==Code for generating and using Lyman-alpha forest emulators== This is the code repository for arXiv:XXXX.XXXXX, Bird et al 2019. It handles creating simulation suites with carefully chosen points, generating simulation parameter files, generating flux power spectra using fake_spectra and making an interpolator from these flux power spectra. It also has a python likelihood function which can be fed to emcee for testing the convergence of the emulator with mock data. To adapt this to your own survey you want to subclass the Emulator class in coarse_grid.py and specify your own parameter set and limits. An example of how to do this can be found in the KnotEmulator class. You may also want to add your cluster (if it is not XSEDE's Stampede) to clusters.py in SimulationRunner Useful submodules: lyaemu.coarse_grid: handles the emulator generation. lyaemu.likelihood: handles the likelihood sampling and the emulator optimization. lyaemu.latin_hypercube: generates points on a unit cube in a maximin latin hypercube lyaemu.gpemulator: fits the interpolation using GPy. lyaemu.mean_flux: models for the redshift evolution of the forest mean flux. Other files: acquisition.py: evaluates the acquisition function for emulator optimization. coarse_grid_plot.py: Makes a few useful plots which show the accuracy of the emulator, as well as the emulator's own error estimate. flux_power.py: generates the flux power spectra, using native bins as a fraction of the simulation box linear_theory.py: linear biasing model for the flux power spectrum linear_emulator.py: emulates the linear biasing model about. For testing purposes, only lightly maintained. lyman_data.py: loads the BOSS DR9 flux power spectrum data. matter_power.py: simple sub-emulator for reading and emulating the matter power spectrum plot_latin_hypercube.py: Small script for visualising latin hypercubes quadratic_emulator.py: Subclass of Emulator that varies one parameter at a time, for quadratic polynomial interpolation. tempdens.py: Prints the IGM thermal parameters, T0 and gamma. plots/ : Contains scripts for making the plots in the paper. Data not included. plots/make_emulator.py gives an example of how to generate an emulator lyaemu/tests: Some simple unit tests. Dependencies: - Python 3 - GPy - numpy - scipy - h5py - matplotlib for the plots - emcee for the sampling - fake_spectra module for generating flux power spectra from a simulation snapshot. - SimulationRunner (not on pip: at https://github.com/sbird/SimulationRunner) for setting up MP-Gadget simulations.