Improved documentation, removed doxygen (#12)

* Improved documentation, removed doxygen

* Added Ewald descirption

Author: simongravelle

docs/Makefile

@@ -1,16 +1,12 @@
-# Docs Makefile - builds Doxygen + Sphinx docs
+# Docs Makefile - builds Sphinx docs only
 
 # Sphinx configuration
 SPHINXBUILD   ?= sphinx-build
 SPHINXOPTS    ?=
 SOURCEDIR     = source
 BUILDDIR      = build
 
-# Doxygen configuration
-DOXYFILE      ?= doxyfile
-DOXYGEN_XML   = $(SOURCEDIR)/xml
-
-.PHONY: help doxygen html clean all
+.PHONY: help html clean all
 
 # Default target: build HTML docs
 all: html
@@ -19,23 +15,17 @@ all: html
 help:
 	@echo "Usage: make [target]"
 	@echo "Targets:"
-	@echo "  html      - build HTML docs (runs Doxygen first)"
-	@echo "  doxygen   - generate Doxygen XML for Sphinx"
+	@echo "  html      - build HTML docs"
 	@echo "  clean     - remove generated files"
 
-# Generate Doxygen XML
-doxygen:
-	@echo "Generating Doxygen XML..."
-	@doxygen $(DOXYFILE)
-
-# Build HTML docs (runs Doxygen first)
-html: doxygen
+# Build HTML docs
+html:
 	@echo "Building Sphinx HTML..."
 	@$(SPHINXBUILD) -b html "$(SOURCEDIR)" "$(BUILDDIR)/html" $(SPHINXOPTS)
 	@echo "HTML docs built in $(BUILDDIR)/html"
 
-# Clean Sphinx build and Doxygen XML
+# Clean Sphinx build
 clean:
-	@echo "Cleaning Sphinx build and Doxygen XML..."
-	@rm -rf $(BUILDDIR) $(DOXYGEN_XML)
+	@echo "Cleaning Sphinx build..."
+	@rm -rf $(BUILDDIR)
 	@echo "Clean complete"

docs/build.sh

@@ -3,23 +3,29 @@ set -euo pipefail
 
 # ------------------------------------------------------------------------------
 # MANIAC-MC Documentation Build Script
-# ------------------------------------------------------------------------------
 # 1. Reads the version number from version.txt (repository root)
 # 2. Updates the 'release' variable in Sphinx conf.py
-# 3. Builds the documentation using the Makefile (Doxygen + Sphinx)
+# 3. Builds the documentation using Sphinx
 # ------------------------------------------------------------------------------
 
 ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
 DOCS_DIR="$ROOT_DIR/docs"
 CONF_FILE="$DOCS_DIR/source/conf.py"
 VERSION_FILE="$ROOT_DIR/version.txt"
 
+# --- Step 0: Optional clean ---------------------------------------------------
+if [[ "${1:-}" == "clean" ]]; then
+    echo "Cleaning build directory..."
+    rm -rf "$DOCS_DIR/build"
+    echo "Clean complete."
+    exit 0
+fi
+
 # --- Step 1: Read version number ---------------------------------------------
 if [[ ! -f "$VERSION_FILE" ]]; then
     echo "Error: version.txt not found at $VERSION_FILE"
     exit 1
 fi
-
 VERSION=$(tr -d '[:space:]' < "$VERSION_FILE")
 echo "Using version: $VERSION"
 
@@ -28,13 +34,11 @@ if [[ ! -f "$CONF_FILE" ]]; then
     echo "Error: conf.py not found at $CONF_FILE"
     exit 1
 fi
-
 echo "Updating conf.py with version: $VERSION"
 sed -i "s/^release = .*/release = '${VERSION}'/" "$CONF_FILE"
 
 # --- Step 3: Build documentation ---------------------------------------------
 cd "$DOCS_DIR"
 echo "Running 'make html'..."
 make html
-
 echo "Documentation build complete."