Use latest pelican

.github/workflows/build-and-deploy.yml

@@ -17,34 +17,24 @@ concurrency:
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     steps:
     - name: Checkout
       uses: actions/checkout@v4
       with:
         submodules: recursive
 
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.7"
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
 
     - name: Install dependencies
       run: |
-        pip install -r requirements.txt
         # tidy-html5 needs to be installed separately via system package manager
         sudo apt-get update && sudo apt-get install -y tidy
 
-    - name: Patch nbconvert to fix filename conflicts
-      run: |
-        # Find nbconvert's extractoutput.py and apply the fix
-        NBCONVERT_PATH=$(python -c "import nbconvert.preprocessors.extractoutput as e; print(e.__file__)")
-        sed -i 's/if filename in resources\['\''outputs'\''\]:/if filename in resources['\''outputs'\''] and False:/' "$NBCONVERT_PATH"
-        echo "Applied nbconvert patch to disable duplicate filename check"
-
     - name: Build site
       run: |
-        python make.py publish
+        uv run --with-requirements ./requirements.txt --python 3.13 python make.py publish
 
     - name: Upload artifact
       uses: actions/upload-pages-artifact@v3

.gitmodules

@@ -4,9 +4,6 @@
 [submodule "content/notebooks/working_with_colors_in_mpl"]
 	path = content/notebooks/working_with_colors_in_mpl
 	url = https://gist.github.com/5636372.git
-[submodule "extras/pelican-plugins"]
-    path = extras/pelican-plugins
-    url = https://github.com/pelson/pelican-plugins.git
 [submodule "content/notebooks/massive_virtual_arrays_with_biggus"]
 	path = content/notebooks/massive_virtual_arrays_with_biggus
 	url = https://gist.github.com/6139282.git
@@ -25,3 +22,6 @@
 [submodule "content/field_notes/coast_path_pt1"]
 	path = content/field_notes/coast_path_pt1
 	url = https://gist.github.com/21fbdc5a944f478bdd896faa95ab3cc7.git
+[submodule "extras/liquid-tags"]
+	path = extras/liquid-tags
+	url =  https://github.com/pelson/liquid-tags.git

README.md

@@ -18,14 +18,16 @@ OR
 
 Next, create an environment:
 
-    conda create -p ./build_env ...
+    uv venv ./venv
+    source ./venv/bin/activate
+    uv pip install -r requirements.txt ./extras/liquid-tags
 
-Finally, for a local server that watches all changed files:
+To run a local server that watches all changed files:
 
     python make.py reload
 
+To update the requirements.txt:
+
+   uv pip compile requirements.in | grep -v pelican-liquid-tags > requirements.txt 
+
 
-Note on branches
-----------------
-The source branch is the master/trunk for the actual source to generate the site, and the master branch is where
-the rendered html lives (this is a result of the way github pages are done). 

extras/theme/templates/base.html

@@ -32,6 +32,9 @@
     <link rel="stylesheet" href="{{ SITEURL }}/theme/font-awesome/css/font-awesome.min.css">
     <link href="//fonts.googleapis.com/css?family=Pacifico" rel="stylesheet" type="text/css">
 
+    {% if EXTRA_HEADER %}
+      {{ EXTRA_HEADER }}
+    {% endif %}
     {% block header %}
     {% endblock %}
   </head>

make.py

@@ -61,7 +61,6 @@ def publish():
             old = os.path.join(root, fname)
             new = os.path.join(new_root, fname)
             if fname.endswith('.html'):
-                print('\nConverting {}:'.format(old))
                 cmd = ['tidy', '-config', 'tidy_config.txt', old]
                 with open(new, 'w') as fh:
                     try:

pelicanconf.py

@@ -40,11 +40,9 @@
 TAG_URL = 'tag/{slug}/'
 TAG_SAVE_AS = 'tag/{slug}/index.html'
 
-PLUGIN_PATHS = ['extras/pelican-plugins']
+PLUGIN_PATHS = ['extras/liquid-tags/pelican/plugins']
 PLUGINS = ['liquid_tags.img', 'liquid_tags.video',
-           'liquid_tags.include_code', 'liquid_tags.notebook', 'summary',
-           'feed_summary']
-FEED_USE_SUMMARY = True
+           'liquid_tags.include_code', 'liquid_tags.notebook']
 
 THEME =  "extras/theme"
 DIRECT_TEMPLATES = ('index', 'archives', 'sitemap', 'announce', 'articles', 'field_notes', 'hints')
@@ -67,3 +65,10 @@
 #MARKDOWN = ['codehilite(noclasses=True, pygments_style=native)', 'extra']  # enable MD options
 
 IGNORE_FILES = ['README.md']
+
+# Include notebook CSS header
+try:
+    with open('_nb_header.html', 'r', encoding='utf-8') as f:
+        EXTRA_HEADER = f.read()
+except FileNotFoundError:
+    EXTRA_HEADER = ''

requirements.in

@@ -1,8 +1,3 @@
-pelican==3.7
-markdown<3.0
-ipython==3.*
-notebook
-nbconvert==5.*
-pygments
-jinja2<3.0
-markupsafe<2.0
+pelican
+markdown
+./extras/liquid-tags/

requirements.txt

@@ -1,57 +1,153 @@
-anyio==3.7.1
-argon2-cffi==23.1.0
-argon2-cffi-bindings==21.2.0
-attrs==24.2.0
-bleach==6.0.0
-blinker==1.6.3
-cffi==1.15.1
+# This file was autogenerated by uv via the following command:
+#    uv pip compile requirements.in
+anyio==4.10.0
+    # via watchfiles
+asttokens==3.0.0
+    # via stack-data
+attrs==25.3.0
+    # via
+    #   jsonschema
+    #   referencing
+beautifulsoup4==4.13.4
+    # via nbconvert
+bleach==6.2.0
+    # via nbconvert
+blinker==1.9.0
+    # via pelican
+decorator==5.2.1
+    # via ipython
 defusedxml==0.7.1
-docutils==0.20.1
-entrypoints==0.4
-exceptiongroup==1.3.0
+    # via nbconvert
+docutils==0.22
+    # via pelican
+executing==2.2.0
+    # via stack-data
 fastjsonschema==2.21.1
-feedgenerator==2.1.0
+    # via nbformat
+feedgenerator==2.2.0
+    # via pelican
 idna==3.10
-importlib-metadata==6.7.0
-importlib-resources==5.12.0
-ipykernel==4.0.1
-ipython==3.2.3
-ipython-genutils==0.2.0
-Jinja2==2.11.3
-jsonschema==4.17.3
-jupyter-server==1.15.6
-jupyter_client==7.4.9
-jupyter_core==4.12.0
-Markdown==2.6.11
-MarkupSafe==1.1.1
-mistune==0.8.4
-nbclassic==1.2.0
-nbconvert==5.6.1
-nbformat==5.8.0
-nest-asyncio==1.6.0
-notebook==6.5.7
-notebook_shim==0.2.4
-packaging==24.0
+    # via anyio
+ipython==9.4.0
+ipython-pygments-lexers==1.1.1
+    # via ipython
+jedi==0.19.2
+    # via ipython
+jinja2==3.1.6
+    # via
+    #   nbconvert
+    #   pelican
+jsonschema==4.25.0
+    # via nbformat
+jsonschema-specifications==2025.4.1
+    # via jsonschema
+jupyter-client==8.6.3
+    # via nbclient
+jupyter-core==5.8.1
+    # via
+    #   jupyter-client
+    #   nbclient
+    #   nbconvert
+    #   nbformat
+jupyterlab-pygments==0.3.0
+    # via nbconvert
+markdown==3.8.2
+    # via -r requirements.in
+markdown-it-py==3.0.0
+    # via rich
+markupsafe==3.0.2
+    # via
+    #   jinja2
+    #   nbconvert
+matplotlib-inline==0.1.7
+    # via ipython
+mdurl==0.1.2
+    # via markdown-it-py
+mistune==3.1.3
+    # via nbconvert
+nbclient==0.10.2
+    # via nbconvert
+nbconvert==7.16.6
+nbformat==5.10.4
+    # via
+    #   nbclient
+    #   nbconvert
+ordered-set==4.1.0
+    # via pelican
+packaging==25.0
+    # via nbconvert
 pandocfilters==1.5.1
-pelican==3.7.0
-pkgutil_resolve_name==1.3.10
-prometheus-client==0.17.1
+    # via nbconvert
+parso==0.8.4
+    # via jedi
+pelican==4.11.0
+    # via
+    #   -r requirements.in
+./extras/liquid-tags/
+    # via -r requirements.in
+pexpect==4.9.0
+    # via ipython
+platformdirs==4.3.8
+    # via jupyter-core
+prompt-toolkit==3.0.51
+    # via ipython
 ptyprocess==0.7.0
-pycparser==2.21
-Pygments==2.17.2
-pyrsistent==0.19.3
+    # via pexpect
+pure-eval==0.2.3
+    # via stack-data
+pygments==2.18.0
+    # via
+    #   ipython
+    #   ipython-pygments-lexers
+    #   nbconvert
+    #   pelican
+    #   rich
 python-dateutil==2.9.0.post0
-pytz==2025.2
-pyzmq==26.2.1
-Send2Trash==1.8.3
+    # via
+    #   jupyter-client
+    #   pelican
+pyzmq==27.0.1
+    # via jupyter-client
+referencing==0.36.2
+    # via
+    #   jsonschema
+    #   jsonschema-specifications
+rich==14.1.0
+    # via pelican
+rpds-py==0.26.0
+    # via
+    #   jsonschema
+    #   referencing
 six==1.17.0
+    # via python-dateutil
 sniffio==1.3.1
-terminado==0.17.1
-testpath==0.6.0
-tornado==6.2
-traitlets==5.9.0
-typing_extensions==4.7.1
-Unidecode==1.4.0
+    # via anyio
+soupsieve==2.7
+    # via beautifulsoup4
+stack-data==0.6.3
+    # via ipython
+tinycss2==1.4.0
+    # via bleach
+tornado==6.5.1
+    # via jupyter-client
+traitlets==5.14.3
+    # via
+    #   ipython
+    #   jupyter-client
+    #   jupyter-core
+    #   matplotlib-inline
+    #   nbclient
+    #   nbconvert
+    #   nbformat
+typing-extensions==4.14.1
+    # via beautifulsoup4
+unidecode==1.4.0
+    # via pelican
+watchfiles==1.1.0
+    # via pelican
+wcwidth==0.2.13
+    # via prompt-toolkit
 webencodings==0.5.1
-websocket-client==1.6.1
-zipp==3.15.0
+    # via
+    #   bleach
+    #   tinycss2