[ik, isp, 1] - self.ib_win[ik, isp, 0] + 1
 # Combine all projectors of the group to one block projector
                 for bl_map in block_maps:
@@ -203,8 +203,8 @@ class ProjectorGroup:
 
         self.hk = np.zeros((ns,nk,ndim,ndim), dtype=np.complex128)
 # Note that 'ns' and 'nk' are the same for all shells
-        for isp in xrange(ns):
+        for isp in range(ns):
-            for ik in xrange(nk):
+            for ik in range(nk):
                 bmin = self.ib_win[ik, isp, 0]
                 bmax = self.ib_win[ik, isp, 1]+1
 
@@ -247,7 +247,7 @@ class ProjectorGroup:
 
         """
 
-        print '\nCalculating complement\n'
+        print('\nCalculating complement\n')
 
         block_maps, ndim = self.get_block_matrix_map()
         _, ns, nk, _, _ = self.shells[0].proj_win.shape
@@ -257,8 +257,8 @@ class ProjectorGroup:
 # Note that 'ns' and 'nk' are the same for all shells
 
 
-        for isp in xrange(ns):
+        for isp in range(ns):
-            for ik in xrange(nk):
+            for ik in range(nk):
                 bmin = self.ib_win[ik, isp, 0]
                 bmax = self.ib_win[ik, isp, 1]+1
 
@@ -335,7 +335,7 @@ class ProjectorGroup:
           1. Orthogonality is ensured on each site (NORMION = True).
              For each site 'ion' we have the following mapping:
 
-                 block_maps = [bl_map[ion] for ion in xrange(shell.nion)
+                 block_maps = [bl_map[ion] for ion in range(shell.nion)
                                            for shell in shells]
 
                  bl_map = [((i1_start, i1_end), (i1_shell, ion)),
@@ -362,7 +362,7 @@ class ProjectorGroup:
                 _shell = self.shells[ish]
                 nion, ns, nk, nlm, nb_max = _shell.proj_win.shape
                 ndim = max(ndim, nlm)
-                for ion in xrange(nion):
+                for ion in range(nion):
                     i1_bl = 0
                     i2_bl = nlm
                     block = {'bmat_range': (i1_bl, i2_bl)}
@@ -378,7 +378,7 @@ class ProjectorGroup:
             for ish in self.ishells:
                 _shell = self.shells[ish]
                 nion, ns, nk, nlm, nb_max = _shell.proj_win.shape
-                for ion in xrange(nion):
+                for ion in range(nion):
                     i2_bl = i1_bl + nlm
                     block = {'bmat_range': (i1_bl, i2_bl)}
                     block['shell_ion'] = (ish, ion)
@@ -456,14 +456,14 @@ class ProjectorGroup:
 
         ib_min = 10000000
         ib_max = 0
-        for isp in xrange(ns_band):
+        for isp in range(ns_band):
-            for ik in xrange(nk):
+            for ik in range(nk):
-                for ib in xrange(nband):
+                for ib in range(nband):
                     en = eigvals[ik, ib, isp]
                     if en >= self.emin:
                         break
                 ib1 = ib
-                for ib in xrange(ib1, nband):
+                for ib in range(ib1, nband):
                     en = eigvals[ik, ib, isp]
                     if en > self.emax:
                         break