Installation

refnx has been tested on Python 3.9, 3.10, 3.11, 3.12. It requires the numpy, scipy, cython packages to work. Additional features require the pytest, h5py, xlrd, uncertainties, attrs, matplotlib, Jupyter, ipywidgets, traitlets, tqdm, pandas, qtpy, pyqt6, periodictable, pymc, pytensor packages. To build the bleeding edge code you will need to have access to a C-compiler to build a couple of Python extensions. C-compilers should be installed on Linux. On OSX you will need to install Xcode and the command line tools. On Windows you will need to install the correct Visual Studio compiler for your Python version.

Installation into a conda environment

Perhaps the easiest way to create a scientific computing environment is to use the miniforge package manager. Once conda has been installed the first step is to create a conda environment.

Creating a conda environment

1. In a shell window create a conda environment and install the dependencies. Note that not all of these dependencies are essential, but they are required to run the full refnx test suite. The -n flag indicates that the environment is called refnx.

   conda create -n refnx python=3.12
   

2. Activate the environment that we’re going to be working in:

   # on OSX
   conda activate refnx
   
   # on windows
   activate refnx
   

3. Install the remaining dependencies:

   python -m pip install refnx[all]
   

Installing with pip

There are refnx wheels available for macOS/Windows/Linux on PyPI. Using the [all] modifier means that all refnx’s optional dependencies will also be installed.

# install refnx and all optional dependencies
python -m pip install refnx[all]

# alternatively just install refnx itself
python -m pip install refnx

Installing into a conda environment from a released version

1. There are pre-built versions on conda-forge:

   conda install -c conda-forge refnx
   

2. Start up a Python interpreter and make sure the tests run:

   >>> import refnx
   >>> refnx.test()
   

Installing from source

The latest source code can be obtained from github. You can build the package from within the refnx git repository.

1. [macOS only] If you wish to enable the parallelised calculation of reflectivity with OpenMP, then you will need to install libomp. This is easily achieved via homebrew, and the setting of environment variables. The refnx kernel that uses OpenMP is not normally any better than the default C version.

   brew install libomp
   export CC=clang
   export CXX=clang++
   export CXXFLAGS="$CXXFLAGS -Xpreprocessor -fopenmp"
   export CFLAGS="$CFLAGS -I/usr/local/opt/libomp/include"
   export CXXFLAGS="$CXXFLAGS -I/usr/local/opt/libomp/include"
   export LDFLAGS="$LDFLAGS -L/usr/local/opt/libomp/lib -lomp"
   export DYLD_LIBRARY_PATH=/usr/local/opt/libomp/lib
   

2. In a shell window navigate into the source directory and build the package. If you are on Windows you’ll need to start a Visual Studio command window.

   pip install .
   

3. Run the tests, they should all work.

   python setup.py test