From ffbb7a1276c787568a2985b8b5a06107761d1d72 Mon Sep 17 00:00:00 2001 From: PennyHow Date: Fri, 3 May 2024 11:10:13 -0100 Subject: [PATCH] joss draft added --- .github/workflows/joss-pdf.yml | 23 +++++++++++ joss/paper.bib | 59 +++++++++++++++++++++++++++ joss/paper.md | 74 ++++++++++++++++++++++++++++++++++ setup.py | 6 ++- 4 files changed, 160 insertions(+), 2 deletions(-) create mode 100644 .github/workflows/joss-pdf.yml create mode 100644 joss/paper.bib create mode 100644 joss/paper.md diff --git a/.github/workflows/joss-pdf.yml b/.github/workflows/joss-pdf.yml new file mode 100644 index 0000000..6a508b7 --- /dev/null +++ b/.github/workflows/joss-pdf.yml @@ -0,0 +1,23 @@ +on: [push] + +jobs: + paper: + runs-on: ubuntu-latest + name: Paper Draft + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Build draft PDF + uses: openjournals/openjournals-draft-action@master + with: + journal: joss + # This should be the path to the paper within your repo. + paper-path: paper.md + - name: Upload + uses: actions/upload-artifact@v1 + 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.pdf diff --git a/joss/paper.bib b/joss/paper.bib new file mode 100644 index 0000000..4e4544a --- /dev/null +++ b/joss/paper.bib @@ -0,0 +1,59 @@ +@article{Pearson:2017, + url = {http://adsabs.harvard.edu/abs/2017arXiv170304627P}, + Archiveprefix = {arXiv}, + Author = {{Pearson}, S. and {Price-Whelan}, A.~M. and {Johnston}, K.~V.}, + Eprint = {1703.04627}, + Journal = {ArXiv e-prints}, + Keywords = {Astrophysics - Astrophysics of Galaxies}, + Month = mar, + Title = {{Gaps in Globular Cluster Streams: Pal 5 and the Galactic Bar}}, + Year = 2017 +} + +@book{Binney:2008, + url = {http://adsabs.harvard.edu/abs/2008gady.book.....B}, + Author = {{Binney}, J. and {Tremaine}, S.}, + Booktitle = {Galactic Dynamics: Second Edition, by James Binney and Scott Tremaine.~ISBN 978-0-691-13026-2 (HB).~Published by Princeton University Press, Princeton, NJ USA, 2008.}, + Publisher = {Princeton University Press}, + Title = {{Galactic Dynamics: Second Edition}}, + Year = 2008 +} + +@article{gaia, + author = {{Gaia Collaboration}}, + title = "{The Gaia mission}", + journal = {Astronomy and Astrophysics}, + archivePrefix = "arXiv", + eprint = {1609.04153}, + primaryClass = "astro-ph.IM", + keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes}, + year = 2016, + month = nov, + volume = 595, + doi = {10.1051/0004-6361/201629272}, + url = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G}, +} + +@article{astropy, + author = {{Astropy Collaboration}}, + title = "{Astropy: A community Python package for astronomy}", + journal = {Astronomy and Astrophysics}, + archivePrefix = "arXiv", + eprint = {1307.6212}, + primaryClass = "astro-ph.IM", + keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools}, + year = 2013, + month = oct, + volume = 558, + doi = {10.1051/0004-6361/201322068}, + url = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A} +} + +@misc{fidgit, + author = {A. M. Smith and K. Thaney and M. Hahnel}, + title = {Fidgit: An ungodly union of GitHub and Figshare}, + year = {2020}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/arfon/fidgit} +} diff --git a/joss/paper.md b/joss/paper.md new file mode 100644 index 0000000..5ac925a --- /dev/null +++ b/joss/paper.md @@ -0,0 +1,74 @@ +--- +title: 'GrIML: A Python package for examining Greenland's ice marginal lakes under a changing climate' +tags: + - Python + - glaciology + - cryospheric science + - remote sensing + - greenland +authors: + - name: Penelope R. How + orcid: 0000-0002-8088-8497 + affiliation: 1 +affiliations: + - name: Geological Survey of Denmark and Greenland (GEUS), Copenhagen, Denmark + index: 1 +date: 3 May 2024 +bibliography: paper.bib +--- + +# Summary + +- GrIML post-processing toolbox description +- GrIML project aim and outline +- GrIML datasets +- Similar toolboxes + +Citations to entries in paper.bib should be in +[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html) +format. + +If you want to cite a software repository URL (e.g. something on GitHub without a preferred +citation) then you can do it with the example BibTeX entry below for @fidgit. + +For a quick reference, the following citation commands can be used: +- `@author:2001` -> "Author et al. (2001)" +- `[@author:2001]` -> "(Author et al., 2001)" +- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)" + +Single dollars ($) are required for inline mathematics e.g. $f(x) = e^{\pi/x}$ + +Double dollars make self-standing equations: + +$$\Theta(x) = \left\{\begin{array}{l} +0\textrm{ if } x < 0\cr +1\textrm{ else} +\end{array}\right.$$ + +You can also use plain \LaTeX for equations +\begin{equation}\label{eq:fourier} +\hat f(\omega) = \int_{-\infty}^{\infty} f(x) e^{i\omega x} dx +\end{equation} +and refer to \autoref{eq:fourier} from text. + +Figures can be included like this: +![Caption for example figure.\label{fig:example}](figure.png) +and referenced from text using \autoref{fig:example}. + +Figure sizes can be customized by adding an optional second parameter: +![Caption for example figure.](figure.png){ width=20% } + + +# Statement of need + +- Need for reproducibility and transparency +- Outlines criteria for ice marginal lake classification + + +# Acknowledgements + +This work is supported by the ESA Living Planet Fellowship (4000136382/21/I-DT-lr) entitled "Examining Greenland's Ice Marginal Lakes under a Changing Climate". Further support is provided by [PROMICE](https://promice.org], funded by the [Geological Survey of Denmark and Greenland (GEUS)](https://www.geus.dk/) and the Danish Ministry of Climate, Energy and Utilities under the Danish Cooperation for Environment in the Arctic (DANCEA). + + +# References + diff --git a/setup.py b/setup.py index ba46956..ac24c9b 100644 --- a/setup.py +++ b/setup.py @@ -17,7 +17,9 @@ }, keywords="glaciology ice lake ESA", classifiers=[ - "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", "License :: OSI Approved :: MIT License", "Development Status :: 4 - Beta", "Intended Audience :: Science/Research", @@ -28,6 +30,6 @@ package_dir={"": "src"}, packages=setuptools.find_packages(where="src"), package_data={"griml.test": ["*"]}, - python_requires=">=3.6", + python_requires=">=3.10", install_requires=['geopandas', 'pandas', 'scipy', 'Shapely', 'rasterio'], )