Start using the updated Pythia theme

_config.yml

@@ -5,7 +5,7 @@ title: Unstructured Grids Visualization Cookbook
 description: Comprehensive showcase of workflows and techniques for visualizing Unstructured Grids using UXarray
 author: the <a href="https://projectpythia.org/">Project Pythia</a> Community
 logo: notebooks/images/logos/pythia_logo-white-rtext.svg
-copyright: "2023"
+copyright: "2024"
 
 execute:
   # To execute notebooks via a Binder instead, replace 'cache' with 'binder'
@@ -41,7 +41,9 @@ 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:
@@ -55,7 +57,12 @@ sphinx:
       extra_navbar: |
         Theme by <a href="https://projectpythia.org">Project Pythia</a>.<br><br>
         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>.<br><br>
-      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
@@ -68,6 +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

_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 */
+}

environment.yml

@@ -15,21 +15,21 @@ dependencies:
   - netcdf4
   - numba
   - numpy
-  - pandas<2.1.0
+  - pandas
   - pathlib
   - pip
   - pre_commit
-  - pyarrow<13.0.0
+  - pyarrow
   - pytest
   - pytest-cov
-  - python>=3.9,<3.12
   - requests
   - scikit-learn
   - scipy
   - shapely
-  - spatialpandas   
+  - spatialpandas
+  - sphinx-pythia-theme
   - uxarray
   - xarray
   - pip:
       - antimeridian
-      - sphinx-pythia-theme
+      - git+https://github.com/UXARRAY/uxarray.git@main #until UXarray's March or April release

notebooks/01-intro/01-unstructured-grid-overview.ipynb

@@ -27,6 +27,16 @@
     "4. Why UXarrary for unstructured grids?"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
+   },
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -240,9 +250,13 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    ":::{note}\n",
-    "This is a very basic example of an unstructured grid with triangles. There are very specialized libraries to create unstructured grids. Often the region of interest is meshed with a finer resolution. The mesh is then coarsened in areas where the resolution is not needed. This is done to reduce the number of elements and improve computational efficiency.\n",
-    ":::"
+    "<div class=\"admonition alert alert-info\">\n",
+    "    <p class=\"admonition-title\" style=\"font-weight:bold\">Note:</p>\n",
+    "    This is a very basic example of an unstructured grid with triangles. There are very specialized libraries to create\n",
+    "    unstructured grids. Often the region of interest is meshed with a finer resolution. The mesh is then coarsened in\n",
+    "    areas where the resolution is not needed. This is done to reduce the number of elements and improve computational\n",
+    "    efficiency.\n",
+    "</div>"
    ]
   },
   {
@@ -272,9 +286,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    ":::{note}\n",
-    "This notebook serves as an introduction to unstructured grids and UXarray. For more information, please visit the UXarray documentation at https://uxarray.readthedocs.io/en/latest/ and specifically see the example section: https://uxarray.readthedocs.io/en/latest/examples.html\n",
-    ":::"
+    "<div class=\"admonition alert alert-info\">\n",
+    "    <p class=\"admonition-title\" style=\"font-weight:bold\">Note:</p>\n",
+    "    This notebook serves as an introduction to unstructured grids and UXarray. For more information, please visit the\n",
+    "    <a href=\"https://uxarray.readthedocs.io/en/latest/\">UXarray documentation</a> and specifically see the \n",
+    "    <a href=\"https://uxarray.readthedocs.io/en/latest/examples.html\">Usage examples</a> section.\n",
+    "</div>"
    ]
   },
   {
@@ -302,7 +319,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.12.2"
   },
   "nbdime-conflicts": {
    "local_diff": [

notebooks/02-methods/01-plotting-libraries.ipynb

@@ -16,9 +16,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    ":::{note}\n",
-    "The following design diagram is actually provided in the [Plotting API](../03-uxarray-vis/01-plot-api.ipynb) section along with key takeaways about it. We highly recommend to check them out as well.\n",
-    ":::"
+    "<div class=\"admonition alert alert-info\">\n",
+    "    <p class=\"admonition-title\" style=\"font-weight:bold\">Note:</p>\n",
+    "    The following design diagram is actually provided in the <a href=\"../03-uxarray-vis/01-plot-api.ipynb\">Plotting\n",
+    "    API</a> section along with key takeaways about it. We highly recommend to check them out as well.\n",
+    "</div>"
    ]
   },
   {
@@ -69,9 +71,13 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    ":::{important}\n",
-    "UXarray takes care of the vital tasks such as recognizing unstructured grids from various formats (such as UGRID, MPAS, Scrip, Exodus, etc.) and representing them in a unified UGRID-like format, providing the data structures and functionality necessary for convenient preprocessing of the grid, and wrapping up HoloViz packages' functionality to enable unstructured grids-specialized, high-level visualization functions.\n",
-    ":::"
+    "<div class=\"admonition alert alert-warning\">\n",
+    "    <p class=\"admonition-title\" style=\"font-weight:bold\">Important!</p>\n",
+    "    UXarray takes care of the vital tasks such as recognizing unstructured grids from various formats (such as UGRID,\n",
+    "    MPAS, Scrip, Exodus, etc.) and representing them in a unified UGRID-like format, providing the data structures and\n",
+    "    functionality necessary for convenient preprocessing of the grid, and wrapping up HoloViz packages' functionality to\n",
+    "    enable unstructured grids-specialized, high-level visualization functions.\n",
+    "</div>"
    ]
   },
   {
@@ -99,9 +105,10 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    ":::{important}\n",
-    "UXarray allows both Matplotlib and Bokeh backends to be chosen in visualization functions as they are provided by Holoviews (in addition to Plotly).\n",
-    ":::"
+    "<div class=\"admonition alert alert-info\">\n",
+    "    <p class=\"admonition-title\" style=\"font-weight:bold\">Note:</p>\n",
+    "    UXarray allows both Matplotlib and Bokeh backends to be chosen in visualization functions as they are provided by Holoviews (in addition to Plotly).\n",
+    "</div>"
    ]
   },
   {
@@ -207,9 +214,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    ":::{warning}\n",
-    "While these conversion functions have already been released, we have observed some issues with the resulting Matplotlib plots after the exceution of these functions, and the bug-fixing of that is WIP. Hence, we don't have an officially released documentation/example about these functions yet.\n",
-    ":::"
+    "<div class=\"admonition alert alert-warning\">\n",
+    "    <p class=\"admonition-title\" style=\"font-weight:bold\">Warning!</p>\n",
+    "    While these conversion functions have already been released, we have observed some issues with the resulting Matplotlib plots after the exceution of\n",
+    "    these functions, and the bug-fixing of that is WIP. Hence, we don't have an officially released documentation/example about these functions yet.\n",
+    "</div>"
    ]
   },
   {
@@ -255,7 +264,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.12.2"
   },
   "nbdime-conflicts": {
    "local_diff": [