[xdmf] annotated tag v1.0 created (now cd5fa7f)
Alastair McKinstry
mckinstry at moszumanska.debian.org
Wed Apr 19 14:32:21 UTC 2017
This is an automated email from the git hooks/post-receive script.
mckinstry pushed a change to annotated tag v1.0
in repository xdmf.
at cd5fa7f (tag)
tagging 891463d8b2cb53e8fc709ad5a448ac5b4c276723 (commit)
tagged by Kenneth Leiter
on Mon Feb 3 11:49:11 2014 -0500
- Log -----------------------------------------------------------------
Version 1.0
Andrew J. Burns (Cont (91):
creating branch with full Python example code
testreadme
Cleaned with full Python example
removing readme
Merge branch 'ajb-dev' of /data/Repository/Xdmf2 into ajb-dev
C++ full examples added
add readme
remove readme
full C++ examples added to documentation
cleaning up files
more example files added, DSM example created but currently being debugged.
DSM example working for previous version of DSM, need to adjust for newer version
Merge branch 'master' of /data/Repository/Xdmf2 into ajb-dev
DSM working with mpich2-1.5
Merge branch 'master' of /data/Repository/Xdmf2 into ajb-dev
changes for hdf5 file splitting and combining xmf files
Merge branch 'ajb-dev', remote-tracking branch 'origin' into ajb-dev
File splitting optimized more
fixed some file output issues
fixed controller addition issue during append
merging from master
function reading capabilities
changes to array to allow for functions
Revert "changes to array to allow for functions"
Revert "function reading capabilities"
changes to file splitting, hyperslab not completely working yet. changes to Fortran to allow for polylines and releasing data after standard write
removed debug statements
fixed some issues with adding to previously created files
removed debug statements
changes to fortran for polylines and file splitting works for single dimensional arrays
minor changes to ensure OutputTestXdmfFortran works properly
Improved backwards compatibility and Fortran interface with file splitting functions
changes for file splitting and functions along with assorted changes to XdmfFortran for possible speed increases
merging in from main branch
Fixed merge issue, class was not defined in header file
was missing header reference for set heavy data writer
Adjusted python interface to properly support XdmfGraph
Fixing improper merge with XdmfFortran header
fixed test errors and added new version of XdmfError
Fixed python wrapping for XdmfGraph and XdmfSparseMatrix
changes to suppress warnings when using -Wall
taking care of the intel compiler warnings
added tests for functions and removed warnings during splitting algorithm
hdf5 write efficiency changes to XdmfFortran and added a test for functions
Formatting changes and removing warnings
Merge branch 'master' of /data/Repository/Xdmf2 into ajb-dev
added nonthreaded DSM, inter program connection hasn't been tested
merged from master
resoving merging conflicts
made some fixes to the documentation
Merge branch 'master' of /data/Repository/Xdmf2 into ajb-dev
cosmetic changes to comments
some cosmetic changes to line length in XdmfArray
made changes for preparations to push to master; still need to finish documentation changes and line length changes
removed warnings
Finished converting documentation to tag-based version; adjusted line length where possible
Update to function code. Added error suppression.
added XdmfSubset
Added subset; modified Array's interaction with Function; added new functionality to XdmfInformation subarrays; adjusted documentation to make more uniform
Added DSM capabilities to Fortran interface, simple array passing; Also added test for Fortran DSM
changed tabs to spaces and pulled dsm to a separate folder under core
fixed documentation to account for new dsm folder; adjusted the test for XdmfError; disabled the WriteHugeArray test
wrapped function and subset into superclass XdmfArrayReference to allow for easier implementation of new array references
removed old function code from main xdmf folder, now placed in core
ensured hdf5 parallel dependancy
small bit of cleaning up in the swig wrapping
removed test files
added include that is not done automaticly in certain versions of cxx compliers
fixing boost includes in Cmake
correcting conversion of int to MPI_Comm in DSM
moved includes around for compatibility with hdf5 1.8.11
adjusted for compatibility with standard hdf5 in addition to hdf5vfd
changed Python Bindings to ensure all of Xdmf is imported
changes to allow for openmpi use
removed unneeded references
fixed dependancy on using core 0 for accept/connect
Merge branch 'ajb-dev' of /data/Repository/Xdmf2
fixed interlace algorithm for unequal sizes
fixed Python DSM bindings to wrap MPIComm correctly
fix for compatibility with Swig 2.0.11, manually defining the missing object type
removed unneeded references
fixed dependancy on using core 0 for accept/connect
fixed interlace algorithm for unequal sizes
fixed Python DSM bindings to wrap MPIComm correctly
fix for compatibility with Swig 2.0.11, manually defining the missing object type
removed duplicate delarations
fixed maps so that they automatically read from hdf5 when needed
Merge branch 'master' of /data/Repository/Xdmf2
fixed default write mode for hdf5 writer when writing to single file
Adjusted Method by Which MPI4PY was included, separating from python proper.
Merge branch 'master' of /data/Repository/Xdmf2
Brian Panneton (77):
Added Ken Renards Java Updates from a patch
Relocated and improved Java and Python SWIG Wrappers
Removed the need for XDMF_SWIG_JAVA macros classpath argument
Added better description for macro and dependencies for XDMF_SWIG_PYTHON
FIX: Deleted duplicate ignores for SWIGJAVA
Copied over testing suite that I made on an old Xdmf2 repo.
Added check for wrapping java to include java test directory
ENH: Added distinction between core and not core with testing suite.
ENH: Added CMake option to build just the core.
ENH: Added 'make clean' support for SWIG Python and SWIG Java extra files
ENH: Added support for 'make clean' into the Testing Suite
FIX: Corrected SWIG overriding equals for Java and Python
ENH: Renamed core/Java and core/Python Test Name
FIX: Added renaming of XdmfSet.hpp methods for getAttribute() const
FIX: Added more SWIG overriding equals for Python
FIX: Fixed Merge Mistake
ENH: Moved the TestingSuite to more of a stand alone format
FIX: Updated Testing Suite to fix Java Parallel Build
FIX: Removed dynamic cast to prevent SWIG java conversion problems
ENH: Added Xdmf Versioning
ENH: Cleaned up some of the CMakeLists.txt file
FIX: Fixed up install to add loki to core, add python core and java libraries.
FIX: Corrected a segfault when two objects are next to each other.
FIX: Corrected how xml content was gathered.
FIX: Cleaned up Version Suite and added the version into XdmfWriter.
FIX: Corrected possible future XdmfVersion header collision problem.
FIX: Corrected accessing Version from Python
Merge branch 'tidyup'
FIX: Added extra headerfiles to install
FIX: Added default version if Git does not exist. (2.X)
FIX: Added XdmfVersions to .gitignore (They will be created on build)
ENH: Initial Windows Conversion
FIX: Added Versioning export for windows and fixed win32 java build
FIX: Added more exports for Win32
FIX: Moved template(ItemVector) from Xdmf.i to XdmfCore.i
ENH: Updated Testing Suite
ENH: Removed test dependency for libraries in LD_PATH and PATH. Fixed Swig Parallel build issue.
ENH: Added some support for XdmfConfig.cmake file.
FIX: Corrected gathering of libxml2 and python locations
FIX: Removed some XdmfConfig.cmake variables set before Carries update.
FIX: Made changes for WinXP Compatability
FIX: Corrected an issue with the Versioning Suite and a Java formatting source code issue.
ADD: Included XdmfVersion.hpp in the install.
FIX: Changed how java builds in order to allow JDK5.
ENH: Added Java support for insertValuesAs*() to allow adding of Java arrays.
Merge branch 'java'
ENH: Changed location of lib files during build for Windows Platforms
ENH: Added headers to support newer compilers.
ENH: Fixed main's arguments for test to prevent warning in updated g++ compiler
ENH: Updated headers to support newer compilers.
FIX: Updated Java tests for change to Polyline
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.
ENH: Fixed some SWIG warnings that appear on 2.0.4
ENH: Corrected library issues for Macs
ENH: Updated the Testing Suite for Test Dependencies. Also fixed Test Option 'dup' to not delete the rest of the arguments.
FIX: Updated Testing Suite to not escape paths with spaces.
FIX: Fixed CMake for utils to build/install on Windows
FIX: Corrected Spelling Error
FIX: Fixed XdmfDiff to allow unsigned int. fabs did not accept it as a param.
Added Windows Support for Utils
Added support to build on Win7 VS2010
Updated XdmfUtils to work with Win7
Updated DSM from Jerome Soumagne.
Reverted changes to core/CMakeLists.txt
Need to link the directory for MPI
Cleaned up some of the CMake files so it should work with HDF5 1.8.5 and 1.8.7
Removed some cmake output
Fixed some CMake issues with linking hdf5 and h5fddsm
Small correction to linking DSM libraries.
Updated XdmfTopologyConverter.cpp to work on Windows
Missed an epsilon when making changes for Windows.
Fixed Java Loading issue. You no longer need to use static { System.loadLibrary() } at the begining of java code
Fixed up some warnings found in Windows.
BUG: Fixed resolving file names with protocol added
FIX: Included hdf5 c include dirs during the build
Added the pass through of MPI libs in CMake
BUG Added header to fix cout not a member of std with gcc 4.1.2
Ken Leiter (Civ (13):
ENH: Initial Commit
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 nodesPerElement) but we still [...]
ENH: Allow XdmfGrids to insert XdmfAttribute elements. Add this to the visitor logic to write to xml.
ENH: Add XdmfAttributeCenter to XdmfAttribute to specify how the attribute values are attached to the grid.
ENH: Start separating XdmfItem properties from their respective classes - XdmfAttributeType.
ENH: Start separating XdmfItem properties from their respective classes - XdmfAttributeCenter.
ENH: Start separating XdmfItem properties from their respective classes - XdmfGeometryType.
ENH: Start separating XdmfItem properties from their respective classes - XdmfTopologyType.
STYLE: Remove const qualifier from return of printSelf() --- it is unecessary
ENH: Add ability to write HDF5 files as part of XdmfVisitor operation.
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.
ENH: Allow for storage, retrieval, and output of datatypes other than int. Incorporate into HDF5 output.
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.
Ken Leiter (Civ ARL/CISD) kleiter (17):
ENH:
ENH: Add Smart Pointers to XdmfArray implementation. Modify some method names to be more clear about whether copying is being
ENH: Remove non const getValuesPointer for now. Rename getValues as getValuesString() and add getValues that returns a smart pointer to the internal array.
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,
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.
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)
Merge branch 'XdmfArraySmartPointer'
ENH: Add BUILD_DOCUMENTATION flag to CMakeLists that builds doxygen documentation for the project.
ENH: Add CTEST to allow for submissions to the Xdmf dashboard.
ENH: Add class level documentation across the project. Remove a couple methods that
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.
ENH: Remove unneccesary private method from XdmfArray. Regenerate python wrappers.
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.
ENH: Add initialize() method that allows user to specify the type of data to store in an XdmfArray if desired.
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.
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.
STYLE: Formatting
Ken Renard (2):
fixes for "transparent root" and "compare"
ENH: Add dimension string to XdmfArray
Kenneth D. Renard (Cont ARL/CISD) kdrenard (7):
ENH: patch to fix problem encountered with "transparent" root object.
ENH: get numpy Array from XdmfArray (for Python)
FIX: Handle error conditions better in XdmfArray.getNumpyArray()
ENH: XdmfArray python object will access HDF5 datasets as numpy arrays via getNumpyArray()
Deleted TestXdmfWriterHDF5ThenXML.cxx
FIX: Updates to reflect API changes in Xdmf2Array
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 XdmfItem->IsEqual()
Kenneth Leiter (250):
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.
ENH: Get Python wrapping working on OS X and regenerate wrappers incorporating recent changes.
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.
ENH: Delete unneeded files from repository
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.
ENH: Add XdmfDataItem which stores array data to write to Xdmf.
ENH: Add XdmfDataItems to XdmfTopology and XdmfGeometry and write them out correctly in the XdmfVisitor. Verified to work with simple Hexahedron file.
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.
ENH: Update Python Wrapping Files
ENH: Add XdmfDomain.
ENH: Make XdmfArray variant visitors private members of XdmfArray.
ENH: Fix up some minor const-correctness issues.
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.
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.
ENH: Add resize() method to XdmfArray.
ENH: Add reserve() and getCapacity() methods to XdmfArray.
ENH: Use unsigned ints where appropriate (sizes, indices, etc.)
ENH: Rename write() operation to accept() which is more consistent for the Visitor pattern. Also, we can
ENH: Remove printSelf() method as it was unnecessary.
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
ENH: Add XdmfItemProperty to genericize properties attached to XdmfItems. Add a pure virtual getItemProperties() method
ENH: Add pure virtual getItemTag method to XdmfItem working to return the tag (same as in XML terminology) for the specific item.
ENH: Modift XdmfWriter to utilize new genericized getItemTag and getItemProperties methods
ENH: Split heavy data writing from XdmfWriter into XdmfHDF5Writer. This paves the way for the possiblity of having multiple
ENH: Use PIMPL idiom to hide hdf5 and libxml2 includes from header files for writers.
ENH: Remove getHDF5Type from XdmfArray and move into XdmfHDF5Writer so all hdf5 interaction is isolated
ENH: Add tests using new XdmfHDF5Writer exclusively. Modify some methods in XdmfHDF5Writer to get everything working as expected.
ENH: Remove group creation when writing HDF5 files. The group paths depend on how the xml
ENH: Add XdmfHDF5Controller so that heavy data can be written and released before light data is written.
ENH: Add reading functionality to XdmfHDF5Controller
ENH: Add ability to read XML files from disk into Xdmf structures in memory.
BUG: Fix incorrect assert() statement causing TestXdmfArray to fail.
ENH: Add XdmfSet. Remove getName() method from ItemProperties.
ENH: Add ability to remove XdmfAttributes and XdmfSets from XdmfGrids.
ENH: Add XdmfGridCollection and begin adding XdmfPartitioner.
ENH: Add test for XdmfGridCollection.
ENH: Continue implementing XdmfPartitioner.
ENH: Split XdmfAttributes in XdmfPartitioner.
ENH: Split XdmfAttributes in XdmfPartitioner.
ENH: Modify ItemProperties to use shared pointers like the rest of Xdmf. Modify swig wrapping to correctly
ENH: Clean up a bit of const-correctness related things.
ENH: Add write modes to HDF5Writer. It can now overwrite (write in the same
ENH: Add XdmfArrayType to store data type / precision information which should make interaction
ENH: Improve python interface by rewriting swig wrapping and moving XdmfObject
ENH: Split Xdmf into XdmfCore and Xdmf libraries in anticipation of NetDMF development. Create a couple abstract base classes
ENH: Move XdmfCore into its own subdirectory. Move XdmfCore specific tests into core subdirectory and modify
ENH: Add skeleton for XdmfTopologyConverter Util
ENH: Make ItemTag const so it is cannot be modified.
ENH: Begin implementing XdmfTopologyConverter. Fix typo in XdmfArray that incorrectly initialized UInt32() type.
ENH: Allow XdmfArrayType to correctly read old xdmf files containing "NumberType" XML attribute, which is the same as DataType.
ENH: Add python wrapping for XdmfUtils and modify some swigisms to get reader working properly in python.
ENH: Add Hexahedron_64() to Hexahedron() Topology Conversion.
ENH: Rename get/set ItemProperties for conciseness. e.g. getAttributeCenter ---> getCenter . This follows
ENH: Add Hexahedron() to Hexahedron_125() Topology Conversion.
ENH: Add XdmfInformation to store key/value pairs.
ENH: Modify XdmfWriter to insert XdmfArray content into most recently created child to allow for creation of multiple XdmfArray children.
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.
ENH: Add Mode to XdmfWriter. Default mode ensures that all heavy data referenced by the XML file being written
ENH: Add XdmfTime and allow it to be attached to XdmfGrid. Add some convenience functions in XdmfGrid
ENH: Remove +x permission from loki files.
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.
ENH: First draft of xpointer respected reading.
ENH: Clean up XInclude additions. Verify that writing reading and writing an XPath/XInclude file produces the same file.
ENH: Finish cleanup of XInclude/XPath additions.
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.
ENH: Remove getLastWrittenDataSet from HDF5Writer and just get that information from the appropriate HDF5Controller attached to the Array.
ENH: Modify all filesystem paths used in xdmf to use the absolute real path - aka "canonical path". Modify tests to ensure this is working.
ENH: Clean up changes to fix absolute/relative path adjustments.
ENH: Modify reading of TopologyType to ignore case.
ENH: Modify reading of XdmfArray dimensions to correctly calculate size for multidimensional arrays.
ENH: Make XdmfGridCollection inherit from XdmfGrid and XdmfDomain, since it is really a unity of the two classes. Modify some details in ItemFactory / Reader.
ENH: Remove XdmfObject since it was unnecessary and broke Java wrapping for NetDMF.
ENH: Remove static New implementation from header files and move to implementation files.
ENH: Fix up some comments, change a couple function names for consistencies sake.
BUG: Fix Python reading with typemaps that has been broken since Xdmf/XdmfCore split.
ENH: Make XdmfSet behave like a real std::set. Modify some writing functionality to make this possible.
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.
ENH: Have all dataitems inherit directly from XdmfArray. Modify writing to support this.
ENH: Get Utils, Python Wrapping, and Tests working for new changes.
ENH: Add XdmfMap which maps nodes across partition boundaries.
ENH: Add ability to XPath a file when opening in order to only read a part of the file.
ENH: Add setHDF5Controllers() to XdmfMap.
ENH: Add XdmfExodusReader for reading ExodusII files into Xdmf. Add ability for XdmfArray::initialize() to take a size value to initialize the array to.
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.
ENH: Add XdmfExodusWriter to utils.
ENH: Commit Ken Renard's patches modifying populateItem and XdmfCoreReader to support some xpath functionality for backwards compatibility.
ENH: Revert changes to XdmfSet to go back to XdmfArray implementation. Add Attributes to XdmfSet.
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.
ENH: Begin adding install rules. Modify bug in XdmfWriter that resulted in XdmfArrays not being written in certain cases.
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).
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.
ENH: Add GLL Spectral Topology Types.
ENH: Clean up some formatting and ignores to use the new function names.
ENH: Modify utils testing to use new testing functionality.
BUG: Fixed dependency issue with java tests causing parallel builds to fail.
ENH: Add macros to simplify adding children to an XdmfItem.
ENH: Add XdmfGridRegular for CoRectilinear (Regular) Structured Grids. Add test for interaction and output.
ENH: Get reading of regular grids partially complete.
ENH: Fix some formatting due to patches.
ENH: Finish IO of XdmfGridRegular. Begin implementation of XdmfGridRectilinear.
ENH: Get equality functions working again, but keep it in the SWIG file rather the polluting the C++.
ENH: Get Java wrapping working again. Add curvilinear grid.
ENH: Get Curvilinear additions wrapped in Python and Java
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.
ENH: Add ID for topology type to support mixed cells. Cleanup some formatting and constness.
ENH: Cleanup to merge changes with Ken Renard.
ENH: Add DSM Support. Update swigging procedures to current code.
Merge to current master
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
ENH: Cleanup comments and inheritance syntax a bit. Remove unnecessary Geometry Types not needed since splitting structured and unstructured grids
COMP: Check SWIG version to be greater than 2.0.0 and fix duplicate "BUILD_TESTING" options.
ENH: Rename all subclasses of XdmfGrid to more syntactically friendly names: i.e. XdmfGridUnstructured to XdmfUnstructuredGrid.
ENH: Modify wrapping of XdmfArray to always use "insert" and not "copy". Also add template specializations to allow for initialize calls.
BUG: Fix writing of single XdmfArray to a file.
Testing permissions of Xdmf repository by commiting dummy change
Check permissions once again.
Check permissions
Check permissions
COMP: Fix compilation of utils tests by including missing directory.
COMP: Mark needed variables as unadvanced before they are found.
STYLE: Transition to friendlier formatting style.
COMP: Fix duplicate BUILD_TESTING and XDMF_BUILD_TESTING in build script.
COMP: Mark DOXYGEN_EXECUTABLE as unadvanced before it is found.
BUG: Add typemap for std::vector<boost::shared_ptr<XdmfItem > > which is a return value from XdmfReader.
Merge branch 'master' of ssh://hsai-dev.arl.army.mil/data/Repository/Xdmf2
ENH: Modify documentation for completeness.
COMP: Fix mixing CMake include preventing xdmf/exodus test from compiling.
COMP: Add missing header files.
COMP: Fix compilation against hdf5 when built with parallel.
COMP: Fix XdmfConfig.cmake generation to install into install directory rather than copying at configure time.
ENH: Add Copyright
COMP: Add header file to get test compiling for newest version of H5FDdsm.
Merge branch 'master' of public.kitware.com:Xdmf2
BUG: Remove duplicate swig typemap for ItemVector.
Merge formatting changes into 'master'
COMP: Move XdmfFunctions.cmake to CMake directory.
ENH: Modify HDF5Controllers to accept start, stride, and count to pull hyperslabs from hdf5 data sets.
ENH: Add assertion to make sure start, stride, and count have the
ENH: Improve how array keeps track of dimensionality in anticipation of working with hyperslabs.
ENH: Modify XdmfHDF5Controller to work with new multidimensional support.
ENH: Modify XdmfHDF5Writer to respect dimensionality in XdmfArrays. This will now be reflected in both light and heavy data.
ENH: Complete hyperslab reading.
ENH: When array is uninitialized return dimensions as [0] and "0"
ENH: Remove trailing whitespace when convert arrays to strings in XdmfArray.
ENH: Add Python test for new multidimensional array handling. Add typemap for swig for the std::vector<unsigned int> necessary for dimensions.
BUG: Fix bug when constructing triangle topology type that caused
BUG: Fix bug causing XdmfAttributes to not be attached to XdmfSets when read
ENH/BUG: Get XdmfInformation to work with older style xdmf format where
ENH: Convert XdmfArrayType to HDF5 data type when reading rather than
BUG: Fix bug found by Di when dealing with text nodes in XML.
BUG: Fix incorrect getNumberElements() in XdmfTopology when Mixed topology
ENH: Enable python test for XdmfSet.
ENH: Get utils building in python.
ENH: Modify how XdmfMap stores data internally. It now follows a form
ENH: Add ability to ignore sets from being partitioned by the partitioner.
ENH: Hide use of boost::shared_ptr and boost::shared_dynamic_cast.
BUG: Fix bug that returned wrong dimensions when array pointer is held
ENH: Add XdmfDiff to compare Xdmf files for equality.
ENH: Add method to getName of XdmfArrayType as a string (useful when printing
ENH: Add option in XdmfHeavyDataWriter to release data from arrays after
ENH: Allow arrays to be attached to XdmfInformation (we use this functionality
ENH: Add option to clobber previous file in XdmfHDF5Writer.
ENH: Add ability to write light data to a stream rather than just to disk.
ENH: Minor include changes to keep consistent style.
ENH: Add specialized getValue in XdmfArray when getting single value.
ENH: Add ability to set boundary communicator map in XdmfMap.
BUG: Fix bug introduced by new GetValue() in XdmfArray. Forgot to return value.
BUG: Fix bug preventing Hexahedron_125 topology from being partitioned.
ENH: Modify how XdmfMaps are attached to XdmfGrids by allowing
BUG: Fix bug that prevented empty maps from being parsed correctly.
BUG: Fix bug causing segmentation fault when reading empty XdmfMap from disk.
BUG: Fix bug in implementation of Polyline topology type.
BUG: Fix bug causing nodal attributes with more than one component to be
COMP: Get rid of some intel compiler warnings in XdmfArray and test.
COMP: Fix testing by using LDPATH = library directories rather than paths
Merge branch 'master' of ssh://hsai-dev.arl.army.mil/data/Repository/Xdmf2
COMP: Fix compilation bug in XdmfSet due to moving using declarations
COMP: Make some relative paths absolute paths (HDF5, LIBXML, H5DSM Lib Dirs)
COMP: Add cstring header to support intel compiler.
BUG: Fix swig wrapping problem involving using declaration.
ENH: Add additional topology types.
ENH: Add additional typemaps for python swig for XdmfMap.
BUG: Update XdmfTopologyConverter test for Hexahedron_64 elements after
BUG: Add Dimensions when writing out Polyvertex topology to remain consistent with old Xdmf format.
COMP: Remove some warnings.
ENH: Upgrade version of metis used by the partitioner to 5.0.
ENH: Allow arbitrary elements to be partitioned by metis.
ENH: Add methods to get faces per element and nodes per element from
ENH: Fix formatting in XdmfArray.hpp
ENH: Add unpartition method to partitioner.
BUG: Fix infinite loop in XdmfCoreReader.cpp
BUG: Fix bug when pulling in href'd xincludes.
ENH: Add ability to convert XdmfRegularGrid to XdmfUnstructuredGrid
ENH: Fix formatting.
ENH: Enable performance improving flags for SWIG wrapper generation in python.
BUG: Fix bug in parse() function that only allowed correct parsing when Xdmf
BUG: Remove --builtin swig optimization since it broke visitor operations
COMP: Add missing include for fopen and fclose (cstdio)
ENH: Add ability to convert Hexahedron to Hexahedron_27 in topology converter.
ENH: Add Fortran updates into trunk.
COMP: Fix some gcc warnings.
ENH: Improve performance of hdf5 writes.
ENH: Performance improvements for HDF5 writer.
ENH: Simplify XdmfArray class.
COMP: Fix a few intel compiler warnings.
ENH: Add ability to unpartition partitioned meshes from command line.
ENH: Add ability to repartition partitioned meshes from command line.
ENH: Performance improvements for large reads/writes
ENH: Add methods in Fortran interface to reuse previously added data.
ENH: Commit Pat's changes for Fortran interface.
BUG: Fix bug in parse caused when xml is parsed from string rather than disk.
ENH: Add method to Fortran interface accepting light data limit.
BUG: Fix previous commit which committed incorrect changes!
ENH: Commit some Fortran tests.
ENH: Add ability to write in parallel to hdf5 file.
ENH: Add string array type
BUG: Fix precision of values when written to XML.
ENH: Make Spectral Topologies have their own type.
BUG: Fix bug in hdf5 chunking mechanism for multi-dimensional datasets.
ENH: Avoid use of boost::get for isInitialized()
BUG: Fix bug causing nested xincludes to not work properly.
ENH: Add graphs to Xdmf.
COMP: Remove unused arguments from functions.
BUG: Fix XdmfTopologyConverter to perform node insertion solely
COMP: Add support for newer versions of boost.
COMP: Get things working again with Intel compiler.
COMP: Get rid of some GCC compiler warnings.
ENH: Add topology setters for polyline and polyvertex.
BUG: Fix off by one error when partitioning graph on one processor.
BUG: Fix insert stride issue with XdmfArray found by Andrew.
ENH: Try to improve performance from Fortran interface.
ENH: Add ability to set heavy data writer in writer after initialization.
BUG: Fix bug in xpointers when writer is used multiple times.
COMP: Fix boost shared_dynamic_cast test for clang compiler.
COMP: Fix a couple tests so that they compile with clang compiler.
ENH: Modify when to retrieve number of datasets from file.
ENH: Store array type precision in string form.
BUG: Add typemap for std::vector<shared_ptr<XdmfItem> >
BUG: Fix bug in python for casting of XdmfGridCollections
ENH: Add executable for conversion between exodus and xdmf.
ENH: Merge minor performance improvements.
Merge branch 'master' of ssh://hsai-dev.arl.army.mil/data/Repository/Xdmf2
Update XdmfPartitioner to more efficiently handle element sets.
BUG: Restore correct parsing of relative file paths for heavy data files.
BUG: Restore correct parsing of relative file paths for heavy data files.
Merge branch 'master' of ssh://hsai-dev.arl.army.mil/data/Repository/Xdmf2
COMP: Fix visitor to not return void - necessary for MSVC compiler.
COMP: Fix compiler errors on clang.
Merge branch 'master' of ssh://hsai-dev.arl.army.mil/data/Repository/Xdmf2
ENH: Enable unpartitioning of files containing temporal collections.
Matthew Bowman (2):
test
sdf
Payton Oliveri (Cont ARL/CISD) poliveri (2):
Added in XdmfError
Added XdmfError Replaced asserts with XdmfError::messages
Sankhesh Jhaveri (1):
Fixed Python wrapping on Linux for SWIG version >= 2.0
panneton (1):
ENH: Added Java Test to make sure the Garbage Collector works correctly
spear (5):
Checking Xdmf Repository permissions on master
Testing permissions for Xdmf2.git
Checking permissions for Xdmf master
Modified Xdmf2 to test master permissions
Added XdmfFunctions.cmake macro, modified XdmfConfig, Added function call and file copy for the XdmfConfig file to the CMakeLists.txt
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