SCIInstitute · jessdtate · Oct 8, 2021 · Jun 8, 2021 · Jun 9, 2021 · Jun 11, 2021
diff --git a/.gitignore b/.gitignore
@@ -24,13 +24,12 @@ src/Doxyfile
 *.orig
 CMakeCache.txt
 CMakeFiles
-Makefile
+src/Makefile
 cmake_install.cmake
 install_manifest.txt
 CTestTestfile.cmake
 DartConfiguration.tcl
 cmake
 
-# docs site
-_site
-.sass-cache
+# Sphinx builds
+docs/_build/
diff --git a/docs/BasicTutorial.md b/docs/BasicTutorial.md
diff --git a/docs/Gemfile b/docs/Gemfile
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# 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) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_config.yml b/docs/_config.yml
diff --git a/docs/_includes/carousel.html b/docs/_includes/carousel.html
diff --git a/docs/_includes/disqus.html b/docs/_includes/disqus.html
diff --git a/docs/_includes/footer.html b/docs/_includes/footer.html
diff --git a/docs/_includes/google_analytics.html b/docs/_includes/google_analytics.html
diff --git a/docs/_includes/header.html b/docs/_includes/header.html
diff --git a/docs/_includes/moduleLink.md b/docs/_includes/moduleLink.md
diff --git a/docs/_includes/modules/AddLinkedNodesToLinearSystem.md b/docs/_includes/modules/AddLinkedNodesToLinearSystem.md
diff --git a/docs/_includes/modules/BuildMappingMatrix.md b/docs/_includes/modules/BuildMappingMatrix.md
diff --git a/docs/_includes/modules/BuildMatrixOfSurfaceNormals.md b/docs/_includes/modules/BuildMatrixOfSurfaceNormals.md
diff --git a/docs/_includes/modules/BuildNoiseColumnMatrix.md b/docs/_includes/modules/BuildNoiseColumnMatrix.md
diff --git a/docs/_includes/modules/BuildSurfaceLaplacianMatrix.md b/docs/_includes/modules/BuildSurfaceLaplacianMatrix.md
diff --git a/docs/_includes/modules/CalcTMP.md b/docs/_includes/modules/CalcTMP.md