From 3874fde510005f389563a140e0ca3e993550f2a5 Mon Sep 17 00:00:00 2001 From: Suraj Ranganath Date: Fri, 12 Jun 2026 09:44:34 -0700 Subject: [PATCH] Fix docs deploy branch and warning noise --- .github/workflows/docs.yml | 4 +- docs/source/changelog.rst | 2 +- docs/source/conf.py | 8 +- docs/source/contributing.rst | 2 +- docs/source/development.rst | 2 +- docs/source/index.rst | 35 ++++++-- docs/source/user_guide/agent_cli.rst | 24 ++++++ pyproject.toml | 1 - uv.lock | 118 +++++---------------------- 9 files changed, 78 insertions(+), 118 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 0f865617..74e0e99a 100644 --- 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 index d9c1b1cb..72d05322 100644 --- 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 index b3107291..5e8be010 100644 --- 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 index d5226922..403e4df0 100644 --- 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 index ed86b16b..5740ced4 100644 --- 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 index 5b539ff9..d5f4fb7a 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -5,16 +5,20 @@ EEGPrep .. raw:: html
-
Standalone EEG preprocessing for researchers
-

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.

+
EEGLAB workflows, modern Python tooling
+

EEGPrep is a modernized Python port of core + EEGLAB preprocessing + workflows for EEG researchers. It preserves familiar concepts such as + EEG, ALLEEG, pop_* commands, + EEGBrowser review, ICA/component workflows, STUDY analyses, and command + history, while making those workflows easier to run, review, automate, + and share from Python.

-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 `_, UCSD, CA, USA +- `Suraj Ranganath `_, 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 index be8a0488..680ba43f 100644 --- 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 index b707724e..ead0098a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,6 @@ docs = [ "sphinx>=7.0", 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