Release 4.0

What's new

Major functionality:

1. Cloudy equilibrium
2. Cloudy/clear photochemistry
3. Patchy cloud climates
4. New correlated-k format (bin files -> hdf5) and computed from OS code within picaso
5. Run photochem to create a spectrum
6. Correlated-K forward modeling
7. Patchy clouds in forward modeling
8. Some integration testing

Enhancements:

1. Climate model has been completely restructured to improve workflow and readability (user input to climate code has changed dramatically for diseq and cloudy runs)
2. Level fluxes output in forward modeling for diagnostics
3. Leave one out climate modeling for individual molecule contributions
4. New get data tutorial auto downloads data that you need incl sonora grids, ck tables, virga files, stellar files, opacities
5. Deprecates pysynphot in place of stsynphot
6. 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

Release 3.3

What's Changed

• Reflected light phase curves by @colinhamill in #192 see accepted paper Hamill et al. 2024 (in press)
• Small additions to picaso+virga doc by @aditya-sengupta in #211
• Stage PR for new reflected light phase curve code by @natashabatalha in #227

New Contributors

• @colinhamill made their first contribution in #192
• @aditya-sengupta made their first contribution in #211

Full Changelog: v3.2...v3.3

Release 3.2.1

What's Changed

• New disequilibrium climate modeling by @sagnickm
• Isos dev by @natashabatalha in #149
• Arraysingular climate bug by @natashabatalha in #182
• Critical hot fix for correct He mass by @natashabatalha in #207

New Contributors

• @nainas2024 made their first contribution in #153
• @logan-pearce made their first contribution in #154
• @dreamjade made their first contribution in #162
• @ayanaman271 made their first contribution in #160
• @Ziva18t made their first contribution in #186

Full Changelog: v3.1...v3.2

Release 3.1

Spherical Harmonics for the 1D Radiative Transfer Equation

• SH harmonics documentation for reflected light (Rooney et al. 2023, resubmitted with minor comments)
• New tutorial on reproduction of Batalha+2019 to test Toon radiative transfer https://github.com/natashabatalha/picaso/blob/9d4cbd672a75c1faf5297c3f1d74074018cd7ef3/docs/notebooks/10a_AnalyzingApproximationsReflectedLightToon.ipynb
• New tutorial on reproduction of Rooney+2023 to test Spherical Harmonics reflected light radiative transfer https://github.com/natashabatalha/picaso/blob/9d4cbd672a75c1faf5297c3f1d74074018cd7ef3/docs/notebooks/10b_AnalyzingApproximationsReflectedLightSH.ipynb
• SH harmonics documentation for thermal emission (Rooney et al. 2023, submitted)
• New tutorial on reproduction of Rooney+2023 to compare spherical harmonics with thermal emission radiative transfer https://github.com/natashabatalha/picaso/blob/9d4cbd672a75c1faf5297c3f1d74074018cd7ef3/docs/notebooks/10c_AnalyzingApproximationsThermal.ipynb
• Added output xarray resources for model preservation and reusability (justdoit.output_xarray)
• New tutorial on model preservation and reuse https://github.com/natashabatalha/picaso/blob/9d4cbd672a75c1faf5297c3f1d74074018cd7ef3/docs/notebooks/ModelStorage.ipynb

Release 3.0

3.0 (2022-10-25)

• First version of climate code (Mukherjee et al. 2022)
• First version of grid fitting tools (JWST Transiting Exoplanet ERS et al. 2022)
• Code help for xarrays
• Reference/citation tools for opacities
• Resampling tutorials
• CK tutorials
• Contribution functions
• Better plotting tools

What to Cite

Mukherjee, et al. "PICASO 3.0: A One-Dimensional Climate Model for Giant Planets and Brown Dwarfs." The Astrophysical Journal (2022): 157

• 1d climate models of brown dwarfs
• 1d climate models of exoplanets

The JWST Transiting Exoplanet Community Early Release Science Team, et al. "Identification of carbon dioxide in an exoplanet atmosphere." Nature (2022)

• Methodology for fitting picaso model grids to data

Release 2.3

• lots of fun 3D functionality (Adams et al 2022)
• phase curves (Robbins-Blanch et al 2022)
• 3D tutorials with xarray
• clearer radiative transfer to be compatible with Toon 89
• Faster chemeq interpolation
• opacity tables pull four nearest neighbors (though option for 1 remains)
• Improvements and additions to plotting functionality
• Minor bug fixes

Release 2.2

• Add evolution tracks
• Add ability to use pre mixed c-k tables
• Expand chemistry to include new Visscher tables
• Add ability to pull out contribution from individual species without running full RT
• Young planet table from ZJ Zhang.
• Separate workshop notebooks for Sagan School 2020, 2021 and ERS
• Add explicit "hard surface" term for thermal flux boundary condition for terrestrial calculations
• Minor bug fixes/improvements

Release 2.1

• Transit Spectroscopy added
• Transit spectroscopy tutorial
• FAQ notebook
• Minor bug fixes/improvements

Release 2.0

Major Changes

• Explicit Brown Dwarf tutorials
• Coupling to brand new python cloud code Virga!!
• Ability to specify wave range in opannection and ability to resample (consult your local theorist before doing this)
• Added "Opacity Factor" so that users can easiy query opacity data without going through SQL
• Removed opacity from git-lfs (was a bad system and users were having trouble)
• Fixed critical spherical integration bug and added more robust steps for 1d vs. 3d. Also added full tutorial to explain differences here.
• Added notebook for surface reflectivity

Functionality Expanded

Scientific functionality : thermal emission, 3d inputs

Major code structure changes:

Because thermal emission was added, we have changed the way the code output is returned:

w,a = case.spectrum()

is now..

df = case.spectrum()

where df is a dictionary with wavenumber, albedo, thermal, fpfs, full_output, pending what the calculation asked for.

All tutorials have been changed to reflect this!

In addition to thermal emission we also include more explicit tutorials for 3d calculations.

NOTE: we opted out of publishing a new paper for this release.