Merge branch 'main' into patch-1

.github/workflows/trigger-replace-links.yaml

@@ -0,0 +1,31 @@
+name: trigger-replace-links
+
+on:
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Find and Replace Repository Name
+        uses: jacobtomlinson/gha-find-replace@v3
+        with:
+          find: "ProjectPythia/cookbook-template"
+          replace: "${{ github.repository_owner }}/${{ github.event.repository.name }}"
+          regex: false
+          exclude: ".github/workflows/trigger-replace-links.yaml"
+
+      - name: Find and Replace Repository ID
+        uses: jacobtomlinson/gha-find-replace@v3
+        with:
+          find: "475509405"
+          replace: "${{ github.repository_id}}"
+          regex: false
+          exclude: ".github/workflows/trigger-replace-links.yaml"
+
+      - name: Push changes
+        uses: stefanzweifel/git-auto-commit-action@v5

.gitignore

@@ -131,3 +131,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Ephemeral .nfs files
+.nfs*

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -10,37 +10,38 @@ repos:
       - id: double-quote-string-fixer
 
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.12.1
     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: 7.0.0
     hooks:
       - id: flake8
 
   - repo: https://github.com/asottile/seed-isort-config
     rev: v2.2.0
     hooks:
       - id: seed-isort-config
+
   - repo: https://github.com/PyCQA/isort
-    rev: 5.11.4
+    rev: 5.13.2
     hooks:
       - id: isort
 
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.7.1
+    rev: v3.1.0
     hooks:
       - id: prettier
         additional_dependencies: [[email protected]]
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.6.1
+    rev: 1.7.1
     hooks:
       - id: nbqa-black
         additional_dependencies: [black]

CITATION.cff

@@ -0,0 +1,48 @@
+cff-version: 1.2.0
+message: "If you use this cookbook, please cite it as below."
+authors:
+  # add additional entries for each author -- see https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md
+  - family-names: Rose
+    given-names: Brian E. J.
+    orcid: https://orcid.org/0000-0002-9961-3821 # optional
+    website: https://github.com/brian-rose # optional
+    affiliation: University at Albany (State University of New York) # optional
+  - 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: Camron
+    given-names: Drew
+    orcid: https://orcid.org/0000-0001-7246-6502
+    website: https://github.com/dcamron
+    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
+  - name: "Cookbook Template contributors" # use the 'name' field to acknowledge organizations
+    website: "https://github.com/ProjectPythia/cookbook-template/graphs/contributors"
+title: "Cookbook Template"
+abstract: "A sample cookbook description."

README.md

@@ -3,7 +3,8 @@
 # (Replace_with_your_title) Cookbook
 
 [![nightly-build](https://github.com/ProjectPythia/cookbook-template/actions/workflows/nightly-build.yaml/badge.svg)](https://github.com/ProjectPythia/cookbook-template/actions/workflows/nightly-build.yaml)
-[![Binder](http://binder.mypythia.org/badge_logo.svg)](http://binder.mypythia.org/v2/gh/ProjectPythia/cookbook-template/main?labpath=notebooks)
+[![Binder](https://binder.projectpythia.org/badge_logo.svg)](https://binder.projectpythia.org/v2/gh/ProjectPythia/cookbook-template/main?labpath=notebooks)
+[![DOI](https://zenodo.org/badge/475509405.svg)](https://zenodo.org/badge/latestdoi/475509405)
 
 This Project Pythia Cookbook covers ... (replace `...` with the main subject of your cookbook ... e.g., _working with radar data in Python_)
 
@@ -35,12 +36,12 @@ This Project Pythia Cookbook covers ... (replace `...` with the main subject of
 
 ## Running the Notebooks
 
-You can either run the notebook using [Binder](https://mybinder.org/) or on your local machine.
+You can either run the notebook using [Binder](https://binder.projectpythia.org/) or on your local machine.
 
 ### Running on Binder
 
 The simplest way to interact with a Jupyter Notebook is through
-[Binder](https://mybinder.org/), which enables the execution of a
+[Binder](https://binder.projectpythia.org/), which enables the execution of a
 [Jupyter Book](https://jupyterbook.org) in the cloud. The details of how this works are not
 important for now. All you need to know is how to launch a Pythia
 Cookbooks chapter via Binder. Simply navigate your mouse to

_config.yml

@@ -4,19 +4,10 @@
 title: Project Pythia Cookbook Template
 author: the <a href="https://projectpythia.org/">Project Pythia</a> Community
 logo: notebooks/images/logos/pythia_logo-white-rtext.svg
-email: [email protected]
-copyright: "2022"
-
-description: A sample cookbook description.
-thumbnail: thumbnail.png
-tags:
-  domains:
-    - sampledomain
-  packages:
-    - samplepackage
+copyright: "2024"
 
 execute:
-  # To execute notebooks via a binder instead, replace 'cache' with 'binder'
+  # To execute notebooks via a Binder instead, replace 'cache' with 'binder'
   execute_notebooks: cache
   timeout: 600
   allow_errors: False # cells with expected failures must set the `raises-exception` cell tag
@@ -36,9 +27,10 @@ parse:
 
 sphinx:
   config:
-    linkcheck_ignore: ["https://doi.org/*",]
+    linkcheck_ignore: ["https://doi.org/*", "https://zenodo.org/badge/*"] # 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)
     html_favicon: notebooks/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:
@@ -48,7 +40,9 @@ sphinx:
       use_issues_button: true
       use_repository_button: true
       use_edit_page_button: true
-      google_analytics_id: G-T52X8HNYE8
+      use_fullscreen_button: true
+      analytics:
+        google_analytics_id: G-T52X8HNYE8
       github_url: https://github.com/ProjectPythia
       twitter_url: https://twitter.com/project_pythia
       icon_links:
@@ -57,13 +51,18 @@ sphinx:
           icon: fab fa-youtube-square
           type: fontawesome
       launch_buttons:
-        binderhub_url: http://binder.mypythia.org
+        binderhub_url: https://binder.projectpythia.org
         notebook_interface: jupyterlab
       extra_navbar: ""
       extra_footer: |
         Theme by <a href="https://projectpythia.org">Project Pythia</a>.
         All code in Pythia Cookbooks 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>.
-      logo_link: https://projectpythia.org
+      logo:
+        link: https://projectpythia.org
+      navbar_start:
+        - navbar-logo
+      navbar_end:
+        - navbar-icon-links
       navbar_links:
         - name: Home
           url: https://projectpythia.org
@@ -76,6 +75,9 @@ sphinx:
         - name: Community
           url: https://projectpythia.org/index.html#join-us
       footer_logos:
-        NCAR: notebooks/images/logos/NCAR-contemp-logo-blue.svg
+        NCAR: notebooks/images/logos/NSF-NCAR_Lockup-UCAR-Dark_102523.svg
         Unidata: notebooks/images/logos/Unidata_logo_horizontal_1200x300.svg
         UAlbany: notebooks/images/logos/UAlbany-A2-logo-purple-gold.svg
+      footer_start:
+        - footer-logos
+        - footer-info

_gallery_info.yml

@@ -0,0 +1,6 @@
+thumbnail: thumbnail.png
+tags:
+  domains:
+    - sampledomain
+  packages:
+    - samplepackage

_static/custom.css

@@ -0,0 +1,6 @@
+.bd-main .bd-content .bd-article-container {
+  max-width: 100%; /* default is 60em */
+}
+.bd-page-width {
+  max-width: 100%; /* default is 88rem */
+}

_toc.yml

@@ -1,6 +1,9 @@
 format: jb-book
 root: README
 parts:
+  - caption: Preamble
+    chapters:
+      - file: notebooks/how-to-cite
   - caption: Introduction
     chapters:
       - file: notebooks/notebook-template

environment.yml

@@ -4,7 +4,4 @@ channels:
 dependencies:
   - jupyter-book
   - jupyterlab
-  - jupyter_server<2
-  - pip
-  - pip:
-      - sphinx-pythia-theme
+  - sphinx-pythia-theme

notebooks/how-to-cite.md

@@ -0,0 +1,7 @@
+# How to Cite This Cookbook
+
+The material in this Project Pythia Cookbook is licensed for free and open consumption and reuse. All code is served under [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0), while all non-code content is licensed under [Creative Commons BY 4.0 (CC BY 4.0)](https://creativecommons.org/licenses/by/4.0/). Effectively, this means you are free to share and adapt this material so long as you give appropriate credit to the Cookbook authors and the Project Pythia community.
+
+The source code for the book is [released on GitHub](https://github.com/ProjectPythia/cookbook-template) and archived on Zenodo. This DOI will always resolve to the latest release of the book source:
+
+[![DOI](https://zenodo.org/badge/475509405.svg)](https://zenodo.org/badge/latestdoi/475509405)

notebooks/notebook-template.ipynb

@@ -295,7 +295,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.10.8"
   },
   "nbdime-conflicts": {
    "local_diff": [