JOSS paper

.github/workflows/BuildJOSSPaper.yml

@@ -0,0 +1,55 @@
+name: Build PDF for JOSS paper
+
+on:
+  push:
+    branches:
+      - "paper"
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: always.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Build Paper
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@85a18372e48f551d8af9ddb7a747de685fbbb01c
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v6
+        id: upload-paper
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf
+      - name: Install Python dependencies
+        run: pip install github3.py
+      - name: Create custom status
+        shell: python {0}
+        run: |
+          import os
+          from github3 import login
+
+          token = "${{ github.token }}"
+          gh = login(token=token)
+
+          owner, repo_name = "${{ github.repository }}".split('/')
+          repo = gh.repository(owner, repo_name)
+
+          sha = "${{ github.sha }}"
+          state = "success"
+          target_url = "${{ steps.upload-paper.outputs.artifact-url }}"
+          description = "Download PDF"
+          context = "${{ github.workflow }} / Preview"
+          repo.create_status(sha, state, target_url, description, context)

paper/paper.bib

@@ -0,0 +1,259 @@
+@article{Oceananigans,
+  author = {Ramadhan, Ali and Wagner, Gregory LeClaire and Hill, Chris and Campin, Jean-Michel and Churavy, Valentin and Besard, Tim and Souza, Andre and Edelman, Alan and Ferrari, Raffaele and Marshall, John},
+  title = {{Oceananigans.jl: Fast and friendly geophysical fluid dynamics on GPUs}},
+  journal = {Journal of Open Source Software},
+  year = {2020},
+  volume = {5},
+  number = {53},
+  pages = {2018},
+  doi = {10.21105/joss.02018}
+}
+
+@article{Siebesma2003,
+  author = {Siebesma, A. Pier and Bretherton, Christopher S. and Brown, Andrew and Chlond, Andreas and Cuxart, Joan and Duynkerke, Peter G. and Jiang, Hongli and Khairoutdinov, Marat and Lewellen, David and Moeng, Chin-Hoh and Sanchez, Enrique and Stevens, Bjorn and Stevens, David E.},
+  title = {A Large Eddy Simulation Intercomparison Study of Shallow Cumulus Convection},
+  journal = {Journal of the Atmospheric Sciences},
+  year = {2003},
+  volume = {60},
+  number = {10},
+  pages = {1201--1219},
+  doi = {10.1175/1520-0469(2003)60<1201:ALESIS>2.0.CO;2}
+}
+
+@article{vanZanten2011,
+  author = {van Zanten, Margreet C. and Stevens, Bjorn and Nuijens, Louise and Siebesma, A. Pier and Ackerman, Andrew S. and Burnet, Fr{\'e}d{\'e}ric and Cheng, Andr{\'e} and Couvreux, Fleur and Jiang, Hongli and Khairoutdinov, Marat and Kogan, Yefim and Lewellen, David C. and Mechem, David and Nakamura, Kozo and Noda, Akira and Shipway, Ben J. and Slawinska, Joanna and Wang, Shuyi and Wyszogrodzki, Andrzej},
+  title = {Controls on precipitation and cloudiness in simulations of trade-wind cumulus as observed during RICO},
+  journal = {Journal of Advances in Modeling Earth Systems},
+  year = {2011},
+  volume = {3},
+  number = {2},
+  pages = {M06001},
+  doi = {10.1029/2011MS000056}
+}
+
+@article{CloudMicrophysics,
+  author = {Jaruga, Anna and Schneider, Tapio},
+  title = {CloudMicrophysics.jl: A Julia package for cloud microphysics modeling},
+  journal = {Journal of Open Source Software},
+  year = {2024},
+  note = {In preparation}
+}
+
+@article{RRTMGP,
+  author = {Pincus, Robert and Mlawer, Eli J. and Delamere, Jennifer S.},
+  title = {Balancing Accuracy, Efficiency, and Flexibility in Radiation Calculations for Dynamical Models},
+  journal = {Journal of Advances in Modeling Earth Systems},
+  year = {2019},
+  volume = {11},
+  number = {10},
+  pages = {3074--3089},
+  doi = {10.1029/2019MS001621}
+}
+
+@software{Churavy_KernelAbstractions_jl,
+  author =	 {Churavy, Valentin},
+  license =	 {MIT},
+  title =	 {{KernelAbstractions.jl}},
+  url =		 {https://github.com/JuliaGPU/KernelAbstractions.jl},
+  doi =		 {10.5281/zenodo.4021259},
+}
+
+@article{Bezanson2017,
+  author = {Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B.},
+  title = {Julia: A Fresh Approach to Numerical Computing},
+  journal = {SIAM Review},
+  year = {2017},
+  volume = {59},
+  number = {1},
+  pages = {65--98},
+  doi = {10.1137/141000671}
+}
+
+@article{Deardorff1980,
+  author = {Deardorff, James W.},
+  title = {Stratocumulus-capped mixed layers derived from a three-dimensional model},
+  journal = {Boundary-Layer Meteorology},
+  year = {1980},
+  volume = {18},
+  number = {4},
+  pages = {495--527},
+  doi = {10.1007/BF00119502}
+}
+
+@book{Stull1988,
+  author = {Stull, Roland B.},
+  title = {An Introduction to Boundary Layer Meteorology},
+  publisher = {Springer Netherlands},
+  year = {1988},
+  doi = {10.1007/978-94-009-3027-8}
+}
+
+@article{OceananigansArxiv,
+  author = {Wagner, Gregory L. and Silvestri, Simone and Constantinou, Navid C. and Ramadhan, Ali and Campin, Jean-Michel and Hill, Chris and Chor, Tomas and Strong-Wright, Jago and Lee, Xin Kai and Poulin, Francis and Souza, Andre and Burns, Keaton J. and Bishnu, Siddhartha and Marshall, John and Ferrari, Raffaele},
+  title = {High-level, high-resolution ocean modeling at all scales with {Oceananigans}},
+  journal = {arXiv preprint arXiv:2502.14148},
+  year = {2025},
+  doi = {10.48550/arXiv.2502.14148},
+  url = {https://arxiv.org/abs/2502.14148}
+}
+
+@article{DALES,
+  author = {Heus, Thijs and van Heerwaarden, Chiel C. and Jonker, Harm J. J. and Pier Siebesma, A. and Axelsen, Simon and van den Dries, Kees and Geoffroy, Olivier and Moene, Arnold F. and Pino, David and de Roode, Stephan R. and Vil{\`a}-Guerau de Arellano, Jordi},
+  title = {Formulation of the {Dutch Atmospheric Large-Eddy Simulation (DALES)} and overview of its applications},
+  journal = {Geoscientific Model Development},
+  year = {2010},
+  volume = {3},
+  number = {2},
+  pages = {415--444},
+  doi = {10.5194/gmd-3-415-2010}
+}
+
+@article{MicroHH,
+  author = {van Heerwaarden, Chiel C. and van Stratum, Bart J. H. and Heus, Thijs and Gibbs, Jeremy A. and Fedorovich, Evgeni and Mellado, Juan Pedro},
+  title = {{MicroHH 1.0}: a computational fluid dynamics code for direct numerical simulation and large-eddy simulation of atmospheric boundary layer flows},
+  journal = {Geoscientific Model Development},
+  year = {2017},
+  volume = {10},
+  number = {8},
+  pages = {3145--3165},
+  doi = {10.5194/gmd-10-3145-2017}
+}
+
+@article{PyCLES,
+  author = {Pressel, Kyle G. and Kaul, Colleen M. and Schneider, Tapio and Tan, Zhihong and Misber, Siddhartha},
+  title = {Large-eddy simulation in an anelastic framework with closed water and entropy balances},
+  journal = {Journal of Advances in Modeling Earth Systems},
+  year = {2015},
+  volume = {7},
+  number = {3},
+  pages = {1425--1456},
+  doi = {10.1002/2015MS000496}
+}
+
+@article{CM1,
+  author = {Bryan, George H. and Fritsch, J. Michael},
+  title = {A Benchmark Simulation for Moist Nonhydrostatic Numerical Models},
+  journal = {Monthly Weather Review},
+  year = {2002},
+  volume = {130},
+  number = {12},
+  pages = {2917--2928},
+  doi = {10.1175/1520-0493(2002)130<2917:ABSFMN>2.0.CO;2}
+}
+
+@techreport{WRF,
+  author = {Skamarock, William C. and Klemp, Joseph B. and Dudhia, Jimy and Gill, David O. and Liu, Zhiquan and Berner, Judith and Wang, Wei and Powers, Jordan G. and Duda, Michael G. and Barker, Dale M. and Huang, Xiang-Yu},
+  title = {A Description of the {Advanced Research WRF Model Version 4}},
+  institution = {National Center for Atmospheric Research},
+  year = {2019},
+  number = {NCAR/TN-556+STR},
+  doi = {10.5065/1dfh-6p97}
+}
+
+@article{MesoNH,
+  author = {Lac, Christine and Chaboureau, Jean-Pierre and Masson, Val{\'e}ry and Pinty, Jean-Pierre and Tulet, Pierre and Escobar, Juan and Leriche, Maud and Barthe, Christelle and Aouizerats, Benjamin and Augros, Cl{\'e}ment and Aumond, Pierre and Auguste, Florian and Bechtold, Peter and Berthet, Sarah and Bielli, S{\`e}verine and Bosseur, Fran{\c{c}}ois and Caumont, Olivier and Cohard, Jean-Martial and Colin, Jeanne and Couvreux, Fleur and Cuxart, Joan and Delautier, Ga{\"e}lle and Dauhut, Thibaut and Ducrocq, V{\'e}ronique and Filippi, Jean-Baptiste and Gazen, Didier and Geoffroy, Olivier and Gheusi, Fran{\c{c}}ois and Honnert, Rachel and Lafore, Jean-Philippe and Lebeaupin Brossier, Cindy and Libois, Quentin and Lunet, Thibaut and Mari, C{\'e}line and Maric, Tomislav and Mascart, Patrick and Mog{\'e}, Maxime and Mo{\"i}se, Gwendal and Molini{\'e}, Guilhem and Peyrot, Fr{\'e}d{\'e}ric and Pergaud, Julien and Perraud, Emilie and Pigeon, Gr{\'e}goire and Redelsperger, Jean-Luc and Riber, D. and Ricard, Didier and Richard, Evelyne and Rinc{\'o}n, Samuel and Rodier, Quentin and Seyfried, Laura and Stein, Jo{\"e}l and S{\"u}hre, Karsten and Taufour, Marie and Thouron, Odile and Turner, S{\'e}bastien and Verrelle, Adrien and Vi{\'e}, Beno{\^i}t and Visentin, Florian and Vionnet, Vincent and Wautelet, Philippe},
+  title = {Overview of the {Meso-NH} model version 5.4 and its applications},
+  journal = {Geoscientific Model Development},
+  year = {2018},
+  volume = {11},
+  number = {5},
+  pages = {1929--1969},
+  doi = {10.5194/gmd-11-1929-2018}
+}
+
+@article{ICON,
+  author = {Z{\"a}ngl, G{\"u}nther and Reinert, Daniel and R{\'\i}podas, Pilar and Baldauf, Michael},
+  title = {The {ICON} ({IC}osahedral {N}on-hydrostatic) modelling framework of {DWD} and {MPI-M}: Description of the non-hydrostatic dynamical core},
+  journal = {Quarterly Journal of the Royal Meteorological Society},
+  year = {2015},
+  volume = {141},
+  number = {687},
+  pages = {563--579},
+  doi = {10.1002/qj.2378}
+}
+
+@article{SAM,
+  author = {Khairoutdinov, Marat F. and Randall, David A.},
+  title = {Cloud Resolving Modeling of the {ARM} Summer 1997 {IOP}: Model Formulation, Results, Uncertainties, and Sensitivities},
+  journal = {Journal of the Atmospheric Sciences},
+  year = {2003},
+  volume = {60},
+  number = {4},
+  pages = {607--625},
+  doi = {10.1175/1520-0469(2003)060<0607:CRMOTA>2.0.CO;2}
+}
+
+@article{PTerodaC3TILES,
+  author = {Thuburn, John},
+  title = {Potential-based thermodynamics with consistent conservative cascade transport for implicit large eddy simulation: {PTerodaC3TILES} version 1.0},
+  journal = {Geoscientific Model Development},
+  year = {2025},
+  volume = {18},
+  number = {11},
+  pages = {3331--3357},
+  doi = {10.5194/gmd-18-3331-2025},
+  url = {https://gmd.copernicus.org/articles/18/3331/2025/}
+}
+
+@article{DPSCREAM,
+  author = {Bogenschutz, P. A. and Clevenger, T. C. and Bradley, A. M. and Caldwell, P. M. and Beydoun, H. and Mahfouz, N. and Keen, N. D. and Guba, O. and Bertagna, L. and Foucar, J. and Zhang, J. and Donahue, A. S.},
+  title = {High Performance, High Fidelity: A {GPU}-Accelerated Doubly-Periodic Configuration of the Simple Cloud-Resolving {E3SM} Atmosphere Model Version 1 ({DP-SCREAMv1})},
+  journal = {Journal of Advances in Modeling Earth Systems},
+  year = {2025},
+  volume = {17},
+  number = {11},
+  doi = {10.1029/2025MS005127},
+  url = {https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2025MS005127},
+  publisher = {American Geophysical Union (AGU)},
+  issn = {1942-2466}
+}
+
+@article{NeuralGCM,
+  author = {Kochkov, Dmitrii and Yuval, Janni and Langmore, Ian and Norgaard, Peter and Smith, Jamie and Mooers, Griffin and Kl{\"o}wer, Milan and Lottes, James and Rasp, Stephan and D{\"u}ben, Peter and Hatfield, Sam and Battaglia, Peter and Sanchez-Gonzalez, Alvaro and Willson, Matthew and Brenner, Michael P. and Hoyer, Stephan},
+  title = {Neural general circulation models for weather and climate},
+  journal = {Nature},
+  year = {2024},
+  volume = {632},
+  number = {8027},
+  pages = {1060--1066},
+  doi = {10.1038/s41586-024-07744-y},
+  url = {https://www.nature.com/articles/s41586-024-07744-y}
+}
+
+@article{Silvestri2025,
+  author = {Silvestri, Simone and Wagner, Gregory L. and Constantinou, Navid C. and Hill, Christopher N. and Campin, Jean-Michel and Souza, Andre N. and Bishnu, Siddhartha and Churavy, Valentin and Marshall, John and Ferrari, Raffaele},
+  title = {A {GPU}-Based Ocean Dynamical Core for Routine Mesoscale-Resolving Climate Simulations},
+  journal = {Journal of Advances in Modeling Earth Systems},
+  year = {2025},
+  volume = {17},
+  number = {4},
+  doi = {10.1029/2024MS004465},
+  url = {https://doi.org/10.1029/2024MS004465},
+  publisher = {American Geophysical Union (AGU)},
+  issn = {1942-2466}
+}
+
+@misc{SpeedyWeather,
+  title = {{SpeedyWeather.jl}: A Julia global atmospheric model for interactivity and extensibility},
+  howpublished = {\url{https://github.com/SpeedyWeather/SpeedyWeather.jl}},
+  note = {Accessed 2025-12-31}
+}
+
+@misc{JAXGCM,
+  title = {{JAX GCM} (Dinosaur): A differentiable dynamical core for global atmospheric modeling},
+  howpublished = {\url{https://github.com/neuralgcm/dinosaur}},
+  note = {Accessed 2025-12-31}
+}
+
+@misc{ClimaCore,
+  title = {{ClimaCore.jl}: Performance-portable spectral-element discretizations for climate modeling},
+  howpublished = {\url{https://github.com/CliMA/ClimaCore.jl}},
+  note = {Accessed 2025-12-31}
+}
+
+@misc{ClimaAtmos,
+  title = {{ClimaAtmos.jl}: An atmosphere model built on {ClimaCore.jl}},
+  howpublished = {\url{https://github.com/CliMA/ClimaAtmos.jl}},
+  note = {Accessed 2025-12-31}
+}
+