# Makefile for Sphinx documentation
#
BINDIR=python ../CGATReport/
XVFB=xvfb-run -a

# You can set these variables from the command line.
SPHINXOPTS    =
SPHINXBUILD   = $(BINDIR)build.py --num-jobs=4 sphinx-build -j 4
SPHINXCLEAN   = $(BINDIR)clean.py
PAPER         =

DIR_PUBLISH = /ifs/public/CGATReport/documentation
URL_SUB="s/\/ifs\/devel\/andreas\/CGATReport\/doc\/doc/http:\/\/www.cgat.org\/downloads\/public\/CGATReport\/documentation/"

# Internal variables.
PAPEROPT_a4     = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS   = -d _build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .

PORT=8080

.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest

help:
	@echo "Please use \`make <target>' where <target> is one of"
	@echo "  html      to make standalone HTML files"
	@echo "  dirhtml   to make HTML files named index.html in directories"
	@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 "  latex     to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
	@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)"
	@echo "  publish   to copy the html code to public_html"

clean:
	$(SPHINXCLEAN) clean

distclean:
	$(SPHINXCLEAN) distclean

# Dump database contents
csvdb_data.txt.gz:
	sqlite3 csvdb .dump | gzip > csvdb_data.txt.gz

# Load database contents
csvdb: csvdb_data.txt.gz
	rm -f $@; gunzip < $< | sqlite3 $@

html: csvdb
	@echo 'building notebooks' 
	ipython nbconvert --to html notebooks/CGATReportTutorial14.ipynb
	ipython nbconvert --to html notebooks/GenomeInformatics2014.ipynb
	$(XVFB) $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) _build/html
	@echo
	@echo "Build finished. The HTML pages are in _build/html."

dirhtml:
	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) _build/dirhtml
	@echo
	@echo "Build finished. The HTML pages are in _build/dirhtml."

server-start:
	if ! test -e static; then ln -s _build/html static; fi 
	nohup nice -19 ./server.py $(PORT) 2>&1 >> server.log &

server-stop:
	pkill "server.py $(PORT)"

pickle:
	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) _build/pickle
	@echo
	@echo "Build finished; now you can process the pickle files."

json:
	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) _build/json
	@echo
	@echo "Build finished; now you can process the JSON files."

htmlhelp:
	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) _build/htmlhelp
	@echo
	@echo "Build finished; now you can run HTML Help Workshop with the" \
	      ".hhp project file in _build/htmlhelp."

qthelp:
	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) _build/qthelp
	@echo
	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
	      ".qhcp project file in _build/qthelp, like this:"
	@echo "# qcollectiongenerator _build/qthelp/Test.qhcp"
	@echo "To view the help file:"
	@echo "# assistant -collectionFile _build/qthelp/Test.qhc"

latex:
	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) _build/latex
	@echo
	@echo "Build finished; the LaTeX files are in _build/latex."
	@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
	      "run these through (pdf)latex."

changes:
	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) _build/changes
	@echo
	@echo "The overview file is in _build/changes."

linkcheck:
	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) _build/linkcheck
	@echo
	@echo "Link check complete; look for any errors in the above output " \
	      "or in _build/linkcheck/output.txt."

doctest:
	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) _build/doctest
	@echo "Testing of doctests in the sources finished, look at the " \
	      "results in _build/doctest/output.txt."

publish:
	-mkdir -p $(DIR_PUBLISH)
	@echo "copying data"
	rsync --size-only -acvz _build/html/ $(DIR_PUBLISH)
	@echo "setting permissions"
	chmod -R a+x $(DIR_PUBLISH)
	chmod -R a+r $(DIR_PUBLISH)
	@echo "fixing URLs"
	find $(DIR_PUBLISH)/ -name "*.html" -exec perl -p -i -e $(URL_SUB) {} \;

