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Merge pull request #77 from BackofenLab/intarna-2
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final doxygen-related changes for 2.0.3 release
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Martin Mann committed May 3, 2017
2 parents fb8c112 + f836259 commit 0368c3e
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3 changes: 3 additions & 0 deletions ChangeLog
@@ -1,4 +1,6 @@

version 2.0.3

170503 Martin Mann :
* README.md :
+ OS X install instructions (thanks to Lars Barquist)
Expand All @@ -13,6 +15,7 @@
* getES*() : enabled
+ tests for NussinovHandler
+ tests for InteractionEnergyBasePair
+ doc/latex-deps : provides required doxygen-latex dependencies

170413 Martin Mann :
* doc/*
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10 changes: 8 additions & 2 deletions doc/Makefile.am
Expand Up @@ -5,6 +5,12 @@

EXTRA_DIST = \
conda.txt \
doxygen.cfg

doxygen.cfg \
latex-deps/adjcalc.sty \
latex-deps/adjustbox.sty \
latex-deps/collectbox.sty \
latex-deps/tc-pgf.def \
latex-deps/tocloft.sty \
latex-deps/trimclip.sty \
latex-deps/xtab.sty

4 changes: 2 additions & 2 deletions doc/doxygen.cfg
Expand Up @@ -654,7 +654,7 @@ SHOW_FILES = YES
# Folder Tree View (if specified).
# The default value is: YES.

SHOW_NAMESPACES = NO
SHOW_NAMESPACES = YES

# The FILE_VERSION_FILTER tag can be used to specify a program or script that
# doxygen should invoke to get the current version for each file (typically from
Expand Down Expand Up @@ -1675,7 +1675,7 @@ LATEX_EXTRA_STYLESHEET =
# markers available.
# This tag requires that the tag GENERATE_LATEX is set to YES.

LATEX_EXTRA_FILES =
LATEX_EXTRA_FILES = doc/latex-deps/adjcalc.sty doc/latex-deps/adjustbox.sty doc/latex-deps/collectbox.sty doc/latex-deps/tc-pgf.def doc/latex-deps/tocloft.sty doc/latex-deps/trimclip.sty doc/latex-deps/xtab.sty

# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
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155 changes: 155 additions & 0 deletions doc/latex-deps/adjcalc.sty
@@ -0,0 +1,155 @@
%% Copyright (C) 2011-2012 by Martin Scharrer <martin@scharrer-online.de>
%% ----------------------------------------------------------------------
%% This work may be distributed and/or modified under the
%% conditions of the LaTeX Project Public License, either version 1.3
%% of this license or (at your option) any later version.
%% The latest version of this license is in
%% http://www.latex-project.org/lppl.txt
%% and version 1.3 or later is part of all distributions of LaTeX
%% version 2005/12/01 or later.
%%
%% This work has the LPPL maintenance status `maintained'.
%%
%% The Current Maintainer of this work is Martin Scharrer.
%%
%% This work consists of the files adjcalc.dtx, adjustbox.ins
%% and the derived file adjcalc.sty.
%% It is part of the larger adjustbox bundle.
%%
\ProvidesPackage{adjcalc}[%
2012/05/16
v1.1
Provides advanced setlength with multiple back-ends (calc, etex, pgfmath)]
\RequirePackage{xkeyval}
\def\adjcalc@atend{%
\begingroup
\expandafter\ifx\csname glueexpr\endcsname\relax
\endgroup
\RequirePackage{calc}%
\adjcalc@calc
\def\adjcalc@etex{\PackageError{adjcalc}{e-TeX not available for current compiler!}}%
\else
\endgroup
\adjcalc@etex
\fi
}
\def\adjcalc@pgfmath{\AtEndOfPackage{\RequirePackage{pgf}}\def\adjcalc@atend{\adjcalc@pgfmath}}
\def\adjcalc@etex{\def\adjcalc@atend{\adjcalc@etex}}
\def\adjcalc@calc{\AtEndOfPackage{\RequirePackage{calc}}\def\adjcalc@atend{\adjcalc@calc}}
\def\adjcalc@overwrite{\AtEndOfPackage{\adjcalc@overwrite}}
\def\adjcalc@defaultunit{bp}%
\DeclareOptionX<adjcalc>{pgfmath}{\adjcalc@pgfmath}
\DeclareOptionX<adjcalc>{etex}{\adjcalc@etex}
\DeclareOptionX<adjcalc>{calc}{\adjcalc@calc}
\DeclareOptionX<adjcalc>{none}{%
\let\adjcalc@atend\relax
\let\adjcalc@overwrite\relax
\def\adjsetlength{\setlength}%
\def\adjaddtolength{\addtolength}%
\def\adjsetcounter{\setcounter}%
\def\adjaddtocounter{\addtocounter}%
}
\DeclareOptionX<adjcalc>{overwrite}{\adjcalc@overwrite}
\DeclareOptionX<adjcalc>{defaultunit}[bp]{%
\begingroup
\def\@tempa{#1}%
\def\@tempb{none}%
\ifx\@tempa\@tempb% 'none':
\endgroup
\def\adjsetlengthdefault{\adjsetlength}%
\else
\ifx\@tempb\adjcalc@defaultunit
\endgroup
% was 'none' before
\let\adjsetlengthdefault\adjsetlengthdefault@
\else
\endgroup
\fi
\fi
\def\adjcalc@defaultunit{#1}%
}
\ProcessOptionsX*<adjcalc>
\disable@keys{adjcalc}{none}
\def\adjcalcset{%
\setkeys{adjcalc}%
}
\def\adjcalc@etex{%
\protected\def\adjsetlength##1##2{%
##1=\glueexpr(##2)\relax
}%
\protected\def\adjaddtolength##1##2{%
\advance##1 by \glueexpr(##2)\relax
}%
\protected\def\adjsetcounter##1##2{%
\@ifundefined{c@##1}%
{\@nocounterr{##1}}%
{\global\csname c@##1\endcsname\numexpr(##2)\relax}%
}%
\protected\def\adjaddtocounter##1##2{%
\@ifundefined{c@##1}%
{\@nocounterr{##1}}%
{\global\advance\csname c@##1\endcsname\numexpr(##2)\relax}%
}%
\def\adjsetlengthdefault@##1##2{%
\@defaultunits##1=\glueexpr##2 \adjcalc@defaultunit\relax\@nnil
}%
\let\adjsetlengthdefault\adjsetlengthdefault@
}
\newif\if@adjcalc@needsdefault
\def\adjcalc@calc{%
\DeclareRobustCommand\adjsetlength{\calc@assign@skip}%
\DeclareRobustCommand\adjaddtolength[1]{\calc@assign@skip{\advance ##1}}%
\DeclareRobustCommand\adjsetcounter[2]{\@ifundefined{c@##1}{\@nocounterr{##1}}{\calc@assign@count{\global\csname c@##1\endcsname}{##2}}}%
\DeclareRobustCommand\adjaddtocounter[2]{\@ifundefined{c@##1}{\@nocounterr{##1}}{\calc@assign@count{\global\advance\csname c@##1\endcsname}{##2}}}%
\def\adjsetlengthdefault@##1##2{%
\begingroup
\def\calc@post@scan####1!{%
\def\@tempa{####1}%
\ifx\@tempa\@empty
\endgroup% to end calc processing
% is number only
\global\@adjcalc@needsdefaulttrue
\else
\endgroup% to end calc processing
% full expression
\global\@adjcalc@needsdefaultfalse
\fi
}%
\calc@assign@skip{##1}{##2 \adjcalc@defaultunit}%
\endgroup
\if@adjcalc@needsdefault
##1=##2 \adjcalc@defaultunit\relax
\else
\calc@assign@skip{##1}{##2}%
\fi
}%
\def\adjcalc@checkdefault##1\@nnil##2##3{%
\ifx\relax##1\relax\else
\calc@assign@skip{##2}{##3}%
\fi
}%
\let\adjsetlengthdefault\adjsetlengthdefault@
}
\def\adjcalc@pgfmath{%
\DeclareRobustCommand\adjsetlength{\pgfmathsetlength}%
\DeclareRobustCommand\adjaddtolength{\pgfmathaddtolength}%
\DeclareRobustCommand\adjsetcounter{\pgfmathsetcounter}%
\DeclareRobustCommand\adjaddtocounter{\pgfmathaddtocounter}%
\def\adjsetlengthdefault@##1##2{%
\edef\pgfmathresultunitscale{1\adjcalc@defaultunit}%
\let\pgfmathpostparse\pgfmathscaleresult
\pgfmathparse{##2}%
##1=\pgfmathresult pt\relax
}%
\let\adjsetlengthdefault\adjsetlengthdefault@
}
\def\adjcalc@overwrite{%
\let\setlength\adjsetlength
\let\addtolength\adjaddtolength
\let\setcounter\adjsetcounter
\let\addtocounter\adjaddtocounter
}
\adjcalc@atend
\endinput
%%
%% End of file `adjcalc.sty'.

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