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 #184
- Merging forked cloudy repo into main repo by @James-Mang in #199
- Merge forked repo developments by @James-Mang in #200
- Merging new disequilibrium chemistry prescriptions by @James-Mang in #202
- Convergence Modifications by @James-Mang in #203
- Changes to include 'final' flag in profile function, works better for… by @James-Mang in #204
- Pull latest from dev into newdev by @James-Mang in #208
- Updates to the Photochem/PICASO coupling by @Nicholaswogan in #212
- Updates to the Photochem/PICASO coupling Part 2 by @Nicholaswogan in #214
- Add surface emissivity to thermal emission calculation by @Nicholaswogan in #217
- update gridtree by @natashabatalha in #223
- Dev by @natashabatalha in #232
- Make ck branch even with master by @natashabatalha in #234
- Syncing master branch changes to newdev by @James-Mang in #236
- Dev by @rewaclarkbush in #235
- Add tutorial series to gridtree branch by @Ziva18t in #237
- Adding functionality for deq+on_fly mixing, and level flux calculations outside of climate by @imalsky in #239
- Added edits to Dominic's HowToAnalyzeExplanetSpectra.ipynb notebook by @rewaclarkbush in #240
- docs: add rewaclarkbush as a contributor for code, and doc by @allcontributors[bot] in #241
- Add the option to save all temperature profiles in a climate run by @aditya-sengupta in #215
- Simple Photochem tutorial for WASP-39b by @Nicholaswogan in #245
- Simplified Picaso-Photochem interface for coupled climate simulations by @Nicholaswogan in #244
- Adding suggestions and fixing typos in first Retrieval Tutorial by @rewaclarkbush in #246
- Newdev cold trapping fixes by @natashabatalha in #247
- Fixed typos and added comments to Retrieval Tutorial 2 by @rewaclarkbush in #248
- docs: add Nicholaswogan as a contributor for tutorial by @allcontributors[bot] in #251
- Faster method for resorting and rebinning k-distributions by @Nicholaswogan in #250
- Small fix to plot all the Rayleigh contributors for plotting by @imalsky in #252
- docs: add kelle as a contributor for test, and code by @allcontributors[bot] in #260
- Fixing comment inconsistency about the temperature for H-bf by @benjaminliberles in #267
- docs: add benjaminliberles as a contributor for doc by @allcontributors[bot] in #268
- Attempting ck, newdev and ck-newdev-merge all back even on dev branch by @natashabatalha in #269
- make dev even with master by @natashabatalha in #270
- Merge all retrieval/grid code to dev by @natashabatalha in #242
- Let's made grid tree even with dev now by @natashabatalha in #271
- Dev by @natashabatalha in #285
- Setup pytest by @kelle in #257
- Add level flux notebook and update correlated-k tutorial by @imalsky in #284
- Reverting to newer justdoit by @imalsky in #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 #281
- Updated 0_GetDataFunctions.ipynb & updated docstrings to analyze.py and opactiy_factory.py by @benjaminliberles in #282
- Updated virga-exo dependency to 0.5 by @zshakespear in #291
- Virga 0.5 to solve trapz problem by @natashabatalha in #293
- Generalized atmsetup to permit any CIA partners by @Nicholaswogan in #294
- Dev by @natashabatalha in #295
- Update packaging by @natashabatalha in #296
- Dev by @natashabatalha in #297
- Test PR for star fix by @Kneeco22 in #301
- Dev by @natashabatalha in #302
- Quick bug fix for photochem run by @James-Mang in #306
- Clean up adjust_quench_chemistry by @James-Mang in #308
- Fran and niall by @natashabatalha in #309
- Feature/html check environ by @natashabatalha in #310
- Refactor data with pooch by @natashabatalha in #311
- Dev by @natashabatalha in #313
- Notes added to demonstarte my knowledge by @Kneeco22 in #303
- Notebook Testing by @James-Mang in #314
- adds unit test to dev by @natashabatalha in #315
- Removed deep isothermal profile issue from CommonClimateBDIssues notebook, can't reproduce it anymore by @James-Mang in #316
- Dev by @natashabatalha in #318
- Plot functionality for dashboard by @Kneeco22 in #322
- Quick fix for get_transit_1d() for python 3.11 by @elijah-mullens in #327
- Improve performance of PICASO-Photochem coupling and improved notebook tutorial by @Nicholaswogan in #336
- Replacing nstr_upper, nstr, and nofczns in user climate inputs with rcb_guess by @James-Mang in #348
- Bump bibtexparser from 1.4.3 to 1.4.4 by @dependabot[bot] in #356
- Dev: Documentation changes to update references and Zenodo links by @James-Mang in #364
- Add tutorial workflow documentation including VS Code Jupytext extension by @natashabatalha in #366
- Fixed missing molecules in photochem tutorial by @Nicholaswogan in #368
- Quick bug fix for new ck files from Zenodo by @James-Mang in #371
- WIP: Full PICASO 4 Release by @natashabatalha in #351
New Contributors
- @Nicholaswogan made their first contribution in #212
- @rewaclarkbush made their first contribution in #235
- @imalsky made their first contribution in #239
- @kelle made their first contribution in #257
- @zshakespear made their first contribution in #291
- @Kneeco22 made their first contribution in #301
- @elijah-mullens made their first contribution in #327
Full Changelog: v3.3...v4.0
Contributors
kelle, natashabatalha, and 12 other contributors