[xdmf] branch debian/master created (now 6301efe)
Alastair McKinstry
mckinstry at moszumanska.debian.org
Fri Apr 1 18:23:00 UTC 2016
This is an automated email from the git hooks/post-receive script.
mckinstry pushed a change to branch debian/master
in repository xdmf.
at 6301efe one little fix to patch needed
This branch includes the following new commits:
new f0246ed ENH: Initial Commit
new b17ab6e ENH: Added XdmfTopologyType to XdmfTopology to handle element types and associated const data like nodesPerElement and name. This resembles "Replace subclass with fields" implementation in Refactoring and does a nice job encapsulating element type data in an enum like way avoiding unneccesary subclassing.
new ac19e9d ENH: Get Python wrapping working on OS X and regenerate wrappers incorporating recent changes.
new 6632e99 ENH: Add XdmfGeometryType to XdmfGeometry in a similar implementation as XdmfTopologyType. Add tests for XdmfGeometry. Add XdmfItem, an abstract class that is able to be traversed by an XdmfVisitor to write out its information to XML and HDF5 or other heavy data formats. Modify XdmfGeometry, XdmfGrid, XdmfTopology, and XdmfAttribute to inherit from XdmfItem.
new c4c3800 ENH: Delete unneeded files from repository
new 6f12cfa ENH: Add write() method to XdmfItem and implement in subclasses. The write() method calls the visitor on the current object which performs some predetermined acivity (writing to heavy data, writing to light data, parallel output, etc.
new 4acdd29 ENH: Replace old way of creating static instances of XdmfTopologyType, XdmfGeometryType, and storing them by reference in their respective topologies. These now work by providing a specific constructor method that returns specific instances of the objects populated with correct values. This was changed because there are some type options in Xdmf where static instances don't make sense (e.g. XdmfTopologyType Polygon can have many different values for nodesPerElemen [...]
new ab806f9 ENH: Allow XdmfGrids to insert XdmfAttribute elements. Add this to the visitor logic to write to xml.
new 250eac6 ENH: Add XdmfAttributeCenter to XdmfAttribute to specify how the attribute values are attached to the grid.
new 46a937d ENH: Start separating XdmfItem properties from their respective classes - XdmfAttributeType.
new 282d5e4 ENH: Start separating XdmfItem properties from their respective classes - XdmfAttributeCenter.
new d9c8a53 ENH: Start separating XdmfItem properties from their respective classes - XdmfGeometryType.
new ed10d43 ENH: Start separating XdmfItem properties from their respective classes - XdmfTopologyType.
new 2be47fe STYLE: Remove const qualifier from return of printSelf() --- it is unecessary
new 1e29d5a ENH: Add XdmfDataItem which stores array data to write to Xdmf.
new 95079f5 ENH: Add XdmfDataItems to XdmfTopology and XdmfGeometry and write them out correctly in the XdmfVisitor. Verified to work with simple Hexahedron file.
new 2922ad7 ENH: Make XdmfAttribute, XdmfTopology, XdmfGeometry inherit from XdmfDataItem. Instead of containing a data item, each is a dataitem of a specific type. This makes setting data items more user friendly --- e.g. once you set the number of elements and set the topology type you don't have to set the number of elements from the dataitem again. This still needs to be figured out for composite dataitems for things like sets.
new 195746b ENH: Update Python Wrapping Files
new 5c28014 ENH: Add XdmfDomain.
new 46189e1 ENH: Add ability to write HDF5 files as part of XdmfVisitor operation.
new 41c12c9 ENH: Add ability to set Light Data Limit for Visitor, which controls how many values there need to be in a DataItem before it writes those values to a heavy data format. Set the default value to 100.
new 436acbe ENH: Allow for storage, retrieval, and output of datatypes other than int. Incorporate into HDF5 output.
new c92bcfa ENH: Use libxml2 to do construction of xml file rather than using the crude stringstream way we were using previously. XML does not own the data, it is used to make constructing XML files easier and libxml2 will be needed eventually anyway to parse xml files.
new 369f62e ENH: Add XdmfArray to store values --- modify XdmfDataItem to contain an XdmfArray. Modify Tests to use new XdmfArray. Modify XdmfVisitor to use new XdmfArray. Add Python Tests and move Cxx tests to their own directory.
new 4e98359 ENH: Add Smart Pointers to XdmfArray implementation. Modify some method names to be more clear about whether copying is being performed when setting values in the array. Modify tests to use new names and regenerate python wrappers.
new e698ae1 ENH: Remove non const getValuesPointer for now. Rename getValues as getValuesString() and add getValues that returns a smart pointer to the internal array.
new 91cfecb BUG: Fix bug when trying to get a smart pointer to a vector type not stored in XdmfArray... If this is the case, just return NULL, This could potentially be very useful.
new 6cde700 ENH: Split visitor operation into a visit and a traverse operation so that logic of how to traverse the xdmf graph is kept with xdmf objects rather than the visitor. The visitor calls this function rather than relying on its own logic.
new 8d06285 ENH: Modify XdmfArray to have a std::vector like interface except for inset, which is replaced in XdmfArray with copyValues (for name clarity and ability to stride) Modify tests to use new functions Significantly modify swig python wrapping to easily store values from python lists in XdmfArrays.
new 4157e30 Merge branch 'XdmfArraySmartPointer'
new 5220c48 ENH: Add BUILD_DOCUMENTATION flag to CMakeLists that builds doxygen documentation for the project.
new 6ff2d20 ENH: Add CTEST to allow for submissions to the Xdmf dashboard.
new 63368ad ENH: Add class level documentation across the project. Remove a couple methods that unnecessarily duplicated functionality.
new 83237ef STYLE: Split XdmfArray.tpp from XdmfArray.hpp --- this will hold template implementations for XdmfArray instead of stuffing them all in XdmfArray.hpp (merely a style difference). Do some minor formatting on some other files.
new de6cba6 ENH: Remove unneccesary private method from XdmfArray. Regenerate python wrappers.
new 5e476e2 ENH: Add swap method to XdmfArray. Swap works by swapping an XdmfArray's contents internally (no copy) between a std::vector<T>, boost::shared_ptr<std::vector<T> > or another XdmfArray. Modify some methods in XdmfArray that did not require visitor operation but can just catch boost::bad_get exceptions.
new e8274ac ENH: Add initialize() method that allows user to specify the type of data to store in an XdmfArray if desired.
new 8e0b09f ENH: Remove XdmfPython.cpp and Xdmf.py from repository. Modify CMake build script to generate wrappers automagically with swig (this will ensure that users always have swig wrapper tailored to their version of python and prevents us from having to regenerate and commit every time something in Xdmf changes). Add a couple extra methods to XdmfArray.cpp --- still need to figure out the rest of XdmfArray functionality.
new 369e953 ENH: Add TestXdmfVisitorValueCounter to demonstrate how to write visitor operations over the Xdmf graph that do something other than write to disk. Separate hexahedron grid example into a header file so that other test cases can use it for testing.
new 395175f STYLE: Formatting
new c4b66df ENH: Make XdmfArray variant visitors private members of XdmfArray.
new 13ce79f ENH: Fix up some minor const-correctness issues.
new 92702e6 ENH: Add ArrayPointer Variant to allow users to use XdmfArray merely as a "pointer holder" for output using Xdmf. See the docs for a more clear explanation. Modify XdmfArray methods to correctly use the ArrayPointer.
new 364fcbb ENH: Add transferOwnership parameter to setValues(std::vector<T> & array) to match other setValues(const T * const array) --- clarification of ownership for non-shared_ptr arrays.
new 9eb1f0c ENH: Add resize() method to XdmfArray.
new 4a0e2da ENH: Add reserve() and getCapacity() methods to XdmfArray.
new b5b2127 ENH: Use unsigned ints where appropriate (sizes, indices, etc.)
new b1ff8b8 ENH: Rename write() operation to accept() which is more consistent for the Visitor pattern. Also, we can do much more to our Xdmf graph structure than just write it using Visitor operations.
new 48eedaa ENH: Remove printSelf() method as it was unnecessary.
new e93ca0f ENH: Create a generic XdmfVisitor class and move writing operations to XdmfWriter. Incorporate Loki library to perform asymmetric visitor operation (allows customizable behavior for eventual Xdmf / NetDMF library split). Modify Loki Visitor to work happily with boost::shared_ptr and modify swig wrapping to properly handle boost::shared_ptr inheritance.
new 08b41ff ENH: Add XdmfItemProperty to genericize properties attached to XdmfItems. Add a pure virtual getItemProperties() method to XdmfItem to force children to implement a way to retrieve properties.
new b9dd679 ENH: Add pure virtual getItemTag method to XdmfItem working to return the tag (same as in XML terminology) for the specific item.
new 0532b59 ENH: Modift XdmfWriter to utilize new genericized getItemTag and getItemProperties methods to write out the Xdmf graph. Modify some random include statements for style.
new 048eaba ENH: Split heavy data writing from XdmfWriter into XdmfHDF5Writer. This paves the way for the possiblity of having multiple heavy data and light data writers. Modify New() macro to accept parameters.
new f8cd665 ENH: Use PIMPL idiom to hide hdf5 and libxml2 includes from header files for writers.
new 5ed3eeb ENH: Remove getHDF5Type from XdmfArray and move into XdmfHDF5Writer so all hdf5 interaction is isolated in XdmfHDF5Writer. Friend the XdmfHDF5Writer from XdmfArray so that it can access the variant to perform typesafe operations on the data stored. Variable macro generation didn't work so reverted the modified code. We may just have to write ugly static New() methods when required.
new 27e3b6e ENH: Add tests using new XdmfHDF5Writer exclusively. Modify some methods in XdmfHDF5Writer to get everything working as expected.
new a7f5d5c ENH: Remove group creation when writing HDF5 files. The group paths depend on how the xml was structured when the dataset was written and we want to fully separate dealing with light and heavy data when creating Xdmf files. This will allow us to move towards complete separation of heavy and light data writing, a Create -> Write -> Release -> Create -> Write -> Release -> Write XML workflow.
new 7a4cb5d ENH: Add XdmfHDF5Controller so that heavy data can be written and released before light data is written. Modify XdmfWriter to accept an XdmfHDF5Writer to use for heavy data writing and allow users to specify XML file name to write to. Add a test that performs the write release write release workflow.
new 5e8d620 ENH: Add reading functionality to XdmfHDF5Controller
new b94acdd ENH: Add ability to read XML files from disk into Xdmf structures in memory.
new 955bbcf BUG: Fix incorrect assert() statement causing TestXdmfArray to fail.
new cd0f247 ENH: Add XdmfSet. Remove getName() method from ItemProperties.
new e31b3ce ENH: Add ability to remove XdmfAttributes and XdmfSets from XdmfGrids.
new 28e67e9 ENH: Add XdmfGridCollection and begin adding XdmfPartitioner.
new f5cd842 ENH: Add test for XdmfGridCollection.
new a1ab48d ENH: Continue implementing XdmfPartitioner.
new dbee693 ENH: Split XdmfAttributes in XdmfPartitioner.
new 0457f2e ENH: Split XdmfAttributes in XdmfPartitioner.
new 94f61d1 ENH: Modify ItemProperties to use shared pointers like the rest of Xdmf. Modify swig wrapping to correctly handle both non const and const shared pointers.
new ef98c86 ENH: Clean up a bit of const-correctness related things.
new 9c5aaf4 ENH: Add write modes to HDF5Writer. It can now overwrite (write in the same location previously written to) and append (write data to end of previously written dataset).
new 5b15354 ENH: Add XdmfArrayType to store data type / precision information which should make interaction between XdmfArray and XdmfHDF5Controller a bit more robust.
new e6f105c ENH: Improve python interface by rewriting swig wrapping and moving XdmfObject destructors to be publicly accessible. Modify tests to work with new wrapping.
new fcfd389 ENH: Split Xdmf into XdmfCore and Xdmf libraries in anticipation of NetDMF development. Create a couple abstract base classes in order to support generic reading from disk.
new 3d1e70f ENH: Move XdmfCore into its own subdirectory. Move XdmfCore specific tests into core subdirectory and modify swig wrapping to create two separate libraries (Xdmf and XdmfCore).
new cb10378 ENH: Add skeleton for XdmfTopologyConverter Util
new 305ffbc ENH: Make ItemTag const so it is cannot be modified.
new 9cf33fd ENH: Begin implementing XdmfTopologyConverter. Fix typo in XdmfArray that incorrectly initialized UInt32() type.
new e7913d9 ENH: Allow XdmfArrayType to correctly read old xdmf files containing "NumberType" XML attribute, which is the same as DataType.
new 12f100b ENH: Add python wrapping for XdmfUtils and modify some swigisms to get reader working properly in python.
new 68d4ee4 ENH: Add Hexahedron_64() to Hexahedron() Topology Conversion.
new 4f65d6c ENH: Rename get/set ItemProperties for conciseness. e.g. getAttributeCenter ---> getCenter . This follows what is done for XdmfArray (getType).
new d07ee80 ENH: Add Hexahedron() to Hexahedron_125() Topology Conversion.
new 03c6c40 ENH: Add XdmfInformation to store key/value pairs.
new f6d3e7c ENH: Modify XdmfWriter to insert XdmfArray content into most recently created child to allow for creation of multiple XdmfArray children.
new 40a27f6 ENH: Add Name property to XdmfArray and accessor functions for getting and setting the name. If no name is specified it is not written to XML. Modify test to verify reading and writing is working.
new 9f1c72b ENH: Add Mode to XdmfWriter. Default mode ensures that all heavy data referenced by the XML file being written exists in a single heavy data file. A DistributedHeavyData mode can be set to allow heavy data referenced by the XML file to exist in more than one hdf5 file.
new e4ed9f6 ENH: Add XdmfTime and allow it to be attached to XdmfGrid. Add some convenience functions in XdmfGrid to get and remove XdmfAttributes and XdmfSets by name.
new 1987ebf ENH: Remove +x permission from loki files.
new 60362c2 ENH: Add XPath writing capabilities to XdmfWriter. Whenever a duplicate XdmfItem is written to disk, instead of writing it twice, XPath the first. We will hopefully mirror this behavior when reading in.
new 326d386 ENH: First draft of xpointer respected reading.
new 7cb7333 ENH: Clean up XInclude additions. Verify that writing reading and writing an XPath/XInclude file produces the same file.
new d0b6406 ENH: Finish cleanup of XInclude/XPath additions.
new 95c92a3 ENH: Fix Absolute/Relative path issues when reading and writing from separate directories. Modify XML attributes to be less verbose e.g. (AttributeType --> Type). Separate XdmfGridCollection from XdmfGrid at the XdmfDomain level.
new 18b3ccf ENH: Remove getLastWrittenDataSet from HDF5Writer and just get that information from the appropriate HDF5Controller attached to the Array.
new 087b6d3 ENH: Modify all filesystem paths used in xdmf to use the absolute real path - aka "canonical path". Modify tests to ensure this is working.
new 63a0aff ENH: Clean up changes to fix absolute/relative path adjustments.
new a34a25c ENH: Modify reading of TopologyType to ignore case.
new 19d96e0 ENH: Modify reading of XdmfArray dimensions to correctly calculate size for multidimensional arrays.
new b612722 ENH: Make XdmfGridCollection inherit from XdmfGrid and XdmfDomain, since it is really a unity of the two classes. Modify some details in ItemFactory / Reader.
new 860ab6c ENH: Remove XdmfObject since it was unnecessary and broke Java wrapping for NetDMF.
new fa56431 ENH: Remove static New implementation from header files and move to implementation files.
new 9c8a905 ENH: Fix up some comments, change a couple function names for consistencies sake.
new 6985f1b BUG: Fix Python reading with typemaps that has been broken since Xdmf/XdmfCore split.
new af48833 ENH: Make XdmfSet behave like a real std::set. Modify some writing functionality to make this possible.
new 99ace67 ENH: Rethink XdmfWriter / XdmfCoreWriter distinction and move XdmfSet to XdmfArray conversion in XdmfSet's traverse method. If conversion is unneeded then do not traverse XdmfSet.
new 996d9c0 ENH: Have all dataitems inherit directly from XdmfArray. Modify writing to support this.
new cb1fe3d ENH: Get Utils, Python Wrapping, and Tests working for new changes.
new 49cd1fb ENH: Add XdmfMap which maps nodes across partition boundaries.
new 7a8eade ENH: Add ability to XPath a file when opening in order to only read a part of the file.
new 732cc4b ENH: Add setHDF5Controllers() to XdmfMap.
new db5298c ENH: Add XdmfExodusReader for reading ExodusII files into Xdmf. Add ability for XdmfArray::initialize() to take a size value to initialize the array to.
new 906019d ENH: Modify several utils to take XdmfHDF5Controller as an argument so that they can write data to hdf5 as generated rather than keeping it all in memory. This is an optional argument.
new ab73bf6 ENH: Add XdmfExodusWriter to utils.
new 983479e ENH: Commit Ken Renard's patches modifying populateItem and XdmfCoreReader to support some xpath functionality for backwards compatibility.
new 16a914c ENH: Revert changes to XdmfSet to go back to XdmfArray implementation. Add Attributes to XdmfSet.
new 259e3eb ENH: Remove XdmfGrid inheritance from XdmfGridCollection. If there is a need for Sets/Attributes at the "global" collection level then we can deal with it in the future.
new 15b20fb ENH: Begin adding install rules. Modify bug in XdmfWriter that resulted in XdmfArrays not being written in certain cases.
new 67bf3fe ENH: Revert back to XdmfGridCollection inheriting from XdmfGrid - we want the flexibility to be able to add global sets (might be necessary for dft work).
new 3613b29 ENH: Change some method names in XdmfArray to be clearer and less verbose. Modify files for documentation clarity. Modify some minor things to prevent -Wall warnings in gcc. Add python install rules and rpathing.
new d5dced0 ENH: Add GLL Spectral Topology Types.
new 10bb623 Added Ken Renards Java Updates from a patch
new 6dfa309 Relocated and improved Java and Python SWIG Wrappers
new f5902b8 Removed the need for XDMF_SWIG_JAVA macros classpath argument
new a1e4069 Added better description for macro and dependencies for XDMF_SWIG_PYTHON
new 6a10c12 FIX: Deleted duplicate ignores for SWIGJAVA
new 5a502ae Copied over testing suite that I made on an old Xdmf2 repo.
new c615f02 Added check for wrapping java to include java test directory
new 1f35bc7 ENH: Added distinction between core and not core with testing suite.
new fac174c ENH: Added CMake option to build just the core.
new c64ed56 ENH: Added 'make clean' support for SWIG Python and SWIG Java extra files
new 267b0f4 ENH: Added support for 'make clean' into the Testing Suite
new f87db32 ENH: Clean up some formatting and ignores to use the new function names.
new 1976fee ENH: Modify utils testing to use new testing functionality.
new f617b9b BUG: Fixed dependency issue with java tests causing parallel builds to fail.
new 87c6965 ENH: Add macros to simplify adding children to an XdmfItem.
new c0e846f ENH: Add XdmfGridRegular for CoRectilinear (Regular) Structured Grids. Add test for interaction and output.
new 8c4b7dd ENH: Get reading of regular grids partially complete.
new f53c300 fixes for "transparent root" and "compare"
new aaf7a98 ENH: Add dimension string to XdmfArray
new c061208 ENH: patch to fix problem encountered with "transparent" root object.
new 15b37b0 ENH: get numpy Array from XdmfArray (for Python)
new 4f077f1 FIX: Handle error conditions better in XdmfArray.getNumpyArray()
new 03208c7 ENH: XdmfArray python object will access HDF5 datasets as numpy arrays via getNumpyArray()
new fe1a440 Deleted TestXdmfWriterHDF5ThenXML.cxx
new 14252b3 FIX: Updates to reflect API changes in Xdmf2Array
new b457fc2 FIX: Corrected SWIG overriding equals for Java and Python
new 7503009 ENH: Renamed core/Java and core/Python Test Name
new 31a8e05 FIX: Added renaming of XdmfSet.hpp methods for getAttribute() const
new c0de466 FIX: Added more SWIG overriding equals for Python
new 86d502b FIX: Fixed Merge Mistake
new 43654bc ENH: Moved the TestingSuite to more of a stand alone format
new 62be8bc ENH: Fix some formatting due to patches.
new be7a634 ENH: Finish IO of XdmfGridRegular. Begin implementation of XdmfGridRectilinear.
new 42286d0 ENH: Get equality functions working again, but keep it in the SWIG file rather the polluting the C++.
new 31b424c ENH: Get Java wrapping working again. Add curvilinear grid.
new b3b0660 ENH: Get Curvilinear additions wrapped in Python and Java
new bddb069 ENH: Add XdmfHeavyDataController base class and make XdmfArray use it. Add XdmfHeavyDataWriter base class and make XdmfWriter use it. This is in preparation to add additional heavy data formats.
new ab5584f ENH: Add ID for topology type to support mixed cells. Cleanup some formatting and constness.
new bacda4b Cleanup: 1. XdmfArray -- took out getElementSize() 2. XdmfArrayType -- took out IsEqual() 3. Xdmf.i -- implement IsEqual() function here for Python and Java in XdmfArrayType and XdmfItem (see #2 and #5) 4. Xdmf.i -- getNumpyArray uses getElementSize on XdmfArrayType instead of on XdmfArray (see #1) 5. XdmfItem -- took out IsEqual() 6. XdmfWriter -- made setDocumentTitle() and setCersionString() protected functions 7. Java test TestXdmfEquals -- took out test of XdmfI [...]
new a328765 ENH: Cleanup to merge changes with Ken Renard.
new 6fd1903 ENH: Add DSM Support. Update swigging procedures to current code.
new bc2792d Merge to current master
new d6c6137 ENH: Added XdmfGridUnstructured and turned XdmfGrid into an abstract base class for all grids (both structured and unstructured). Modified a bunch of utils and other classes to fit this new hierarchy.
new cf8f263 ENH: Cleanup comments and inheritance syntax a bit. Remove unnecessary Geometry Types not needed since splitting structured and unstructured grids into separate hierarchies.
new 8f51370 COMP: Check SWIG version to be greater than 2.0.0 and fix duplicate "BUILD_TESTING" options.
new e742494 ENH: Rename all subclasses of XdmfGrid to more syntactically friendly names: i.e. XdmfGridUnstructured to XdmfUnstructuredGrid.
new ea06eaa ENH: Modify wrapping of XdmfArray to always use "insert" and not "copy". Also add template specializations to allow for initialize calls.
new b20b648 BUG: Fix writing of single XdmfArray to a file.
new f3e961e FIX: Updated Testing Suite to fix Java Parallel Build
new e0c4fa3 FIX: Removed dynamic cast to prevent SWIG java conversion problems
new d7e90ba ENH: Added Xdmf Versioning
new 9f46334 ENH: Cleaned up some of the CMakeLists.txt file
new 02e1a0e FIX: Fixed up install to add loki to core, add python core and java libraries.
new 43de25a FIX: Corrected a segfault when two objects are next to each other.
new 7560d54 FIX: Corrected how xml content was gathered.
new 413c427 FIX: Cleaned up Version Suite and added the version into XdmfWriter.
new 913d465 FIX: Corrected possible future XdmfVersion header collision problem.
new 1c0eff9 Testing permissions of Xdmf repository by commiting dummy change
new 833c47a Checking Xdmf Repository permissions on master
new ba87ec0 Check permissions once again.
new 587f76b Check permissions
new a2056ef Testing permissions for Xdmf2.git
new 30a391b Check permissions
new 8098dfa Checking permissions for Xdmf master
new e58278d Modified Xdmf2 to test master permissions
new 2bc4f25 FIX: Corrected accessing Version from Python
new 198c3f5 Merge branch 'tidyup'
new 810800f FIX: Added extra headerfiles to install
new fd40266 FIX: Added default version if Git does not exist. (2.X)
new 4a43c7b FIX: Added XdmfVersions to .gitignore (They will be created on build)
new 62fe124 ENH: Initial Windows Conversion
new 0831d7b FIX: Added Versioning export for windows and fixed win32 java build
new 3614907 COMP: Fix compilation of utils tests by including missing directory.
new 3f126cb COMP: Mark needed variables as unadvanced before they are found. Makes identifying required variables easier for users, especially for hdf5 variables where only the C library is needed for linking.
new da547f3 FIX: Added more exports for Win32
new 4d39280 STYLE: Transition to friendlier formatting style.
new 088bda6 COMP: Fix duplicate BUILD_TESTING and XDMF_BUILD_TESTING in build script.
new 894a861 COMP: Mark DOXYGEN_EXECUTABLE as unadvanced before it is found.
new 7844ab7 BUG: Add typemap for std::vector<boost::shared_ptr<XdmfItem > > which is a return value from XdmfReader.
new bc1150f Merge branch 'master' of ssh://hsai-dev.arl.army.mil/data/Repository/Xdmf2
new 36ed6d0 ENH: Modify documentation for completeness.
new e245b7f COMP: Fix mixing CMake include preventing xdmf/exodus test from compiling.
new 6616dd1 COMP: Add missing header files.
new af68e41 COMP: Fix compilation against hdf5 when built with parallel.
new a0fb276 FIX: Moved template(ItemVector) from Xdmf.i to XdmfCore.i
new 7239e25 ENH: Updated Testing Suite
new 5eecc6c ENH: Removed test dependency for libraries in LD_PATH and PATH. Fixed Swig Parallel build issue.
new ecff3e6 ENH: Added some support for XdmfConfig.cmake file.
new 0ae7134 FIX: Corrected gathering of libxml2 and python locations
new 30a38ee Added XdmfFunctions.cmake macro, modified XdmfConfig, Added function call and file copy for the XdmfConfig file to the CMakeLists.txt
new 8c5c106 COMP: Fix XdmfConfig.cmake generation to install into install directory rather than copying at configure time.
new e924050 ENH: Add Copyright
new dedf4c9 COMP: Add header file to get test compiling for newest version of H5FDdsm.
new 48abd2f FIX: Removed some XdmfConfig.cmake variables set before Carries update.
new ce20ec5 FIX: Made changes for WinXP Compatability
new e86e334 test
new a6ebba8 sdf
new 062e094 Merge branch 'master' of public.kitware.com:Xdmf2
new 8f2dc16 BUG: Remove duplicate swig typemap for ItemVector.
new 03fb2f8 Merge formatting changes into 'master'
new 42147d3 COMP: Move XdmfFunctions.cmake to CMake directory.
new 7fdf00c FIX: Corrected an issue with the Versioning Suite and a Java formatting source code issue.
new ae80f9d ADD: Included XdmfVersion.hpp in the install.
new dca545e ENH: Modify HDF5Controllers to accept start, stride, and count to pull hyperslabs from hdf5 data sets.
new 889c1c2 ENH: Add assertion to make sure start, stride, and count have the same dimension.
new b8ea021 ENH: Improve how array keeps track of dimensionality in anticipation of working with hyperslabs.
new 64ae383 ENH: Modify XdmfHDF5Controller to work with new multidimensional support.
new b56afa1 ENH: Modify XdmfHDF5Writer to respect dimensionality in XdmfArrays. This will now be reflected in both light and heavy data.
new 08bfa4e ENH: Complete hyperslab reading.
new f46b9dc ENH: When array is uninitialized return dimensions as [0] and "0" rather than empty array or empty string.
new e5f0a64 ENH: Remove trailing whitespace when convert arrays to strings in XdmfArray.
new f25f692 ENH: Add Python test for new multidimensional array handling. Add typemap for swig for the std::vector<unsigned int> necessary for dimensions.
new cd1e7ae FIX: Changed how java builds in order to allow JDK5.
new 0aa8831 Added in XdmfError
new e08245f Added XdmfError Replaced asserts with XdmfError::messages
new 207cdd6 BUG: Fix bug when constructing triangle topology type that caused comparisons between topology types to fail.
new 901ed4b BUG: Fix bug causing XdmfAttributes to not be attached to XdmfSets when read from a file.
new 9524a6d ENH/BUG: Get XdmfInformation to work with older style xdmf format where values could be stored as content instead of just as attributes.
new e7d6f95 ENH: Convert XdmfArrayType to HDF5 data type when reading rather than relying on the hdf5 data type in the file to always correspond to the XdmfArrayType. This will allow hdf5 to handle datatype conversion (e.g. from int to double) if this is required. It also further decouples light and heavy data descriptions.
new 403f36e ENH: Added Java support for insertValuesAs*() to allow adding of Java arrays.
new bb75885 Merge branch 'java'
new 8c860bb ENH: Changed location of lib files during build for Windows Platforms
new 86ae327 BUG: Fix bug found by Di when dealing with text nodes in XML.
new a6be5bf BUG: Fix incorrect getNumberElements() in XdmfTopology when Mixed topology type is specified. Previously, for mixed topology types, this would return 0.0. This would result in unreadable xdmf files being written to disk.
new 8028748 ENH: Added headers to support newer compilers.
new b1686a9 ENH: Fixed main's arguments for test to prevent warning in updated g++ compiler
new ce93f59 ENH: Enable python test for XdmfSet.
new 52708d7 ENH: Get utils building in python.
new ccbfa35 ENH: Modify how XdmfMap stores data internally. It now follows a form used in other FEM codes, in a manner that makes it easy to assemble nodal forces.
new 518b583 ENH: Add ability to ignore sets from being partitioned by the partitioner.
new 5aa71a6 ENH: Hide use of boost::shared_ptr and boost::shared_dynamic_cast.
new 1c814a2 BUG: Fix bug that returned wrong dimensions when array pointer is held by XdmfArray.
new ea5dbd1 ENH: Add XdmfDiff to compare Xdmf files for equality.
new c04961b ENH: Add method to getName of XdmfArrayType as a string (useful when printing error messages in client codes).
new 72f5461 ENH: Add option in XdmfHeavyDataWriter to release data from arrays after writing to disk.
new 63991cd ENH: Allow arrays to be attached to XdmfInformation (we use this functionality in client code to store input parameters).
new 10a0025 ENH: Add option to clobber previous file in XdmfHDF5Writer.
new e058cc5 ENH: Add ability to write light data to a stream rather than just to disk.
new cd83004 ENH: Minor include changes to keep consistent style.
new 72ba85b ENH: Add specialized getValue in XdmfArray when getting single value.
new 720346e ENH: Add ability to set boundary communicator map in XdmfMap.
new c231d85 BUG: Fix bug introduced by new GetValue() in XdmfArray. Forgot to return value.
new 57773d2 BUG: Fix bug preventing Hexahedron_125 topology from being partitioned.
new 01d89e5 ENH: Updated headers to support newer compilers.
new 8186bbf ENH: Modify how XdmfMaps are attached to XdmfGrids by allowing more than one map to be attached.
new 1e964a2 BUG: Fix bug that prevented empty maps from being parsed correctly.
new 5fe29ae BUG: Fix bug causing segmentation fault when reading empty XdmfMap from disk.
new f45699a BUG: Fix bug in implementation of Polyline topology type.
new 21b2305 BUG: Fix bug causing nodal attributes with more than one component to be partitioned incorrectly by the partitioner.
new 6fa7fe7 FIX: Updated Java tests for change to Polyline
new 0a99426 ENH: Added Java Test to make sure the Garbage Collector works correctly
new fcf4fcc FIX: Corrected Java issue with BaseVisitor delete() trying to delete the concrete object even though it was receiving a shared pointer. This issue would occur whenever the garbage collector would run and try to delete an old XdmfWriter object. Also hid some SWIG warning for Java.
new c179c4d ENH: Fixed some SWIG warnings that appear on 2.0.4
new 20bd7a4 ENH: Corrected library issues for Macs
new f0d7d68 ENH: Updated the Testing Suite for Test Dependencies. Also fixed Test Option 'dup' to not delete the rest of the arguments.
new c314e51 FIX: Updated Testing Suite to not escape paths with spaces.
new 007a4a8 FIX: Fixed CMake for utils to build/install on Windows
new 1ef7304 FIX: Corrected Spelling Error
new 863de4f FIX: Fixed XdmfDiff to allow unsigned int. fabs did not accept it as a param.
new 5d35918 Added Windows Support for Utils
new 066763b Added support to build on Win7 VS2010
new 5e08005 Updated XdmfUtils to work with Win7
new 976c274 Updated DSM from Jerome Soumagne.
new 38d4a20 Reverted changes to core/CMakeLists.txt
new 5655c26 Need to link the directory for MPI
new 9ec81c6 Cleaned up some of the CMake files so it should work with HDF5 1.8.5 and 1.8.7
new aadf2a4 Removed some cmake output
new 0f90839 Fixed some CMake issues with linking hdf5 and h5fddsm
new 65d1f84 Small correction to linking DSM libraries.
new 4bb47fc COMP: Get rid of some intel compiler warnings in XdmfArray and test.
new 6d64b4a COMP: Fix testing by using LDPATH = library directories rather than paths to the libraries.
new 814a4c6 Merge branch 'master' of ssh://hsai-dev.arl.army.mil/data/Repository/Xdmf2
new 5c05105 COMP: Fix compilation bug in XdmfSet due to moving using declarations around to prevent compiler warnings.
new 5015de6 COMP: Make some relative paths absolute paths (HDF5, LIBXML, H5DSM Lib Dirs)
new 360f2e5 COMP: Add cstring header to support intel compiler.
new 3ada9fd BUG: Fix swig wrapping problem involving using declaration. This looks like a bug in swig since the fix is not proper C++ Surrounded by a ifdef swig block. If anyone has a better fix for this I'd like to use - this is a hack.
new 5d773b0 ENH: Add additional topology types.
new dc67273 ENH: Add additional typemaps for python swig for XdmfMap.
new c4b5ec5 Updated XdmfTopologyConverter.cpp to work on Windows
new 42c73cf Missed an epsilon when making changes for Windows.
new c8d2c32 BUG: Update XdmfTopologyConverter test for Hexahedron_64 elements after node connectivity has been changed.
new 4388f29 Fixed Java Loading issue. You no longer need to use static { System.loadLibrary() } at the begining of java code
new aa04762 Fixed up some warnings found in Windows.
new e579eee BUG: Add Dimensions when writing out Polyvertex topology to remain consistent with old Xdmf format.
new 848412f COMP: Remove some warnings.
new 6afc622 ENH: Upgrade version of metis used by the partitioner to 5.0.
new 86eefce ENH: Allow arbitrary elements to be partitioned by metis.
new 0d48e72 ENH: Add methods to get faces per element and nodes per element from XdmfTopologyType.
new dd6850a ENH: Fix formatting in XdmfArray.hpp
new f73576e ENH: Add unpartition method to partitioner.
new d11ee07 BUG: Fix infinite loop in XdmfCoreReader.cpp
new 4fe6147 BUG: Fix bug when pulling in href'd xincludes.
new 294c383 BUG: Fixed resolving file names with protocol added
new b9d23a5 ENH: Add ability to convert XdmfRegularGrid to XdmfUnstructuredGrid
new fa50bf2 ENH: Fix formatting.
new 48c377c ENH: Enable performance improving flags for SWIG wrapper generation in python.
new dd5eeb0 BUG: Fix bug in parse() function that only allowed correct parsing when Xdmf fragment was surrounded by an <Xdmf> tag.
new 80c53e8 BUG: Remove --builtin swig optimization since it broke visitor operations when writing out file to disk.
new 04f0957 FIX: Included hdf5 c include dirs during the build
new 37844fc COMP: Add missing include for fopen and fclose (cstdio)
new 4537750 ENH: Add ability to convert Hexahedron to Hexahedron_27 in topology converter.
new 32ae603 ENH: Add Fortran updates into trunk.
new 51b36c5 COMP: Fix some gcc warnings.
new decc7dd ENH: Improve performance of hdf5 writes.
new d5ebbc9 ENH: Performance improvements for HDF5 writer.
new 3eb2d34 ENH: Simplify XdmfArray class.
new 0dee627 COMP: Fix a few intel compiler warnings.
new ae42e9d ENH: Add ability to unpartition partitioned meshes from command line.
new 8c27cc2 ENH: Add ability to repartition partitioned meshes from command line.
new 7bcbfe7 ENH: Performance improvements for large reads/writes
new 895f33c ENH: Add methods in Fortran interface to reuse previously added data.
new 71b4e1a Added the pass through of MPI libs in CMake
new c728834 ENH: Commit Pat's changes for Fortran interface.
new fcb4261 BUG: Fix bug in parse caused when xml is parsed from string rather than disk.
new 7b0f5e8 ENH: Add method to Fortran interface accepting light data limit.
new 9c1652a BUG: Fix previous commit which committed incorrect changes!
new ab7e226 creating branch with full Python example code
new 7c2cfcc testreadme
new 63798d2 ENH: Commit some Fortran tests.
new 0803282 Cleaned with full Python example
new 3a71f5d removing readme
new de5d523 Merge branch 'ajb-dev' of /data/Repository/Xdmf2 into ajb-dev
new 752922c C++ full examples added
new db80e15 add readme
new f709ab4 remove readme
new 804c9d8 full C++ examples added to documentation
new bef0a66 cleaning up files
new eee28dc more example files added, DSM example created but currently being debugged.
new 521435d ENH: Add ability to write in parallel to hdf5 file.
new 7755f6b DSM example working for previous version of DSM, need to adjust for newer version
new b08e567 Merge branch 'master' of /data/Repository/Xdmf2 into ajb-dev
new c5929b5 ENH: Add string array type
new d85b477 DSM working with mpich2-1.5
new f91048a Merge branch 'master' of /data/Repository/Xdmf2 into ajb-dev
new ef76d17 BUG: Fix precision of values when written to XML.
new 275c67a ENH: Make Spectral Topologies have their own type.
new 15d33cb BUG Added header to fix cout not a member of std with gcc 4.1.2
new 4b1c1d0 changes for hdf5 file splitting and combining xmf files
new 4084f4e Merge branch 'ajb-dev', remote-tracking branch 'origin' into ajb-dev
new 62b1231 BUG: Fix bug in hdf5 chunking mechanism for multi-dimensional datasets.
new 734d4cf ENH: Avoid use of boost::get for isInitialized()
new 0cb8d44 BUG: Fix bug causing nested xincludes to not work properly.
new 0382f13 File splitting optimized more
new 88ed353 fixed some file output issues
new d51c5f3 ENH: Add graphs to Xdmf.
new b76c0b7 COMP: Remove unused arguments from functions.
new c7fdba2 fixed controller addition issue during append
new 76a9b91 BUG: Fix XdmfTopologyConverter to perform node insertion solely based on connectivity.
new 158f4ab COMP: Add support for newer versions of boost.
new 456d231 COMP: Get things working again with Intel compiler.
new 26bed71 COMP: Get rid of some GCC compiler warnings.
new 87bb27a merging from master
new f386e63 function reading capabilities
new df13c70 changes to array to allow for functions
new 8858e32 Revert "changes to array to allow for functions"
new cf18fe6 Revert "function reading capabilities"
new f1f7237 ENH: Add topology setters for polyline and polyvertex.
new 1133c56 changes to file splitting, hyperslab not completely working yet. changes to Fortran to allow for polylines and releasing data after standard write
new 73ceb40 removed debug statements
new d28d761 fixed some issues with adding to previously created files
new b8e830b removed debug statements
new 4f7ac2f BUG: Fix off by one error when partitioning graph on one processor.
new 1c4b3e2 changes to fortran for polylines and file splitting works for single dimensional arrays
new 98c7f46 BUG: Fix insert stride issue with XdmfArray found by Andrew.
new 861177e minor changes to ensure OutputTestXdmfFortran works properly
new f5c88a9 Improved backwards compatibility and Fortran interface with file splitting functions
new 19c5991 ENH: Try to improve performance from Fortran interface.
new 6748b23 ENH: Add ability to set heavy data writer in writer after initialization.
new d860685 changes for file splitting and functions along with assorted changes to XdmfFortran for possible speed increases
new c24e1ba merging in from main branch
new 897473c Fixed merge issue, class was not defined in header file
new d7626db was missing header reference for set heavy data writer
new 5006a19 Adjusted python interface to properly support XdmfGraph
new 0b37c6e Fixing improper merge with XdmfFortran header
new af08f05 fixed test errors and added new version of XdmfError
new f23f1be Fixed python wrapping for XdmfGraph and XdmfSparseMatrix
new b5dd776 changes to suppress warnings when using -Wall
new 273290a taking care of the intel compiler warnings
new 6699fb8 added tests for functions and removed warnings during splitting algorithm
new 03e031e hdf5 write efficiency changes to XdmfFortran and added a test for functions
new 817cd64 BUG: Fix bug in xpointers when writer is used multiple times.
new c804396 COMP: Fix boost shared_dynamic_cast test for clang compiler.
new 70882ed COMP: Fix a couple tests so that they compile with clang compiler.
new a72f400 Formatting changes and removing warnings
new 5d41d4c Merge branch 'master' of /data/Repository/Xdmf2 into ajb-dev
new e5f83ed ENH: Modify when to retrieve number of datasets from file.
new 5bae079 ENH: Store array type precision in string form.
new 004113f BUG: Add typemap for std::vector<shared_ptr<XdmfItem> >
new 9075be3 added nonthreaded DSM, inter program connection hasn't been tested
new 25380d0 merged from master
new 75b28f5 resoving merging conflicts
new 058ce90 made some fixes to the documentation
new 7ea61be BUG: Fix bug in python for casting of XdmfGridCollections
new 3249266 Merge branch 'master' of /data/Repository/Xdmf2 into ajb-dev
new 317d6f8 cosmetic changes to comments
new 3bce6df some cosmetic changes to line length in XdmfArray
new 11e9f68 made changes for preparations to push to master; still need to finish documentation changes and line length changes
new a5f74bf removed warnings
new ae817cd ENH: Add executable for conversion between exodus and xdmf.
new dc686f8 Finished converting documentation to tag-based version; adjusted line length where possible
new 6db38e9 ENH: Merge minor performance improvements.
new 5e38d23 Update to function code. Added error suppression.
new 101ba7b added XdmfSubset
new 8a80f9a Added subset; modified Array's interaction with Function; added new functionality to XdmfInformation subarrays; adjusted documentation to make more uniform
new 6e0d6c9 Added DSM capabilities to Fortran interface, simple array passing; Also added test for Fortran DSM
new e8b8549 changed tabs to spaces and pulled dsm to a separate folder under core
new 59106d9 fixed documentation to account for new dsm folder; adjusted the test for XdmfError; disabled the WriteHugeArray test
new 1a27ab8 wrapped function and subset into superclass XdmfArrayReference to allow for easier implementation of new array references
new 65d2636 removed old function code from main xdmf folder, now placed in core
new 03fc01b ensured hdf5 parallel dependancy
new 31b11e1 small bit of cleaning up in the swig wrapping
new a3f4e1d removed test files
new 82a7a83 added include that is not done automaticly in certain versions of cxx compliers
new c6357a2 fixing boost includes in Cmake
new d0cfaf9 correcting conversion of int to MPI_Comm in DSM
new 0590766 moved includes around for compatibility with hdf5 1.8.11
new 9998cb0 adjusted for compatibility with standard hdf5 in addition to hdf5vfd
new 053a30b changed Python Bindings to ensure all of Xdmf is imported
new 8e14630 Merge branch 'master' of ssh://hsai-dev.arl.army.mil/data/Repository/Xdmf2
new 261e07a changes to allow for openmpi use
new dda62b5 Update XdmfPartitioner to more efficiently handle element sets.
new 2c8248a removed unneeded references
new 9499b32 fixed dependancy on using core 0 for accept/connect
new c8b356a Merge branch 'ajb-dev' of /data/Repository/Xdmf2
new e3018ed Fixed Python wrapping on Linux for SWIG version >= 2.0
new aa51d51 BUG: Restore correct parsing of relative file paths for heavy data files.
new 0453f9d fixed interlace algorithm for unequal sizes
new f4adbc2 fixed Python DSM bindings to wrap MPIComm correctly
new ae10af4 fix for compatibility with Swig 2.0.11, manually defining the missing object type
new 56bdaad removed unneeded references
new c873ea1 fixed dependancy on using core 0 for accept/connect
new c67ebed BUG: Restore correct parsing of relative file paths for heavy data files.
new 65e96db fixed interlace algorithm for unequal sizes
new 550c1aa fixed Python DSM bindings to wrap MPIComm correctly
new b233dc7 fix for compatibility with Swig 2.0.11, manually defining the missing object type
new 9bc2ad7 Merge branch 'master' of ssh://hsai-dev.arl.army.mil/data/Repository/Xdmf2
new e08cae0 COMP: Fix visitor to not return void - necessary for MSVC compiler.
new 5269a83 removed duplicate delarations
new d0bc892 COMP: Fix compiler errors on clang.
new 3f9f3c6 fixed maps so that they automatically read from hdf5 when needed
new bfdf7d5 Merge branch 'master' of /data/Repository/Xdmf2
new 1d618f9 fixed default write mode for hdf5 writer when writing to single file
new 3d85b62 Merge branch 'master' of ssh://hsai-dev.arl.army.mil/data/Repository/Xdmf2
new 8df5716 ENH: Enable unpartitioning of files containing temporal collections.
new 354c9ad Adjusted Method by Which MPI4PY was included, separating from python proper.
new 891463d Merge branch 'master' of /data/Repository/Xdmf2
new 1f57c1b fixed typographical error in XdmfFortran header
new df2dcfc Edited Fortran Include file for Fixed Form compatibility
new 7e2f2a9 ENH: Translate element blocks correctly back to exodus.
new 0483f8b BUG: Fix bug in conversion of blocks back to exodus.
new 7c111ef ENH: Adjust exodus writer to utilize material blocks.
new 95ad91e added include required for newer versions of gcc
new 7231f8a Merge branch 'master' of /data/Repository/Xdmf2
new 89a31eb Added include for linux sleep command, it isn't automatically included in newer versions of gcc
new eb3575d added controller multi-open, dsm tests, and fortran tests
new 366b7b3 Added Fortran bindings for multiopen code
new 39a4f8e ENH: Initial commit of binary heavy data file support.
new 3e4a11f ENH: Support default attribute values for ArrayType (Float32) and AttributeType (Scalar). Also enable parsing of deprecated DataStructure tag, synonym of DataItem.
new 65ac92d ENH: Trim whitespace of XML content - to be friendlier to hand-edited files.
new 4117b09 ENH: Parse with XML_PARSE_NOENT to resolve XML entities.
new 55717ca ENH: Actually commit binary reader test.
new dc68e15 ENH: Remove unneccesary try catch blocks.
new 06c633a BUG: Fix parsing of nested xincludes.
new 0e3f8a5 ENH: Relax requirement for XdmfSet to contain Name attribute.
new 975536e ENH: Enable flexibility in specifying dimensionality of light data description.
new 7f5d700 Rework of HeavyDataController and HDF5Controller to remove extra code and move HeavyDataController away from being too dependent on hdf5 style XdmfFunction now supports negative numbers in addition to the - operator Reworked the interaction between array references and reading Cleaned up some warnings that showed up in pedantic Adjusted mpi tests to test against the MPIEXEC variable as opposed to hard calling mpirun Still needs to be changed to work better with Cray [...]
new ce12619 bug fixes for merge
new d46a7a6 added include for PGI compatibility
new 5f4fe7f Merge branch 'master' of /data/Repository/Xdmf2
new a3cefa8 fixed an issue with CMake lists and fixed Fortran bindings to work with intel style booleans
new d663dd9 refining CMake to convert install prefix to absolute path and to add some variables to the config file for FindXdmf
new 09136d0 removed unreachable code
new 6a2647c Merge branch 'master' of hsai-dev.arl.army.mil:/data/Repository/Xdmf2
new da24996 XdmfFunction read legacy files, small fortran changes
new caf2954 Improving the auto detection for MPI4PY and HDF5
new d4babe1 added FindMPI4Py link
new d61eee2 fixed unistd include guarding
new b92bfe9 fixed sleep command include
new 7863e93 Merge branch 'master' of hsai-dev.arl.army.mil:/data/Repository/Xdmf2
new db257fe Improving test output
new 939ff6c cleaning up code
new fa4993f minor bug fixes
new 96f6b25 COMP: Fix includes in tests for iostream.
new 643784c fix for version 1.8.x of OpenMPI
new 05106ef fixing type comparisons for python wrappers
new 6fe7f5d Merge branch 'master' of hsai-dev.arl.army.mil:/data/Repository/Xdmf2
new 76260f7 fixing version check as newer versions of OpenMPI output to stdout instead of stderr
new 1d1a19a fix for CMake 3.0.0
new 94e66e0 adjusted for mpi other than openmpi
new 5c29c74 fixed python linking error due to changes for CMake 3.0.0
new 4548469 fixed installation of Python libs and took care of polymorphism issue with std::floor
new 7cd7798 fix for polymorphism on std::log for pgi compiler
new 12cdf56 Fixing issues with arrays not currently read to disk when dealing with functions
new 5aef23f debugging function changes
new 43e68a4 Fix for Set compatibility with functions while having child Attributes
new bf7182d Fixed child Attributes not getting added to parent
new 06d2b52 BUG: Fix bug causing missed shared vertices in topology converter.
new 1524081 xdmf-2.1.dfsg.1
new 2db2f8e Debian 2.1.dfsg.1-11
new b9d2419 * Build against hdf5 for 1.8.15 transition
new 37a3a92 Add missing files
new b1e155c Remove kernel version from header for reproducibility
new ca1ed86 SV : 3.9.7
new 3b5c937 Fix for c++11 compilation
new 6301efe one little fix to patch needed
The 527 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
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