This addresses the 2D part of issue 168: the ability to specify which meteo parameter and time step to read/write from/to a 2D grid. This should be the prefered reading method in the future, since it leaves to the plugin the task of building the file name, extension, database table, etc This also provides added metadata and more control over the writing process.

A lot of writes were using std::endl for end of line, which forces a buffer flush. This lead to a visible performance cost (as shown by the profiling project made in collaboration with HES_SO). These have been replaced by "\n" that lets ostream manage its buffer as it wants.

Because POPC does not properly support std::cout and requires cout instead, this has been fixed in the code, with the necessary "using namespace" added. Only one std::cout remains (in IOUtils) and will be removed if absolutely necessary later.

Removed some unecessary variables in exceptions catching (this should remove VC++ (rightful) warnings).

Some Visual C++ warnings have been turned off (namely, that it can not generate a copy constructor) in MeteoIO.h, so each application using MeteoIO would benefit from it (and avoid being polluted by unecessary warnings). 

Exception catching is now done by const reference, as recommended in our coding style.

More size_t related issues have been found (thanks to the new snowpack server) and fixed. Basically, please remember that any variable used with/for the return value of a call to size() MUST be of type size_t (this becomes specially relevant in 64 bits).

The water triple point pressure has been updated to a better value.

Fixed some bad naming in DynamicLibrary, silenced an unnecessary warning from Visual C++ (urging us to use non standard library calls), fixed some DLL exports for Visual C++.

The arrays are now using the vector filling methods when possible. A specialized template for convertString(unsigned int) has been written. 

A two segments linear fit (for elevation detrending) has been implemented with a fixed inflection point. This is quite primitive but allows the LLIDW spatial interpolation to use it and therefore to behave like the traditional SLF SnowFit program. More work will be needed for fully configurable regression algorithm choice though... 

Some namming issues have been fixed in COSMOXML. A better emissivity handling has been implemented in SNIO to be closer to the original Snowpack (ie: compute clear sky ILWR when no cloudiness/emissivity is given).

The changes to the IOInterface (no more vec<vec<StationData>>) have been propagated into all plugins.

BUGFIX: When adding a key on the fly to the ConfigReader object it disappeared when accessing it in a plugin. Reason: The dynamic instantiation used the filename parameter in the constructor of the plugins instead of the ConfigReader object itself. Architectural change inside DynamicLibrary was necessary.

Overall all include statements within in the library have been replaced by angle brackets, the default install path for the include file is $CMAKE_INSTALL_DIR/include/meteoio, the meteoio libraries (static and shared) will be installed in $CMAKE_INSTALL_DIR/lib per default.

The plugins will be installed in the subdirectory $CMAKE_INSTALL_DIR/lib/meteoio/plugins

Then, the remaining namespace issues with doxygen have been fixed, by enclosing the full class implementation in the namespace (as seen for the libstdc++). This removes all these irritating issues. But the popc version has been broken by the change (as seen in LegacyIO).

Some uncommitted fixes to the documentation are now committed. Hopefully all the namespace issues (ie: broken links) are now fixed!

Changed the name of the Date_IO class to Date. In case of namespace conflicts, just use mio::Date to reference the MeteoIO Date class.

The COORDSYS, COORDPARAM keywords of the output section are consitently used when writing out meteo data and 2D grids

changed the way we deal with the projection parameters within the io.ini. COORDSYS must be declared in the [Input] section and is optional for the [Output] section (it becomes mandatory if a function is to be used, that creates output)

The parsing of the ConfigReader object is done in IOUtils, this is not the final solution on that.

The input and output parameters were looked for in the [INPUT] and [OUTPUT] sections. This naming was not consistent with the rest of io.ini, they have been renamed in [Input] and [Output].

Some documentation was missing and has been added (plugin documentation)

a new function called: readStationData has been added. It expects a date and a vector<StationData> as parameters and returns the meta data for the required date (often this date is irrelevant, because stations are fixed, then just pass any date).

The new structure of the io.ini shall have an [Input], [Output], [General], [Interpolations2D] and [Filters] section. Some of the keys have changed names: COORDIN is COORDSYS, instead of DEMSRC it's just DEM in the [Input] section and so on.

A new function is introduced into the IOInterface: writeMeteoData. It expects one vector<vector<MeteoData>> and one vector<vector<StationData>> as well as an optional string (for database info, file name, etc). The relevant io.ini tag is:
METEODEST = GEOTOP

Only GeotopIO has this method fully implemented thus enabling to convert all meteo data captured from any other source to a GEOtop compliant meteo files. The relevant tags are:
METEODESTPATH = /tmp
METEODESTSEQ	= WindS WindDir RelHum AirT SWglobal Iprec

METEODESTPATH determines where the files will be written to and METEODESTSEQ determines the order in which the meteo parameters will be written into the CSV file

A problem was found during the intialization of the plugins (as well as A3DIO): the parameters that were passed to initialize the local copies were not always initialized with the raw parameters passed to the constructor but usually with the copy of the previous element. This lead to some copies not to be up to date when calling their constructor (see A3DIO.cc for a clearer view!!).

The write2DGrid members of the plugins now use the features of the Coords object to output the grid in the input coordinate system (as specified in the io.ini file). A copy of the Coords object is made, so that it does not change the given grid. This is fixing issue 3

The plugin's interface (IOInterface) has been slightly modified: readSpecialPoints now returns a vector of Coords. This means that a plugin can provide coordinates as (lat,long) or (easting, northing) or (grid_i, grid_j). All the plugins have been modified accordingly and POINTS and POINTSArray have been removed from Array.h

Finally, the implementation of issue 35 is here... A few bugs left with the Coords class have been fixed (namely, the methods take 1 optional parameter and not more, because for this usage scenario it was way too dangerous and the user (myself in this case!) could call the method with the wrong parameter left empty). New mebers have been added: grid_i and grid_j as well as methods to deal with them. These contain the grid indices matching the position. Since these indices depend on the chosen DEM/grid, they are NOT updated by Coords but by Grid2DObject or Grid3DObject instead. If the user calls Coords::setLatLon() or Coords::setXY(), then these grid parameters are reset to nodata.

A bug in a constructor of StationData has also been fixed (assigning a temporary object to a member of the class). Some bugs/unlucky deletes in the examples have been fixed (this is the price to pay for work too late at night!)

New constants "lat_epsilon" and "lon_epsilon" have been created in IOUtils. They represent the smallest latitude/longitude resolution (ie: two points within lat_epsilon are considered to have the same latitude)

The constructor Coords(ConfigReader) was a bad idea... Convenient, but way too specific. It has been removed. The documentation in the Coords class has been updated.

A saner handling of nodata values by the plugins has been implemented. Now, each plugin should properly get its own internal definition of nodata and return data using IOUtils::nodata to the caller. A new method has been implemented in IOUtils to help cleaning a parameter for nodata.

A check for xmlParseFile (used for compiling the Boschung plugin) was working poorly and has been commented out in configure.ac.

Finally, more cleanup in the ph files has been performed.

The new Coords object is now used by all grids (Grid2DObject, Grid3DObject, DEMObject) as well as by all plugins (but checking proper operation was not possible for GSNIO because of missing libraries on my system...). The documentation has been updated as well as the code examples. A few extra methods have been added when usage has shown the need/convenience of having them (specially for standardazing some processing called by the plugins). A few small bugs have been fixed (possibility of not updating or improperly updating the coordinates in some rare cases).

The proper marshalling for Grid3DObject has been implemented (it was more or less a dummy method until now). One bug has been fixed for Proj4 support. The code of most of the plugins has been cleaned up in order to get rid of the few remaining "using namespace" in header files. 

The class Stationdata now properly uses the new Coords class. All usual dependencies have been fixed (A3DIO.cc) but not (yet) the optional plugins. The Coords class has been modified so that it computes the matching coordinates as soon as possible instead of the previous implementation that was delaying it as much as possible (thus making "const Coords..." impossible).

The includes have been cleaned up (compilation was failing because of multiple "using namespace" in header files) and all "using namespace" have been removed from header files (please don't put any of these back!!). The doxygen comments has been updated.

The MapProj class has been renamed in Coords. It now contains the coordinates (lat,long) and (xcoord, ycoord) and should therefore be used as a storage and conversion class. The necessary changes have been made to the rest of the code so it uses this class, but it still does NOT use it as a storage of coordinates (which will have to be done in the future). This addressed partially issue 35.

The Special_PTS and CSpecialPointsArray structures have been renamed in "POINT" and "POINTSArray" (there was no reason to call them "special points"). 

A few new methods have been added to DEMObject: getPointsBetween that returns a vector containing the indices of all points located on the line between two points (given by their real world (x,y) coordinates), horizontalDistance that returns the horizontal distance between two points and terrainDistance that returns the distance between two point accros the terrain as described by the DEM (ie: going up and down the terrain).

The successfull call of MeteoIO from Java has been implemented by Cyril Perot but needed a few adjustments in MeteoIO. This commit makes the said adjustments: a few more "#ifdef _POPC_", a missing ConfgReader.addKey(key, section, value) and some previously private members of Meteo2DInterpolator now exposed. 

The plugin unloading sections have been protected by ifndef _METEOIO_JNI because the current implementation of such Java integration uses JNI and does its own plugin loading/unloading.

A new slope computation algorithm has bee added: CARD It computes the slope using Corripio and then discretizes the azimuth along 8 cardinal directions and the slope by degrees. This should be all that GEOtop needs for its drainage direction (then simply calling a dem.update("CARDINAL")).

The copyright notices have been put in place in all files (headers and cc) with proper attribution of copyright.

The documentation has been improved, specially fixing issue 22. Warning messages of doxygen have been fixed. An example subdirectory has been created in /doc and contains (currently) 2 examples of code using MeteoIO.

A small but irrtating bug in the Makefile has been fixed (failure to install when the parallel version had not yet been compiled). 

The doxygen documentation has been updated with the documentation of the plugins (from a user point of view). The data assimilation reading methods have been slightly tweaked (so that they read a time stamp containing minutes and not only hours). 

The Makefile.in has been modified so that a new keyword has been added for proj4. This is not yet user-friendly (and it might never be so, since we are moving to CMake instead) but at least it prepares a full, convenient integration.

Mostly code clean up: removed some unnecessary comments.

A parameter has been added to DEMObject::update in order to specify which algorithm to use. It can either take a member from a specifc enum or a string like "HICK" or "CORRIPIO".

The isSameGeolocalization method has been added to Grid2DObject in order to allow comparing the geolocalization attributes of two grids. It does not compare the xllcorner/yllcorner parameters since these might have been tweaked for convenience. The code checking the match between lat/long and xll/yll has been commented out since this prevents the correct operations when using a local grid. This method (checkCoordinates) will have to be completely redesigned.

The ISWR and LWR methods have been uncommented for the Meteo2DInterpolator. 

The (very dirty) hack that would have interpreted the grid coordinates differently depending on their value (as lat/long or swiss coordinates) in ARCIO and GRASSIO has been removed (this is now replaced by the much cleaner projection class). If the COORDPARAM key is missing in the io.ini file, it is quietly ignored instead of throwing an exception.

The meteoio_demo program has been updated to reflect these changes

	* Changed method call to readDEM so that polymorphism is not used anymore.

* MapProj is a new class that deals with all kinds of map projections (some can be implemented directly, like CH1903, others can be based on the Proj.4 library)
* changes in map projections made it necessary to adapt the children of IOInterface that have an implementation of readMeteoData or read2DGrid

The spatial interpolation class has been modified so that it works with Grid2DObjects instead of Array2D. This makes room for being able (one day) to work with a DEM bigger than the requested grid... (yes, this would be so sexy!)

Warnings have been silenced in GrassIO.cc

Fixed a few bugs in GrassIO - it will remain unusable until the new coordinate reprojection calculations are committed