species v0.8.4

• Several small fixes in the retrieval framework (thanks @wbalmer!)
• Added flux_units parameter to get_mcmc_photometry
• Support for fitting multiple disk_teff and disk_radius parameters in FitModel
• Support for fitting the combined photometry of unresolved binary stars with different parallaxes
• Multiple improvements for fitting a combination of two spectra in FitModel
• Support for flux ratio prior for filters when fitting a binary system
• Check for NaNs in the uncertainties when adding a spectrum with add_object
• Updated plot_posterior for showing posteriors from binary systems
• Returning the individual binary components with get_mcmc_spectra
• Added support for coolTLUSTY Y dwarf spectra
• Tutorial for comparing data with a model grid of spectra
• Support for fitting separate ism_ext parameters for a binary system
• Support for PHOENIX Husser et al. (2013) models
• Major refactoring of FitModel, improved extinction accuracy, faster interpolation based on Teff prior
• Added optional database_file parameter to SpeciesInit
• Added fixed_param parameter to add_samples
• Added tag parameter and several improvements in get_residuals
• Changed the values added with inc_loglike to ln(L)
• Included chi2 and n_dof in ResidualBox
• Fixed indentation problem in CompareSpectra
• Robust implementation for filenames by using the pathlib instead of the os module
• Using pooch instead of urllib for downloading files
• Fixed bug in get_samples with reading normal priors
• Fixed bug with storing the log-likelihood after running run_multinest
• Fixed Windows issue with the Linder et al. (2019) isochrones
• Check for NaN and inf when calculating the goodness-of-fit statistic in CompareSpectra
• Exclude SpeX spectra that can not be flux calibrated when adding with add_spectra
• Updated dependency versions
• Overall code maintenance, many minor improvements, and updated tutorials

species v0.8.3

Another fix in setup.py! Adding a missing JSON file to the package_data.

species v0.8.2

Fixing issue with setup.py to include the JSON files in the package on PyPI

species v0.8.1

• Fixed issue with max_prob parameter in plot_posterior
• Included uniform_priors and normal_priors to SamplesBox
• Added show_priors parameter to plot_posterior
• Fixed issue with wavelength precision in Exo-Rem grid
• Added verbose parameter to list_filters method of ReadObject
• Implemented the units parameter in plot_spectrum
• Added convert_from parameter to convert_units function
• Extended the BT-NextGen grid to 5 mm
• Allowing to fix the parallax when fitting with FitModel
• Including the blackbody radius (calculated from disk_teff) in the posterior with inc_luminosity=True in plot_posterior
• Added the add_simple_object method to Database for retrieving data from the SIMPLE Database
• Support for providing a spectrum array directly to the spectrum parameter of add_object
• Retrieving the f_sed parameter for each cloud species individually by setting global_fsed=False
• Added spec_res attribute to ModelBox
• Support for Sonora Elf Owl L-, T-, and Y-type grids
• Fixed issue with appending mode for opening the HDF5 database
• Fixed issue with package_data in setup.py

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

species v0.7.4

• Added the contrast_to_mass method to ReadIsochrone for converting contrast values for a given filter into masses
• Support for clear and cloudy model spectra of the petitCODE grid that is used for the isochrones from Linder et al. (2019)
• Possibility to include only photometric fluxes when comparing a grid of model spectra with CompareSpectra

species v0.7.3

• Removed deprecated update_spectra function
• Some minor maintenance of util and plot functions
• Updated notebook tutorials

species v0.7.2

• Updated the type annotations so they are compatible with Python 3.11
• Tested the notebook tutorials and fixed several small issues due to code changes

species v0.7.1

• SPHINX model spectra: add_model('sphinx')
• BEX isochrones from Linder et al. (2019): add_isochrones('linder2019')
• Keck NIRC Y-band filter: add_filter('Keck/NIRC.Y')

species v0.7.0

• Added support for Python 3.11 and dropped support for Python 3.8
• Added a check in ReadColorMagnitude for selecting an incorrect filter name that is not part of a photometric library
• Retrieving free abundances that vary with altitude using AtmosphericRetrieval
• Included FitEvolution for estimating ages and masses from luminosities
• Changed use of interp2d to RegularGridInterpolator
• Optimization in CompareSpectra so it runs faster
• Added plot_abundances function to plot_retrieval module
• Added the res_mode and lbl_opacity_sampling parameters to AtmosphericRetrieval
• Changed lbl_species parameter of AtmosphericRetrieval to ccf_species
• Added lbl_opacity_sampling parameter to ReadRadtrans
• Generalized the implementation of the mean_molecular_weight function
• Changed photometric uncertainty inflation in FitModel to relative to the uncertainties instead of relative to the flux
• Changed weights parameter in FitModel to apply_weights and improved its functionality
• Added convert_units_plot function to plot_util
• Capital sensitive unit conversion with convert_units function
• Added inc_abund parameter to plot_posterior
• Added units parameter to add_object
• Added extra_param parameter to plot_grid_statistic
• Added plot_model_spectra to plot_comparison module
• Maintenance of plot_comparison functions
• Updated dependency versions, documentation, and docstrings
• A lot of small improvements and maintenance!