Add website

.github/workflows/docs_build_and _deploy.yml

@@ -0,0 +1,46 @@
+name: Build and Deploy Sphinx Docs
+
+# Generate the documentation on all merges to main, all pull requests, or by
+# manual workflow dispatch. The build job can be used as a CI check that the
+# docs still build successfully. The deploy job only runs when a tag is
+# pushed and actually moves the generated html to the gh-pages branch
+# (which triggers a GitHub pages deployment).
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  pull_request:
+  merge_group:
+  workflow_dispatch:
+
+jobs:
+  linting:
+    # scheduled workflows should not run on forks
+    if: (${{ github.event_name == 'schedule' }} && ${{ github.repository_owner == 'neuroinformatics-unit' }} && ${{ github.ref == 'refs/heads/main' }}) || (${{ github.event_name != 'schedule' }})
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/lint@v2
+
+  build_sphinx_docs:
+    name: Build Sphinx Docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/build_sphinx_docs@main
+        with:
+          python-version: 3.12
+          use-make: true
+
+  deploy_sphinx_docs:
+    name: Deploy Sphinx Docs
+    needs: build_sphinx_docs
+    permissions:
+      contents: write
+    if: (github.event_name == 'push' && github.ref_type == 'tag') || github.event_name == 'workflow_dispatch'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/deploy_sphinx_docs@main
+        with:
+          secret_input: ${{ secrets.GITHUB_TOKEN }}
+          use-make: true

docs/CNAME

@@ -1 +1 @@
-python-cookiecutter.neuroinformatics.dev
+python-cookiecutter.neuroinformatics.dev

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

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+linkify-it-py
+myst-parser
+nbsphinx
+pydata-sphinx-theme
+setuptools-scm
+sphinx
+sphinx-autodoc-typehints
+sphinx-copybutton
+sphinx-design
+sphinx-gallery
+sphinx-notfound-page
+sphinx-sitemap
+sphinx-togglebutton

docs/source/_static/css/custom.css

@@ -0,0 +1,64 @@
+html[data-theme=dark] {
+    --pst-color-primary: #04B46D;
+    --pst-color-link: var(--pst-color-primary);
+  }
+
+html[data-theme=light] {
+  --pst-color-primary: #03A062;
+  --pst-color-link: var(--pst-color-primary);
+}
+
+body .bd-article-container {
+max-width: 100em !important;
+}
+
+.col {
+flex: 0 0 50%;
+max-width: 50%;
+}
+
+.img-sponsor {
+height: 50px;
+padding-top: 5px;
+padding-right: 5px;
+padding-bottom: 5px;
+padding-left: 5px;
+}
+
+.things-in-a-row {
+display: flex;
+flex-wrap: wrap;
+justify-content: space-between;
+}
+
+/* grids to match theme colors */
+.sd-card-icon {
+  color: var(--sd-color-primary);
+  font-size: 1.5em;
+  margin-bottom: 0.5rem;
+}
+
+.sd-card {
+  padding: 1.5rem;
+  transition: transform 0.2s;
+}
+
+.sd-card:hover {
+  transform: translateY(-5px);
+}
+
+/* Ensuring content area uses full width when sidebar is hidden */
+.bd-page-width {
+  max-width: 90% !important;
+}
+
+/* Hide sidebar on pages with hide-sidebar metadata */
+body[data-hide-sidebar="true"] .bd-sidebar-primary {
+  display: none !important;
+}
+
+/* Expand content width when sidebar hidden */
+body[data-hide-sidebar="true"] .bd-main {
+  flex-grow: 1;
+  max-width: 75%;
+}

docs/source/_templates/footer_end.html

@@ -0,0 +1,7 @@
+<div class="things-in-a-row">
+    <a href="https://neuroinformatics.dev/" target="_blank" >
+        <img src="{{ pathto('_static/light-logo-niu.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
+        <img src="{{ pathto('_static/dark-logo-niu.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
+    </a>
+    <p class="sphinx-version">python-cookiecutter is based on <a href="https://github.com/napari/napari-plugin-template" target="_blank">cookiecutter-napari-plugin</a>.</p>
+</div>

docs/source/_templates/footer_start.html

@@ -0,0 +1,9 @@
+<p class="sphinx-version">
+    {% trans sphinx_version=sphinx_version|e %}Created using <a href="https://www.sphinx-doc.org/" target="_blank" >Sphinx</a> {{ sphinx_version }}.{% endtrans %}
+    <br/>
+    </p>
+    <p class="theme-version">
+    {{ _("Built with the") }}
+    <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html" target="_blank" >PyData Sphinx Theme</a>
+    {{ theme_version }}.
+    </p>

docs/source/_templates/sidebar-nav.html

@@ -0,0 +1,7 @@
+<div class="sidebar-header-items__center">
+    <nav class="bd-links" id="bd-docs-nav" aria-label="Main navigation">
+      <div class="bd-toc-item navbar-nav">
+        {{ toctree(maxdepth=2, includehidden=True, collapse=False) }}
+      </div>
+    </nav>
+  </div>

docs/source/conf.py

@@ -0,0 +1,142 @@
+# conf.py
+# Configuration file for the Sphinx documentation builder.
+import setuptools_scm
+
+
+project = "python-cookiecutter"
+copyright = "2025, University College London"
+author = "Neuroinformatics Unit"
+try:
+    full_version = setuptools_scm.get_version(root="../..", relative_to=__file__)
+    # Splitting the release on '+' to remove the commit hash
+    release = full_version.split('+', 1)[0]
+except LookupError:
+    # if git is not initialised, still allow local build
+    # with a dummy version
+    release = "0.0.0"
+
+# -- General configuration ---------------------------------------------------
+extensions = [
+    "myst_parser",
+    "sphinx_design",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.githubpages",
+    "sphinx_autodoc_typehints",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "sphinx_sitemap",
+    "nbsphinx",
+]
+
+# Configure MyST Parser
+myst_enable_extensions = [
+    "colon_fence",
+    "deflist",
+    "fieldlist",
+    "html_admonition",
+    "html_image",
+    "linkify",
+    "replacements",
+    "smartquotes",
+    "substitution",
+    "tasklist",
+    "attrs_inline"
+]
+
+myst_heading_anchors = 4
+
+source_suffix = {
+    '.md': 'markdown',
+    '.rst': 'restructuredtext'
+}
+
+templates_path = ['_templates']
+exclude_patterns = [
+    "**.ipynb_checkpoints",
+    "**/includes/**",
+]
+
+# -- HTML output options -----------------------------------------------------
+html_theme = 'pydata_sphinx_theme'
+html_logo = "_static/dark-logo-niu.png"
+html_static_path = ["_static"]
+html_title = "Python Cookiecutter"
+html_favicon = "_static/favicon.ico"
+
+
+html_theme_options = {
+    "navbar_start": ["navbar-logo"],
+    "navbar_center": ["navbar-nav"],
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/neuroinformatics-unit/python-cookiecutter",
+            "icon": "fa-brands fa-github",
+            "type": "fontawesome",
+        },
+        {
+            "name": "Zulip (chat)",
+            "url": "https://neuroinformatics.zulipchat.com/#narrow/channel/406003-Python-cookiecutter",
+            "icon": "fa-solid fa-comments",
+            "type": "fontawesome",
+        },
+    ],
+    "logo": {
+        "text": f"{project}",
+    },
+    "footer_start": ["footer_start"],
+    "footer_end": ["footer_end"],
+    "external_links": [],
+}
+
+# Sitemap configuration
+github_user = "neuroinformatics-unit"
+html_baseurl = "https://python-cookiecutter.neuroinformatics.dev"
+sitemap_url_scheme = "{link}"
+
+
+# -- HTML sidebar configuration ---------------------------------------------
+html_sidebars = {
+    # Apply sidebar to ALL pages except index
+    "**": ["sidebar-nav.html"],  
+    "index": []  
+}
+html_show_sourcelink = False
+
+
+def setup(app):
+    app.add_css_file("css/custom.css")
+
+
+# What to show on the 404 page
+notfound_context = {
+    "title": "Page Not Found",
+    "body": """
+    <h1>Page Not Found</h1>
+
+    <p>Sorry, we couldn't find that page.</p>
+
+    <p>We occasionally restructure the python-cookiecutter website, and some links may have broken.</p> 
+
+    <p>Try using the search box or go to the homepage.</p>
+""",
+}
+
+# needed for GH pages (vs readthedocs),
+# because we have no '/<language>/<version>/' in the URL
+notfound_urls_prefix = None
+
+# The linkcheck builder will skip verifying that anchors exist when checking
+# these URLs
+linkcheck_anchors_ignore_for_url = [
+    "https://neuroinformatics.zulipchat.com/",
+    "https://neuroinformatics.zulipchat.com/#narrow/channel/406003-Python-cookiecutter",
+    "https://github.com/pypa/setuptools_scm#default-versioning-scheme",
+]
+# A list of regular expressions that match URIs that should not be checked
+linkcheck_ignore = [
+    "https://github.com/",
+    "https://opensource.org/license/bsd-3-clause/",  # to avoid odd 403 error
+]