From 25b8ee39b0c1013daaeb8d56496e2d5dcfc0a803 Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Mon, 14 Jul 2025 20:11:02 -0400 Subject: [PATCH 01/16] updated various numpy citations, created bib page --- core/bibliography.md | 3 ++ core/numpy/intermediate-numpy.ipynb | 4 +- core/numpy/numpy-basics.ipynb | 3 +- myst.yml | 2 + references.bib | 78 ++++++++--------------------- 5 files changed, 32 insertions(+), 58 deletions(-) create mode 100644 core/bibliography.md diff --git a/core/bibliography.md b/core/bibliography.md new file mode 100644 index 000000000..c46bdad75 --- /dev/null +++ b/core/bibliography.md @@ -0,0 +1,3 @@ +# References +```{bibliography} +``` \ No newline at end of file diff --git a/core/numpy/intermediate-numpy.ipynb b/core/numpy/intermediate-numpy.ipynb index a87ad168a..78100d410 100644 --- a/core/numpy/intermediate-numpy.ipynb +++ b/core/numpy/intermediate-numpy.ipynb @@ -650,7 +650,9 @@ "metadata": {}, "source": [ "## Resources and references\n", - "The [NumPy Users Guide](https://numpy.org/devdocs/user/quickstart.html#less-basic) expands further on some of these topics, as well as suggests various [Tutorials](https://numpy.org/learn/), lectures, and more at this stage." + "The [NumPy Users Guide](https://numpy.org/devdocs/user/quickstart.html#less-basic) expands further on some of these topics, as well as suggests various [Tutorials](https://numpy.org/learn/), lectures, and more at this stage.\n", +"\n", +"{cite}'harris2020array'" ] } ], diff --git a/core/numpy/numpy-basics.ipynb b/core/numpy/numpy-basics.ipynb index ee2a9925c..121529a80 100644 --- a/core/numpy/numpy-basics.ipynb +++ b/core/numpy/numpy-basics.ipynb @@ -1007,7 +1007,8 @@ "source": [ "## Resources and references\n", "- [NumPy User Guide](http://docs.scipy.org/doc/numpy/user/)\n", - "- [SciPy Lecture Notes](https://scipy-lectures.org/)" + "- [SciPy Lecture Notes](https://scipy-lectures.org/)\n", + "- {cite}'harris2020array'" ] } ], diff --git a/myst.yml b/myst.yml index f80ed4378..530d8a525 100644 --- a/myst.yml +++ b/myst.yml @@ -5,6 +5,8 @@ extends: project: title: Pythia Foundations github: https://github.com/projectpythia/pythia-foundations + bibtex_bibfiles: + - references.bib author: - Project Pythia Community copyright: '2024' diff --git a/references.bib b/references.bib index 783ec6aa5..33b432409 100644 --- a/references.bib +++ b/references.bib @@ -1,56 +1,22 @@ ---- ---- - -@inproceedings{holdgraf_evidence_2014, - address = {Brisbane, Australia, Australia}, - title = {Evidence for {Predictive} {Coding} in {Human} {Auditory} {Cortex}}, - booktitle = {International {Conference} on {Cognitive} {Neuroscience}}, - publisher = {Frontiers in Neuroscience}, - author = {Holdgraf, Christopher Ramsay and de Heer, Wendy and Pasley, Brian N. and Knight, Robert T.}, - year = {2014} -} - -@article{holdgraf_rapid_2016, - title = {Rapid tuning shifts in human auditory cortex enhance speech intelligibility}, - volume = {7}, - issn = {2041-1723}, - url = {http://www.nature.com/doifinder/10.1038/ncomms13654}, - doi = {10.1038/ncomms13654}, - number = {May}, - journal = {Nature Communications}, - author = {Holdgraf, Christopher Ramsay and de Heer, Wendy and Pasley, Brian N. and Rieger, Jochem W. and Crone, Nathan and Lin, Jack J. and Knight, Robert T. and Theunissen, Frédéric E.}, - year = {2016}, - pages = {13654}, - file = {Holdgraf et al. - 2016 - Rapid tuning shifts in human auditory cortex enhance speech intelligibility.pdf:C\:\\Users\\chold\\Zotero\\storage\\MDQP3JWE\\Holdgraf et al. - 2016 - Rapid tuning shifts in human auditory cortex enhance speech intelligibility.pdf:application/pdf} -} - -@inproceedings{holdgraf_portable_2017, - title = {Portable learning environments for hands-on computational instruction using container-and cloud-based technology to teach data science}, - volume = {Part F1287}, - isbn = {978-1-4503-5272-7}, - doi = {10.1145/3093338.3093370}, - abstract = {© 2017 ACM. There is an increasing interest in learning outside of the traditional classroom setting. This is especially true for topics covering computational tools and data science, as both are challenging to incorporate in the standard curriculum. These atypical learning environments offer new opportunities for teaching, particularly when it comes to combining conceptual knowledge with hands-on experience/expertise with methods and skills. Advances in cloud computing and containerized environments provide an attractive opportunity to improve the effciency and ease with which students can learn. This manuscript details recent advances towards using commonly-Available cloud computing services and advanced cyberinfrastructure support for improving the learning experience in bootcamp-style events. We cover the benets (and challenges) of using a server hosted remotely instead of relying on student laptops, discuss the technology that was used in order to make this possible, and give suggestions for how others could implement and improve upon this model for pedagogy and reproducibility.}, - booktitle = {{ACM} {International} {Conference} {Proceeding} {Series}}, - author = {Holdgraf, Christopher Ramsay and Culich, A. and Rokem, A. and Deniz, F. and Alegro, M. and Ushizima, D.}, - year = {2017}, - keywords = {Teaching, Bootcamps, Cloud computing, Data science, Docker, Pedagogy} -} - -@article{holdgraf_encoding_2017, - title = {Encoding and decoding models in cognitive electrophysiology}, - volume = {11}, - issn = {16625137}, - doi = {10.3389/fnsys.2017.00061}, - abstract = {© 2017 Holdgraf, Rieger, Micheli, Martin, Knight and Theunissen. Cognitive neuroscience has seen rapid growth in the size and complexity of data recorded from the human brain as well as in the computational tools available to analyze this data. This data explosion has resulted in an increased use of multivariate, model-based methods for asking neuroscience questions, allowing scientists to investigate multiple hypotheses with a single dataset, to use complex, time-varying stimuli, and to study the human brain under more naturalistic conditions. These tools come in the form of “Encoding” models, in which stimulus features are used to model brain activity, and “Decoding” models, in which neural features are used to generated a stimulus output. Here we review the current state of encoding and decoding models in cognitive electrophysiology and provide a practical guide toward conducting experiments and analyses in this emerging field. Our examples focus on using linear models in the study of human language and audition. We show how to calculate auditory receptive fields from natural sounds as well as how to decode neural recordings to predict speech. The paper aims to be a useful tutorial to these approaches, and a practical introduction to using machine learning and applied statistics to build models of neural activity. The data analytic approaches we discuss may also be applied to other sensory modalities, motor systems, and cognitive systems, and we cover some examples in these areas. In addition, a collection of Jupyter notebooks is publicly available as a complement to the material covered in this paper, providing code examples and tutorials for predictive modeling in python. The aimis to provide a practical understanding of predictivemodeling of human brain data and to propose best-practices in conducting these analyses.}, - journal = {Frontiers in Systems Neuroscience}, - author = {Holdgraf, Christopher Ramsay and Rieger, J.W. and Micheli, C. and Martin, S. and Knight, R.T. and Theunissen, F.E.}, - year = {2017}, - keywords = {Decoding models, Encoding models, Electrocorticography (ECoG), Electrophysiology/evoked potentials, Machine learning applied to neuroscience, Natural stimuli, Predictive modeling, Tutorials} -} - -@book{ruby, - title = {The Ruby Programming Language}, - author = {Flanagan, David and Matsumoto, Yukihiro}, - year = {2008}, - publisher = {O'Reilly Media} -} +@Article{ harris2020array, + title = {Array programming with {NumPy}}, + author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J. + van der Walt and Ralf Gommers and Pauli Virtanen and David + Cournapeau and Eric Wieser and Julian Taylor and Sebastian + Berg and Nathaniel J. Smith and Robert Kern and Matti Picus + and Stephan Hoyer and Marten H. van Kerkwijk and Matthew + Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del + R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre + G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and + Warren Weckesser and Hameer Abbasi and Christoph Gohlke and + Travis E. Oliphant}, + year = {2020}, + month = sep, + journal = {Nature}, + volume = {585}, + number = {7825}, + pages = {357--362}, + doi = {10.1038/s41586-020-2649-2}, + publisher = {Springer Science and Business Media {LLC}}, + url = {https://doi.org/10.1038/s41586-020-2649-2} +} From 9c554178554b9f3a8e14169a74b3bfbb63c19119 Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Mon, 14 Jul 2025 20:15:21 -0400 Subject: [PATCH 02/16] citation formatting fixed --- core/numpy/intermediate-numpy.ipynb | 2 +- core/numpy/numpy-basics.ipynb | 2 +- core/numpy/numpy-broadcasting.ipynb | 3 ++- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/core/numpy/intermediate-numpy.ipynb b/core/numpy/intermediate-numpy.ipynb index 78100d410..fbd0022d4 100644 --- a/core/numpy/intermediate-numpy.ipynb +++ b/core/numpy/intermediate-numpy.ipynb @@ -652,7 +652,7 @@ "## Resources and references\n", "The [NumPy Users Guide](https://numpy.org/devdocs/user/quickstart.html#less-basic) expands further on some of these topics, as well as suggests various [Tutorials](https://numpy.org/learn/), lectures, and more at this stage.\n", "\n", -"{cite}'harris2020array'" +"{cite:p}`harris2020array`" ] } ], diff --git a/core/numpy/numpy-basics.ipynb b/core/numpy/numpy-basics.ipynb index 121529a80..8f27e04bd 100644 --- a/core/numpy/numpy-basics.ipynb +++ b/core/numpy/numpy-basics.ipynb @@ -1008,7 +1008,7 @@ "## Resources and references\n", "- [NumPy User Guide](http://docs.scipy.org/doc/numpy/user/)\n", "- [SciPy Lecture Notes](https://scipy-lectures.org/)\n", - "- {cite}'harris2020array'" + "- {cite:p}`harris2020array`" ] } ], diff --git a/core/numpy/numpy-broadcasting.ipynb b/core/numpy/numpy-broadcasting.ipynb index 3d636bc02..68abafd1c 100644 --- a/core/numpy/numpy-broadcasting.ipynb +++ b/core/numpy/numpy-broadcasting.ipynb @@ -912,7 +912,8 @@ "metadata": {}, "source": [ "## Resources and references\n", - "* [NumPy Broadcasting Documentation](https://docs.scipy.org/doc/numpy/user/basics.broadcasting.html)" + "* [NumPy Broadcasting Documentation](https://docs.scipy.org/doc/numpy/user/basics.broadcasting.html)\n", +"* {cite:p}`harris2020array`" ] } ], From 7d39cf238584d9828f9bdd7a233d1abb8354100b Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Mon, 14 Jul 2025 20:21:18 -0400 Subject: [PATCH 03/16] updated matplotlib references --- .../annotations-colorbars-layouts.ipynb | 3 ++- .../histograms-piecharts-animation.ipynb | 3 ++- core/matplotlib/matplotlib-basics.ipynb | 3 ++- references.bib | 15 +++++++++++++++ 4 files changed, 21 insertions(+), 3 deletions(-) diff --git a/core/matplotlib/annotations-colorbars-layouts.ipynb b/core/matplotlib/annotations-colorbars-layouts.ipynb index 0fc49775b..64d5b66c7 100644 --- a/core/matplotlib/annotations-colorbars-layouts.ipynb +++ b/core/matplotlib/annotations-colorbars-layouts.ipynb @@ -645,7 +645,8 @@ "- [Plot Types Cheat Sheet](https://lnkd.in/dD5fE8V)\n", "- [Choosing Colormaps in Matplotlib](https://matplotlib.org/stable/tutorials/colors/colormaps.html)\n", "- [Making custom colormaps](https://matplotlib.org/stable/tutorials/colors/colormap-manipulation.html)\n", - "- [Complex figure and subplot composition](https://matplotlib.org/stable/tutorials/provisional/mosaic.html#)" + "- [Complex figure and subplot composition](https://matplotlib.org/stable/tutorials/provisional/mosaic.html#)\n", +"{cite:p}`Hunter:2007`" ] }, { diff --git a/core/matplotlib/histograms-piecharts-animation.ipynb b/core/matplotlib/histograms-piecharts-animation.ipynb index 1414ca84a..7114771a4 100644 --- a/core/matplotlib/histograms-piecharts-animation.ipynb +++ b/core/matplotlib/histograms-piecharts-animation.ipynb @@ -420,7 +420,8 @@ "## Additional Resources\n", "- [Plot Types Cheat Sheet](https://lnkd.in/dD5fE8V)\n", "- [Matplotlib Documentation: Basic Pie Charts](https://matplotlib.org/stable/gallery/pie_and_polar_charts/pie_features.html)\n", - "- [Matplotlib Documentation: Histograms](https://matplotlib.org/stable/gallery/statistics/hist.html)" + "- [Matplotlib Documentation: Histograms](https://matplotlib.org/stable/gallery/statistics/hist.html)\n", +"{cite:p}`Hunter:2007`" ] }, { diff --git a/core/matplotlib/matplotlib-basics.ipynb b/core/matplotlib/matplotlib-basics.ipynb index 8dcbbf813..89b0f2b40 100644 --- a/core/matplotlib/matplotlib-basics.ipynb +++ b/core/matplotlib/matplotlib-basics.ipynb @@ -875,7 +875,8 @@ "The goal of this tutorial is to provide an overview of the use of the Matplotlib library. It covers creating simple line plots, but it is by no means comprehensive. For more information, try looking at the following documentation:\n", "- [Matplotlib documentation](http://matplotlib.org)\n", "- [Matplotlib examples gallery](https://matplotlib.org/stable/gallery/index.html)\n", - "- [GeoCAT examples gallery](https://geocat-examples.readthedocs.io/en/latest/gallery/index.html)" + "- [GeoCAT examples gallery](https://geocat-examples.readthedocs.io/en/latest/gallery/index.html)\n", +"{cite:p}`Hunter:2007`" ] } ], diff --git a/references.bib b/references.bib index 33b432409..0f992fd02 100644 --- a/references.bib +++ b/references.bib @@ -20,3 +20,18 @@ @Article{ harris2020array publisher = {Springer Science and Business Media {LLC}}, url = {https://doi.org/10.1038/s41586-020-2649-2} } + +@Article{Hunter:2007, + 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 +} \ No newline at end of file From 232186d7c7d5e45c5c050e6bee3080fc94f7357d Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Mon, 14 Jul 2025 20:23:26 -0400 Subject: [PATCH 04/16] fixed formatting --- core/matplotlib/annotations-colorbars-layouts.ipynb | 2 +- core/matplotlib/histograms-piecharts-animation.ipynb | 2 +- core/matplotlib/matplotlib-basics.ipynb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/core/matplotlib/annotations-colorbars-layouts.ipynb b/core/matplotlib/annotations-colorbars-layouts.ipynb index 64d5b66c7..7c25a1b59 100644 --- a/core/matplotlib/annotations-colorbars-layouts.ipynb +++ b/core/matplotlib/annotations-colorbars-layouts.ipynb @@ -646,7 +646,7 @@ "- [Choosing Colormaps in Matplotlib](https://matplotlib.org/stable/tutorials/colors/colormaps.html)\n", "- [Making custom colormaps](https://matplotlib.org/stable/tutorials/colors/colormap-manipulation.html)\n", "- [Complex figure and subplot composition](https://matplotlib.org/stable/tutorials/provisional/mosaic.html#)\n", -"{cite:p}`Hunter:2007`" + "- {cite:p}`Hunter:2007`" ] }, { diff --git a/core/matplotlib/histograms-piecharts-animation.ipynb b/core/matplotlib/histograms-piecharts-animation.ipynb index 7114771a4..8b4cc9a81 100644 --- a/core/matplotlib/histograms-piecharts-animation.ipynb +++ b/core/matplotlib/histograms-piecharts-animation.ipynb @@ -421,7 +421,7 @@ "- [Plot Types Cheat Sheet](https://lnkd.in/dD5fE8V)\n", "- [Matplotlib Documentation: Basic Pie Charts](https://matplotlib.org/stable/gallery/pie_and_polar_charts/pie_features.html)\n", "- [Matplotlib Documentation: Histograms](https://matplotlib.org/stable/gallery/statistics/hist.html)\n", -"{cite:p}`Hunter:2007`" + "- {cite:p}`Hunter:2007`" ] }, { diff --git a/core/matplotlib/matplotlib-basics.ipynb b/core/matplotlib/matplotlib-basics.ipynb index 89b0f2b40..9f0307138 100644 --- a/core/matplotlib/matplotlib-basics.ipynb +++ b/core/matplotlib/matplotlib-basics.ipynb @@ -876,7 +876,7 @@ "- [Matplotlib documentation](http://matplotlib.org)\n", "- [Matplotlib examples gallery](https://matplotlib.org/stable/gallery/index.html)\n", "- [GeoCAT examples gallery](https://geocat-examples.readthedocs.io/en/latest/gallery/index.html)\n", -"{cite:p}`Hunter:2007`" + "- {cite:p}`Hunter:2007`" ] } ], From c0cee547c2650e28694725d0302bf299c9b6a81f Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Mon, 14 Jul 2025 20:27:15 -0400 Subject: [PATCH 05/16] updated cartopy references --- core/cartopy/cartopy.ipynb | 3 ++- references.bib | 8 ++++++++ 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/core/cartopy/cartopy.ipynb b/core/cartopy/cartopy.ipynb index ac349eb11..5aa434c1f 100644 --- a/core/cartopy/cartopy.ipynb +++ b/core/cartopy/cartopy.ipynb @@ -724,7 +724,8 @@ "2. [Full list of projections in Cartopy](https://scitools.org.uk/cartopy/docs/latest/reference/crs.html) \n", "3. [Maps with Cartopy (Ryan Abernathey)](https://rabernat.github.io/research_computing_2018/maps-with-cartopy.html)\n", "4. [Map Projections (GeoCAT)](https://geocat-examples.readthedocs.io/en/latest/gallery/index.html#map-projections)\n", - "5. [NCAR xdev Cartopy Tutorial Video](https://www.youtube.com/watch?v=ivmd3RluMiw)" + "5. [NCAR xdev Cartopy Tutorial Video](https://www.youtube.com/watch?v=ivmd3RluMiw)\n", + "6. {cite:p}`Cartopy`" ] } ], diff --git a/references.bib b/references.bib index 0f992fd02..a8fc2b777 100644 --- a/references.bib +++ b/references.bib @@ -34,4 +34,12 @@ @Article{Hunter:2007 publisher = {IEEE COMPUTER SOC}, doi = {10.1109/MCSE.2007.55}, year = 2007 +} + +@manual{Cartopy, +author = {{Met Office}}, +title = {Cartopy: a cartographic python library with a Matplotlib interface}, +year = {2010 - 2025}, +address = {Exeter, Devon }, +url = {https://scitools.org.uk/cartopy} } \ No newline at end of file From ebe71219c719961bc4f9de2338d8336c44840e45 Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Mon, 14 Jul 2025 20:35:46 -0400 Subject: [PATCH 06/16] updated pandas references --- core/pandas/pandas.ipynb | 3 ++- references.bib | 9 +++++++++ 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/core/pandas/pandas.ipynb b/core/pandas/pandas.ipynb index 147640ff3..efc5e39c6 100644 --- a/core/pandas/pandas.ipynb +++ b/core/pandas/pandas.ipynb @@ -1222,7 +1222,8 @@ "## Resources and References\n", "1. [ENSO data used in this example](https://www.ncei.noaa.gov/access/monitoring/enso/sst)\n", "1. [Getting Started with Pandas](https://pandas.pydata.org/docs/getting_started/index.html#getting-started)\n", - "1. [Pandas User Guide](https://pandas.pydata.org/docs/user_guide/index.html#user-guide)" + "1. [Pandas User Guide](https://pandas.pydata.org/docs/user_guide/index.html#user-guide)\n", + "1. {cite:p}`mckinney-proc-scipy-2010`" ] }, { diff --git a/references.bib b/references.bib index a8fc2b777..d478d6b39 100644 --- a/references.bib +++ b/references.bib @@ -42,4 +42,13 @@ @manual{Cartopy year = {2010 - 2025}, address = {Exeter, Devon }, url = {https://scitools.org.uk/cartopy} +} + +@InProceedings{ mckinney-proc-scipy-2010, + author = { Wes McKinney }, + title = { Data Structures for Statistical Computing in Python }, + booktitle = { Proceedings of the 9th Python in Science Conference }, + pages = { 51 - 56 }, + year = { 2010 }, + editor = { St\'efan van der Walt and Jarrod Millman } } \ No newline at end of file From 893122bf03aedc252f6dbe1c10faed7d1b7d6c70 Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Mon, 14 Jul 2025 20:44:47 -0400 Subject: [PATCH 07/16] added xarray references --- core/xarray/computation-masking.ipynb | 3 ++- core/xarray/dask-arrays-xarray.ipynb | 1 + core/xarray/enso-xarray.ipynb | 3 ++- core/xarray/xarray-intro.ipynb | 4 +++- references.bib | 12 ++++++++++++ 5 files changed, 20 insertions(+), 3 deletions(-) diff --git a/core/xarray/computation-masking.ipynb b/core/xarray/computation-masking.ipynb index 4f4bfe70c..670dcd5c8 100644 --- a/core/xarray/computation-masking.ipynb +++ b/core/xarray/computation-masking.ipynb @@ -875,7 +875,8 @@ "- `weighted`: [Useful for weighting data before applying reductions](https://xarray.pydata.org/en/stable/user-guide/computation.html#weighted-array-reductions)\n", "\n", "- [More xarray tutorials and videos](https://docs.xarray.dev/en/stable/getting-started-guide/tutorials-and-videos.html)\n", - "- [Xarray Documentation - Masking with `where()`](https://xarray.pydata.org/en/stable/user-guide/indexing.html#masking-with-where)" + "- [Xarray Documentation - Masking with `where()`](https://xarray.pydata.org/en/stable/user-guide/indexing.html#masking-with-where)\n", + "- {cite:p}`hoyer2017xarray`" ] } ], diff --git a/core/xarray/dask-arrays-xarray.ipynb b/core/xarray/dask-arrays-xarray.ipynb index c4c68b065..e86d3a7e6 100644 --- a/core/xarray/dask-arrays-xarray.ipynb +++ b/core/xarray/dask-arrays-xarray.ipynb @@ -654,6 +654,7 @@ " * [Dask Blog](https://blog.dask.org/)\n", " \n", " * [Xarray Docs](https://xarray.pydata.org/)\n", + " * {cite:p}`hoyer2017xarray`}\n", " \n", "* If you require assistance with a specific issue involving Xarray or Dask, the following resources may be of use:\n", " * Dask tag on StackOverflow, for usage questions\n", diff --git a/core/xarray/enso-xarray.ipynb b/core/xarray/enso-xarray.ipynb index a419fd5f3..0d86fcfd5 100644 --- a/core/xarray/enso-xarray.ipynb +++ b/core/xarray/enso-xarray.ipynb @@ -366,7 +366,8 @@ "\n", "- [Niño 3.4 index](https://climatedataguide.ucar.edu/climate-data/nino-sst-indices-nino-12-3-34-4-oni-and-tni)\n", "- [Matplotlib's `fill_between` method](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.fill_between.html)\n", - "- [Matplotlib's `axhline` method](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.axhline.html) (see also its analogous `axvline` method)" + "- [Matplotlib's `axhline` method](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.axhline.html) (see also its analogous `axvline` method)\n", + "- {cite:p}`hoyer2017xarray`}" ] }, { diff --git a/core/xarray/xarray-intro.ipynb b/core/xarray/xarray-intro.ipynb index aabf7ee0c..6a64a75bb 100644 --- a/core/xarray/xarray-intro.ipynb +++ b/core/xarray/xarray-intro.ipynb @@ -910,7 +910,9 @@ "- [Quick overview](http://xarray.pydata.org/en/stable/getting-started-guide/quick-overview.html#)\n", "- [Example gallery](http://xarray.pydata.org/en/stable/gallery.html)\n", "\n", - "Another resource you may find useful is this [Xarray Tutorial collection](https://xarray-contrib.github.io/xarray-tutorial/), created from content hosted on GitHub." + "Another resource you may find useful is this [Xarray Tutorial collection](https://xarray-contrib.github.io/xarray-tutorial/), created from content hosted on GitHub.", + "\n", + "{cite:p}`hoyer2017xarray`}" ] } ], diff --git a/references.bib b/references.bib index d478d6b39..e60d0379b 100644 --- a/references.bib +++ b/references.bib @@ -51,4 +51,16 @@ @InProceedings{ mckinney-proc-scipy-2010 pages = { 51 - 56 }, year = { 2010 }, editor = { St\'efan van der Walt and Jarrod Millman } +} + +@article{hoyer2017xarray, + title = {xarray: {N-D} labeled arrays and datasets in {Python}}, + author = {Hoyer, S. and J. Hamman}, + journal = {Journal of Open Research Software}, + volume = {5}, + number = {1}, + year = {2017}, + publisher = {Ubiquity Press}, + doi = {10.5334/jors.148}, + url = {https://doi.org/10.5334/jors.148} } \ No newline at end of file From d53436d5aaf082d91e2f35fb726331555cd5bf46 Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Mon, 14 Jul 2025 20:49:32 -0400 Subject: [PATCH 08/16] fixed formatting --- core/xarray/xarray-intro.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/xarray/xarray-intro.ipynb b/core/xarray/xarray-intro.ipynb index 6a64a75bb..19fcabafa 100644 --- a/core/xarray/xarray-intro.ipynb +++ b/core/xarray/xarray-intro.ipynb @@ -910,7 +910,7 @@ "- [Quick overview](http://xarray.pydata.org/en/stable/getting-started-guide/quick-overview.html#)\n", "- [Example gallery](http://xarray.pydata.org/en/stable/gallery.html)\n", "\n", - "Another resource you may find useful is this [Xarray Tutorial collection](https://xarray-contrib.github.io/xarray-tutorial/), created from content hosted on GitHub.", + "Another resource you may find useful is this [Xarray Tutorial collection](https://xarray-contrib.github.io/xarray-tutorial/), created from content hosted on GitHub.\n", "\n", "{cite:p}`hoyer2017xarray`}" ] From 9a45ed36869d4414253470b8170ace77043ee6e6 Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Fri, 18 Jul 2025 18:12:20 -0400 Subject: [PATCH 09/16] remove unnecessary file --- core/bibliography.md | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 core/bibliography.md diff --git a/core/bibliography.md b/core/bibliography.md deleted file mode 100644 index c46bdad75..000000000 --- a/core/bibliography.md +++ /dev/null @@ -1,3 +0,0 @@ -# References -```{bibliography} -``` \ No newline at end of file From 01a2376aa2b622b16dc94dd95a5d5ab1569d6970 Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Tue, 22 Jul 2025 15:26:48 -0400 Subject: [PATCH 10/16] updated reference list --- references.bib | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/references.bib b/references.bib index e60d0379b..4baf790dd 100644 --- a/references.bib +++ b/references.bib @@ -63,4 +63,15 @@ @article{hoyer2017xarray publisher = {Ubiquity Press}, doi = {10.5334/jors.148}, url = {https://doi.org/10.5334/jors.148} -} \ No newline at end of file +} + +@software{reback2020pandas, + author = {{The 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} +} From 786953f9d1848ea5866a1446ec1f6d6fc26517c1 Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Tue, 22 Jul 2025 15:28:19 -0400 Subject: [PATCH 11/16] updated cartopy files --- core/cartopy.md | 2 +- core/cartopy/cartopy.ipynb | 9 ++++----- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/core/cartopy.md b/core/cartopy.md index 03a47555a..6abf7da96 100644 --- a/core/cartopy.md +++ b/core/cartopy.md @@ -1,6 +1,6 @@ # Cartopy -This section contains tutorials on plotting maps with [Cartopy](https://scitools.org.uk/cartopy/docs/latest/); it is cross-referenced with tutorials on [Xarray](xarray) and [Matplotlib](matplotlib). +This section contains tutorials on plotting maps with [Cartopy](https://scitools.org.uk/cartopy/docs/latest/) {cite:p}`Cartopy`; it is cross-referenced with tutorials on [Xarray](xarray) and [Matplotlib](matplotlib). --- diff --git a/core/cartopy/cartopy.ipynb b/core/cartopy/cartopy.ipynb index 5aa434c1f..3f65b71b3 100644 --- a/core/cartopy/cartopy.ipynb +++ b/core/cartopy/cartopy.ipynb @@ -30,7 +30,7 @@ "2. Exploring some of Cartopy's map projections\n", "3. Creating regional maps\n", "\n", - "This tutorial will lead you through some basics of creating maps with specified projections using Cartopy, and adding geographical features (like coastlines and borders) to those maps.\n", + "This tutorial will lead you through some basics of creating maps with specified projections using Cartopy {cite:p}`Cartopy`, and adding geographical features (like coastlines and borders) to those maps.\n", "\n", "Plotting data on map projections will be covered in later tutorials." ] @@ -43,7 +43,7 @@ "\n", "| Concepts | Importance | Notes |\n", "| --- | --- | --- |\n", - "| [Matplotlib](../matplotlib) | Necessary | |\n", + "| [Matplotlib](../matplotlib) | Necessary | {cite:t}`Hunter:2007` |\n", "\n", "- **Time to learn**: 30 minutes" ] @@ -718,14 +718,13 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Resources and References\n", + "## Additional Resources\n", "\n", "1. [Cartopy Documentation](https://scitools.org.uk/cartopy/docs/latest/)\n", "2. [Full list of projections in Cartopy](https://scitools.org.uk/cartopy/docs/latest/reference/crs.html) \n", "3. [Maps with Cartopy (Ryan Abernathey)](https://rabernat.github.io/research_computing_2018/maps-with-cartopy.html)\n", "4. [Map Projections (GeoCAT)](https://geocat-examples.readthedocs.io/en/latest/gallery/index.html#map-projections)\n", - "5. [NCAR xdev Cartopy Tutorial Video](https://www.youtube.com/watch?v=ivmd3RluMiw)\n", - "6. {cite:p}`Cartopy`" + "5. [NCAR xdev Cartopy Tutorial Video](https://www.youtube.com/watch?v=ivmd3RluMiw)\n" ] } ], From 1cc113df96c490ef9610a94aef6207dcc9adbbdd Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Tue, 22 Jul 2025 15:29:57 -0400 Subject: [PATCH 12/16] updated matplotlib files --- core/matplotlib.md | 2 +- core/matplotlib/annotations-colorbars-layouts.ipynb | 13 ++++++------- .../matplotlib/histograms-piecharts-animation.ipynb | 7 +++---- core/matplotlib/matplotlib-basics.ipynb | 9 ++++----- 4 files changed, 14 insertions(+), 17 deletions(-) diff --git a/core/matplotlib.md b/core/matplotlib.md index 184519f98..7f27f31fa 100644 --- a/core/matplotlib.md +++ b/core/matplotlib.md @@ -2,7 +2,7 @@ ![Matplotlib logo](https://matplotlib.org/stable/_images/sphx_glr_logos2_003.png) -[Matplotlib](https://matplotlib.org) is the go-to library for plotting within Python. Numerous packages and libraries build off of Matplotlib, making it the de facto standard Python plotting package. If you were to learn a single plotting tool to keep in your toolbox, this is it. +[Matplotlib](https://matplotlib.org) {cite:p}`Hunter:2007` is the go-to library for plotting within Python. Numerous packages and libraries build off of Matplotlib, making it the de facto standard Python plotting package. If you were to learn a single plotting tool to keep in your toolbox, this is it. ## Why Matplotlib? diff --git a/core/matplotlib/annotations-colorbars-layouts.ipynb b/core/matplotlib/annotations-colorbars-layouts.ipynb index 7c25a1b59..515f83814 100644 --- a/core/matplotlib/annotations-colorbars-layouts.ipynb +++ b/core/matplotlib/annotations-colorbars-layouts.ipynb @@ -31,10 +31,10 @@ "## Prerequisites\n", "\n", "\n", - "| Concepts | Importance |\n", - "| --- | --- |\n", - "| [NumPy Basics](../numpy/numpy-basics) | Necessary |\n", - "| [Matplotlib Basics](matplotlib-basics) | Necessary |\n", + "| Concepts | Importance | Notes |\n", + "| --- | --- | --- |\n", + "| [NumPy Basics](../numpy/numpy-basics) | Necessary | {cite:t}`harris2020array` |\n", + "| [Matplotlib Basics](matplotlib-basics) | Necessary | {cite:t}`Hunter:2007` |\n", "\n", "- **Time to learn**: *30-40 minutes*" ] @@ -635,7 +635,7 @@ "* You can create your own colormaps with Matplotlib\n", "* Various subplots and corresponding `Axes` objects in a figure can share colorbars\n", " \n", - "## Resources and references\n", + "## Additional Resources\n", "- [Matplotlib text documentation](https://matplotlib.org/stable/api/text_api.html#matplotlib.text.Text.set_math_fontfamily)\n", "- [Matplotlib annotation documentation](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.annotate.html)\n", "- [Matplotlib's annotation examples](https://matplotlib.org/stable/tutorials/text/annotations.html)\n", @@ -645,8 +645,7 @@ "- [Plot Types Cheat Sheet](https://lnkd.in/dD5fE8V)\n", "- [Choosing Colormaps in Matplotlib](https://matplotlib.org/stable/tutorials/colors/colormaps.html)\n", "- [Making custom colormaps](https://matplotlib.org/stable/tutorials/colors/colormap-manipulation.html)\n", - "- [Complex figure and subplot composition](https://matplotlib.org/stable/tutorials/provisional/mosaic.html#)\n", - "- {cite:p}`Hunter:2007`" + "- [Complex figure and subplot composition](https://matplotlib.org/stable/tutorials/provisional/mosaic.html#)\n" ] }, { diff --git a/core/matplotlib/histograms-piecharts-animation.ipynb b/core/matplotlib/histograms-piecharts-animation.ipynb index 8b4cc9a81..6b94973a0 100644 --- a/core/matplotlib/histograms-piecharts-animation.ipynb +++ b/core/matplotlib/histograms-piecharts-animation.ipynb @@ -33,8 +33,8 @@ "## Prerequisites\n", "| Concepts | Importance | Notes |\n", "| --- | --- | --- |\n", - "| [NumPy Basics](../numpy/numpy-basics) | Necessary | |\n", - "| [Matplotlib Basics](matplotlib-basics) | Necessary | |\n", + "| [NumPy Basics](../numpy/numpy-basics) | Necessary | {cite:t}`harris2020array` |\n", + "| [Matplotlib Basics](matplotlib-basics) | Necessary | {cite:t}`Hunter:2007` |\n", "\n", "* **Time to Learn**: 30 minutes" ] @@ -420,8 +420,7 @@ "## Additional Resources\n", "- [Plot Types Cheat Sheet](https://lnkd.in/dD5fE8V)\n", "- [Matplotlib Documentation: Basic Pie Charts](https://matplotlib.org/stable/gallery/pie_and_polar_charts/pie_features.html)\n", - "- [Matplotlib Documentation: Histograms](https://matplotlib.org/stable/gallery/statistics/hist.html)\n", - "- {cite:p}`Hunter:2007`" + "- [Matplotlib Documentation: Histograms](https://matplotlib.org/stable/gallery/statistics/hist.html)\n" ] }, { diff --git a/core/matplotlib/matplotlib-basics.ipynb b/core/matplotlib/matplotlib-basics.ipynb index 9f0307138..053a3b3c2 100644 --- a/core/matplotlib/matplotlib-basics.ipynb +++ b/core/matplotlib/matplotlib-basics.ipynb @@ -15,7 +15,7 @@ "source": [ "---\n", "## Overview\n", - "We will cover the basics of using the Matplotlib library to create plots in Python, including a few different plots available within the library. This page is laid out as follows:\n", + "We will cover the basics of using the Matplotlib {cite:p}`Hunter:2007` library to create plots in Python, including a few different plots available within the library. This page is laid out as follows:\n", "\n", "1. Why Matplotlib?\n", "1. Figure and axes\n", @@ -37,7 +37,7 @@ "## Prerequisites\n", "| Concepts | Importance | Notes |\n", "| --- | --- | --- |\n", - "| [NumPy Basics](../numpy/numpy-basics) | Necessary | |\n", + "| [NumPy Basics](../numpy/numpy-basics) | Necessary | {cite:t}`harris2020array` |\n", "| MATLAB plotting experience | Helpful | |\n", "\n", "* **Time to Learn**: 30 minutes" @@ -870,13 +870,12 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Resources and References\n", + "## Additional Resources\n", "\n", "The goal of this tutorial is to provide an overview of the use of the Matplotlib library. It covers creating simple line plots, but it is by no means comprehensive. For more information, try looking at the following documentation:\n", "- [Matplotlib documentation](http://matplotlib.org)\n", "- [Matplotlib examples gallery](https://matplotlib.org/stable/gallery/index.html)\n", - "- [GeoCAT examples gallery](https://geocat-examples.readthedocs.io/en/latest/gallery/index.html)\n", - "- {cite:p}`Hunter:2007`" + "- [GeoCAT examples gallery](https://geocat-examples.readthedocs.io/en/latest/gallery/index.html)\n" ] } ], From 07e248bf676497acb68c26af8ff8f294cc9b9ba5 Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Tue, 22 Jul 2025 15:31:19 -0400 Subject: [PATCH 13/16] updated numpy files --- core/numpy.md | 2 +- core/numpy/intermediate-numpy.ipynb | 7 +++---- core/numpy/numpy-basics.ipynb | 7 +++---- core/numpy/numpy-broadcasting.ipynb | 7 +++---- 4 files changed, 10 insertions(+), 13 deletions(-) diff --git a/core/numpy.md b/core/numpy.md index eb4cecb06..fa8d37b1a 100644 --- a/core/numpy.md +++ b/core/numpy.md @@ -5,7 +5,7 @@ :width: 250 ::: -This section contains tutorials on array computing with [NumPy](https://numpy.org). +This section contains tutorials on array computing with [NumPy](https://numpy.org) {cite:p}`harris2020array`. --- diff --git a/core/numpy/intermediate-numpy.ipynb b/core/numpy/intermediate-numpy.ipynb index fbd0022d4..1ef29dd86 100644 --- a/core/numpy/intermediate-numpy.ipynb +++ b/core/numpy/intermediate-numpy.ipynb @@ -29,7 +29,7 @@ "\n", "| Concepts | Importance | Notes |\n", "| --- | --- | --- |\n", - "| [NumPy Basics](numpy-basics) | Necessary | |\n", + "| [NumPy Basics](numpy-basics) | Necessary | {cite:t}`harris2020array` |\n", "\n", "* **Time to learn**: 20 minutes\n", "---" @@ -649,10 +649,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Resources and references\n", + "## Additional Resources\n", "The [NumPy Users Guide](https://numpy.org/devdocs/user/quickstart.html#less-basic) expands further on some of these topics, as well as suggests various [Tutorials](https://numpy.org/learn/), lectures, and more at this stage.\n", -"\n", -"{cite:p}`harris2020array`" +"\n" ] } ], diff --git a/core/numpy/numpy-basics.ipynb b/core/numpy/numpy-basics.ipynb index 8f27e04bd..ac39c8260 100644 --- a/core/numpy/numpy-basics.ipynb +++ b/core/numpy/numpy-basics.ipynb @@ -16,7 +16,7 @@ "metadata": {}, "source": [ "## Overview\n", - "Welcome to your first Python library - NumPy! NumPy is the fundamental package for numerical operations with Python. It contains among other things:\n", + "Welcome to your first Python library - NumPy! NumPy is the fundamental package for numerical operations with Python {cite:p}`harris2020array`. It contains among other things:\n", "\n", "- a powerful N-dimensional array object\n", "- sophisticated (broadcasting) functions\n", @@ -1005,10 +1005,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Resources and references\n", + "## Additional Resources\n", "- [NumPy User Guide](http://docs.scipy.org/doc/numpy/user/)\n", - "- [SciPy Lecture Notes](https://scipy-lectures.org/)\n", - "- {cite:p}`harris2020array`" + "- [SciPy Lecture Notes](https://scipy-lectures.org/)\n" ] } ], diff --git a/core/numpy/numpy-broadcasting.ipynb b/core/numpy/numpy-broadcasting.ipynb index 68abafd1c..5604b6f9b 100644 --- a/core/numpy/numpy-broadcasting.ipynb +++ b/core/numpy/numpy-broadcasting.ipynb @@ -29,7 +29,7 @@ "\n", "| Concepts | Importance | Notes |\n", "| --- | --- | --- |\n", - "| [NumPy Basics](numpy-basics) | Necessary | |\n", + "| [NumPy Basics](numpy-basics) | Necessary | {cite:t}`harris2020array` |\n", "| [Intermediate NumPy](intermediate-numpy) | Helpful | |\n", "| [Conceptual guide to broadcasting](https://numpy.org/doc/stable/user/theory.broadcasting.html#array-broadcasting-in-numpy) | Helpful | |\n", "\n", @@ -911,9 +911,8 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Resources and references\n", - "* [NumPy Broadcasting Documentation](https://docs.scipy.org/doc/numpy/user/basics.broadcasting.html)\n", -"* {cite:p}`harris2020array`" + "## Additional Resources\n", + "* [NumPy Broadcasting Documentation](https://docs.scipy.org/doc/numpy/user/basics.broadcasting.html)\n" ] } ], From 093b1ac17ed2d5bbfbf0c59f3c8c4d01682a672b Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Tue, 22 Jul 2025 15:31:58 -0400 Subject: [PATCH 14/16] updated pandas files --- core/pandas.md | 2 +- core/pandas/pandas.ipynb | 9 ++++----- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/core/pandas.md b/core/pandas.md index 680210b1b..43022df39 100644 --- a/core/pandas.md +++ b/core/pandas.md @@ -8,7 +8,7 @@ This section will contain tutorials on using [pandas](https://pandas.pydata.org) --- -From the [official documentation](https://pandas.pydata.org/), Pandas "is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language." +From the [official documentation](https://pandas.pydata.org/), Pandas {cite:p}`reback2020pandas` "is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language." Pandas is a very powerful library for working with tabular data (e.g., spreadsheets, comma-separated-value files, or database printouts; all of these are quite common for geoscientific data). It allows us to use labels for our data; this, in turn, allows us to write expressive and robust code to manipulate the data. diff --git a/core/pandas/pandas.ipynb b/core/pandas/pandas.ipynb index efc5e39c6..9005ad47f 100644 --- a/core/pandas/pandas.ipynb +++ b/core/pandas/pandas.ipynb @@ -18,7 +18,7 @@ "metadata": {}, "source": [ "## Overview\n", - "1. Introduction to pandas data structures\n", + "1. Introduction to pandas {cite:p}`reback2020pandas` data structures\n", "1. How to slice and dice pandas dataframes and dataseries\n", "1. How to use pandas for exploratory data analysis\n", "\n", @@ -27,7 +27,7 @@ "| Concepts | Importance | Notes |\n", "| --- | --- | --- |\n", "| [Python Quickstart](../../foundations/quickstart) | Necessary | Intro to `dict` |\n", - "| [Numpy Basics](../numpy/numpy-basics) | Necessary | |\n", + "| [Numpy Basics](../numpy/numpy-basics) | Necessary | {cite:t}`harris2020array` |\n", "\n", "* **Time to learn**: 60 minutes" ] @@ -1219,11 +1219,10 @@ "### What's Next?\n", "In the next notebook, we will look more into using pandas for more in-depth data analysis.\n", "\n", - "## Resources and References\n", + "## Additional Resources\n", "1. [ENSO data used in this example](https://www.ncei.noaa.gov/access/monitoring/enso/sst)\n", "1. [Getting Started with Pandas](https://pandas.pydata.org/docs/getting_started/index.html#getting-started)\n", - "1. [Pandas User Guide](https://pandas.pydata.org/docs/user_guide/index.html#user-guide)\n", - "1. {cite:p}`mckinney-proc-scipy-2010`" + "1. [Pandas User Guide](https://pandas.pydata.org/docs/user_guide/index.html#user-guide)\n" ] }, { From 909db63d4ecd37e82cbfebbf09bd6a5f794c91dc Mon Sep 17 00:00:00 2001 From: Brittany Freeman Date: Tue, 22 Jul 2025 15:33:02 -0400 Subject: [PATCH 15/16] updated xarray files --- core/xarray.md | 2 +- core/xarray/computation-masking.ipynb | 7 +++---- core/xarray/dask-arrays-xarray.ipynb | 5 ++--- core/xarray/enso-xarray.ipynb | 7 +++---- core/xarray/xarray-intro.ipynb | 11 +++++------ 5 files changed, 14 insertions(+), 18 deletions(-) diff --git a/core/xarray.md b/core/xarray.md index 7d37a20bd..90cab47bf 100644 --- a/core/xarray.md +++ b/core/xarray.md @@ -2,7 +2,7 @@ ![xarray Logo](https://docs.xarray.dev/en/stable/_static/Xarray_Logo_RGB_Final.svg "xarray Logo") -This section contains tutorials on using [Xarray][xarray home]. Xarray is used widely in the geosciences and beyond for analysis of gridded N-dimensional datasets. +This section contains tutorials on using [Xarray][xarray home]. Xarray {cite:p}`hoyer2017xarray` is used widely in the geosciences and beyond for analysis of gridded N-dimensional datasets. --- diff --git a/core/xarray/computation-masking.ipynb b/core/xarray/computation-masking.ipynb index 670dcd5c8..be27ec45f 100644 --- a/core/xarray/computation-masking.ipynb +++ b/core/xarray/computation-masking.ipynb @@ -49,7 +49,7 @@ "\n", "| Concepts | Importance | Notes |\n", "| --- | --- | --- |\n", - "| [Introduction to Xarray](xarray-intro) | Necessary | |\n", + "| [Introduction to Xarray](xarray-intro) | Necessary | {cite:t}`hoyer2017xarray` |\n", "\n", "\n", "- **Time to learn**: 60 minutes" @@ -865,7 +865,7 @@ "id": "374de3a3-807a-47be-9014-e1af98909456", "metadata": {}, "source": [ - "## Resources and References\n", + "## Additional Resources\n", "\n", "- `groupby`: [Useful for binning/grouping data and applying reductions and/or transformations on those groups](https://xarray.pydata.org/en/stable/user-guide/groupby.html)\n", "- `resample`: [Functionality similar to groupby, specialized for time dimensions. Can be used for temporal upsampling and downsampling](https://xarray.pydata.org/en/stable/user-guide/time-series.html#resampling-and-grouped-operations)\n", @@ -875,8 +875,7 @@ "- `weighted`: [Useful for weighting data before applying reductions](https://xarray.pydata.org/en/stable/user-guide/computation.html#weighted-array-reductions)\n", "\n", "- [More xarray tutorials and videos](https://docs.xarray.dev/en/stable/getting-started-guide/tutorials-and-videos.html)\n", - "- [Xarray Documentation - Masking with `where()`](https://xarray.pydata.org/en/stable/user-guide/indexing.html#masking-with-where)\n", - "- {cite:p}`hoyer2017xarray`" + "- [Xarray Documentation - Masking with `where()`](https://xarray.pydata.org/en/stable/user-guide/indexing.html#masking-with-where)\n" ] } ], diff --git a/core/xarray/dask-arrays-xarray.ipynb b/core/xarray/dask-arrays-xarray.ipynb index e86d3a7e6..af4749543 100644 --- a/core/xarray/dask-arrays-xarray.ipynb +++ b/core/xarray/dask-arrays-xarray.ipynb @@ -32,7 +32,7 @@ "\n", "| Concepts | Importance | Notes |\n", "| --- | --- | --- |\n", - "| [Introduction to NumPy](../numpy/numpy-basics) | Necessary | Familiarity with Data Arrays |\n", + "| [Introduction to NumPy](../numpy/numpy-basics) | Necessary | Familiarity with Data Arrays; {cite:t}`hoyer2017xarray` |\n", "| [Introduction to Xarray](xarray-intro) | Necessary | Familiarity with Xarray Data Structures |\n", "\n", "\n", @@ -645,7 +645,7 @@ "id": "c282d878-a11f-41a2-9737-caee406ad5c3", "metadata": {}, "source": [ - "## Resources and references\n", + "## Additional Resources\n", "\n", "* To find specific reference information about Dask and Xarray, see the official documentation pages listed below:\n", " * [Dask Docs](https://dask.org/)\n", @@ -654,7 +654,6 @@ " * [Dask Blog](https://blog.dask.org/)\n", " \n", " * [Xarray Docs](https://xarray.pydata.org/)\n", - " * {cite:p}`hoyer2017xarray`}\n", " \n", "* If you require assistance with a specific issue involving Xarray or Dask, the following resources may be of use:\n", " * Dask tag on StackOverflow, for usage questions\n", diff --git a/core/xarray/enso-xarray.ipynb b/core/xarray/enso-xarray.ipynb index 0d86fcfd5..8a66898c3 100644 --- a/core/xarray/enso-xarray.ipynb +++ b/core/xarray/enso-xarray.ipynb @@ -41,7 +41,7 @@ "\n", "| Concepts | Importance | Notes |\n", "| --- | --- | --- |\n", - "| [Introduction to Xarray](xarray-intro) | Necessary | |\n", + "| [Introduction to Xarray](xarray-intro) | Necessary | {cite:t}`hoyer2017xarray` |\n", "| [Computation and Masking](computation-masking) | Necessary | |\n", "\n", "\n", @@ -362,12 +362,11 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Resources and References\n", + "## Additional Resources\n", "\n", "- [Niño 3.4 index](https://climatedataguide.ucar.edu/climate-data/nino-sst-indices-nino-12-3-34-4-oni-and-tni)\n", "- [Matplotlib's `fill_between` method](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.fill_between.html)\n", - "- [Matplotlib's `axhline` method](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.axhline.html) (see also its analogous `axvline` method)\n", - "- {cite:p}`hoyer2017xarray`}" + "- [Matplotlib's `axhline` method](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.axhline.html) (see also its analogous `axvline` method)\n" ] }, { diff --git a/core/xarray/xarray-intro.ipynb b/core/xarray/xarray-intro.ipynb index 19fcabafa..591907bc9 100644 --- a/core/xarray/xarray-intro.ipynb +++ b/core/xarray/xarray-intro.ipynb @@ -22,7 +22,7 @@ "source": [ "## Overview\n", "\n", - "The examples in this tutorial focus on the fundamentals of working with gridded, labeled data using Xarray. Xarray works by introducing additional abstractions into otherwise ordinary data arrays. In this tutorial, we demonstrate the usefulness of these abstractions. The examples in this tutorial explain how the proper usage of Xarray abstractions generally leads to simpler, more robust code.\n", + "The examples in this tutorial focus on the fundamentals of working with gridded, labeled data using Xarray {cite:p}`hoyer2017xarray`. Xarray works by introducing additional abstractions into otherwise ordinary data arrays. In this tutorial, we demonstrate the usefulness of these abstractions. The examples in this tutorial explain how the proper usage of Xarray abstractions generally leads to simpler, more robust code.\n", "\n", "The following topics will be covered in this tutorial:\n", "\n", @@ -43,10 +43,10 @@ "\n", "| Concepts | Importance | Notes |\n", "| --- | --- | --- |\n", - "| [NumPy Basics](../numpy/numpy-basics) | Necessary | |\n", + "| [NumPy Basics](../numpy/numpy-basics) | Necessary | {cite:t}`harris2020array` |\n", "| [Intermediate NumPy](../numpy/intermediate-numpy) | Helpful | Familiarity with indexing and slicing arrays |\n", "| [NumPy Broadcasting](../numpy/numpy-broadcasting) | Helpful | Familiarity with array arithmetic and broadcasting |\n", - "| [Introduction to Pandas](../pandas/pandas) | Helpful | Familiarity with labeled data |\n", + "| [Introduction to Pandas](../pandas/pandas) | Helpful | Familiarity with labeled data; {cite:t}`reback2020pandas` |\n", "| [Datetime](../datetime/datetime) | Helpful | Familiarity with time formats and the `timedelta` object |\n", "| [Understanding of NetCDF](some-link-to-external-resource) | Helpful | Familiarity with metadata structure |\n", "\n", @@ -901,7 +901,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Resources and references\n", + "## Additional Resources\n", "\n", "This tutorial contains content adapted from the material in [Unidata's Python Training](https://unidata.github.io/python-training/workshop/XArray/xarray-and-cf/).\n", "\n", @@ -911,8 +911,7 @@ "- [Example gallery](http://xarray.pydata.org/en/stable/gallery.html)\n", "\n", "Another resource you may find useful is this [Xarray Tutorial collection](https://xarray-contrib.github.io/xarray-tutorial/), created from content hosted on GitHub.\n", - "\n", - "{cite:p}`hoyer2017xarray`}" + "\n" ] } ], From 6264dffb10909613c1b396bdb72155428e081beb Mon Sep 17 00:00:00 2001 From: bl-freeman <105937999+bl-freeman@users.noreply.github.com> Date: Wed, 23 Jul 2025 11:05:05 -0400 Subject: [PATCH 16/16] Update core/xarray/xarray-intro.ipynb Declutter table by removing citation Co-authored-by: Brian Rose --- core/xarray/xarray-intro.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/xarray/xarray-intro.ipynb b/core/xarray/xarray-intro.ipynb index 591907bc9..dca1d5e80 100644 --- a/core/xarray/xarray-intro.ipynb +++ b/core/xarray/xarray-intro.ipynb @@ -46,7 +46,7 @@ "| [NumPy Basics](../numpy/numpy-basics) | Necessary | {cite:t}`harris2020array` |\n", "| [Intermediate NumPy](../numpy/intermediate-numpy) | Helpful | Familiarity with indexing and slicing arrays |\n", "| [NumPy Broadcasting](../numpy/numpy-broadcasting) | Helpful | Familiarity with array arithmetic and broadcasting |\n", - "| [Introduction to Pandas](../pandas/pandas) | Helpful | Familiarity with labeled data; {cite:t}`reback2020pandas` |\n", + "| [Introduction to Pandas](../pandas/pandas) | Helpful | Familiarity with labeled data |\n", "| [Datetime](../datetime/datetime) | Helpful | Familiarity with time formats and the `timedelta` object |\n", "| [Understanding of NetCDF](some-link-to-external-resource) | Helpful | Familiarity with metadata structure |\n", "\n",