Fix dup search bar

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.github/workflows/deploy-docs.yml

@@ -23,16 +23,11 @@ jobs:
         with:
           persist-credentials: false
 
-      - name: Set up Python
-        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
-        with:
-          python-version: "3.x"
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@a09b6247153796b190642a2b53fac4241043cf6f  # v0.10.0
 
       - name: Build documentation
-        run: >
-          set -e
-          && pip install "jupyter-book<2"
-          && jupyter-book build jupyterbook
+        run: pixi run jb
 
       - name: GitHub Pages action
         if: success() && github.event_name == 'release'

.github/workflows/docs-linkchecker.yml

@@ -11,20 +11,16 @@ on:
 jobs:
   build-docs:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
 
     steps:
       - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
-          fetch-depth: 0
           persist-credentials: false
 
-      - name: Set up Python
-        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
-        with:
-          python-version: "3.x"
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@a09b6247153796b190642a2b53fac4241043cf6f  # v0.10.0
 
-      - name: Linkcheck
-        run: >
-          set -e
-          && pip install "jupyter-book<2"
-          && jupyter-book build jupyterbook --builder linkcheck
+      - name: Build documentation
+        run: pixi run linkcheck

.gitignore

@@ -2,3 +2,7 @@
 *.swp
 .ipynb_checkpoints/
 index.html
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+pixi.lock

.pre-commit-config.yaml

@@ -34,7 +34,7 @@ repos:
       - id: add-trailing-comma
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.20
+    rev: v0.15.22
     hooks:
       - id: ruff
 
@@ -55,7 +55,7 @@ repos:
       - id: nb-strip-paths
 
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.26.1
+    rev: v1.28.0
     hooks:
       - id: zizmor
 

jupyterbook/_config.yml

@@ -1,5 +1,5 @@
 # Book settings
-title: The U.S. Integrated Ocean Observing System (IOOS) # The title of the book. Will be placed in the left navbar.
+title: The U.S. Integrated Ocean Observing System (IOOS)
 author: IOOS # The author of the book
 logo: images/IOOS_logo.png # A path to the book logo
 
@@ -44,7 +44,8 @@ html:
   use_edit_page_button: false # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in
   use_repository_button: true # Whether to add a link to your repository button
   use_issues_button: true # Whether to add an "open an issue" button
-  extra_navbar: <a href="https://ioos.us">IOOS</a> # Will be displayed underneath the left navbar.
+  # Hitting https://github.com/jupyter-book/jupyter-book/issues/1966
+  extra_navbar: <a href="https://ioos.us">IOOS</a>
   extra_footer: <a href=https://ioos.noaa.gov> ioos.noaa.gov </a> &nbsp
     <a href=https://www.facebook.com/usioosgov> Facebook </a> &nbsp
     <a href=https://www.twitter.com/usioosgov> Twitter </a> &nbsp

jupyterbook/add_header.py

@@ -0,0 +1,24 @@
+from pathlib import Path
+
+path = Path(__file__).absolute().parent
+
+
+def add_header(fname):
+    ioos_ui_components_min_js = """\n<script src="https://dgd6r9iiqa8y9.cloudfront.net/ioos-ui-components.min.js"></script>\n"""
+    ioos_header = """\n<ioos-header variant="compact" theme="auto"></ioos-header>\n"""
+
+    with open(fname) as f:
+        lines = f.readlines()
+
+    with open(fname, "w") as out:
+        for line in lines:
+            if line.strip().startswith("<title"):
+                line = line + f"\n{ioos_ui_components_min_js}"
+            if line.strip().startswith("<body"):
+                line = line + f"\n{ioos_header}"
+            out.write(line)
+
+
+if "__main__" == __name__:
+    for fname in path.glob("_build/html/**/*.html"):
+        add_header(fname)

jupyterbook/content/code_gallery/data_management_notebooks/2017-05-14-running_compliance_checker.ipynb

@@ -48,7 +48,7 @@
     "\n",
     "Created: 2017-05-14\n",
     "\n",
-    "The IOOS Compliance Checker is a Python-based tool that helps users check the meta data compliance of a netCDF file. This software can be run in a web interface here: [https://ioos.github.io/compliance-checker-wasm-web/ioos_cc_browser.html](https://ioos.github.io/compliance-checker-wasm-web/ioos_cc_browser.html) The checker can also be run as a Python tool either on the command line or in a Python script.  This notebook demonstrates the python usage of the Compliance Checker.\n",
+    "The IOOS Compliance Checker is a Python-based tool that helps users check the meta data compliance of a netCDF file. This software can be run in a web interface here: [https://compliance.ioos.us/](https://compliance.ioos.us/) The checker can also be run as a Python tool either on the command line or in a Python script.  This notebook demonstrates the python usage of the Compliance Checker.\n",
     "\n",
     "## Purpose:\n",
     "\n",
@@ -249,7 +249,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.4"
+   "version": "3.14.5"
   }
  },
  "nbformat": 4,

pixi.toml

@@ -0,0 +1,15 @@
+[workspace]
+authors = ["Filipe Fernandes <ocefpaf@gmail.com>"]
+channels = ["conda-forge"]
+name = "ioos_code_lab"
+platforms = ["linux-64"]
+version = "0.1.0"
+
+[tasks]
+build_html = { cmd = ["jupyter-book", "build", "jupyterbook"] }
+jb = { cmd = "python jupyterbook/add_header.py", depends-on=["build_html"] }
+linkcheck = { cmd = "jupyter-book build jupyterbook --builder linkcheck" }
+
+[dependencies]
+jupyter-book = ">=1.0.4,<2"
+pydata-sphinx-theme = "==0.16.1"