research-copilot 0.1.0

package/lib/skills/builtin/paper-writing/templates/neurips2025/Makefile

@@ -0,0 +1,36 @@
+FIGURES_FOLDER := figures
+PDFS := \
+$(filter-out $(wildcard $(FIGURES_FOLDER)/*-crop.pdf),$(wildcard $(FIGURES_FOLDER)/*.pdf)) \
+$(filter-out $(wildcard $(FIGURES_FOLDER)/**/*-crop.pdf),$(wildcard $(FIGURES_FOLDER)/**/*.pdf))
+CROPPED_PDFS := $(PDFS:.pdf=-crop.pdf)
+
+all: main.pdf
+
+%.pdf: %.tex Makefile $(CROPPED_PDFS)
+	pdflatex -synctex=1 -interaction=nonstopmode $<
+	-bibtex $*.aux
+	pdflatex -synctex=1 -interaction=nonstopmode $<
+	pdflatex -synctex=1 -interaction=nonstopmode $<
+
+.PHONY: figures
+figures: $(CROPPED_PDFS)
+
+.PRECIOUS: $(CROPPED_PDFS)
+%-crop.pdf: %.pdf Makefile
+	pdfcrop $<
+
+.PHONY: clean upgrade
+clean:
+	find . -maxdepth 1 \
+		\( -name "*.aux" -o -name "*.bbl" -o -name "*.blg" -o \
+	           -name "*.log" -o -name "*.out" -o -name "*.pdf" -o \
+		   -name "*.synctex.gz" \) | xargs $(RM)
+	find $(FIGURES_FOLDER) -name "*-crop.pdf" | xargs $(RM)
+
+YEAR := 2025
+
+upgrade:
+	curl -O https://media.neurips.cc/Conferences/NeurIPS$(YEAR)/Styles.zip
+	unzip -u Styles.zip
+	mv Styles/neurips_${YEAR}.sty neurips.sty
+	$(RM) -r Styles.zip Styles

package/lib/skills/builtin/paper-writing/templates/neurips2025/extra_pkgs.tex

@@ -0,0 +1,53 @@
+\usepackage[export]{adjustbox}
+\usepackage[ruled]{algorithm2e}
+\usepackage[inline, shortlabels]{enumitem}
+\usepackage[T1]{fontenc}
+\usepackage{hyperref}
+\usepackage{microtype}
+\usepackage{pifont}
+\usepackage{xcolor}
+\usepackage{xurl}
+% Figures and Tables
+\usepackage{graphicx}
+\usepackage{booktabs}
+\usepackage{tabularray}
+% Monospaced Code Blocks
+\usepackage{listings}
+% Math Packages
+\usepackage{amsmath, amsfonts}
+\usepackage{nicefrac}
+
+\UseTblrLibrary{booktabs}
+
+\lstset{
+  backgroundcolor=\color{white},   % choose the background color; you must add \usepackage{color} or \usepackage{xcolor}; should come as last argument
+  basicstyle=\ttfamily,            % the size of the fonts that are used for the code
+  breakatwhitespace=false,         % sets if automatic breaks should only happen at whitespace
+  breaklines=true,                 % sets automatic line breaking
+  captionpos=b,                    % sets the caption-position to bottom
+  columns=fullflexible,            % reduce the column spacing
+  commentstyle=\color{gray},       % comment style
+  deletekeywords={},               % if you want to delete keywords from the given language
+  escapeinside={\%*}{*)},          % if you want to add LaTeX within your code
+  extendedchars=true,              % lets you use non-ASCII characters; for 8-bits encodings only, does not work with UTF-8
+  frame=none,                      % adds no frame around the code
+  keepspaces=true,                 % keeps spaces in text, useful for keeping indentation of code (possibly needs columns=flexible)
+  keywordstyle=\color{blue},       % keyword style
+  language=C++,                    % the language of the code
+  morekeywords={},                 % if you want to add more keywords to the set
+  numbers=none,                    % where to put the line-numbers; possible values are (none, left, right)
+  numbersep=5pt,                   % how far the line-numbers are from the code
+  numberstyle=\color{black},       % the style that is used for the line-numbers
+  rulecolor=\color{black},         % if not set, the frame-color may be changed on line-breaks within not-black text (e.g. comments (green here))
+  showspaces=false,                % show spaces everywhere adding particular underscores; it overrides 'showstringspaces'
+  showstringspaces=false,          % underline spaces within strings only
+  showtabs=false,                  % show tabs within strings adding particular underscores
+  stepnumber=1,                    % the step between two line-numbers. If it's 1, each line will be numbered
+  stringstyle=\color{red},         % string literal style
+  tabsize=4,                       % sets default tabsize to 4 spaces
+}
+
+\makeatletter
+\newcommand{\ssymbol}[1]{\@fnsymbol{#1}}
+\newcommand{\romanNumeral}[1]{\expandafter\@slowromancap\romannumeral #1@}
+\makeatother

package/lib/skills/builtin/paper-writing/templates/neurips2025/main.tex

@@ -0,0 +1,38 @@
+\documentclass{article}
+
+\usepackage[nonatbib, final]{neurips}
+\usepackage[numbers]{natbib}
+
+\makeatletter
+\renewcommand{\@noticestring}{
+  \centering
+  
+}
+\makeatother
+
+\input{extra_pkgs}
+
+\usepackage{physics}
+\usepackage{mathtools}
+\DeclarePairedDelimiter\p{(}{)}
+\DeclarePairedDelimiter\n{|}{|}
+\DeclarePairedDelimiter\B{[}{]}
+
+\title{}
+
+\author{
+    Bojian Zheng \\
+    University of Toronto \\
+    \href{mailto:bojian@cs.toronto.edu}{bojian@cs.toronto.edu}
+}
+
+\begin{document}
+
+\maketitle
+
+
+
+% \bibliographystyle{plainnat}
+% \bibliography{bibliography}
+
+\end{document}

package/lib/skills/builtin/paper-writing/templates/neurips2025/neurips.sty

@@ -0,0 +1,382 @@
+% partial rewrite of the LaTeX2e package for submissions to the
+% Conference on Neural Information Processing Systems (NeurIPS):
+%
+% - uses more LaTeX conventions
+% - line numbers at submission time replaced with aligned numbers from
+%   lineno package
+% - \nipsfinalcopy replaced with [final] package option
+% - automatically loads times package for authors
+% - loads natbib automatically; this can be suppressed with the
+%   [nonatbib] package option
+% - adds foot line to first page identifying the conference
+% - adds preprint option for submission to e.g. arXiv
+% - conference acronym modified
+%
+% Roman Garnett (garnett@wustl.edu) and the many authors of
+% nips15submit_e.sty, including MK and drstrip@sandia
+%
+% last revision: April 2025
+
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{neurips_2025}[2025/04/02 NeurIPS 2025 submission/camera-ready style file]
+
+% declare final option, which creates camera-ready copy
+\newif\if@neuripsfinal\@neuripsfinalfalse
+\DeclareOption{final}{
+  \@neuripsfinaltrue
+}
+
+% declare nonatbib option, which does not load natbib in case of
+% package clash (users can pass options to natbib via
+% \PassOptionsToPackage)
+\newif\if@natbib\@natbibtrue
+\DeclareOption{nonatbib}{
+  \@natbibfalse
+}
+
+% declare preprint option, which creates a preprint version ready for
+% upload to, e.g., arXiv
+\newif\if@preprint\@preprintfalse
+\DeclareOption{preprint}{
+  \@preprinttrue
+}
+
+\ProcessOptions\relax
+
+% determine whether this is an anonymized submission
+\newif\if@submission\@submissiontrue
+\if@neuripsfinal\@submissionfalse\fi
+\if@preprint\@submissionfalse\fi
+
+% fonts
+\renewcommand{\rmdefault}{ptm}
+\renewcommand{\sfdefault}{phv}
+
+% change this every year for notice string at bottom
+\newcommand{\@neuripsordinal}{39th}
+\newcommand{\@neuripsyear}{2025}
+\newcommand{\@neuripslocation}{San Diego}
+
+% acknowledgments
+\usepackage{environ}
+\newcommand{\acksection}{\section*{Acknowledgments and Disclosure of Funding}}
+\NewEnviron{ack}{%
+  \acksection
+  \BODY
+}
+
+
+% load natbib unless told otherwise
+\if@natbib
+  \RequirePackage{natbib}
+\fi
+
+% set page geometry
+\usepackage[verbose=true,letterpaper]{geometry}
+\AtBeginDocument{
+  \newgeometry{
+    textheight=9in,
+    textwidth=5.5in,
+    top=1in,
+    headheight=12pt,
+    headsep=25pt,
+    footskip=30pt
+  }
+  \@ifpackageloaded{fullpage}
+    {\PackageWarning{neurips_2025}{fullpage package not allowed! Overwriting formatting.}}
+    {}
+}
+
+\widowpenalty=10000
+\clubpenalty=10000
+\flushbottom
+\sloppy
+
+
+% font sizes with reduced leading
+\renewcommand{\normalsize}{%
+  \@setfontsize\normalsize\@xpt\@xipt
+  \abovedisplayskip      7\p@ \@plus 2\p@ \@minus 5\p@
+  \abovedisplayshortskip \z@ \@plus 3\p@
+  \belowdisplayskip      \abovedisplayskip
+  \belowdisplayshortskip 4\p@ \@plus 3\p@ \@minus 3\p@
+}
+\normalsize
+\renewcommand{\small}{%
+  \@setfontsize\small\@ixpt\@xpt
+  \abovedisplayskip      6\p@ \@plus 1.5\p@ \@minus 4\p@
+  \abovedisplayshortskip \z@  \@plus 2\p@
+  \belowdisplayskip      \abovedisplayskip
+  \belowdisplayshortskip 3\p@ \@plus 2\p@   \@minus 2\p@
+}
+\renewcommand{\footnotesize}{\@setfontsize\footnotesize\@ixpt\@xpt}
+\renewcommand{\scriptsize}{\@setfontsize\scriptsize\@viipt\@viiipt}
+\renewcommand{\tiny}{\@setfontsize\tiny\@vipt\@viipt}
+\renewcommand{\large}{\@setfontsize\large\@xiipt{14}}
+\renewcommand{\Large}{\@setfontsize\Large\@xivpt{16}}
+\renewcommand{\LARGE}{\@setfontsize\LARGE\@xviipt{20}}
+\renewcommand{\huge}{\@setfontsize\huge\@xxpt{23}}
+\renewcommand{\Huge}{\@setfontsize\Huge\@xxvpt{28}}
+
+% sections with less space
+\providecommand{\section}{}
+\renewcommand{\section}{%
+  \@startsection{section}{1}{\z@}%
+                {-2.0ex \@plus -0.5ex \@minus -0.2ex}%
+                { 1.5ex \@plus  0.3ex \@minus  0.2ex}%
+                {\large\bf\raggedright}%
+}
+\providecommand{\subsection}{}
+\renewcommand{\subsection}{%
+  \@startsection{subsection}{2}{\z@}%
+                {-1.8ex \@plus -0.5ex \@minus -0.2ex}%
+                { 0.8ex \@plus  0.2ex}%
+                {\normalsize\bf\raggedright}%
+}
+\providecommand{\subsubsection}{}
+\renewcommand{\subsubsection}{%
+  \@startsection{subsubsection}{3}{\z@}%
+                {-1.5ex \@plus -0.5ex \@minus -0.2ex}%
+                { 0.5ex \@plus  0.2ex}%
+                {\normalsize\bf\raggedright}%
+}
+\providecommand{\paragraph}{}
+\renewcommand{\paragraph}{%
+  \@startsection{paragraph}{4}{\z@}%
+                {1.5ex \@plus 0.5ex \@minus 0.2ex}%
+                {-1em}%
+                {\normalsize\bf}%
+}
+\providecommand{\subparagraph}{}
+\renewcommand{\subparagraph}{%
+  \@startsection{subparagraph}{5}{\z@}%
+                {1.5ex \@plus 0.5ex \@minus 0.2ex}%
+                {-1em}%
+                {\normalsize\bf}%
+}
+\providecommand{\subsubsubsection}{}
+\renewcommand{\subsubsubsection}{%
+  \vskip5pt{\noindent\normalsize\rm\raggedright}%
+}
+
+% float placement
+\renewcommand{\topfraction      }{0.85}
+\renewcommand{\bottomfraction   }{0.4}
+\renewcommand{\textfraction     }{0.1}
+\renewcommand{\floatpagefraction}{0.7}
+
+\newlength{\@neuripsabovecaptionskip}\setlength{\@neuripsabovecaptionskip}{7\p@}
+\newlength{\@neuripsbelowcaptionskip}\setlength{\@neuripsbelowcaptionskip}{\z@}
+
+\setlength{\abovecaptionskip}{\@neuripsabovecaptionskip}
+\setlength{\belowcaptionskip}{\@neuripsbelowcaptionskip}
+
+% swap above/belowcaptionskip lengths for tables
+\renewenvironment{table}
+  {\setlength{\abovecaptionskip}{\@neuripsbelowcaptionskip}%
+   \setlength{\belowcaptionskip}{\@neuripsabovecaptionskip}%
+   \@float{table}}
+  {\end@float}
+
+% footnote formatting
+\setlength{\footnotesep }{6.65\p@}
+\setlength{\skip\footins}{9\p@ \@plus 4\p@ \@minus 2\p@}
+\renewcommand{\footnoterule}{\kern-3\p@ \hrule width 12pc \kern 2.6\p@}
+\setcounter{footnote}{0}
+
+% paragraph formatting
+\setlength{\parindent}{\z@}
+\setlength{\parskip  }{5.5\p@}
+
+% list formatting
+\setlength{\topsep       }{4\p@ \@plus 1\p@   \@minus 2\p@}
+\setlength{\partopsep    }{1\p@ \@plus 0.5\p@ \@minus 0.5\p@}
+\setlength{\itemsep      }{2\p@ \@plus 1\p@   \@minus 0.5\p@}
+\setlength{\parsep       }{2\p@ \@plus 1\p@   \@minus 0.5\p@}
+\setlength{\leftmargin   }{3pc}
+\setlength{\leftmargini  }{\leftmargin}
+\setlength{\leftmarginii }{2em}
+\setlength{\leftmarginiii}{1.5em}
+\setlength{\leftmarginiv }{1.0em}
+\setlength{\leftmarginv  }{0.5em}
+\def\@listi  {\leftmargin\leftmargini}
+\def\@listii {\leftmargin\leftmarginii
+              \labelwidth\leftmarginii
+              \advance\labelwidth-\labelsep
+              \topsep  2\p@ \@plus 1\p@    \@minus 0.5\p@
+              \parsep  1\p@ \@plus 0.5\p@ \@minus 0.5\p@
+              \itemsep \parsep}
+\def\@listiii{\leftmargin\leftmarginiii
+              \labelwidth\leftmarginiii
+              \advance\labelwidth-\labelsep
+              \topsep    1\p@ \@plus 0.5\p@ \@minus 0.5\p@
+              \parsep    \z@
+              \partopsep 0.5\p@ \@plus 0\p@ \@minus 0.5\p@
+              \itemsep \topsep}
+\def\@listiv {\leftmargin\leftmarginiv
+              \labelwidth\leftmarginiv
+              \advance\labelwidth-\labelsep}
+\def\@listv  {\leftmargin\leftmarginv
+              \labelwidth\leftmarginv
+              \advance\labelwidth-\labelsep}
+\def\@listvi {\leftmargin\leftmarginvi
+              \labelwidth\leftmarginvi
+              \advance\labelwidth-\labelsep}
+
+% create title
+\providecommand{\maketitle}{}
+\renewcommand{\maketitle}{%
+  \par
+  \begingroup
+    \renewcommand{\thefootnote}{\fnsymbol{footnote}}
+    % for perfect author name centering
+    \renewcommand{\@makefnmark}{\hbox to \z@{$^{\@thefnmark}$\hss}}
+    % The footnote-mark was overlapping the footnote-text,
+    % added the following to fix this problem               (MK)
+    \long\def\@makefntext##1{%
+      \parindent 1em\noindent
+      \hbox to 1.8em{\hss $\m@th ^{\@thefnmark}$}##1
+    }
+    \thispagestyle{empty}
+    \@maketitle
+    \@thanks
+    \@notice
+  \endgroup
+  \let\maketitle\relax
+  \let\thanks\relax
+}
+
+% rules for title box at top of first page
+\newcommand{\@toptitlebar}{
+  \hrule height 4\p@
+  \vskip 0.25in
+  \vskip -\parskip%
+}
+\newcommand{\@bottomtitlebar}{
+  \vskip 0.29in
+  \vskip -\parskip
+  \hrule height 1\p@
+  \vskip 0.09in%
+}
+
+% create title (includes both anonymized and non-anonymized versions)
+\providecommand{\@maketitle}{}
+\renewcommand{\@maketitle}{%
+  \vbox{%
+    \hsize\textwidth
+    \linewidth\hsize
+    \vskip 0.1in
+    \@toptitlebar
+    \centering
+    {\LARGE\bf \@title\par}
+    \@bottomtitlebar
+    \if@submission
+      \begin{tabular}[t]{c}\bf\rule{\z@}{24\p@}
+        Anonymous Author(s) \\
+        Affiliation \\
+        Address \\
+        \texttt{email} \\
+      \end{tabular}%
+    \else
+      \def\And{%
+        \end{tabular}\hfil\linebreak[0]\hfil%
+        \begin{tabular}[t]{c}\bf\rule{\z@}{24\p@}\ignorespaces%
+      }
+      \def\AND{%
+        \end{tabular}\hfil\linebreak[4]\hfil%
+        \begin{tabular}[t]{c}\bf\rule{\z@}{24\p@}\ignorespaces%
+      }
+      \begin{tabular}[t]{c}\bf\rule{\z@}{24\p@}\@author\end{tabular}%
+    \fi
+    \vskip 0.3in \@minus 0.1in
+  }
+}
+
+% add conference notice to bottom of first page
+\newcommand{\ftype@noticebox}{8}
+\newcommand{\@notice}{%
+  % give a bit of extra room back to authors on first page
+  \enlargethispage{2\baselineskip}%
+  \@float{noticebox}[b]%
+    \footnotesize\@noticestring%
+  \end@float%
+}
+
+% abstract styling
+\renewenvironment{abstract}%
+{%
+  \vskip 0.075in%
+  \centerline%
+  {\large\bf Abstract}%
+  \vspace{0.5ex}%
+  \begin{quote}%
+}
+{
+  \par%
+  \end{quote}%
+  \vskip 1ex%
+}
+
+% For the paper checklist
+\newcommand{\answerYes}[1][]{\textcolor{blue}{[Yes] #1}}
+\newcommand{\answerNo}[1][]{\textcolor{orange}{[No] #1}}
+\newcommand{\answerNA}[1][]{\textcolor{gray}{[NA] #1}}
+\newcommand{\answerTODO}[1][]{\textcolor{red}{\bf [TODO]}}
+\newcommand{\justificationTODO}[1][]{\textcolor{red}{\bf [TODO]}}
+
+% handle tweaks for camera-ready copy vs. submission copy
+\if@preprint
+  \newcommand{\@noticestring}{%
+    Preprint. Under review.%
+  }
+\else
+  \if@neuripsfinal
+    \newcommand{\@noticestring}{%
+      \@neuripsordinal\/ Conference on Neural Information Processing Systems
+      (NeurIPS \@neuripsyear).%, \@neuripslocation.%
+    }
+  \else
+    \newcommand{\@noticestring}{%
+      Submitted to \@neuripsordinal\/ Conference on Neural Information
+      Processing Systems (NeurIPS \@neuripsyear). Do not distribute.%
+    }
+
+    % hide the acknowledgements
+    \NewEnviron{hide}{}
+    \let\ack\hide
+    \let\endack\endhide
+
+    % line numbers for submission
+    \RequirePackage{lineno}
+    \linenumbers
+
+    % fix incompatibilities between lineno and amsmath, if required, by
+    % transparently wrapping linenomath environments around amsmath
+    % environments
+    \AtBeginDocument{%
+      \@ifpackageloaded{amsmath}{%
+        \newcommand*\patchAmsMathEnvironmentForLineno[1]{%
+          \expandafter\let\csname old#1\expandafter\endcsname\csname #1\endcsname
+          \expandafter\let\csname oldend#1\expandafter\endcsname\csname end#1\endcsname
+          \renewenvironment{#1}%
+                          {\linenomath\csname old#1\endcsname}%
+                          {\csname oldend#1\endcsname\endlinenomath}%
+        }%
+        \newcommand*\patchBothAmsMathEnvironmentsForLineno[1]{%
+          \patchAmsMathEnvironmentForLineno{#1}%
+          \patchAmsMathEnvironmentForLineno{#1*}%
+        }%
+        \patchBothAmsMathEnvironmentsForLineno{equation}%
+        \patchBothAmsMathEnvironmentsForLineno{align}%
+        \patchBothAmsMathEnvironmentsForLineno{flalign}%
+        \patchBothAmsMathEnvironmentsForLineno{alignat}%
+        \patchBothAmsMathEnvironmentsForLineno{gather}%
+        \patchBothAmsMathEnvironmentsForLineno{multline}%
+      }
+      {}
+    }
+  \fi
+\fi
+
+
+\endinput