Work in progress: Journal of Open Source Science paper

.github/workflows/main.yml

@@ -4,8 +4,14 @@ on:
   push:
     branches:
       - main
+    paths-ignore:
+      - "paper/**"
+      - "README.md"
   pull_request:
     types: [opened, synchronize, reopened]
+    paths-ignore:
+      - "paper/**"
+      - "README.md"
 
 env:
   EO_TIDES_TIDE_MODELS: ./tests/data/tide_models
@@ -58,6 +64,7 @@ jobs:
       #   run: uv run gdalinfo --format GTiff
 
       - name: Run Python unit tests
+        timeout-minutes: 10
         run: uv run python -m pytest tests --cov --cov-config=pyproject.toml --cov-report=xml --verbose
 
       - name: Run Jupyter Notebook integration tests

.github/workflows/paper.yml

@@ -0,0 +1,30 @@
+name: Draft paper PDF
+on:
+  push:
+    branches:
+      - main
+      - JOSS_paper
+    paths:
+      - paper/**
+      - .github/workflows/paper.yml
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Generate paper draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # 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

paper/paper.bib

@@ -0,0 +1,208 @@
+@misc{pytmd,
+  author       = {Sutterley, T.C. and Alley, K. and Brunt, K. and Howard, S., and Padman, L., and Siegried, M.},
+  title        = {pyTMD: Python-based tidal prediction software},
+  year         = 2017,
+  publisher    = {Zenodo},
+  doi          = {10.5281/zenodo.5555395},
+  url          = {https://doi.org/10.5281/zenodo.5555395},
+}
+
+@software{reback2020pandas,
+    author       = {pandas development team},
+    title        = {pandas-dev/pandas: Pandas},
+    month        = feb,
+    year         = 2020,
+    publisher    = {Zenodo},
+    version      = {latest},
+    doi          = {10.5281/zenodo.3509134},
+    url          = {https://doi.org/10.5281/zenodo.3509134}
+}
+
+@InProceedings{ mckinney-proc-scipy-2010,
+  author    = { {W}es {M}c{K}inney },
+  title     = { {D}ata {S}tructures for {S}tatistical {C}omputing in {P}ython },
+  booktitle = { {P}roceedings of the 9th {P}ython in {S}cience {C}onference },
+  pages     = { 56 - 61 },
+  year      = { 2010 },
+  editor    = { {S}t\'efan van der {W}alt and {J}arrod {M}illman },
+  doi       = { 10.25080/Majora-92bf1922-00a }
+}
+
+@article{Hoyer_xarray_N-D_labeled_2017,
+  author = {Hoyer, Stephan and Joseph, Hamman},
+  doi = {10.5334/jors.148},
+  journal = {Journal of Open Research Software},
+  month = apr,
+  number = {1},
+  title = {{xarray}: N-D labeled Arrays and Datasets in Python},
+  volume = {5},
+  year = {2017}
+}
+
+@misc{odcgeo,
+  author       = {odc-geo development team},
+  title        = {opendatacube/{odc-geo}},
+  license      = {Apache 2.0},
+  publisher    = {GitHub},
+  journal      = {GitHub repository},
+  year         = 2024,
+  url          = {https://github.com/opendatacube/odc-geo},
+}
+
+@article{murray2012continental,
+  title={Continental scale mapping of tidal flats across East Asia using the Landsat archive},
+  author={Murray, Nicholas J and Phinn, Stuart R and Clemens, Robert S and Roelfsema, Chris M and Fuller, Richard A},
+  journal={Remote Sensing},
+  volume={4},
+  number={11},
+  pages={3417--3426},
+  year={2012},
+  publisher={Molecular Diversity Preservation International (MDPI)}
+}
+
+@article{sagar2017item,
+  title={Extracting the intertidal extent and topography of the Australian coastline from a 28 year time series of Landsat observations},
+  author={Sagar, S. and Roberts, D. and Bala, B. and Lymburner, L.},
+  journal={Remote Sensing of Environment},
+  volume={195},
+  pages={153--169},
+  year={2017},
+  publisher={Elsevier}
+}
+
+@inproceedings{carrere2022new,
+  title={A new barotropic tide model for global ocean: FES2022},
+  author={Carrere, Loren and Lyard, Florent and Cancet, Mathilde and Allain, Damien and Dabat, Mei-Ling and Fouchet, Ergane and Sahuc, Etienne and Faugere, Yannice and Dibarboure, Gerald and Picot, Nicolas},
+  booktitle={2022 Ocean Surface Topography Science Team Meeting},
+  pages={43},
+  year={2022}
+}
+
+@article{GESLAv3,
+  author = {Haigh, Ivan D. and Marcos, Marta and Talke, Stefan A. and Woodworth, Philip L. and Hunter, John R. and Hague, Ben S. and Arns, Arne and Bradshaw, Elizabeth and Thompson, Philip},
+  title = {GESLA Version 3: A major update to the global higher-frequency sea-level dataset},
+  journal = {Geoscience Data Journal},
+  volume = {10},
+  number = {3},
+  pages = {293-314},
+  keywords = {sea level records, sea level rise, storm surges, storm tides, tide gauge},
+  doi = {https://doi.org/10.1002/gdj3.174},
+  url = {https://rmets.onlinelibrary.wiley.com/doi/abs/10.1002/gdj3.174},
+  eprint = {https://rmets.onlinelibrary.wiley.com/doi/pdf/10.1002/gdj3.174},
+  abstract = {Abstract This paper describes a major update to the quasi-global, higher-frequency sea-level dataset known as GESLA (Global Extreme Sea Level Analysis). Versions 1 (released 2009) and 2 (released 2016) of the dataset have been used in many published studies, across a wide range of oceanographic and coastal engineering-related investigations concerned with evaluating tides, storm surges, extreme sea levels, and other related processes. The third version of the dataset (released 2021), presented here, contains double the number of years of data, and nearly four times the number of records, compared to Version 2. The dataset consists of records obtained from multiple sources around the world. This paper describes the assembly of the dataset, its processing, and its format, and outlines potential future improvements.},
+  year = {2023}
+}
+
+@misc{krause2021dea,
+  title={{Digital Earth Australia} notebooks and tools repository},
+  author={Krause, C. and Dunn, B. and Bishop-Taylor, R. and Adams, C. and Burton, C. and Alger, M. and Chua, S. and Phillips, C. and Newey, V. and Kouzoubov, K. and Leith, A. and Ayers, D. and Hicks, A.},
+  year={2021},
+  publisher={Commonwealth of Australia (Geoscience Australia)},
+  url={https://doi.org/10.26186/145234},
+  howpublished={\url{https://github.com/GeoscienceAustralia/dea-notebooks/}},
+  doi={10.26186/145234}
+}
+
+@misc{deaintertidal,
+  title={{Digital Earth Australia Intertidal}},
+  author={Bishop-Taylor, R. and Phillips, C. and Newey, V. and Sagar, S},
+  year={2024},
+  publisher={Commonwealth of Australia (Geoscience Australia)},
+  url={https://dx.doi.org/10.26186/149403},
+  doi={10.26186/149403}
+}
+
+@article{Fitzpatrick2024,
+  doi = {10.21105/joss.06683},
+  url = {https://doi.org/10.21105/joss.06683},
+  year = {2024},
+  publisher = {The Open Journal},
+  volume = {9},
+  number = {99},
+  pages = {6683},
+  author = {Sharon Fitzpatrick and Daniel Buscombe and Jonathan A. Warrick and Mark A. Lundine and Kilian Vos},
+  title = {CoastSeg: an accessible and extendable hub for satellite-derived-shoreline (SDS) detection and mapping},
+  journal = {Journal of Open Source Software}
+}
+
+@article{eleveld2014estuarine,
+  title={Estuarine suspended particulate matter concentrations from sun-synchronous satellite remote sensing: Tidal and meteorological effects and biases},
+  author={Eleveld, Marieke A and Van der Wal, Daphne and Van Kessel, Thijs},
+  journal={Remote Sensing of Environment},
+  volume={143},
+  pages={204--215},
+  year={2014},
+  publisher={Elsevier}
+}
+
+@article{bishop2021mapping,
+  title={Mapping {Australia}'s {Dynamic Coastline} at {Mean Sea Level} Using {Three Decades of Landsat Imagery}},
+  author={Bishop-Taylor, R. and Nanson, R. and Sagar, S. and Lymburner, L.},
+  journal={Remote Sensing of Environment},
+  volume={267},
+  pages={112734},
+  year={2021},
+  publisher={Elsevier},
+  doi={10.1016/j.rse.2021.112734},
+  url={https://doi.org/10.1016/j.rse.2021.112734}
+}
+
+@article{bishop2019NIDEM,
+  title={Between the tides: Modelling the elevation of Australia's exposed intertidal zone at continental scale},
+  author={Bishop-Taylor, R. and Sagar, S. and Lymburner, L. and Beaman, R.J.},
+  journal={Estuarine, Coastal and Shelf Science},
+  volume={223},
+  pages={115-128},
+  year={2019},
+  publisher={Elsevier},
+  doi={10.1016/j.ecss.2019.03.006},
+  url={https://doi.org/10.1016/j.ecss.2019.03.006}
+}
+
+@article{sagar2018composites,
+  title={Generating Continental Scale Pixel-Based Surface Reflectance Composites in Coastal Regions with the Use of a Multi-Resolution Tidal Model},
+  author={Sagar, S. and Phillips, C. and Bala, B. and Roberts, D. and Lymburner, L. and Beaman, R.J.},
+  journal={Remote Sensing},
+  volume={10(3)},
+  pages={480},
+  year={2018},
+  publisher={MDPI},
+  doi={10.3390/rs10030480},
+  url={https://doi.org/10.3390/rs10030480}
+}
+
+@article{vitousek2023future,
+  title={The future of coastal monitoring through satellite remote sensing},
+  author={Vitousek, S. and Buscombe, D. and Vos, K. and Barnard, P. L. and Ritchie, A. C. and Warrick, J. A.},
+  journal={Cambridge Prisms: Coastal Futures},
+  volume={1},
+  pages={e10},
+  year={2023},
+  publisher={Cambridge University Press},
+  doi={10.1017/cft.2022.4},
+  url={https://doi.org/10.1017/cft.2022.4}
+}
+
+@article{turner2021satellite,
+  title={Satellite optical imagery in {Coastal Engineering}},
+  author={Turner, I. L. and Harley, M. D. and Almar, R. and Bergsma, E. W. J.},
+  journal={Coastal Engineering},
+  volume={167},
+  pages={103919},
+  year={2021},
+  publisher={Elsevier},
+  doi={10.1016/j.coastaleng.2021.103919},
+  url={https://doi.org/10.1016/j.coastaleng.2021.103919}
+}
+
+@article{vos2019coastsat,
+  title={{CoastSat}: {A} {Google Earth Engine}-enabled {Python} toolkit to extract shorelines from publicly available satellite imagery},
+  author={Vos, K. and Splinter, K. D. and Harley, M. D. and Simmons, J. A. and Turner, I. L.},
+  journal={Environmental Modelling \& Software},
+  volume={122},
+  pages={104528},
+  year={2019},
+  doi={10.1016/j.envsoft.2019.104528},
+  url={https://doi.org/10.1016/j.envsoft.2019.104528},
+  publisher={Elsevier}
+}