PICASO Release 4.0

What's new Major functionality: Cloudy equilibrium Cloudy/clear photochemistry Patchy cloud climates New correlated-k format (bin files -> hdf5) and computed from OS code within picaso Run photochem to create a spectrum Correlated-K forward modeling Patchy clouds in forward modeling Some integration testing Enhancements: Climate model has been completely restructured to improve workflow and readability (user input to climate code has changed dramatically for diseq and cloudy runs) Level fluxes output in forward modeling for diagnostics Leave one out climate modeling for individual molecule contributions New get data tutorial auto downloads data that you need incl sonora grids, ck tables, virga files, stellar files, opacities Deprecates pysynphot in place of stsynphot Opacity files starting with v3 now has zenodo DOI in meta data. Full changelog Dev and gridtree merge by @natashabatalha in https://github.com/natashabatalha/picaso/pull/184 Merging forked cloudy repo into main repo by @James-Mang in https://github.com/natashabatalha/picaso/pull/199 Merge forked repo developments by @James-Mang in https://github.com/natashabatalha/picaso/pull/200 Merging new disequilibrium chemistry prescriptions by @James-Mang in https://github.com/natashabatalha/picaso/pull/202 Convergence Modifications by @James-Mang in https://github.com/natashabatalha/picaso/pull/203 Changes to include 'final' flag in profile function, works better for… by @James-Mang in https://github.com/natashabatalha/picaso/pull/204 Pull latest from dev into newdev by @James-Mang in https://github.com/natashabatalha/picaso/pull/208 Updates to the Photochem/PICASO coupling by @Nicholaswogan in https://github.com/natashabatalha/picaso/pull/212 Updates to the Photochem/PICASO coupling Part 2 by @Nicholaswogan in https://github.com/natashabatalha/picaso/pull/214 Add surface emissivity to thermal emission calculation by @Nicholaswogan in https://github.com/natashabatalha/picaso/pull/217 update gridtree by @natashabatalha in https://github.com/natashabatalha/picaso/pull/223 Dev by @natashabatalha in https://github.com/natashabatalha/picaso/pull/232 Make ck branch even with master by @natashabatalha in https://github.com/natashabatalha/picaso/pull/234 Syncing master branch changes to newdev by @James-Mang in https://github.com/natashabatalha/picaso/pull/236 Dev by @rewaclarkbush in https://github.com/natashabatalha/picaso/pull/235 Add tutorial series to gridtree branch by @Ziva18t in https://github.com/natashabatalha/picaso/pull/237 Adding functionality for deq+on_fly mixing, and level flux calculations outside of climate by @imalsky in https://github.com/natashabatalha/picaso/pull/239 Added edits to Dominic's HowToAnalyzeExplanetSpectra.ipynb notebook by @rewaclarkbush in https://github.com/natashabatalha/picaso/pull/240 docs: add rewaclarkbush as a contributor for code, and doc by @allcontributors[bot] in https://github.com/natashabatalha/picaso/pull/241 Add the option to save all temperature profiles in a climate run by @aditya-sengupta in https://github.com/natashabatalha/picaso/pull/215 Simple Photochem tutorial for WASP-39b by @Nicholaswogan in https://github.com/natashabatalha/picaso/pull/245 Simplified Picaso-Photochem interface for coupled climate simulations by @Nicholaswogan in https://github.com/natashabatalha/picaso/pull/244 Adding suggestions and fixing typos in first Retrieval Tutorial by @rewaclarkbush in https://github.com/natashabatalha/picaso/pull/246 Newdev cold trapping fixes by @natashabatalha in https://github.com/natashabatalha/picaso/pull/247 Fixed typos and added comments to Retrieval Tutorial 2 by @rewaclarkbush in https://github.com/natashabatalha/picaso/pull/248 docs: add Nicholaswogan as a contributor for tutorial by @allcontributors[bot] in https://github.com/natashabatalha/picaso/pull/251 Faster method for resorting and rebinning k-distributions by @Nicholaswogan in https://github.com/natashabatalha/picaso/pull/250 Small fix to plot all the Rayleigh contributors for plotting by @imalsky in https://github.com/natashabatalha/picaso/pull/252 docs: add kelle as a contributor for test, and code by @allcontributors[bot] in https://github.com/natashabatalha/picaso/pull/260 Fixing comment inconsistency about the temperature for H-bf by @benjaminliberles in https://github.com/natashabatalha/picaso/pull/267 docs: add benjaminliberles as a contributor for doc by @allcontributors[bot] in https://github.com/natashabatalha/picaso/pull/268 Attempting ck, newdev and ck-newdev-merge all back even on dev branch by @natashabatalha in https://github.com/natashabatalha/picaso/pull/269 make dev even with master by @natashabatalha in https://github.com/natashabatalha/picaso/pull/270 Merge all retrieval/grid code to dev by @natashabatalha in https://github.com/natashabatalha/picaso/pull/242 Let's made grid tree even with dev now by @natashabatalha in https://github.com/natashabatalha/picaso/pull/271 Dev by @natashabatalha in https://github.com/natashabatalha/picaso/pull/285 Setup pytest by @kelle in https://github.com/natashabatalha/picaso/pull/257 Add level flux notebook and update correlated-k tutorial by @imalsky in https://github.com/natashabatalha/picaso/pull/284 Reverting to newer justdoit by @imalsky in https://github.com/natashabatalha/picaso/pull/286 Energy Injection ported over from newdev, updated docustrings for climate and jdi, notebook updates/reorganization, and hot fix for constant kz by @James-Mang in https://github.com/natashabatalha/picaso/pull/281 Updated 0_GetDataFunctions.ipynb & updated docstrings to analyze.py and opactiy_factory.py by @benjaminliberles in https://github.com/natashabatalha/picaso/pull/282 Updated virga-exo dependency to 0.5 by @zshakespear in https://github.com/natashabatalha/picaso/pull/291 Virga 0.5 to solve trapz problem by @natashabatalha in https://github.com/natashabatalha/picaso/pull/293 Generalized atmsetup to permit any CIA partners by @Nicholaswogan in https://github.com/natashabatalha/picaso/pull/294 Dev by @natashabatalha in https://github.com/natashabatalha/picaso/pull/295 Update packaging by @natashabatalha in https://github.com/natashabatalha/picaso/pull/296 Dev by @natashabatalha in https://github.com/natashabatalha/picaso/pull/297 Test PR for star fix by @Kneeco22 in https://github.com/natashabatalha/picaso/pull/301 Dev by @natashabatalha in https://github.com/natashabatalha/picaso/pull/302 Quick bug fix for photochem run by @James-Mang in https://github.com/natashabatalha/picaso/pull/306 Clean up adjust_quench_chemistry by @James-Mang in https://github.com/natashabatalha/picaso/pull/308 Fran and niall by @natashabatalha in https://github.com/natashabatalha/picaso/pull/309 Feature/html check environ by @natashabatalha in https://github.com/natashabatalha/picaso/pull/310 Refactor data with pooch by @natashabatalha in https://github.com/natashabatalha/picaso/pull/311 Dev by @natashabatalha in https://github.com/natashabatalha/picaso/pull/313 Notes added to demonstarte my knowledge by @Kneeco22 in https://github.com/natashabatalha/picaso/pull/303 Notebook Testing by @James-Mang in https://github.com/natashabatalha/picaso/pull/314 adds unit test to dev by @natashabatalha in https://github.com/natashabatalha/picaso/pull/315 Removed deep isothermal profile issue from CommonClimateBDIssues notebook, can't reproduce it anymore by @James-Mang in https://github.com/natashabatalha/picaso/pull/316 Dev by @natashabatalha in https://github.com/natashabatalha/picaso/pull/318 Plot functionality for dashboard by @Kneeco22 in https://github.com/natashabatalha/picaso/pull/322 Quick fix for get_transit_1d() for python 3.11 by @elijah-mullens in https://github.com/natashabatalha/picaso/pull/327 Improve performance of PICASO-Photochem coupling and improved notebook tutorial by @Nicholaswogan in https://github.com/natashabatalha/picaso/pull/336 Replacing nstr_upper, nstr, and nofczns in user climate inputs with rcb_guess by @James-Mang in https://github.com/natashabatalha/picaso/pull/348 Bump bibtexparser from 1.4.3 to 1.4.4 by @dependabot[bot] in https://github.com/natashabatalha/picaso/pull/356 Dev: Documentation changes to update references and Zenodo links by @James-Mang in https://github.com/natashabatalha/picaso/pull/364 Add tutorial workflow documentation including VS Code Jupytext extension by @natashabatalha in https://github.com/natashabatalha/picaso/pull/366 Fixed missing molecules in photochem tutorial by @Nicholaswogan in https://github.com/natashabatalha/picaso/pull/368 Quick bug fix for new ck files from Zenodo by @James-Mang in https://github.com/natashabatalha/picaso/pull/371 WIP: Full PICASO 4 Release by @natashabatalha in https://github.com/natashabatalha/picaso/pull/351 New Contributors @Nicholaswogan made their first contribution in https://github.com/natashabatalha/picaso/pull/212 @rewaclarkbush made their first contribution in https://github.com/natashabatalha/picaso/pull/235 @imalsky made their first contribution in https://github.com/natashabatalha/picaso/pull/239 @kelle made their first contribution in https://github.com/natashabatalha/picaso/pull/257 @zshakespear made their first contribution in https://github.com/natashabatalha/picaso/pull/291 @Kneeco22 made their first contribution in https://github.com/natashabatalha/picaso/pull/301 @elijah-mullens made their first contribution in https://github.com/natashabatalha/picaso/pull/327 Full Changelog: https://github.com/natashabatalha/picaso/compare/v3.3...v4.0