sccn · arnodelorme · Jun 12, 2026 · Jun 12, 2026
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -3,7 +3,6 @@ name: Documentation Build and Deploy
 on:
   push:
     branches:
-      - master
       - develop
     paths:
       - 'docs/**'
@@ -12,7 +11,6 @@ on:
       - '.github/workflows/docs.yml'
   pull_request:
     branches:
-      - master
       - develop
     paths:
       - 'docs/**'
@@ -59,7 +57,7 @@ jobs:
   deploy:
     name: Deploy to GitHub Pages
     needs: build
-    if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+    if: github.event_name == 'push' && github.ref == 'refs/heads/develop'
     runs-on: ubuntu-latest
     permissions:
       contents: write

diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -230,7 +230,7 @@ Or from source:
 
 .. code-block:: bash
 
-    git pull origin main
+    git pull origin develop
     pip install -e .
 
 Checking Your Version

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -14,7 +14,7 @@
 
 # -- Project information -------------------------------------------------------
 project = "eegprep"
-copyright = "2024 - , EEGPrep contributors"
+copyright = "2024-2026, EEGPrep contributors"
 author = "EEGPrep contributors"
 
 # Import version from eegprep package
@@ -38,7 +38,6 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.intersphinx",
     "sphinx_gallery.gen_gallery",
-    "sphinx_autodoc_typehints",
     "myst_parser",
     "sphinx_design",
     "sphinx_copybutton",
@@ -65,7 +64,7 @@
     # Navigation structure
     "navbar_start": ["navbar-logo"],
     "navbar_center": ["navbar-nav"],
-    "navbar_end": ["search-button.html", "navbar-icon-links"],
+    "navbar_end": ["theme-switcher", "search-button.html", "navbar-icon-links"],
     "navbar_persistent": [],
     "primary_sidebar_end": [],
     "footer_start": ["copyright"],
@@ -92,8 +91,9 @@
 html_context = {
     "github_user": "sccn",
     "github_repo": "eegprep",
-    "github_version": "main",
+    "github_version": "develop",
     "doc_path": "docs/source",
+    "default_mode": "light",
 }
 
 # -- Options for autodoc -------------------------------------------------------

diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
@@ -235,7 +235,7 @@ Before Submitting
 .. code-block:: bash
 
     git fetch upstream
-    git rebase upstream/main
+    git rebase upstream/develop
 
 2. Run tests locally:
 

diff --git a/docs/source/development.rst b/docs/source/development.rst
@@ -585,7 +585,7 @@ Git Conflicts
 .. code-block:: bash
 
     git fetch upstream
-    git rebase upstream/main
+    git rebase upstream/develop
     # Resolve conflicts in your editor
     git add .
     git rebase --continue

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -5,16 +5,20 @@ EEGPrep
 .. raw:: html
 
    <div class="eegprep-hero">
-     <div class="eegprep-kicker">Standalone EEG preprocessing for researchers</div>
-     <p>EEGPrep is a Python application for loading, cleaning, reviewing, and
-     scripting EEG datasets. It keeps familiar EEG workflow concepts where they
-     help, but the package, GUI, console, help, examples, and documentation are
-     EEGPrep-owned and work without a MATLAB or EEGLAB checkout.</p>
+     <div class="eegprep-kicker">EEGLAB workflows, modern Python tooling</div>
+     <p>EEGPrep is a modernized Python port of core
+     <a href="https://sccn.ucsd.edu/eeglab/">EEGLAB</a> preprocessing
+     workflows for EEG researchers. It preserves familiar concepts such as
+     <code>EEG</code>, <code>ALLEEG</code>, <code>pop_*</code> commands,
+     EEGBrowser review, ICA/component workflows, STUDY analyses, and command
+     history, while making those workflows easier to run, review, automate,
+     and share from Python.</p>
    </div>
 
-Use this manual as a working path, not only as an API index. Start with the
-sample datasets in ``sample_data/``, move between the Qt GUI and
-``eegprep-console``, then reuse the recorded ``pop_*`` commands in scripts.
+Use this manual to move from a first dataset to a reproducible workflow. Start
+with the sample data, try the same steps in the GUI and ``eegprep-console``,
+then turn the recorded ``pop_*`` history into scripts, pipelines, or
+agent-assisted analyses.
 
 .. grid:: 1 1 2 2
    :gutter: 2
@@ -53,6 +57,13 @@ sample datasets in ``sample_data/``, move between the Qt GUI and
 
       Convert menu history into reusable Python scripts and batch workflows.
 
+   .. grid-item-card:: Work With Research Agents
+      :link: user_guide/agent_cli
+      :link-type: doc
+
+      Use the EEGPrep CLI, JSON outputs, manifests, pipeline plans, and bundled
+      agent skill guidance for AI-assisted EEG research projects.
+
 Manual
 ======
 
@@ -125,6 +136,14 @@ Where EEGLAB Users Should Go First
    * - MNE-Python interop
      - :doc:`user_guide/mne_integration`
 
+Core Maintainers
+================
+
+- `Arnaud Delorme <https://arnauddelorme.com/>`_, UCSD, CA, USA
+- `Suraj Ranganath <https://surajr.dev/>`_, UCSD, CA, USA
+- Christian Kothe, Intheon, CA, USA
+- Bruno Aristimunha Pinto, Inria, France
+
 Indices
 =======
 

diff --git a/docs/source/user_guide/agent_cli.rst b/docs/source/user_guide/agent_cli.rst
@@ -9,10 +9,34 @@ reproducible preprocessing pipelines. It complements the human-facing
 ``eegprep-gui`` and ``eegprep-console`` entry points; it does not replace the
 shared GUI plus console workspace.
 
+To get started, point your AI agent at this page or at the EEGPrep repository.
+The documentation, bundled CLI skill, and repository ``AGENTS.md`` file provide
+the context agents need to use EEGPrep commands safely and reproducibly.
+
 The CLI is organized around researcher workflows rather than internal modules:
 inspect, validate, filter, rereference, resample, epoch, ICA, QC, reports,
 pipelines, BIDS, and EEGLAB migration helpers.
 
+For EEG Researchers Working With Agents
+=======================================
+
+Start agents from EEGPrep's machine-readable CLI instead of asking them to guess
+Python calls from prose documentation. A practical workflow is:
+
+* use ``eegprep skills get eegprep-cli`` to give the agent version-matched
+  EEGPrep CLI rules and examples;
+* use ``eegprep inspect`` and ``eegprep validate`` before changing data;
+* use ``eegprep pipeline plan`` or ``--dry-run`` before expensive processing;
+* use ``--json`` and manifests so the agent can make decisions from structured
+  results and provenance;
+* review generated HTML reports and QC summaries before accepting changes.
+
+When an agent is working inside the EEGPrep source repository rather than on
+your research data, use the project skills under ``.agents/skills/``:
+``eegprep-extension-development`` for creating extensions,
+``eegprep-feature-development`` for contributing EEGPrep features, and
+``eeglab-gui-visual-parity`` for GUI parity work.
+
 Agent Contract
 ==============
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -58,7 +58,6 @@ docs = [
   "sphinx>=7.0",
   "pydata-sphinx-theme>=0.14.0",
   "sphinx-gallery>=0.14.0",
-  "sphinx-autodoc-typehints>=1.25.0",
   "numpydoc>=1.6.0",
   "sphinx-design>=0.5.0",
   "myst-parser>=1.0.0",