BP3 Deserialization:
Getting subfile seeks and intersection info
Set host language in bindings for row-major and zero-index info

Passed ctest (MPI and nonMPI) excluding ADIOS1 engine, and Python bindings
HDF5, C bindings and C++ tests working
Introduced BeginStep EndStep functions
Renamed IO GetVariable/Attribute to InquireVariable/Attribute

Getting and defining available Variables at Open
Storing Variable position in Metadata, added to VariableBase
mpidummy: Added support for MPI_Reduce, MPI_Gatherv
Added utils and BPLS

Implemented basic buffer reading functionality
Added threading for bp serialization/deserialization
Refactored MPI functionality
Engine is now a reference
Initial Read API

bool flag checks are implicit
Removed single letter enums in ADIOSTypes.h
All enums are enum class in ADIOSTypes.h using CamelCase
ADIOS uses delegating constructor
Using return type of emplace for IO (in ADIOS) and Variable (in IO)
Removed all base class include from inl template file

1 Now IO (replaced Method) and is the factory for Variables and Engines
2 Reduced core components to user-public objects only
3 Moved and reorganized all helper functions to helper directory
4 Engines are now lightweight (except for ADIOS1Reader WIP) using MACRO
5 HF5Common and ADIOS1Common (except for Readers WIP) are now part of the toolkit so they can be reused by Engines
6 TransportMan is a new layer for transport management (file is default)
7 DataMan will be implemented under toolkit/transportman/dataman
8 Template separation (tcc and inl) applied all over the code
9 Improved Doxygen documentation

Runtime Issues:
DataMan library compilation (cacheman)
ADIOS1 Warning
TestADIOSInterfaceWrite catches exceptions

Fix hello examples with new DefineVariable() syntax, for BP, timeBP and ADIOS1. Missing HDF5 and DataMan

- Added examples/groupless/multistep writer example to the build
- Added ADIOS1 reader but it does not work yet
- Added heat transfer example reader

helloBPWriter and timeBPWriter

Now file.bp/profiling.log is generating capturing I/O profile info

Started implementation of bindings/python using boost::python
Modified Makefile to allow for dynamic library compilation

To do:
Work on time aggregation

Now printing last variable values with bpls. 

Need to fix so payload offset is set for all variables correctly. 

Replaced vectors with map containers for Variables to avoid iterator
invalidation when adding element to a container. 

Metadata is correctly interpreted by ADIOS 1.0 bpls

To do:
Need to debug values from bpls -d option

Continued debugging BP1 Writer for a single variable write

examples/hello/bpWriter working

To do:

BPReader examples and BP1Reader class

Testing

see examples/hello/dataman and examples/hello/writer for working
examples

Corrected bug by including cmath in adiosFunctions.cpp

Removed helloWriter.cpp and helloDataMan.cpp, now using
helloDataMan_OOP.cpp and helloWriter_OOP.cpp

Tested memory leaks with valgrind for simple example
Verifying if variable index is written correctly

Added ./src/format/BP1Writer.cpp

To do:
Need to test for array index and payload write

Propagate GetType<T> in Group, Engine and Support classes

To do:

Test ./examples/hello/writer/helloWriter_OOP.cpp

BP1Writer: Continue working on functions to write data and metadata

Group: added Dims alias and SetDimensions function, so dimensions can be built from a Var List put in an std::initializer_list<Var>

Added a bool flag in Variable to know if it is a dimension


To do:
Allow for passing values at DefineVariable

rather than handlers

Group&, Method& and the polymorphic std::shared_ptr<Engine> will be
returned by DeclareGroup, DeclareMethod and Open.

Added Group functions DefineVariable to be a template
Now using adios::Var when creating a variable (still a variable name
string).

Uses more C++ OO + templates features

Compiled and tested with ./examples/hello/helloWriter_OOP.cpp , mpi and
no-mpi versions