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Installation

Qubefit has been tested on both macOS as well as Linux (Red Hat 7). To install the code clone or download the latest version from github: qubefit. After downloading the code (and unzipping if necessary), open up a terminal window, navigate to the directory where the code lives, which contains the setup.py file, and type:

python setup.py install

If everything goes correctly, this installs the code. To test if the installation was successful, see if the GUI loads. Use the command line to put yourself Inside the examples folder qubefit/examples and then type:

qubemom WolfeDiskCube.fits

and :

qfgui WolfeDiskSetup.py

If this brings up the two GUIs such as shown in the section guis, the code was installed correctly.

Dependencies

Qubefit has been tested on python 3.8 and depends heavily on the following packages, where the version numbers are the version used for testing the code:

  • numpy (v1.19.2)
  • scipy (v1.5.2)
  • astropy (v4.0.2)
  • matplotlib (v3.3.2)
  • h5py (2.10.0)
  • scikit-image (v0.17.2)
  • tqdm (v4.50.2)
  • emcee (v3.0.2)
  • corner (v2.1.0)

The first four packages are standard packages that you probably already have installed on your computer. For these the version number is probably not particularly important except for numpy, which pre v.1.15 will throw an error because of certain missing functions.

The following four packages can simply be installed using conda e.g.,:

conda install h5py
conda install scikit-image
conda install tqdm
conda install -c conda-forge emcee

It should be noted that the top three packages are normally installed in the full installation of conda (v4.9.2). Alternatively, these programs can also be installed using pip. See the repsective websites for each program: h5py, scikit image, tqdm, emcee. scikit-image package is only needed to generate masks, and if you want to make your own masks, it does not need to be installed. The tqdm package provides the progress bar used in the MCMC chain.

Warning

It is very important to use version 3.X or higher for emcee, because version 2.X or earlier of this code will result in errors. Further details are given in the documentation for emcee v3.0.

Although the corner package is not required to run the fitting routine, it is recommended for displaying the output of the fitting routine, and is necessary to create the diagnostic plots. It can be installed using pip, see the documentation for corner.