Deltares-research · dalmijn · Jun 1, 2026 · Jun 2, 2026 · Jun 2, 2026
diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml
@@ -54,13 +54,13 @@ jobs:
           pixi run -e docs docs-html
           echo "DOC_VERSION=$(pixi run --locked -e docs python -c 'from workflowpy import __version__ as v; print("dev" if "dev" in v else "v"+v.replace(".dev",""))')" >> $GITHUB_ENV
 
-      # - name: Upload to GitHub Pages
-      #   if: ${{ github.event_name != 'pull_request' && !github.event.act }}
-      #   uses: peaceiris/actions-gh-pages@84c30a85c19949d7eee79c4ff27748b70285e453
-      #   with:
-      #     github_token: ${{ secrets.GITHUB_TOKEN }}
-      #     publish_dir: ./docs/_build/html
-      #     exclude_assets: .buildinfo,_sources/*,_examples/*.ipynb
-      #     destination_dir: ./${{ env.DOC_VERSION }}
-      #     keep_files: false
-      #     full_commit_message: Deploy ${{ env.DOC_VERSION }} to GitHub Pages
+      - name: Upload to GitHub Pages
+        if: ${{ !github.event.act }}
+        uses: peaceiris/actions-gh-pages@84c30a85c19949d7eee79c4ff27748b70285e453
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/_build/html
+          exclude_assets: .buildinfo,_sources/*,_examples/*.ipynb
+          destination_dir: ./${{ env.DOC_VERSION }}
+          keep_files: false
+          full_commit_message: Deploy ${{ env.DOC_VERSION }} to GitHub Pages
diff --git a/docs/_static/icon.svg b/docs/_static/icon.svg
diff --git a/docs/_templates/autosummary/class_pydantic.rst b/docs/_templates/autosummary/class_pydantic.rst
@@ -0,0 +1,38 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :member-order: bysource
+   :class-doc-from: class
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+      :nosignatures:
+   {% for item in methods %}
+      {% if item not in inherited_members %}
+      {%- if not item.startswith('_') %}
+      ~{{ name }}.{{ item }}
+      {%- endif -%}
+      {%- endif %}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      {% if item not in inherited_members %}
+      ~{{ name }}.{{ item }}
+      {%- endif %}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
diff --git a/docs/_templates/autosummary/module.rst b/docs/_templates/autosummary/module.rst
@@ -0,0 +1,4 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+   :members:
diff --git a/docs/api.rst b/docs/api.rst
diff --git a/docs/api/core.rst b/docs/api/core.rst
@@ -0,0 +1,55 @@
+.. currentmodule:: workflowpy
+
+.. raw:: html
+
+    <style>
+        /* Default (light mode) */
+        html[data-theme="light"] h2 {
+            border-bottom: 1px solid #000;
+        }
+        /* Dark mode */
+        html[data-theme="dark"] h2 {
+            border-bottom: 1px solid #d1d5db;
+        }
+    </style>
+
+.. _api_core:
+
+Core functionality
+==================
+These are the core functions & classes of workflowpy.
+
+Workflow
+--------
+
+.. autosummary::
+   :toctree: ../_generated
+   :template: autosummary/class_pydantic.rst
+   :nosignatures:
+
+   Workflow
+   WorkflowConfig
+
+Rule
+----
+
+.. autosummary::
+   :toctree: ../_generated
+   :template: autosummary/class_pydantic.rst
+   :nosignatures:
+
+   Rule
+   Wildcards
+
+Method
+------
+
+.. autosummary::
+   :toctree: ../_generated
+   :template: autosummary/class_pydantic.rst
+   :nosignatures:
+
+   Method
+   ExpandMethod
+   ReduceMethod
+   Parameters
diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -0,0 +1,29 @@
+.. _api_index:
+
+=============
+API reference
+=============
+
+This is the API reference of workflowpy.
+
+
+.. list-table::
+   :widths: 30 70
+   :header-rows: 1
+
+   * - Section
+     - Information
+   * - :ref:`api_core`
+     - All core functionality of workflowpy
+   * - :ref:`api_methods`
+     - The built-in methods
+   * - :ref:`api_utils`
+     - The utiliy functions
+
+.. toctree::
+    :maxdepth: 1
+    :hidden:
+
+    core.rst
+    methods.rst
+    utils.rst
diff --git a/docs/api/methods.rst b/docs/api/methods.rst
@@ -0,0 +1,42 @@
+.. currentmodule:: workflowpy.methods
+
+.. raw:: html
+
+    <style>
+        /* Default (light mode) */
+        html[data-theme="light"] h2 {
+            border-bottom: 1px solid #000;
+        }
+        /* Dark mode */
+        html[data-theme="dark"] h2 {
+            border-bottom: 1px solid #d1d5db;
+        }
+    </style>
+
+.. _api_methods:
+
+Methods
+=======
+These are the built-in methods of workflowpy.
+
+Script Method
+---------------------
+
+Python scripts can directly be added to a workflow using the `ScriptMethod` class.
+
+.. autosummary::
+   :toctree: ../_generated
+   :template: autosummary/class.rst
+
+   script.ScriptMethod
+
+Script Method parameters
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autosummary::
+   :toctree: ../_generated
+   :template: autosummary/class.rst
+
+   script.ScriptInput
+   script.ScriptOutput
+   script.ScriptParams
diff --git a/docs/api/utils.rst b/docs/api/utils.rst
@@ -0,0 +1,29 @@
+.. currentmodule:: workflowpy
+
+.. raw:: html
+
+    <style>
+        /* Default (light mode) */
+        html[data-theme="light"] h2 {
+            border-bottom: 1px solid #000;
+        }
+        /* Dark mode */
+        html[data-theme="dark"] h2 {
+            border-bottom: 1px solid #d1d5db;
+        }
+    </style>
+
+.. _api_utils:
+
+Utility
+=======
+These are the utility functions of workflowpy.
+
+Logging
+-------
+
+.. autosummary::
+   :toctree: ../_generated
+
+   log.setuplog
+   log.add_filehandler
diff --git a/docs/conf.py b/docs/conf.py
@@ -64,7 +64,7 @@ def remove_dir_content(path: str) -> None:
 source_suffix = ".rst"
 templates_path = ["_templates"]
 
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "links.rst"]
 language = "en"
 master_doc = "index"
 pygments_style = "sphinx"
@@ -89,8 +89,8 @@ def remove_dir_content(path: str) -> None:
 }
 
 html_css_files = ["theme.css"]
-# html_favicon = "_static/icon.svg"
-# html_logo = "_static/icon.svg"
+html_favicon = "_static/icon.svg"
+html_logo = "_static/icon.svg"
 html_show_sourcelink = False
 html_static_path = ["_static"]
 html_theme = "pydata_sphinx_theme"
@@ -128,6 +128,11 @@ def remove_dir_content(path: str) -> None:
 
 remove_from_toctrees = ["_generated/*"]
 
+# Add information to the back of every page
+rst_epilog = ""
+with open("links.rst") as f:
+    rst_epilog += f.read()
+
 # -- Options for manual page output ---------------------------------------
 
 man_pages = [(master_doc, "workflowpy", "workflowpy Documentation", [author], 1)]

diff --git a/docs/dev/index.rst b/docs/dev/index.rst
@@ -7,7 +7,6 @@ These pages provide guidelines on how to contribute to workflowpy.
 Furthermore it informs you on planned developments and new features.
 
 .. toctree::
-   :caption: Table of Contents
    :maxdepth: 2
    :hidden:
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -4,7 +4,7 @@
    :titlesonly:
    :hidden:
 
-   setup_guide/index.rst
+   overview/index.rst
    user_guide/index.rst
-   api.rst
+   api/index.rst
    dev/index.rst
diff --git a/docs/links.rst b/docs/links.rst
@@ -0,0 +1,2 @@
+.. _SnakeMake: https://snakemake.readthedocs.io/en/stable/
+.. _CWL: https://www.commonwl.org/
diff --git a/docs/overview/index.rst b/docs/overview/index.rst
@@ -0,0 +1,50 @@
+.. _overview_index:
+
+===============
+Getting started
+===============
+
+.. grid:: 2
+    :gutter: 1
+
+    .. grid-item-card::
+        :text-align: center
+        :link: overview_install_guide
+        :link-type: ref
+
+        :octicon:`gear;10em`
+        +++
+        Installation guide
+
+    .. grid-item-card::
+        :text-align: center
+        :link: user_guide_index
+        :link-type: ref
+
+        :octicon:`book;10em`
+        +++
+        User guide
+
+    .. grid-item-card::
+        :text-align: center
+        :link: user_guide_examples
+        :link-type: ref
+
+        :octicon:`graph;10em`
+        +++
+        Examples
+
+    .. grid-item-card::
+        :text-align: center
+        :link: api_index
+        :link-type: ref
+
+        :octicon:`list-unordered;10em`
+        +++
+        API reference
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+   install.rst
diff --git a/docs/overview/install.rst b/docs/overview/install.rst
@@ -0,0 +1,4 @@
+.. _overview_install_guide:
+
+Installation guide
+==================
diff --git a/docs/setup_guide/index.rst b/docs/setup_guide/index.rst
diff --git a/docs/user_guide/create.rst b/docs/user_guide/create.rst
@@ -0,0 +1,4 @@
+.. _user_guide_create:
+
+Create your own
+===============
diff --git a/docs/user_guide/example.rst b/docs/user_guide/example.rst
@@ -0,0 +1,4 @@
+.. _user_guide_examples:
+
+Examples
+========
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		.. _SnakeMake: https://snakemake.readthedocs.io/en/stable/
		.. _CWL: https://www.commonwl.org/