species v0.8.0

• Improved package structure by including additional subpackages and modules
• The implicit import of classes and functions is removed from the initialization of the package, instead these should be explicitly imported by the user
• Started with implementing improved output printing, added print_section function in core_util
• Support for BT-NextGen subsolar metallicity grid (tag='bt-nextgen-subsolar')
• Changed default transmission threshold from 0.05 to 0.01 in SyntheticPhotometry
• GJ 758 B included in companion_data.json (thanks @mperrin!)
• Tutorial included for plotting companion properties
• Fitting a flux scaling and offset in FitModel
• Updated add_model_grid such that only spectra files are unpacked within the selected teff_range
• Added unpack_tar parameter to add_model
• Update links in tutorials and documentation pages
• Added verbose parameter to available_models and list_companions
• Fixed issue with float type returned by likelihood function
• Fixed issue with np.inf in the likelihood that can not be handled by UltraNest
• Added setup_retrieval method to AtmosphericRetrieval
• Added gradient P-T parameterization from Zhang et al. 2023 (thanks @wbalmer!)
• Support for nested sampling with Dynesty in AtmosphericRetrieval with run_dynesty method (thanks @wbalmer!)
• Refactoring of the prior function in FitModel so it is shared by the sampling routines
• Added normal_prior parameter to FitModel and deprecated the prior parameter in run_multinest and run_ultranest
• Added resume and kwargs_multinest parameters to run_multinest
• Added resume and kwargs_ultranest parameters to run_ultranest
• Spectra are no longer removed when rerunning add_object with different spectrum labels
• Changed scipy.interpolate.interp1d to numpy.interp which produces the same output but interp1d is considered a legacy function
• Added calc_phot parameter to contrast_to_mass
• Retrieving log_p_base with physical clouds instead of using the condensation profile
• Added param_fmt parameter to plot_spectrum
• Fixed issue with appending to database during multiprocessing
• Added verbose parameter to get_median_sample, get_probably_sample, and get_compare_sample
• Store priors from FitModel in the database results
• Removed interp_method from configuration so linear interpolation is used
• Added rad_vel and vsini as optional retrieval parameters in AtmosphericRetrieval
• Added support for nested sampling with Dynesty in FitModel with run_dynesty method
• Renamed the spec_res parameter in add_model to wavel_sampling
• Deprecated the smooth parameter in ReadModel and ReadPlanck since the spec_res parameter is sufficient
• Renamed the get_spec_res method in ReadModel to get_sampling
• Moved the convert_model_name function to the model_util module
• Added option to use wavel_range parameter without setting wavel_sampling in order to not resample but store a restricted wavelength range
• Increased dependency versions in requirements.txt
• Updated documentation and tutorials
• Many small enhancements and several minor bug fixes