JOSE paper

.github/workflows/paper-preview.yml

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+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: jose
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        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
+        # These lines have been added following
+        # https://github.com/openjournals/openjournals-draft-action/issues/15
+      - name: save pdf to repo
+        uses: stefanzweifel/git-auto-commit-action@v6
+        with:
+          commit_message: Saved new PDF of paper

paper/paper.bib

@@ -0,0 +1,300 @@
+@software{cosimaCookbook,
+  author       = {Constantinou, Navid C. and
+                  Hogg, Andy McC. and
+                  Gibson, Angus and
+                  Steketee, Anton and
+                  Beucher, Romain and
+                  Proft, Max and
+                  Heerdegen, Aidan and
+                  Neme, Julia and
+                  Holmes, Ryan M. and
+                  Morrison, Adele and
+                  Fierro-Arcos, Denisse and
+                  Kiss, Andrew E. and
+                  Oliveira, Micael and
+                  Yung, Claire and
+                  Doddridge, Edward and
+                  Huneke, Wilma and
+                  Bhagtani, Dhruv and
+                  Ong, Ellie Q. Y. and
+                  Munroe, James and
+                  Schmidt, Christina and
+                  Dawson, Hannah and
+                  Squire, Dougal T. and
+                  Dias, Fabio Boeira and
+                  Jeffree, Jemma and
+                  Moorman, Ruth and
+                  Martínez-Moreno, Josué and
+                  Zika, Jan and
+                  Meijer, Jan Jaap and
+                  Auger, Matthis and
+                  Aguiar, Wilton and
+                  Moore, Thomas and
+                  Vilela da Silva, Felipe and
+                  Yang, Luwei and
+                  White, Marc and
+                  Sohail, Taimoor and
+                  Barnes, Ashley J. and
+                  Spence, Paul and
+                  Turner, Charles and
+                  Rosevear, Madelaine G. and
+                  Bull, Christopher Yit Sen and
+                  Day, Noah and
+                  Li, Minghang and
+                  Ellepola, Anupiya and
+                  Narayanan, Aditya},
+  title = {{COSIMA Cookbook: A cookbook of recipes for analysing ocean and sea ice model output}},
+  year = {2026},
+  doi = {10.5281/zenodo.14353852},
+  url = {https://doi.org/10.5281/zenodo.14353852}
+}
+
+@software{sphinx,
+  author       = {Komiya, Takeshi and
+                  Brandl, Georg and
+                  Turner, Adam and
+                  Bakosi, Jean-Francois and
+                  Shimizukawa, Takayuki and
+                  Andersen, Jakob Lykke and
+                  Neuh{\"a}user, Daniel and
+                  Finucane, Stephen and
+                  Lehmann, Robert and
+                  Mason, Jacob and
+                  Kampik, Timotheus and
+                  Addison, James and
+                  Magin, Justus and
+                  Dufresne, Jon and
+                  Waltman, Jonathan and
+                  Eades, Daniel and
+                  Cano Rodr{\'i}guez, Juan Luis and
+                  Ronacher, Armin and
+                  Geier, Matthias and
+                  Shachnev, Dmitry and
+                  Shibukawa, Yoshiki and
+                  Tran, B{\'e}n{\'e}dikt and
+                  Dangoor, Adam and
+                  Sewell, Chris and
+                  Ruana, Rob and
+                  Virtanen, Pauli and
+                  Hoffmann, Tim and
+                  Li{\v{s}}ka, Martin and
+                  Freitag, Fran{\c c}ois},
+  title        = {{sphinx-doc/sphinx: Sphinx 9.1.0}},
+  year         = {2025},
+  publisher    = {Zenodo},
+  version      = {v9.1.0},
+  doi          = {10.5281/zenodo.18109073},
+  url          = {https://doi.org/10.5281/zenodo.18109073}
+}
+
+@article{kiss2020accessom2,
+  author = {Kiss, Andrew E. and Woodward, Melanie J. and Hollings, T. and Mu, Minyu and Fiedler, Raquel and Steven, Andrew D. L. and Lenton, Andrew and Matear, Richard and Chamberlain, Matthew A. and Oke, Peter R. and Alves, Orly and Griffies, Stephen M. and Hill, Catherine and Kovach, Alexander and Marsland, Simon J. and Fiedler, Rebecca and Waters, Judith and Yang, Chun-Hsu and Zhou, Xiaobing and Savita, Abha and Rymph, Stacey and Bi, D. and Griffin, David and Mackallah, Christian and Underwood, Stuart and Druken, Karina A. and Merati, Nasim and Hogg, Andrew McC.},
+  title = {ACCESS-OM2 v1.0: a global ocean-sea ice model at three resolutions},
+  journal = {Geoscientific Model Development},
+  year = {2020},
+  volume = {13},
+  number = {2},
+  pages = {401--442},
+  doi = {10.5194/gmd-13-401-2020},
+  url = {https://doi.org/10.5194/gmd-13-401-2020}
+}
+
+@article{hoyer2017xarray,
+  author = {Hoyer, Stephan and Hamman, Joseph J.},
+  title = {{xarray: N-D labeled arrays and datasets in Python}},
+  journal = {Journal of Open Research Software},
+  year = {2017},
+  volume = {5},
+  number = {1},
+  pages = {10},
+  doi = {10.5334/jors.148},
+  url = {https://doi.org/10.5334/jors.148}
+}
+
+@incollection{kluyver2016jupyter,
+  author = {Kluyver, Thomas and Ragan-Kelley, Benjamin and P{\'e}rez, Fernando and Granger, Brian and Bussonnier, Matthias and Frederic, Jonathan and Kelley, Kyle and Hamrick, Jessica and Grout, Jason and Corlay, Sylvain and Ivanov, Paul and Avila, Dami{\'a}n and Abdalla, Safia and Willing, Carol},
+  title = {Jupyter Notebooks---a publishing format for reproducible computational workflows},
+  booktitle = {Positioning and Power in Academic Publishing: Players, Agents and Agendas},
+  editor = {Loizides, Fernando and Schmidt, Birgit},
+  publisher = {IOS Press},
+  address = {Amsterdam},
+  year = {2016},
+  pages = {87--90},
+  doi = {10.3233/978-1-61499-649-1-87},
+  url = {https://doi.org/10.3233/978-1-61499-649-1-87}
+}
+
+@article{barnes2024regionalmom6,
+  author = {Barnes, Ashley J. and Constantinou, Navid C. and Gibson, Angus H. and Kiss, Andrew E. and Chapman, Chris and Reilly, John and Bhagtani, Dhruv and Yang, Luwei},
+  title = {{regional-mom6: A Python package for automatic generation of regional configurations for the Modular Ocean Model 6}},
+  journal = {Journal of Open Source Software},
+  year = {2024},
+  volume = {9},
+  number = {100},
+  pages = {6857},
+  doi = {10.21105/joss.06857},
+  url = {https://doi.org/10.21105/joss.06857}
+}
+
+@software{cartopy,
+  author       = {Phil Elson and
+                  Elliott Sales de Andrade and
+                  Greg Lucas and
+                  Ryan May and
+                  Richard Hattersley and
+                  Ed Campbell and
+                  Ruth Comer and
+                  Andrew Dawson and
+                  Bill Little and
+                  Stephane Raynaud and
+                  scmc72 and
+                  Alan D. Snow and
+                  lgolston and
+                  Byron Blay and
+                  Peter Killick and
+                  lbdreyer and
+                  Patrick Peglar and
+                  Nat Wilson and
+                  Andrew and
+                  Jon Szymaniak and
+                  Adrien Berchet and
+                  Corinne Bosley and
+                  Luke Davis and
+                  Filipe and
+                  John Krasting and
+                  Matthew Bradbury and
+                  stephenworsley and
+                  Daniel Kirkham},
+  title        = {{SciTools/cartopy: v0.24.1}},
+  month        = oct,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {v0.24.1},
+  doi          = {10.5281/zenodo.13905945},
+  url          = {https://doi.org/10.5281/zenodo.13905945},
+}
+
+@manual{intake,
+  author = {{Intake developers}},
+  title = {Intake: a lightweight package for finding, investigating, loading and disseminating data},
+  year = {2026},
+  url = {https://intake.readthedocs.io/en/reader/}
+}
+
+@Article{Delandmeter-vanSebille-2019,
+  author = {Delandmeter, P. and van Sebille, E.},
+  title = {The Parcels v2.0 Lagrangian framework: new field interpolation schemes},
+  journal = {Geoscientific Model Development},
+  volume = {12},
+  year = {2019},
+  number = {8},
+  pages = {3571--3584},
+  doi = {10.5194/gmd-12-3571-2019}
+}
+
+@article{lange2017parcels,
+  author = {Lange, Michael and van Sebille, Erik},
+  title = {Parcels v0.9: prototyping a {Lagrangian} ocean analysis framework for the petascale age},
+  journal = {Geoscientific Model Development},
+  year = {2017},
+  volume = {10},
+  number = {11},
+  pages = {4175--4186},
+  doi = {10.5194/gmd-10-4175-2017},
+  url = {https://doi.org/10.5194/gmd-10-4175-2017}
+}
+
+@Manual{dask,
+  title = {Dask: Library for dynamic task scheduling},
+  author = {{Dask Development Team}},
+  year = {2016},
+  url = {http://dask.pydata.org},
+}
+
+@software{xgcm,
+  author       = {Abernathey, Ryan P. and
+                  Busecke, Julius J. M. and
+                  Smith, Timothy Andrew and
+                  Deauna, Josephine Dianne and
+                  Banihirwe, Anderson and
+                  Nicholas, Thomas and
+                  Fernandes, Filipe and
+                  James, Bourbeau and
+                  Dussin, Raphael and
+                  Cherian, Deepak A. and
+                  Caneill, Romain and
+                  Sinha, Anirban and
+                  Uieda, Leonardo and
+                  Rath, Willi and
+                  Balwada, Dhruv and
+                  Constantinou, Navid C. and
+                  Ponte, Aurélien and
+                  Zhou, Yuxin and
+                  Uchida, Takaya and
+                  Thielen, Jon},
+  title        = {{xgcm}},
+  month        = nov,
+  year         = 2022,
+  publisher    = {Zenodo},
+  version      = {v0.8.1},
+  doi          = {10.5281/zenodo.7348619},
+  url          = {https://doi.org/10.5281/zenodo.7348619},
+}
+
+@software{xesmf,
+  author       = {Jiawei Zhuang and
+                  Raphael Dussin and
+                  Pascal Bourgault and
+                  David Huard and
+                  Anderson Banihirwe and
+                  Stephane Raynaud and
+                  Brewster Malevich and
+                  Martin Schupfner and
+                  Charles Gauthier and
+                  Filipe and
+                  Sam Levang and
+                  Mattia Almansi and
+                  André Jüling and
+                  RichardScottOZ and
+                  RondeauG and
+                  Stephan Rasp and
+                  Trevor James Smith and
+                  Aaron G. Meyer and
+                  Ben Mares and
+                  Bill Sacks and
+                  Jemma Stachelek and
+                  Matthew Plough and
+                  Pierre and
+                  Ray Bell and
+                  Romain Caneill and
+                  Xianxiang Li},
+  title = {{pangeo-data/xESMF: v0.9.2}},
+  year = {2025},
+  doi = {10.5281/zenodo.4294774},
+  url = {https://doi.org/10.5281/zenodo.4294774}
+}
+
+@InProceedings{rocklin2015dask,
+  author    = {Matthew Rocklin},
+  title     = {Dask: Parallel Computation with Blocked algorithms and Task Scheduling},
+  booktitle = {Proceedings of the 14th Python in Science Conference},
+  pages     = {130--136},
+  year      = {2015},
+  editor    = {Kathryn Huff and James Bergstra},
+  doi       = {10.25080/Majora-7b98e3ed-013}
+}
+
+@Article{Hunter2007matplotlib,
+  Author    = {Hunter, J. D.},
+  Title     = {Matplotlib: A 2D graphics environment},
+  Journal   = {Computing in Science \& Engineering},
+  Volume    = {9},
+  Number    = {3},
+  Pages     = {90--95},
+  abstract  = {Matplotlib is a 2D graphics package used for Python for
+  application development, interactive scripting, and publication-quality
+  image generation across user interfaces and operating systems.},
+  publisher = {IEEE COMPUTER SOC},
+  doi       = {10.1109/MCSE.2007.55},
+  year      = 2007
+}