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Fix PDF documentation build configuration
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‎package/doc/sphinx/Makefile‎

Lines changed: 132 additions & 132 deletions
Original file line numberDiff line numberDiff line change
@@ -1,132 +1,132 @@
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# Makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS =
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SPHINXBUILD = sphinx-build -v -W
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PAPER =
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BUILDDIR = ..
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# Internal variables.
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PAPEROPT_a4 = -D latex_paper_size=a4
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PAPEROPT_letter = -D latex_paper_size=letter
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ALLSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
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.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
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help:
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@echo "Please use \`make <target>' where <target> is one of"
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@echo " html to make standalone HTML files"
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@echo " dirhtml to make HTML files named index.html in directories"
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@echo " singlehtml to make a single large HTML file"
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@echo " pickle to make pickle files"
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@echo " json to make JSON files"
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@echo " htmlhelp to make HTML files and a HTML help project"
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@echo " qthelp to make HTML files and a qthelp project"
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@echo " devhelp to make HTML files and a Devhelp project"
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@echo " epub to make an epub"
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@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
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@echo " latexpdf to make LaTeX files and run them through pdflatex"
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@echo " text to make text files"
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@echo " man to make manual pages"
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@echo " changes to make an overview of all changed/added/deprecated items"
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@echo " linkcheck to check all external links for integrity"
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@echo " doctest to run all doctests embedded in the documentation (if enabled)"
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clean:
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for i in html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex text man changes linkcheck doctest; do \
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rm -rf $(BUILDDIR)/$$i; \
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done
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html:
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$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
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dirhtml:
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$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
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singlehtml:
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$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
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@echo
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@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
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pickle:
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$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
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@echo
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@echo "Build finished; now you can process the pickle files."
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json:
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$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
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@echo
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@echo "Build finished; now you can process the JSON files."
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htmlhelp:
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$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
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@echo
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@echo "Build finished; now you can run HTML Help Workshop with the" \
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".hhp project file in $(BUILDDIR)/htmlhelp."
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qthelp:
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$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
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@echo
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@echo "Build finished; now you can run "qcollectiongenerator" with the" \
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".qhcp project file in $(BUILDDIR)/qthelp, like this:"
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@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/MDAnalysis.qhcp"
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@echo "To view the help file:"
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@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/MDAnalysis.qhc"
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devhelp:
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$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
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@echo
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@echo "Build finished."
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@echo "To view the help file:"
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@echo "# mkdir -p $$HOME/.local/share/devhelp/MDAnalysis"
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@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/MDAnalysis"
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@echo "# devhelp"
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epub:
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$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
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@echo
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@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
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latex:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo
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@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
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@echo "Run \`make' in that directory to run these through (pdf)latex" \
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"(use \`make latexpdf' here to do that automatically)."
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latexpdf:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo "Running LaTeX files through pdflatex..."
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make -C $(BUILDDIR)/latex all-pdf
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@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
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text:
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$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
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@echo
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@echo "Build finished. The text files are in $(BUILDDIR)/text."
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man:
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$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
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@echo
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@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
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changes:
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$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
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@echo
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@echo "The overview file is in $(BUILDDIR)/changes."
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linkcheck:
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$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
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@echo
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@echo "Link check complete; look for any errors in the above output " \
127-
"or in $(BUILDDIR)/linkcheck/output.txt."
128-
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doctest:
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$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
131-
@echo "Testing of doctests in the sources finished, look at the " \
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"results in $(BUILDDIR)/doctest/output.txt."
1+
# Makefile for Sphinx documentation
2+
#
3+
4+
# You can set these variables from the command line.
5+
SPHINXOPTS =
6+
SPHINXBUILD = sphinx-build -v -W
7+
PAPER =
8+
BUILDDIR = ..
9+
10+
# Internal variables.
11+
PAPEROPT_a4 = -D latex_paper_size=a4
12+
PAPEROPT_letter = -D latex_paper_size=letter
13+
ALLSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
14+
15+
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
16+
17+
help:
18+
@echo "Please use \`make <target>' where <target> is one of"
19+
@echo " html to make standalone HTML files"
20+
@echo " dirhtml to make HTML files named index.html in directories"
21+
@echo " singlehtml to make a single large HTML file"
22+
@echo " pickle to make pickle files"
23+
@echo " json to make JSON files"
24+
@echo " htmlhelp to make HTML files and a HTML help project"
25+
@echo " qthelp to make HTML files and a qthelp project"
26+
@echo " devhelp to make HTML files and a Devhelp project"
27+
@echo " epub to make an epub"
28+
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
29+
@echo " latexpdf to make LaTeX files and run them through pdflatex"
30+
@echo " text to make text files"
31+
@echo " man to make manual pages"
32+
@echo " changes to make an overview of all changed/added/deprecated items"
33+
@echo " linkcheck to check all external links for integrity"
34+
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
35+
36+
clean:
37+
for i in html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex text man changes linkcheck doctest; do \
38+
rm -rf $(BUILDDIR)/$$i; \
39+
done
40+
41+
html:
42+
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
43+
@echo
44+
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
45+
46+
dirhtml:
47+
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
48+
@echo
49+
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
50+
51+
singlehtml:
52+
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
53+
@echo
54+
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
55+
56+
pickle:
57+
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
58+
@echo
59+
@echo "Build finished; now you can process the pickle files."
60+
61+
json:
62+
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
63+
@echo
64+
@echo "Build finished; now you can process the JSON files."
65+
66+
htmlhelp:
67+
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
68+
@echo
69+
@echo "Build finished; now you can run HTML Help Workshop with the" \
70+
".hhp project file in $(BUILDDIR)/htmlhelp."
71+
72+
qthelp:
73+
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
74+
@echo
75+
@echo "Build finished; now you can run "qcollectiongenerator" with the" \
76+
".qhcp project file in $(BUILDDIR)/qthelp, like this:"
77+
@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/MDAnalysis.qhcp"
78+
@echo "To view the help file:"
79+
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/MDAnalysis.qhc"
80+
81+
devhelp:
82+
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
83+
@echo
84+
@echo "Build finished."
85+
@echo "To view the help file:"
86+
@echo "# mkdir -p $$HOME/.local/share/devhelp/MDAnalysis"
87+
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/MDAnalysis"
88+
@echo "# devhelp"
89+
90+
epub:
91+
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
92+
@echo
93+
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
94+
95+
latex:
96+
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
97+
@echo
98+
@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
99+
@echo "Run \`make' in that directory to run these through (pdf)latex" \
100+
"(use \`make latexpdf' here to do that automatically)."
101+
102+
latexpdf:
103+
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
104+
@echo "Running LaTeX files through pdflatex..."
105+
make -C $(BUILDDIR)/latex all-pdf
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@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
107+
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text:
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$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
110+
@echo
111+
@echo "Build finished. The text files are in $(BUILDDIR)/text."
112+
113+
man:
114+
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
115+
@echo
116+
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
117+
118+
changes:
119+
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
120+
@echo
121+
@echo "The overview file is in $(BUILDDIR)/changes."
122+
123+
linkcheck:
124+
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
125+
@echo
126+
@echo "Link check complete; look for any errors in the above output " \
127+
"or in $(BUILDDIR)/linkcheck/output.txt."
128+
129+
doctest:
130+
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
131+
@echo "Testing of doctests in the sources finished, look at the " \
132+
"results in $(BUILDDIR)/doctest/output.txt."

‎package/doc/sphinx/conf.py‎

Lines changed: 12 additions & 0 deletions
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autodoc_mock_imports = [
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"mdahole2",
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"PathSimAnalysis",
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"waterdynamics",
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]
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latex_engine = "pdflatex"
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latex_elements = {
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"papersize": "letterpaper",
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"pointsize": "10pt",
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"extraclassoptions": "openany,oneside",
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}

‎package/doc/sphinx/doc/sphinx/source/documentation_pages/references.rst‎

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