Add website

.gitattributes

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+* text=auto eol=lf

.github/workflows/cookiecutter_docs.yml

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+name: Documentation
+on:
+  push:
+    branches: [main]
+    tags: ['*']
+
+jobs:
+  deploy-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.13'
+
+    - name: Install dependencies
+      run: |
+        pip install -r docs/requirements.txt
+
+    - name: Build docs
+      run: |
+        cd docs
+        make clean && make html
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs/build/html

docs/Makefile

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+# 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

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+@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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+myst-parser
+pydata-sphinx-theme
+sphinx

docs/source/_static/css/custom.css

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+/* Top navbar */
+.navbar {
+    display: flex;
+    justify-content: space-between;
+    align-items: center;
+    padding: 0.8rem 2rem;
+    background: transparent;
+}
+
+.navbar-brand {
+    flex: 0 0 auto;
+}
+
+.navbar-center-group {
+    flex: 1;
+    display: flex;
+    justify-content: center;
+    gap: 2rem;
+    margin: 0 2rem;
+    float: right;
+}
+
+.navbar-nav {
+    display: flex;
+    gap: 1.5rem;
+    margin: 0;
+    padding: 0;
+    align-items: center;
+}
+
+.navbar-icons {
+    display: flex;
+    gap: 1.5rem;
+    align-items: center;
+}
+
+.navbar-brand-logo img { height: 40px; }
+.nav-link { color: white !important; font-weight: 500; }
+.icon-link { color: white !important; font-size: 1.2rem; }
+.bd-sidebar-secondary { display: none !important; }
+
+/* Mobile responsiveness */
+@media (max-width: 768px) {
+    .navbar {
+        flex-wrap: wrap;
+        padding: 0.8rem;
+    }
+
+    .navbar-center-group {
+        order: 2;
+        width: 100%;
+        margin: 1rem 0;
+        justify-content: center;
+    }
+
+    .navbar-brand {
+        order: 1;
+    }
+}

docs/source/_templates/navbar.html

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+<nav class="bd-navbar navbar">
+  <!-- Center: Navigation items -->
+  <div class="navbar-center-group">
+    <ul class="nav navbar-nav">
+      <li class="nav-item">
+        <a class="nav-link" href="{{ pathto('index') }}">About</a>
+      </li>
+      <li class="nav-item">
+        <a class="nav-link" href="{{ pathto('contributing') }}">Contribute</a>
+      </li>
+    </ul>
+  </div>
+
+</nav>

docs/source/_templates/sidebar-nav.html

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+<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

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+# conf.py
+# Configuration file for the Sphinx documentation builder.
+project = 'cookiecutter-python'
+copyright = "2025, Neuroinformatics Unit"
+author = 'NIU'
+release = "1.0.0"
+
+# -- 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/logo.png"
+html_static_path = ["_static"]
+html_title = "Python Cookiecutter"
+html_favicon = "_static/favicon.ico"
+html_show_sourcelink = False
+
+html_theme_options = {
+    "navbar_start": ["navbar-logo"],
+    "navbar_center": ["navbar.html"],
+    "navbar_end": ["theme-switcher", "navbar-icon-links"],
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/neuroinformatics-unit/python-cookiecutter",
+            "icon": "fa-brands fa-github",
+            "type": "fontawesome",
+        }
+    ],
+    "logo": {
+        "text": "Python Cookiecutter",
+        "image_light": "logo.png",
+        "image_dark": "logo.png",
+    },
+    "show_nav_level": 2,
+    "navigation_depth": 3,
+    "collapse_navigation": True,
+}
+
+# Sitemap configuration
+html_baseurl = "https://neuroinformatics-unit.github.io/python-cookiecutter/"
+sitemap_url_scheme = "{link}"
+
+
+html_sidebars = {
+    "**": ["sidebar-nav.html"]
+}
+
+def setup(app):
+    app.add_css_file("css/custom.css")

docs/source/contributing.md

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+# Contributing to cookiecutter-python
+
+Thank you for considering contributing to cookiecutter-python! We welcome contributions that improve the project, whether it's code,
+documentation, or enhancements.
+
+Please follow the guidelines below to ensure a smooth process.
+
+1. **Fork and Clone the Repository** Fork the main repository on
+    GitHub, then clone your fork locally:
+
+    ``` sh
+    git clone https://github.com/<your-username>/python-cookiecutter.git
+    cd python-cookiecutter
+    ```
+
+2. **Create a New Branch** Create and switch to a new branch for your
+    changes:
+
+    ``` sh
+    git checkout -b my_new_feature
+    ```
+
+3. **Make Your Changes** Edit the content, code, or
+    documentation as needed. When you're ready, add and commit your
+    changes with a descriptive message:
+
+    ``` sh
+    git add .
+    git commit -m "Describe your changes in short here"
+    ```
+
+4. **Push Your Branch and Create a Pull Request** Push the new branch
+    to GitHub:
+
+    ``` sh
+    git push origin --set-upstream origin my_new_feature
+    ```
+
+    Then, open a pull request against the ``main`` branch of the main repository. This will automatically trigger a GitHub Action to verify that the builds correctly.
+
+5. **Review and Merge** If the build checks pass, assign someone to review your pull request. Once approved and merged into the ``main`` branch, another GitHub Action will build and add your changes to the ``main`` branch.
+
+
+## Documentation Local Testing
+
+If you are contributing to the Documentation, Before pushing your changes, you can test locally:
+
+-   **First-Time Setup:** Install the required dependencies and build
+    the docs:
+
+    ``` sh
+    pip install -r docs/requirements.txt
+    sphinx-build docs/source docs/build
+    ```
+
+Alternatively, you can use the following commands to install the
+dependencies and build the docs:
+
+ ``` sh
+pip install -r docs/requirements.txt
+cd docs
+make html
+```
+
+- **Rebuilding:** Each time you update the documentation,
+    rebuild the docs by running:
+
+    ``` sh
+    rm -rf docs/build && sphinx-build docs/source docs/build
+    ```
+    or
+
+    ```sh
+    cd docs
+    make clean && make html
+    ```
+
+    Then, open `docs/build/index.html` in your browser to preview the changes.
+
+
+Thank you for your contributions!

docs/source/documentation.md

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+# Documentation
+
+Software documentation is important for effectively communicating how to use the software to others as well as to your future self.
+
+If you want to include documentation in your package, make sure to respond with `1 - Yes` when prompted during the `cookiecutter` setup. This will instantiate a `docs` folder with a skeleton documentation system, that you can build upon.
+
+The documentation source files are located in the `docs/source` folder and should be written in either [reStructuredText](https://docutils.sourceforge.io/rst.html) or [markdown](https://myst-parser.readthedocs.io/en/stable/syntax/typography.html). The `index.rst` file corresponds to the main page of the documentation website. Other `.rst`  or `.md` files can be included in the main page via the `toctree` directive.
+
+The documentation is built using [Sphinx](https://www.sphinx-doc.org/en/master/) and the [PyData Sphinx Theme](https://pydata-sphinx-theme.readthedocs.io/en/latest/). The `docs/source/conf.py` file contains the `Sphinx` configuration.
+
+## Building the documentation locally
+You can build and view the documentation website locally, on your machine. To do so, run the following commands from the root of your project:
+
+```sh
+# Install the documentation build dependencies
+pip install -r docs/requirements.txt
+# Build the documentation
+sphinx-build docs/source docs/build
+```
+This should create a `docs/build` folder. You can view the local build by opening `docs/build/index.html` in a browser.
+To refresh the documentation, after making changes, remove the `docs/build` folder and re-run the above command:
+
+```sh
+rm -rf docs/build
+sphinx-build docs/source docs/build
+```
+
+### Publishing the documentation
+We have included an extra GitHub actions workflow in `.github/workflows/docs_build_and_deploy.yml` that will build the documentation and deploy it to [GitHub pages](https://pages.github.com/).
+* The build step is triggered every time a pull request is opened or a push is made to the `main` branch. This way you can make sure that the documentation does not break before merging your changes.
+* The deployment is triggered only when a tag is present (see [Automated versioning](versioning.md)). This ensures that new documentation versions are published in tandem with the release of a new package version on PyPI (see [GitHub actions workflow](github_actions_setup.md)).
+* The published docs are by default hosted at `https://<github_username_or_organization>.github.io/<package_name>/`. To enable hosting, you will need to go to the settings of your repository, and under the "Pages" section, select the `gh-pages` branch as the source for your GitHub pages site.
+* A popular alternative to GitHub pages for hosting the documentation is [Read the Docs](https://readthedocs.org/). To enable hosting on Read the Docs, you will need to create an account on the website and follow the instructions to link your GitHub repository to your Read the Docs account.
+
+### Docstrings and API documentation
+The journey towards good documentation starts with writing docstrings for all functions in your module code. In the example `math.py` and `greetings.py` modules you will find some docstrings that you can use as a template. We have written the example docstrings following the [numpy style](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html) but you may also choose another widely used style, such as the [Google style](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
+
+Once you have written docstrings for all your functions, API documentation can be automatically generated via the [Sphinx autodoc extension](https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html). We have given examples of how to do this in the `docs/source/api_index.rst` file.

docs/source/github_actions_setup.md

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+# GitHub actions workflow
+
+A GitHub actions workflow (`.github/workflows/test_and_deploy.yml`) has been set up to run (on each commit/PR):
+* Linting checks (pre-commit).
+* Testing (only if linting checks pass)
+* Release to PyPI (only if a git tag is present and if tests pass). Requires `TWINE_API_KEY` from PyPI to be set in repository secrets.
+
+This automation ensures that each commit or pull request is validated and that releases are published only when all checks pass.