.github/dependabot.yml

@@ -4,8 +4,8 @@ updates:
   #   directory: "/"
   #   schedule:
   #     interval: daily
-  - package-ecosystem: 'github-actions'
-    directory: '/'
+  - package-ecosystem: "github-actions"
+    directory: "/"
     schedule:
       # Check for updates once a week
-      interval: 'weekly'
+      interval: "weekly"

.github/workflows/nightly-build.yaml

@@ -3,7 +3,7 @@ name: nightly-build
 on:
   workflow_dispatch:
   schedule:
-    - cron: '0 0 * * *' # Daily “At 00:00”
+    - cron: "0 0 * * *" # Daily “At 00:00”
 
 jobs:
   build:

.github/workflows/publish-book.yaml

@@ -16,5 +16,3 @@ jobs:
   deploy:
     needs: build
     uses: ProjectPythia/cookbook-actions/.github/workflows/deploy-book.yaml@main
-    with:
-      cname: foundations.projectpythia.org

.github/workflows/trigger-preview.yaml

@@ -17,8 +17,7 @@ jobs:
     with:
       artifact_name: book-zip-${{ needs.find-pull-request.outputs.number }}
       destination_dir: _preview/${{ needs.find-pull-request.outputs.number }} # deploy to subdirectory labeled with PR number
-      is_preview: 'true'
-      cname: foundations.projectpythia.org
+      is_preview: "true"
 
   preview-comment:
     needs: find-pull-request

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -10,17 +10,17 @@ repos:
       - id: double-quote-string-fixer
 
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 25.1.0
     hooks:
       - id: black
 
   - repo: https://github.com/keewis/blackdoc
-    rev: v0.3.8
+    rev: v0.3.9
     hooks:
       - id: blackdoc
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
 
@@ -29,17 +29,12 @@ repos:
     hooks:
       - id: seed-isort-config
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 6.0.0
     hooks:
       - id: isort
 
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.7.1
-    hooks:
-      - id: prettier
-
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+    rev: 1.9.1
     hooks:
       - id: nbqa-black
         additional_dependencies: [black]

CITATION.cff

@@ -0,0 +1,74 @@
+cff-version: 1.2.0
+message: "If you use this resource, please cite it as below."
+authors:
+  - family-names: Rose
+    given-names: Brian E. J.
+    orcid: https://orcid.org/0000-0002-9961-3821
+    website: https://github.com/brian-rose
+    affiliation: University at Albany (State University of New York)
+  - family-names: Kent
+    given-names: Julia
+    orcid: https://orcid.org/0000-0002-5611-8986
+    website: https://github.com/jukent
+    affiliation: UCAR/NCAR
+  - family-names: Tyle
+    given-names: Kevin
+    orcid: https://orcid.org/0000-0001-5249-9665
+    website: https://github.com/ktyle
+    affiliation: University at Albany (State University of New York)
+  - family-names: Clyne
+    given-names: John
+    orcid: https://orcid.org/0000-0003-2788-9017
+    website: https://github.com/clyne
+    affiliation: UCAR/NCAR
+  - family-names: Banihirwe
+    given-names: Anderson
+    orcid: https://orcid.org/0000-0001-6583-571X
+    website: https://github.com/andersy005
+  - family-names: Camron
+    given-names: Drew
+    orcid: https://orcid.org/0000-0001-7246-6502
+    website: https://github.com/dcamron
+    affiliation: UCAR/Unidata
+  - family-names: May
+    given-names: Ryan
+    orcid: https://orcid.org/0000-0003-2907-038X
+    website: https://github.com/dopplershift
+    affiliation: UCAR/Unidata
+  - family-names: Grover
+    given-names: Maxwell
+    orcid: https://orcid.org/0000-0002-0370-8974
+    website: https://github.com/mgrover1
+    affiliation: Argonne National Laboratory
+  - family-names: Ford
+    given-names: Robert R.
+    orcid: https://orcid.org/0000-0001-5483-4965
+    website: https://github.com/r-ford
+    affiliation: University at Albany (State University of New York)
+  - family-names: Paul
+    given-names: Kevin
+    orcid: https://orcid.org/0000-0001-8155-8038
+    website: https://github.com/kmpaul
+    affiliation: NVIDIA
+  - family-names: Morley
+    given-names: James
+    orcid: https://orcid.org/0009-0005-5193-7981
+    website: https://github.com/jnmorley
+  - family-names: Eroglu
+    given-names: Orhan
+    orcid: https://orcid.org/0000-0003-3099-8775
+    website: https://github.com/erogluorhan
+    affiliation: UCAR/NCAR
+  - family-names: Kailyn
+    given-names: Lily
+    orcid: https://orcid.org/0009-0002-0125-5091
+    website: https://github.com/lkailynncar
+    affiliation: UCAR/NCAR
+  - family-names: Zacharias
+    given-names: Anissa
+    orcid: https://orcid.org/0000-0002-2666-8493
+    website: https://github.com/anissa111
+    affiliation: UCAR/NCAR
+title: "Pythia Foundations"
+version: v2023.05.01
+doi: 10.5281/zenodo.7884571

README.md

@@ -1,6 +1,7 @@
 # Pythia Foundations
 
 [![nightly-build](https://github.com/ProjectPythia/pythia-foundations/actions/workflows/nightly-build.yaml/badge.svg)](https://github.com/ProjectPythia/pythia-foundations/actions/workflows/nightly-build.yaml)
+[![DOI](https://zenodo.org/badge/338145160.svg)](https://zenodo.org/badge/latestdoi/338145160)
 
 This is the source repository for the Pythia Foundations content collection.
 

_config.yml

@@ -5,7 +5,7 @@ title: Pythia Foundations
 author: the <a href="https://projectpythia.org/">Project Pythia</a> Community
 logo: images/logos/pythia_logo-white-rtext.svg
 email: projectpythia@ucar.edu
-copyright: '2022'
+copyright: "2024"
 
 exclude_patterns:
   - README.md
@@ -76,34 +76,37 @@ bibtex_bibfiles:
 #   use_issues_button: true
 #   use_repository_button: true
 #   use_edit_page_button: true
-#   extra_navbar: |
-#     Theme by <a href="https://projectpythia.org">Project Pythia</a>.<br>
-#     All code in Pythia Foundations is licensed under Apache 2.0. All other non-code content is licensed under <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons BY 4.0 (CC BY 4.0)</a>.
 #   extra_footer: |
 #     <img src="/_static/footer-logo-nsf.png" style="float:left;width:60px;height:60px;margin-right:1rem;">
 #     This material is based upon work supported by the National
 #     Science Foundation under Grant Nos. 2026863 and 2026899. Any
 #     opinions, findings, and conclusions or recommendations expressed
 #     in this material are those of the author(s) and do not necessarily
-#     reflect the views of the National Science Foundation.
+#     reflect the views of the National Science Foundation.<br><br>
+#     Theme by <a href="https://projectpythia.org">Project Pythia</a>.<br>
+#     All code in Pythia Foundations is licensed under Apache 2.0. All other non-code content is licensed
+#     under <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons BY 4.0 (CC BY 4.0)</a>.
 
 sphinx:
   config:
+    nb_execution_raise_on_error: true # raise exception in build if there are notebook errors (this flag is ignored if building on binder)
     linkcheck_request_headers:
-      'https://docs.github.com/':
+      "https://docs.github.com/":
         User-Agent: Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:24.0) Gecko/20100101 Firefox/24.0
     html_favicon: images/icons/favicon.ico
-    html_last_updated_fmt: '%-d %B %Y'
+    html_last_updated_fmt: "%-d %B %Y"
     html_theme: sphinx_pythia_theme
     html_permalinks_icon: '<i class="fas fa-link"></i>'
     html_theme_options:
-      google_analytics_id: 'G-G57FLM9M46'
+      analytics:
+        google_analytics_id: "G-G57FLM9M46"
       home_page_in_toc: true
       repository_url: https://github.com/ProjectPythia/pythia-foundations # Online location of your book
       repository_branch: main # Which branch of the repository should be used when creating links (optional)
       use_issues_button: true
       use_repository_button: true
       use_edit_page_button: true
+      use_fullscreen_button: true
       github_url: https://github.com/ProjectPythia
       twitter_url: https://twitter.com/project_pythia
       icon_links:
@@ -112,14 +115,15 @@ sphinx:
           icon: fab fa-youtube-square
           type: fontawesome
       launch_buttons:
-        binderhub_url: https://mybinder.org
+        binderhub_url: https://binder.projectpythia.org
         notebook_interface: jupyterlab
       extra_navbar: |
-        Theme by <a href="https://projectpythia.org">Project Pythia</a>.<br><br>
-        All code in Pythia Foundations is licensed under Apache 2.0. All other non-code content is licensed under <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons BY 4.0 (CC BY 4.0)</a>.<br><br>
         We want your feedback! Fill out this <a href="https://docs.google.com/forms/d/e/1FAIpQLSeVa1TC9xM-dk7qIE2e8bsgSrIP82yYDNw3wew3J46eREJa4w/viewform?usp=sf_link">Google Form</a>
         or see our <a href="https://foundations.projectpythia.org/appendix/how-to-contribute.html">Contributor's Guide</a>.
-      logo_link: https://projectpythia.org
+      logo:
+        link: https://projectpythia.org
+      navbar_start:
+        - navbar-logo
       navbar_links:
         - name: Home
           url: https://projectpythia.org
@@ -131,7 +135,16 @@ sphinx:
           url: https://projectpythia.org/resource-gallery.html
         - name: Community
           url: https://projectpythia.org/index.html#join-us
+        - name: Blog
+          url: https://projectpythia.org/blog.html
+      navbar_end:
+        - navbar-icon-links
       footer_logos:
-        NCAR: images/logos/NCAR-contemp-logo-blue.svg
+        NCAR: images/logos/NSF-NCAR_Lockup-UCAR-Dark_102523.svg
         Unidata: images/logos/Unidata_logo_horizontal_1200x300.svg
         UAlbany: images/logos/UAlbany-A2-logo-purple-gold.svg
+      footer_start:
+        - footer-logos
+        - footer-menu
+        - footer-info
+        - footer-extra

_static/custom.css

@@ -1,3 +1,10 @@
+.bd-main .bd-content .bd-article-container {
+  max-width: 100%; /* default is 60em */
+}
+.bd-page-width {
+  max-width: 100%; /* default is 88rem */
+}
+
 kbd {
   /* Based on: https://dylanatsmith.com/wrote/styling-the-kbd-element */
 

_templates/footer-extra.html

@@ -1,5 +1,14 @@
 <div class="container-fluid footer-extra">
   <div class="container">
+    <center>
+      Theme by <a href="https://projectpythia.org">Project Pythia</a>. All code
+      in Pythia Foundations is licensed under Apache 2.0. All other non-code
+      content is licensed under
+      <a href="https://creativecommons.org/licenses/by/4.0/">
+        Creative Commons BY 4.0 (CC BY 4.0)</a
+      >.
+    </center>
+    <br /><br />
     <div class="row">
       <p class="m-0">
         <img

_templates/footer-menu.html

@@ -1,3 +1,4 @@
+{% set ext_icon = '<i class="fas fa-external-link-alt"></i>' %}
 <div class="container-fluid footer-menu pt-4">
   <div class="container">
     <div class="row justify-content-center">
@@ -20,6 +21,14 @@ <h1>{{ _("About") }}</h1>
               >{{ _("The Project Team") }}</a
             >
           </li>
+          <li>
+            <a href="https://projectpythia.org/#how-to-cite"
+              >{{ _("How to Cite") }}</a
+            >
+          </li>
+          <li>
+            <a href="https://projectpythia.org/metrics">{{ _("Metrics") }}</a>
+          </li>
         </ul>
       </div>
       <div class="col-9 col-sm-4 col-md-4 col-lg-3 footer-menu-col">
@@ -29,15 +38,8 @@ <h1>{{ _("Give Feedback") }}</h1>
             <a href="mailto:projectpythia@ucar.edu">{{ _("Email us!") }}</a>
           </li>
           <li>
-            <a
-              href="https://github.com/ProjectPythia/projectpythia.github.io/discussions"
-              >{{ _("Project Pythia Discussions") }}</a
-            >
-          </li>
-          <li>
-            <a
-              href="https://github.com/ProjectPythia/pythia-foundations/discussions"
-              >{{ _("Pythia Foundations Discussions") }}</a
+            <a href="https://discourse.pangeo.io/c/education/project-pythia/60s"
+              >{{ _("Pangeo Discourse") }}</a
             >
           </li>
         </ul>
@@ -50,12 +52,6 @@ <h1>{{ _("Contribute") }}</h1>
               >{{ _("How to contribute to Project Pythia") }}</a
             >
           </li>
-          <li>
-            <a
-              href="https://foundations.projectpythia.org/appendix/how-to-contribute.html"
-              >{{ _("How to contribute to Pythia Foundations") }}</a
-            >
-          </li>
           <li>
             <a href="https://projectpythia.org/code_of_conduct.html"
               >{{ _("Our code of conduct") }}</a

_toc.yml

@@ -4,6 +4,7 @@ parts:
   - caption: Preamble
     chapters:
       - file: preamble/how-to-use
+      - file: preamble/how-to-cite
   - caption: Foundational skills
     chapters:
       - file: foundations/overview

appendix/template.ipynb

@@ -4,6 +4,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "# Project Pythia Notebook Template\n",
+    "\n",
     "## How to Use This Page\n",
     "\n",
     "This page is designed as a template. As such, each section contains instructions for the content added to the equivalent section of a new notebook, with the exception of this section, and the Setting Up a New Notebook section. Because this is not a tutorial, the overall structure of the page does not need to be cohesive.\n",
@@ -23,7 +25,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Project Pythia Notebook Template\n",
+    "## Project Pythia Notebook Template\n",
     "\n",
     "Each notebook must be properly titled with a top level Markdown header, i.e., a header title prefixed by a single # mark. Nowhere else in the notebook should you use a top level header. This header will be automatically used by the Pythia book-building process to generate the page title, which will then be added to the navbar, table of contents, etc. As such, the header needs to be short, concise, and descriptive. After the header line, add a separate Jupyter Notebook cell with the text `---`. This adds a separating line used to separate the title from the overview and prerequisites. This technique will also be used later to separate other sections."
    ]

core/data-formats/netcdf-cf.ipynb

@@ -575,13 +575,13 @@
     "lon_var[:] = lon\n",
     "lon_var.units = 'degrees_east'\n",
     "lon_var.standard_name = 'longitude'  # Optional\n",
-    "lon_var.long_name = 'longitude'\n",
+    "lon_var.long_name = 'longitude coordinate'\n",
     "\n",
     "lat_var = nc.createVariable('lat', np.float64, ('y', 'x'))\n",
     "lat_var[:] = lat\n",
     "lat_var.units = 'degrees_north'\n",
     "lat_var.standard_name = 'latitude'  # Optional\n",
-    "lat_var.long_name = 'latitude'"
+    "lat_var.long_name = 'latitude coordinate'"
    ]
   },
   {
@@ -983,7 +983,6 @@
     "\n",
     "- [CF Conventions doc (1.7)](http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html)\n",
     "- [Jonathan Gregory's old CF presentation](http://cfconventions.org/Data/cf-documents/overview/viewgraphs.pdf)\n",
-    "- [NASA ESDS \"Dataset Interoperability Recommendations for Earth Science\"](https://earthdata.nasa.gov/user-resources/standards-and-references/dataset-interoperability-recommendations-for-earth-science)\n",
     "- [CF Data Model (cfdm) python package tutorial](https://ncas-cms.github.io/cfdm/tutorial.html)\n",
     "- [Tim Whiteaker's cfgeom python package (GitHub repo)](https://github.com/twhiteaker/CFGeom) and [(tutorial)]( https://twhiteaker.github.io/CFGeom/tutorial.html)\n",
     "- [netCDF4 Documentation](https://unidata.github.io/netcdf4-python/)"
@@ -1013,7 +1012,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,