fixed documentation build erros and added makefile.

.gitignore

@@ -1,3 +1,3 @@
 *.swp
 doctrees
-
+build

Makefile

@@ -1,34 +1,183 @@
 # Makefile for Sphinx documentation
 #
+
 GH_SOURCE_DIRS = source 
-GH_BUILT_DIRS = 
+GH_BUILT_DIRS = _images _sources people projects papers 
+GH_BUILT_FILES = index.html
 
-GH_CURRENT_BRANCH = $(shell git branch 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/\1/')
 GH_SOURCE_BRANCH = source
 GH_BUILD_BRANCH = master
 
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = ./build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
 
-.PHONY: help gh-preview gh-pages
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  gh-preview to update branch $(GH_BUILD_BRANCH) with new HTML based on content"
-	@echo "                  from branch $(GH_CURRENT_BRANCH) for previewing"
-	@echo "  gh-pages   to update branch $(GH_BUILD_BRANCH) with new HTML based on content"
-	@echo "                  from branch $(GH_SOURCE_BRANCH) and push it to the server LIVE"
+	@echo "  gh-preview to build HTML in directory $BUILDDIR for testing"
+	@echo "  gh-revert  to cleanup HTML build in directory $BUILDDIR after testing"
+	@echo "  gh-pages   final build and push from source branch to master branch"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
-gh-preview:
-	git checkout $(GH_BUILD_BRANCH)
-	git checkout $(GH_CURRENT_BRANCH) $(GH_SOURCE_DIRS)
-	git reset HEAD 
-	make html
-	make gh-install
+clean:
+	-rm -rf $(GH_BUILT_DIRS) $(GH_BUILT_FILES)
+
+gh-preview html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)."
+
+gh-revert:
+	-rm -rf $(BUILDDIR)
 
 gh-pages:
 	git checkout $(GH_BUILD_BRANCH)
-	git checkout $(GH_SOURCE_BRANCH) $(GH_SOURCE_DIRS)
+	git checkout $(GH_SOURCE_BRANCH) -- $(GH_SOURCE_DIRS)
 	git reset HEAD 
 	make html
-	make gh-install
-	make gh-push
+	rsync -a $(BUILDDIR)/* .
+	rm -rf $(GH_SOURCE_DIRS) build
+	git add -A 
+	git commit -m "Generated $(GH_BUILD_BRANCH) for `git log $(GH_SOURCE_BRANCH) -1 --pretty=short --abbrev-commit`" && git push origin $(GH_BUILD_BRANCH)
+	git checkout $(GH_SOURCE_BRANCH)
+
+htmlclean cleanhtml: clean html
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/UW-MadisonComputationalNuclearEngineeringResearchGroupCNERG.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/UW-MadisonComputationalNuclearEngineeringResearchGroupCNERG.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/UW-MadisonComputationalNuclearEngineeringResearchGroupCNERG"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/UW-MadisonComputationalNuclearEngineeringResearchGroupCNERG"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+install:
+	rsync -a $(BUILDDIR)build/html/* .
+	rm -rf $(BUILDDIR)build/html/*
 

source/basics/main.rst

@@ -11,7 +11,7 @@ Cyclus Fundamentals
    roadmap
    ecosystem
    glossary
-
+   acknowledgements
 
 .. stuff not converted yet
 

source/devdoc/main.rst

@@ -36,16 +36,10 @@ Core Concepts and Expectations
    :maxdepth: 1
 
    sim_init
-   control_flow
-   time_steps
-   commodities_and_markets
    resources
    materials_and_isotopes
+   discrete_materials
    decay
-   message_passing
-   transactions
-   facility_deployment
-   using_prototypes
 
 Utilities and Components
 ------------------------
@@ -56,19 +50,14 @@ Utilities and Components
    logger
    output_dbase
    output_usecases
-   module_building_blocks
 
 Software Development Aids
 --------------------------
 .. toctree::
    :maxdepth: 1
 
-   code_documentation
    ../basics/roadmap
-   cycamore
-   cycstub
    contributing_to_cyclus
-   git_worflows
    make-models/main
    testing
    style_guide