Merge pull request #36 from brian-rose/references

Add proper citations and bibliography

Author: brian-rose

_config.yml

@@ -24,10 +24,14 @@ parse:
     - smartquotes
     - substitution
 
+bibtex_bibfiles:
+    - references.bib
+
 sphinx:
   config:
     linkcheck_ignore: ["https://doi.org/*"] # don't run link checker on DOI links since they are immutable
     nb_execution_raise_on_error: true # raise exception in build if there are notebook errors (this flag is ignored if building on binder)
+    bibtex_reference_style: author_year
     html_favicon: notebooks/images/icons/favicon.ico
     html_last_updated_fmt: "%-d %B %Y"
     html_theme: sphinx_pythia_theme

_toc.yml

@@ -10,3 +10,6 @@ parts:
   - caption: Example workflows
     chapters:
       - file: notebooks/example-workflows/key-figures.ipynb
+  - caption: Appendix
+    chapters:
+      - file: references

notebooks/example-workflows/key-figures.ipynb

@@ -26,7 +26,7 @@
    "metadata": {},
    "source": [
     "## Overview\n",
-    "This notebook demonstrates how one might use the NCAR Community Earth System Model (CESM) Large Ensemble (LENS) data hosted on AWS S3. The notebook shows how to reproduce figures 2 and 4 from the [Kay et al. (2015) paper](https://doi.org/10.1175/BAMS-D-13-00255.1) describing the CESM LENS dataset.\n",
+    "This notebook demonstrates how one might use the NCAR Community Earth System Model (CESM) Large Ensemble (LENS) data hosted on AWS S3. The notebook shows how to reproduce figures 2 and 4 from the [Kay et al. (2015) paper](https://doi.org/10.1175/BAMS-D-13-00255.1) describing the CESM LENS dataset {cite:p}`Kay:2015a`.\n",
     "\n",
     "This resource is intended to be helpful for people not familiar with elements of the [Pangeo](https://pangeo.io/) framework including Jupyter Notebooks, [Xarray](https://docs.xarray.dev/en/stable/), and [Zarr](https://zarr.readthedocs.io/en/stable/) data format, or with the original paper, so it includes additional explanation."
    ]
@@ -488,7 +488,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Get observations for Figure 2 (HadCRUT4; Morice et al. 2012)"
+    "### Get observations for Figure 2 (HadCRUT4)\n",
+    "\n",
+    "The HadCRUT4 temperature dataset is described by {cite:t}`Morice:2012a`."
    ]
   },
   {
@@ -756,14 +758,18 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This is observational time series data for comparison with ensemble average (NASA GISS Surface Temperature Analysis, https://data.giss.nasa.gov/gistemp/)."
+    "This is observational time series data for comparison with ensemble average. Here we are using the [GISS Surface Temperature Analysis (GISTEMP v4)](https://data.giss.nasa.gov/gistemp/) from NASA's Goddard Institute of Space Studies {cite:p}`Lenssen:2019a`."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<div class=\"alert alert-info\"><b>NOTE: </b>We will point to Project Pythia's <a href=\"https://jetstream-cloud.org\"> Jetstream2</a> object-store copy of the original time series dataset, in Zarr format.</div>"
+    "```{note}\n",
+    "We will point to Project Pythia's [Jetstream2](https://jetstream-cloud.org) object-store copy of the original time series dataset, in Zarr format. \n",
+    "\n",
+    "The dataset was obtained from [NASA's GISTEMP website](https://data.giss.nasa.gov/gistemp/) in May 2024. \n",
+    "```"
    ]
   },
   {
@@ -1019,8 +1025,21 @@
    "metadata": {},
    "source": [
     "## Resources and references\n",
-    "[Original notebook in the Pangeo Gallery](https://gallery.pangeo.io/repos/NCAR/cesm-lens-aws/notebooks/kay-et-al-2015.v3.html)"
+    "\n",
+    "1. [Original notebook in the (no longer maintained) Pangeo Gallery](https://gallery.pangeo.io/repos/NCAR/cesm-lens-aws/notebooks/EnhancedIntakeCatalogDemo.html)\n",
+    "2. [Kay et al. (2015): _The Community Earth System Model (CESM) Large Ensemble Project_, BAMS, doi:10.1175/BAMS-D-13-00255.1](https://doi.org/10.1175/BAMS-D-13-00255.1)\n",
+    "3. [CESM LENS Data Sets on AWS](https://doi.org/10.26024/wt24-5j82)\n",
+    "4. [Morice et al. (2012) paper on HadCRUT4 dataset](https://doi.org/10.1029/2011JD017187)\n",
+    "5. [NASS GISTEMP dataset](https://data.giss.nasa.gov/gistemp/)\n",
+    "6. [Lenssen et al. (2019) paper on latest GISTEMP methods](https://doi.org/10.1029/2018JD029522)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

notebooks/foundations/enhanced-catalog.ipynb

@@ -26,7 +26,7 @@
    "metadata": {},
    "source": [
     "## Overview\n",
-    "This notebook compares one [Intake-ESM](https://intake-esm.readthedocs.io/en/stable/) catalog with an enhanced version that includes additional attributes. Both catalogs are an inventory of the NCAR Community Earth System Model (CESM) Large Ensemble (LENS) data hosted on AWS S3 ([doi:10.26024/wt24-5j82](https://doi.org/10.26024/wt24-5j82))."
+    "This notebook compares one [Intake-ESM](https://intake-esm.readthedocs.io/en/stable/) catalog with an enhanced version that includes additional attributes. Both catalogs are an inventory of the [NCAR Community Earth System Model (CESM) Large Ensemble (LENS) data hosted on AWS S3](https://doi.org/10.26024/wt24-5j82)."
    ]
   },
   {
@@ -522,18 +522,27 @@
     "In this notebook, we used Intake-ESM to explore a catalog of CESM LENS data. We then worked through some helpful features of the enhanced catalog.\n",
     "\n",
     "### What's next?\n",
-    "We will use this data to recreate some figures from a [paper published in BAMS that describes the CESM LENS project](https://journals.ametsoc.org/view/journals/bams/96/8/bams-d-13-00255.1.xml)."
+    "We will use this data to recreate some figures from a paper published in [BAMS](https://www.ametsoc.org/index.cfm/ams/publications/bulletin-of-the-american-meteorological-society-bams/) that describes the CESM LENS project: {cite:t}`Kay:2015a`"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "## Resources and references\n",
-    "[Original notebook in the Pangeo Gallery](https://gallery.pangeo.io/repos/NCAR/cesm-lens-aws/notebooks/EnhancedIntakeCatalogDemo.html)\n",
     "\n",
-    "[Intake-esm documentation](https://intake-esm.readthedocs.io)"
+    "1. [Original notebook in the (no longer maintained) Pangeo Gallery](https://gallery.pangeo.io/repos/NCAR/cesm-lens-aws/notebooks/EnhancedIntakeCatalogDemo.html)\n",
+    "2. [Intake-esm documentation](https://intake-esm.readthedocs.io)\n",
+    "3. [Kay et al. (2015): _The Community Earth System Model (CESM) Large Ensemble Project_, BAMS, doi:10.1175/BAMS-D-13-00255.1](https://doi.org/10.1175/BAMS-D-13-00255.1)\n",
+    "4. [Community Earth System Model Large Ensemble (CESM LENS) Data Sets on AWS](https://doi.org/10.26024/wt24-5j82)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -552,7 +561,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.15"
+   "version": "3.11.9"
   },
   "nbdime-conflicts": {
    "local_diff": [

references.bib

@@ -0,0 +1,45 @@
+%% This BibTeX bibliography file was created using BibDesk.
+%% https://bibdesk.sourceforge.io/
+
+%% Created for Rose, Brian at 2024-06-03 11:56:53 -0400 
+
+
+%% Saved with string encoding Unicode (UTF-8) 
+
+
+
+@article{Lenssen:2019a,
+	author = {Lenssen, N. and Schmidt, G. and Hansen, J. and Menne, M. and Persin, A. and Ruedy, R. and Zyss, D.},
+	date-added = {2024-06-03 09:15:01 -0400},
+	date-modified = {2024-06-03 09:15:01 -0400},
+	doi = {10.1029/2018JD029522},
+	journal = {Journal of Geophysical Research: Atmospheres},
+	number = {12},
+	pages = {6307--6326},
+	title = {Improvements in the GISTEMP uncertainty model},
+	volume = {124},
+	year = {2019},
+	bdsk-url-1 = {https://doi.org/10.1029/2018JD029522}}
+
+@article{Morice:2012a,
+	author = {Colin P. Morice and John J. Kennedy and Nick A. Rayner and Phil D. Jones},
+	date-added = {2024-06-03 09:12:29 -0400},
+	date-modified = {2024-06-03 09:12:56 -0400},
+	doi = {10.1029/2011JD017187},
+	journal = {J. Geophys. Res. Atmos.},
+	number = {D8},
+	title = {Quantifying uncertainties in global and regional temperature change using an ensemble of observational estimates: The {HadCRUT4} data set},
+	url = {https://doi.org/10.1029/2011JD017187},
+	volume = {117},
+	year = {2012},
+	bdsk-file-1 = {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}}
+
+@article{Kay:2015a,
+	author = {J. E. Kay and C. Deser and A. Phillips and A. Mai and C. Hannay and G. Strand and J. M. Arblaster and S. C. Bates and G. Danabasoglu and J. Edwards and M. Holland and P. Kushner and J.-F. Lamarque and D. Lawrence and K. Lindsday and A. Middleton and E. Munoz and R. Neale and K. Oleson and L. Polvani and M. Vertenstein},
+	date-added = {2024-06-03 09:09:36 -0400},
+	date-modified = {2024-06-03 09:13:11 -0400},
+	doi = {10.1175/BAMS-D-13-00255.1},
+	journal = {Bull. Amer. Meteor. Soc.},
+	title = {The Community Earth System Model ({CESM}) Large Ensemble Project},
+	year = {2015},
+	bdsk-file-1 = {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}}

references.md

@@ -0,0 +1,5 @@
+# References
+
+```{bibliography}
+:style: plain
+```