https://github.com/hyperbrowser/genomic-hyperbrowser
Tip revision: 9b0c9522903291f70e7e97ed2eeaf6151c78aa02 authored by Sveinung Gundersen on 07 December 2018, 21:55:56 UTC
Added documentation of Conda support. Bumped to v1.1
Added documentation of Conda support. Bumped to v1.1
Tip revision: 9b0c952
Makefile
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = build
SPHINXAPIDOC = sphinx-apidoc
# 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
GENERATED_RST = source/api/api.rst source/api/ts_api.rst source/dev/schema.rst
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext updaterst
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 " 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)"
@echo " updaterst to update Sphinx RST files for lib/ to reflect code structure changes"
schema.md: parse_gx_xsd.py schema_template.md ../lib/galaxy/tools/xsd/galaxy.xsd ## Build Github-flavored Markdown from Galaxy Tool XSD (expects libxml in environment)
python parse_gx_xsd.py schema_template.md ../lib/galaxy/tools/xsd/galaxy.xsd > $@
source/api/api.rst: source/lib/galaxy.webapps.galaxy.api.rst
printf "Galaxy API\n==========\n" > $@
tail -n +11 source/lib/galaxy.webapps.galaxy.api.rst >> $@
sed -i.bak -e 's/^galaxy\\\.webapps\\\.galaxy\\\.api\\\.//' $@
rm -f $@.bak
source/api/ts_api.rst: source/lib/galaxy.webapps.tool_shed.api.rst
printf "Tool Shed API\n=============\n" > $@
tail -n +11 source/lib/galaxy.webapps.tool_shed.api.rst >> $@
sed -i.bak -e 's/^galaxy\\\.webapps\\\.tool\\_shed\\\.api\\\.//' $@
rm -f $@.bak
source/dev/schema.rst: schema.md ## Convert Galaxy Tool XSD Markdown docs into reStructuredText (expects pandoc in environment)
pandoc schema.md -f markdown_github-hard_line_breaks -s -o $@
./fix_schema_rst.sh $@
# might also want to do
# cd source/lib; hg revert; rm *.rst.orig; or not.
clean:
-rm -rf $(BUILDDIR)/* schema.md $(GENERATED_RST)
html: $(GENERATED_RST)
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
dirhtml: $(GENERATED_RST)
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
singlehtml: $(GENERATED_RST)
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
pickle: $(GENERATED_RST)
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
json: $(GENERATED_RST)
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
htmlhelp: $(GENERATED_RST)
$(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: $(GENERATED_RST)
$(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/Galaxy.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Galaxy.qhc"
devhelp: $(GENERATED_RST)
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/Galaxy"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Galaxy"
@echo "# devhelp"
epub: $(GENERATED_RST)
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
latex: $(GENERATED_RST)
$(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: $(GENERATED_RST)
$(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: $(GENERATED_RST)
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
man: $(GENERATED_RST)
$(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: $(GENERATED_RST)
$(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: $(GENERATED_RST)
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
changes: $(GENERATED_RST)
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
linkcheck: $(GENERATED_RST)
$(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: $(GENERATED_RST)
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
# Update Sphinx RST files for lib/ to reflect code structure changes
updaterst:
$(SPHINXAPIDOC) -M --force -o source/lib/ ../lib/