Creating documentation and update eegprep functions

.github/workflows/docs.yml

@@ -0,0 +1,56 @@
+name: Documentation Build and Deploy
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - main
+      - develop
+
+permissions:
+  contents: write
+
+jobs:
+  build-docs:
+    name: Build Documentation
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[all]"
+
+      - name: Build HTML documentation
+        run: |
+          cd docs
+          make html
+        env:
+          SPHINXOPTS: ""
+
+      - name: Upload documentation artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: documentation
+          path: docs/build/html/
+          retention-days: 7
+
+      - name: Deploy to GitHub Pages
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/build/html
+          publish_branch: gh-pages

.gitignore

@@ -101,3 +101,9 @@ matlab/clean_rawdata
 
 # for now excluded; may introduce for purposes of hard-locking dev deps
 uv.lock
+
+*.DS_Store
+
+# Sphinx documentation
+docs/build/
+docs/source/auto_examples/

README.md

@@ -1,7 +1,12 @@
 # EEGPrep
 
+[![Documentation Status](https://github.com/sccn/eegprep/actions/workflows/docs.yml/badge.svg)](https://github.com/sccn/eegprep/actions/workflows/docs.yml)
+[![GitHub Pages](https://github.com/sccn/eegprep/actions/workflows/pages.yml/badge.svg)](https://sccn.github.io/eegprep/)
+
 EEGPrep is a Python package that reproduces the EEGLAB default preprocessing pipeline with numerical accuracy down to 1e-5 uV, including clean_rawdata and ICLabel, enabling MATLAB-to-Python equivalence for EEG analysis. It takes BIDS data as input and produces BIDS derivative dataset as output, which can then be reimported into other packages as needed (EEGLAB, Fieldtrip, Brainstorm, MNE). It does produce plots. The package will be fully documented for conversion, packaging, and testing workflows, with installation available via PyPI.
 
+**📚 [View Full Documentation](https://sccn.github.io/eegprep/)** | **🔧 [GitHub Pages Setup Guide](docs/GITHUB_PAGES_SETUP.md)**
+
 ## Pre-Release
 
 EEGPrep is currently in a pre-release phase. It functions end-to-end (bids branch) but has not yet been tested with multiple BIDS datasets. The documentation is incomplete, and use is at your own risk. The planned release is scheduled for the end of 2025.

docs/Makefile

@@ -0,0 +1,83 @@
+# Makefile for Sphinx documentation
+#
+# You can set these variables from the command line.
+SPHINXBUILD   ?= sphinx-build
+SPHINXOPTS    ?= --keep-going
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make help" is always printed when you enter `make` without arguments
+.PHONY: help
+help:
+	@echo "Sphinx documentation build targets:"
+	@echo ""
+	@echo "  make html       - Build HTML documentation"
+	@echo "  make clean      - Remove build artifacts"
+	@echo "  make linkcheck  - Check for broken links"
+	@echo "  make spelling   - Check spelling"
+	@echo "  make serve      - Serve documentation locally on port 8000"
+	@echo ""
+	@echo "Variables:"
+	@echo "  SPHINXBUILD   = $(SPHINXBUILD)"
+	@echo "  SPHINXOPTS    = $(SPHINXOPTS)"
+	@echo "  SOURCEDIR     = $(SOURCEDIR)"
+	@echo "  BUILDDIR      = $(BUILDDIR)"
+
+# Clean build artifacts
+.PHONY: clean
+clean:
+	@echo "Removing build artifacts..."
+	@rm -rf $(BUILDDIR)
+	@rm -rf $(SOURCEDIR)/auto_examples
+	@echo "Build artifacts removed successfully."
+
+# Build HTML documentation
+.PHONY: html
+html:
+	@echo "Building HTML documentation..."
+	@$(SPHINXBUILD) -b html $(SPHINXOPTS) $(SOURCEDIR) $(BUILDDIR)/html
+	@if [ $$? -eq 0 ]; then \
+		echo ""; \
+		echo "Build finished successfully! The HTML pages are in $(BUILDDIR)/html"; \
+	else \
+		echo "Build failed!"; \
+		exit 1; \
+	fi
+
+# Check for broken links
+.PHONY: linkcheck
+linkcheck:
+	@echo "Checking for broken links..."
+	@$(SPHINXBUILD) -b linkcheck $(SPHINXOPTS) $(SOURCEDIR) $(BUILDDIR)/linkcheck
+	@if [ $$? -eq 0 ]; then \
+		echo ""; \
+		echo "Link check finished! Results are in $(BUILDDIR)/linkcheck"; \
+	else \
+		echo "Link check failed!"; \
+		exit 1; \
+	fi
+
+# Check spelling
+.PHONY: spelling
+spelling:
+	@echo "Checking spelling..."
+	@$(SPHINXBUILD) -b spelling $(SPHINXOPTS) $(SOURCEDIR) $(BUILDDIR)/spelling
+	@if [ $$? -eq 0 ]; then \
+		echo ""; \
+		echo "Spelling check finished! Results are in $(BUILDDIR)/spelling"; \
+	else \
+		echo "Spelling check failed!"; \
+		exit 1; \
+	fi
+
+# Serve documentation locally
+.PHONY: serve
+serve: html
+	@echo "Serving documentation on http://localhost:8000"
+	@echo "Press Ctrl+C to stop the server"
+	@cd $(BUILDDIR)/html && python -m http.server 8000
+
+# 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) -b $@ $(SPHINXOPTS) $(SOURCEDIR) $(BUILDDIR)/$@