INSTALL

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Building and installing the C/C++ library

Requirements:
   A C++11 compiler, clang++ (v3.3 or later) or g++ (v4.7 or later)
   Make (GNU make is OK)


Note: clang++ is the default (and preferred) compiler as it produces 
faster code (in our tests, the difference in speed is about 20%). 
If you'd like to use g++ instead, please edit the first line of 
IsoSpec++/Makefile appropriately.

Next, execute the following commands:

cd IsoSpec++
make

You may copy the resulting .so file to a convenient location.
If you wish to develop software using this library, you will also 
have to place the header files (*.hpp/*.h) somewhere your C/C++
compiler can find them.

On Windows, you should turn on the MANN_LIBRARY pre-processor directive when
building the library.

------------------------------------------
Building and installing the Python package

IMPORTANT: please note that the Python package is standalone, in the
sense that it does not need the C/C++ library to be installed separately.

IsoSpecPy is compatible with both CPython and PyPy, running on Unix,
Cygwin or in MinGW environment.

The preferred method of installation is by using the pip package manager.
In order to do that, simply issue the following command, replacing 
"<python>" with your Python executable (python/python3/pypy/...)

<python> -m pip install IsoSpecPy

If, instead, you wish to install the package manually, follow these 
instructions:

Requirements:
    Python (obviously) (v2 and v3 are supported)
    C++11 compiler, clang++ (v3.3 or later) or g++ (v4.7 or later)
    setuptools
    cffi (this, if not present, will be automatically downloaded and
          installed by the setup script, however you may prefer to use 
          your distribution's package manager to install that)

Execute the following commands:
cd IsoSpecPy
sudo python setup.py install

Again, clang++ is the preferred compiler and will be used if found by the 
setup script. If you want to override the behaviour (if you have clang++ 
installed, but still want to use g++) you will have to replace the last 
command with:

ISO_USE_DEFAULT_CXX=TRUE sudo python setup.py install


------------------------------------------
Building and installing the R package
	
The preferred installation method is to use the CRAN package installer.
To do that, simply issue the command:

install.packages('IsoSpecR')

in your R session. However it is possible to install the package manually,
from source, by following these instructions:

Requirements:
	R (>= 3.2.1)
	Rcpp package from CRAN
	C++11 compiler, clang++ (v3.3 or later) or g++ (v4.7 or later)

Move to the folder containing the IsoSpecR folder. Then run in terminal:

	R CMD build IsoSpecR 
	R CMD INSTALL IsoSpecR_*.tar.gz  

All necessary packages should download automatically.