Cleaning up Python build process

2c39cb5e · Peter Eastman · 1a50d0c1 · 2c39cb5e · 1a50d0c1 · 2c39cb5e
Commit 2c39cb5e authored Mar 23, 2011 by Peter Eastman
6 changed files
--- a/wrappers/python/CMakeLists.txt
+++ b/wrappers/python/CMakeLists.txt
@@ -55,58 +55,58 @@ foreach(INIT_FILE ${STAGING_INPUT_FILES})
    # message("STAGING_OUTPUT_FILE = " ${outfile})
 endforeach(INIT_FILE ${STAGING_INPUT_FILES})

-# Swig wrapper need to be rebuilt if the API has changed
-set(OPENMM_PYTHON_BUILD_SWIG ON CACHE BOOL "Whether to rebuild swig wrappers vs using the premade ones.")
-if(OPENMM_PYTHON_BUILD_SWIG)
-    # Look in ~/bin/swig first, more likely to be latest version on build machines
-    find_program(SWIG_EXECUTABLE swig PATHS
+########################################################
+### Rebuild the Swig wrappers if the API has changed ###
+########################################################
+# Look in ~/bin/swig first, more likely to be latest version on build machines
+find_program(SWIG_EXECUTABLE swig PATHS
    "$ENV{HOME}/bin" "/Users/builder/bin" "/home/builder/bin"
    NO_DEFAULT_PATH)
-    find_program(SWIG_EXECUTABLE swig)
-    if(SWIG_EXECUTABLE)
+find_program(SWIG_EXECUTABLE swig)
+if(SWIG_EXECUTABLE)
    execute_process(COMMAND ${SWIG_EXECUTABLE} -version
        OUTPUT_VARIABLE SWIG_VERSION_output ERROR_VARIABLE SWIG_VERSION_output)
    string(REGEX REPLACE ".*SWIG Version[^0-9.]*\([0-9.]+\).*" "\\1"
        SWIG_VERSION_output "${SWIG_VERSION_output}")
    set(SWIG_VERSION ${SWIG_VERSION_output} CACHE STRING "Swig version" FORCE)
-    else(SWIG_EXECUTABLE)
+else(SWIG_EXECUTABLE)
    set(SWIG_VERSION "0.0.0" CACHE STRING "Swig version" FORCE)
-    endif(SWIG_EXECUTABLE)
-    # Enforce swig version
-    string(COMPARE LESS "${SWIG_VERSION}" "1.3.39" SWIG_VERSION_ERROR)
-    if(SWIG_VERSION_ERROR)
+endif(SWIG_EXECUTABLE)
+# Enforce swig version
+string(COMPARE LESS "${SWIG_VERSION}" "1.3.39" SWIG_VERSION_ERROR)
+if(SWIG_VERSION_ERROR)
    message("Swig version must be 1.3.39 or greater! (You have ${SWIG_VERSION})")
-    endif(SWIG_VERSION_ERROR)
+endif(SWIG_VERSION_ERROR)

-    find_package(Doxygen REQUIRED)
-    mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
+find_package(Doxygen REQUIRED)
+mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)

-    find_package(Java REQUIRED)
-    mark_as_advanced(CLEAR JAVA_RUNTIME)
+find_package(Java REQUIRED)
+mark_as_advanced(CLEAR JAVA_RUNTIME)

-    # SWIG_OPENMM_DIR is package area where swig files will be created/used
-    set(SWIG_OPENMM_DIR "${OPENMM_PYTHON_STAGING_DIR}/src/swig_doxygen")
-    file(MAKE_DIRECTORY ${SWIG_OPENMM_DIR}/swig_lib/python)
+# SWIG_OPENMM_DIR is package area where swig files will be created/used
+set(SWIG_OPENMM_DIR "${OPENMM_PYTHON_STAGING_DIR}/src/swig_doxygen")
+file(MAKE_DIRECTORY ${SWIG_OPENMM_DIR}/swig_lib/python)

-    ### Create OpenMM_headers.xml ###
-    # Step 1 - Create Doxyfile to point to OpenMM headers
-    configure_file(
+### Create OpenMM_headers.xml ###
+# Step 1 - Create Doxyfile to point to OpenMM headers
+configure_file(
    ${CMAKE_CURRENT_SOURCE_DIR}/src/swig_doxygen/doxygen/Doxyfile.in
    ${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/Doxyfile
    @ONLY
-    )
+)

-    # Step 2 - Run doxygen in non-package area
-    add_custom_command(
+# Step 2 - Run doxygen in non-package area
+add_custom_command(
    OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/index.xml" "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/combine.xslt"
    COMMAND "${DOXYGEN_EXECUTABLE}"
    DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/Doxyfile"
    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen"
    COMMENT "Parsing OpenMM header files with doxygen..."
-    )
+)

-    # Step 3 - Run xslt to create combined xml file
-    add_custom_command(
+# Step 3 - Run xslt to create combined xml file
+add_custom_command(
    OUTPUT "${SWIG_OPENMM_DIR}/OpenMM_headers.xml"
    COMMAND ${JAVA_RUNTIME}
        -jar "${CMAKE_SOURCE_DIR}/wrappers/saxonb9-1-0-7j/saxon9.jar"
@@ -117,27 +117,27 @@ if(OPENMM_PYTHON_BUILD_SWIG)
    DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/index.xml" "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/combine.xslt"
    WORKING_DIRECTORY "${SWIG_OPENMM_DIR}"
    COMMENT "Creating combined OpenMM API xml file..."
-    )
-    add_custom_target(CreateCombinedXmlFile DEPENDS
+)
+add_custom_target(CreateCombinedXmlFile DEPENDS
    "${SWIG_OPENMM_DIR}/OpenMM_headers.xml"
    "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/index.xml"
    "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml/combine.xslt"
    ${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/Doxyfile)

-    # OpenMM REFERENCE platform first
+# OpenMM REFERENCE platform first

-    # Files which will be created by python script and used by swig (dynamically generated)
-    set(SWIG_INPUT_FILES_REF
+# Files which will be created by python script and used by swig (dynamically generated)
+set(SWIG_INPUT_FILES_REF
    "${SWIG_OPENMM_DIR}/swig_lib/python/pythonprepend.i"
    "${SWIG_OPENMM_DIR}/swig_lib/python/pythonappend.i"
    "${SWIG_OPENMM_DIR}/OpenMM_docstring.i"
    "${SWIG_OPENMM_DIR}/OpenMM_headers.i"
    # "${SWIG_OPENMM_DIR}/OpenMM.i"
-    )
+)

-    # Swig input files which should have been copied from source tree
-    # file(GLOB SWIG_INPUT_FILES2 "${SWIG_OPENMM_DIR}/swig_lib/python/*.i")
-    set(SWIG_INPUT_FILES2
+# Swig input files which should have been copied from source tree
+# file(GLOB SWIG_INPUT_FILES2 "${SWIG_OPENMM_DIR}/swig_lib/python/*.i")
+set(SWIG_INPUT_FILES2
    "${SWIG_OPENMM_DIR}/swig_lib/python/exceptions.i"
    "${SWIG_OPENMM_DIR}/swig_lib/python/extend.i"
    "${SWIG_OPENMM_DIR}/swig_lib/python/features.i"
@@ -145,10 +145,10 @@ if(OPENMM_PYTHON_BUILD_SWIG)
    "${SWIG_OPENMM_DIR}/swig_lib/python/pythoncode.i"
    "${SWIG_OPENMM_DIR}/swig_lib/python/typemaps.i"
    "${SWIG_OPENMM_DIR}/swig_lib/python/pythonprepend_all.i"
-    )
+)

-    # Create input files for swig
-    add_custom_command(
+# Create input files for swig
+add_custom_command(
    OUTPUT ${SWIG_INPUT_FILES_REF}
    COMMAND ${PYTHON_EXECUTABLE} "${SWIG_OPENMM_DIR}/swigInputBuilder.py"
        -i OpenMM_headers.xml
@@ -163,15 +163,15 @@ if(OPENMM_PYTHON_BUILD_SWIG)
        "${SWIG_OPENMM_DIR}/swigInputBuilder.py"
        "${SWIG_OPENMM_DIR}/OpenMM_headers.xml"
    COMMENT "Creating OpenMM Python swig input files..."
-    )
+)

-    #~ swig -python -c++ \
-    #~      -outdir $PYTHON_PACKAGE_DIR \
-    #~      -o OpenMMSwig.cxx \
-    #~      OpenMM.i
+#~ swig -python -c++ \
+#~      -outdir $PYTHON_PACKAGE_DIR \
+#~      -o OpenMMSwig.cxx \
+#~      OpenMM.i

-    # Run swig
-    add_custom_command(
+# Run swig
+add_custom_command(
    OUTPUT "${SWIG_OPENMM_DIR}/OpenMMSwig.cxx" "${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm/openmm.py"
    COMMAND ${SWIG_EXECUTABLE}
        -python -c++
@@ -184,17 +184,14 @@ if(OPENMM_PYTHON_BUILD_SWIG)
        ${SWIG_INPUT_FILES_REF}
        ${SWIG_INPUT_FILES2}
    COMMENT "Creating OpenMM Python module sources with swig..."
-    )
-    add_custom_target(RunSwig DEPENDS 
+)
+add_custom_target(RunSwig DEPENDS 
    "${SWIG_OPENMM_DIR}/OpenMMSwig.cxx"
    "${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm/openmm.py")

-    set (STAGING_OUTPUT_FILES ${STAGING_OUTPUT_FILES}
+set (STAGING_OUTPUT_FILES ${STAGING_OUTPUT_FILES}
    "${OPENMM_PYTHON_STAGING_DIR}/src/swig_doxygen/OpenMMSwig.cxx"
    "${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm/openmm.py")
-else(OPENMM_PYTHON_BUILD_SWIG)
-    add_custom_target(RunSwig)
-endif(OPENMM_PYTHON_BUILD_SWIG)

 ##################################################################################################
 ### Make a list of all folders containing include files the wrappers must be compiled against. ###

--- a/wrappers/python/README.txt
+++ b/wrappers/python/README.txt
-===========================================
- PyOpenMM: Python wrappers for OpenMM
-===========================================
-
-URL: https://simtk.org/home/pyopenmm
-
-PyOpenMM is a python API that allows access to OpenMM, which is a library
-that provides tools for performing GPU accelerated molecular simulations.
-See the OpenMM project home page for more details:
-https://simtk.org/home/openmm
-
-Note that you do *not* need to download the OpenMM package.  This
-package includes all requried OpenMM libraries for Windows, Mac OS X,
-Linux, and 64 bit Linux. However, if you wish to make use of the
-GPU acceleration, you will need to have a supported GPU, and you will
-need to install the associated CUDA Toolkit and drivers.
-
-
-INTENDED AUDIENCE:
-This README is intended for people who downloaded the PyOpenMM package
-from the simtk.org website.
-
-
-ADVANCED USERS:
-if you are building or installing your own OpenMM libraries, you will also
-need to rebuild the python wrappers.  Note that most users will not
-need (or want) to do this.  If you really do need to rebuild the python
-wrappers, change to the following subdirectory and read its README.txt file,
-then return here to finish the installation:
-cd src/swig_doxygen
-
-
-REQUIREMENTS
-1) Python 2.6 (Pythons 2.4 and 2.5 no longer supported; Python 2.7 might work)
-2) One of the OS types supported by OpenMM:
-  a) Windows XP or better
-  b) Mac Leopard
-  c) Snow Leopard, assuming 32-bit python. See the README_MAC_64bit.txt file.
-  d) Linux (we test using CentOS 5, but others also should work)
-  e) Linux64 (we test using CentOS 5, but others should work)
-3) A C/C++ compiler.
-  a) For Windows, we suggest Visual Studio 2008
-  b) For Mac Leopard and Snow Leopard, you may need to install Apple's Xcode
-     development environment (this will install otool and install_name_tool
-     which might also be needed).
-  c) For Linux, we use gcc-c++ 4.1
-
-
-INSTALL
-First unzip the package, change to the new directory, and run
-the following two commands from a command line:
- python setup.py build
- python setup.py install
-
-
-TEST INSTALL
-Next run the following test to see if the install worked (it
-should report "OK"):
- python test/test_openmm.py
-This should return "OK"
-
-
-USING A GPU
-If you would like to make use of OpenMM's GPU acceleration, you
-will have to have one of the supported GPU's, and you will need
-to install the Cuda libraries.  To download the Cuda libraries,
-check the NVIDIA website (try
-http://www.nvidia.com/object/cuda_get.html).
-For more help, see the OpenMM discussion forums at the following URL:
-https://simtk.org/forum/?group_id=161)
-
-Once the Cuda librareis are installed, python may need help finding
-them.  One easy way to do this on Unix type machines is to set the
-LD_LIBRARY_PATH to point to the Cuda installation.
-On my Bash system, I could do the following at the command line:
- export LD_LIBRARY_PATH=/usr/local/cuda/lib
-On a windows machine, adding the Cuda installation path to
-your system PATH variable should work.
-
-After installing you may need to reboot.
-
-TEST GPU
-If you have a GPU, run the following to see if PyOpenMM is accessing it:
- python scripts/pluginLoadingCheck.py
-If you do not have a GPU, or it is not found, you should get the following:
- OpenMM found no plugins
-If you have a GPU and it's found, you will see a list of GPU libraries that
-have been loaded.  For example, on my system I see the following:
- OpenMM loaded the following plugin(s)
- $PYTHONPATH/simtk/chem/OpenMM/plugins/libOpenMMCuda.so
-
-If you are unable to load the GPU (Cuda) plugins, check that you installed
-the Cuda drivers and Toolkit correctly.
-
-
-PYOPENMM USAGE EXAMPLES
-Once you have tested the installation, switch to the example
-directory (cd examples), and try running one of the simulations.
-For example, run the argon simulation by changing to the examples/argon
-directory and typing the following:
- python runArgon.py argon.pdb
-
-If all goes well, this will produce a PDB formatted file called argon.pdb,
-which can be visualized using a program such as VMD.
-
-
-FEEDBACK
-Please address all comments, criticisms, suggestions, etc to one of us:
-Mark Friedrichs at friedrim@stanford.edu
-Peter Eastman at cmbruns@stanford.edu 
-Randy Radmer at radmer@stanford.edu 
-
-
--- a/wrappers/python/pysetup.cmake.in
+++ b/wrappers/python/pysetup.cmake.in
 set(ENV{OPENMM_INCLUDE_PATH} "@WRAPPER_INCLUDE_DIRS@")
-file(TO_NATIVE_PATH "@CMAKE_BINARY_DIR@" OPENMM_LIB_PATH)
+file(TO_NATIVE_PATH "@OPENMM_INSTALL_PREFIX@/lib" OPENMM_LIB_PATH)
 set(ENV{OPENMM_LIB_PATH} "${OPENMM_LIB_PATH}")
 message("OPENMM_LIB_PATH = " $ENV{OPENMM_LIB_PATH})
 message("OPENMM_INCLUDE_PATH = " $ENV{OPENMM_INCLUDE_PATH})

--- a/wrappers/python/src/swig_doxygen/OpenMMSwig.cxx
+++ b/wrappers/python/src/swig_doxygen/OpenMMSwig.cxx
--- a/wrappers/python/src/swig_doxygen/README.txt
+++ b/wrappers/python/src/swig_doxygen/README.txt
-This swig based, wrapper code only works from a Bash shell.
-
-You *must* have the following installed:
-1) Python 2.5 or 2.6
-2) swig 2.0.0 or better (earlier versions are likely to fail)
-3) Some type of XSLT processor (xsltproc, saxon, etc)
-4) Doxygen (tested with version 1.4.7, but others should also work)
-5) py-dom-xpath (tested with version 0.1, but others should also work):
-   http://code.google.com/p/py-dom-xpath
-
-
-To build the wrapper codes, the following must be done
-1) Run doxygen to generate xml files containing OpenMM API info (doxygen
-   uses the OpenMM header files to do this).
-2) Run a python script that builds SWIG input files based on info in the
-   doxygen xml files
-3) Run SWIG to generate python and C code that wraps the OpenMM libraries
-
-We have created a single Bash script that does the full build for you.
-But before running it, you must create and export environment variables
-containing the OpenMM lib path (OPENMM_LIB_PATH) and the include directory
-path (OPENMM_INCLUDE_PATH).  The include directory should contain the "OpenMM.h"
-file and an "openmm" directory.  The lib directory should contain
-the OpenMM dynamic library (OpenMM.dll, libOpenMM.so or libOpenMM.dylib) and
-plugins.  For example, when I build OpenMM on a Bash system, I set the
-install dir to $HOME (in ccmake). Then I type the following two lines at
-the command line:
-export OPENMM_LIB_PATH=$HOME/lib
-export OPENMM_INCLUDE_PATH=$HOME/include
-
-Next run the Bash build script as follows:
-/bin/bash buildSwigWrapper.sh
-
-You may need to edit this script to work on your system
-
-If all went well, the wrapper code is now updated; cd ../.. and follow
-instuctions for building the PyOpenMM libraries.
-
-
-1. Edit swigInputConfig.py to add new classes, ...
-2. Add template <class T> to XmlSerializer (serialize/deserialize)
-
-    class XmlSerializer {
-    public:
-    
-       %apply std::ostream & OUTPUT { std::ostream & stream };
-       template <class T>static void serialize(const T *object, const std::string
-    &rootName, std::ostream &stream) ;
-       %clear std::ostream & stream;
-       %apply std::istream & OUTPUT { std::istream & stream };
-       template <class T>static T* deserialize(std::istream &stream) ;
-       %clear std::istream & stream;
-    };
-
-
-
--- a/wrappers/python/src/swig_doxygen/buildSwigWrapper.sh
+++ b/wrappers/python/src/swig_doxygen/buildSwigWrapper.sh
-#!/bin/bash
-
-rm -f *.xml
-rm -f OpenMM_headers*
-rm -f *.cxx
-
-SWIG_REV_FILE_OPENMM=RevisionNumber_OpenMM.txt
-SWIG_REV_FILE_PYOPENMM=RevisionNumber_pyopenmm.txt
-
-PYTHON_PACKAGE_DIR=../../simtk/openmm
-
-
-if [ -n "$OPENMM_SVN_PATH" ] ; then
-  SVN_INFO=$(svn info $OPENMM_SVN_PATH 2>/dev/null | awk '$0~/^Revision:/{print $2}')
-  if [ -n "$SVN_INFO" ] ; then
-    echo  $SVN_INFO >| $SWIG_REV_FILE_OPENMM
-  fi
-fi
-
-if [ -z "$OPENMM_INCLUDE_PATH" ] ; then
-  OPENMM_INCLUDE_PATH=../../OpenMM/include
-fi
-
-SVN_INFO=$(svn info 2>/dev/null | awk '$0~/^Revision:/{print $2}')
-if [ -n "$SVN_INFO" ] ; then
-  echo  $SVN_INFO >| $SWIG_REV_FILE_PYOPENMM
-fi
-
-cd doxygen
-rm -rf xml/ html/
-echo "Calling doxygen >| doxygen.out 2>| doxygen.err"
-doxygen >| doxygen.out 2>| doxygen.err
-if [ "$?" -ne "0" ]; then
-  echo "ERROR: doxygen did not run"
-  echo "       See doxygen/doxygen.out and doxygen/doxygen.err!"
-  echo "Exiting!"
-  exit 1
-fi
-cd xml
-echo "Calling xsltproc combine.xslt index.xml >| ../../OpenMM_headers.xml"
-xsltproc combine.xslt index.xml >| ../../OpenMM_headers.xml
-cd ../../
-
-
-#Build ref platform only
-echo "Calling swigInputBuilder.py -i OpenMM_headers.xml -c swigInputConfig.py -o OpenMM_headers.i -d OpenMM_docstring.i -a swig_lib/python/pythonprepend.i  -z swig_lib/python/pythonappend.i "
-python swigInputBuilder.py -i OpenMM_headers.xml \
-                           -c swigInputConfig.py \
-                           -o OpenMM_headers.i \
-                           -d OpenMM_docstring.i \
-                           -a swig_lib/python/pythonprepend.i \
-                           -z swig_lib/python/pythonappend.i \
-                        >| swigInputBuilder.out 
-
-USING_SWIG_VERSION=$(swig -version | awk '/^SWIG Version/{print $3}')
-USING_SWIG_VERSION_NUM=$(echo $USING_SWIG_VERSION | awk -F. '{print 1000*(1000*$1+$2)+$3}')
-if (( $USING_SWIG_VERSION_NUM < 2000000 )) ; then
-   echo "ERROR: Using swig $USING_SWIG_VERSION.  Must use 2.0.0 or better"
-   exit 1
-fi
-
-echo "calling swig -python -c++ -Wall -outdir $PYTHON_PACKAGE_DIR -o OpenMMSwig.cxx OpenMM.i"
-swig -python -c++ -Wall \
-     -outdir $PYTHON_PACKAGE_DIR \
-     -o OpenMMSwig.cxx \
-     OpenMM.i
-
-
-echo "Done: swig -python -c++\n"
-