academia-mcp 1.7.1__tar.gz → 1.7.3__tar.gz

{academia_mcp-1.7.1 → academia_mcp-1.7.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: academia-mcp
-Version: 1.7.1
+Version: 1.7.3
 Summary: MCP server that provides different tools to search for scientific publications
 Author-email: Ilya Gusev <phoenixilya@gmail.com>
 Project-URL: Homepage, https://github.com/IlyaGusev/academia_mcp

academia_mcp-1.7.3/academia_mcp/latex_templates/agents4science_2025/agents4science_2025.tex

@@ -0,0 +1,459 @@
+\documentclass{article}
+
+% if you need to pass options to natbib, use, e.g.:
+%     \PassOptionsToPackage{numbers, compress}{natbib}
+% before loading agents4science_2025
+
+% ready for submission
+% \usepackage{agents4science_2025}
+
+% to compile a preprint version, e.g., for submission to arXiv, add the
+% [preprint] option:
+\usepackage[preprint]{agents4science_2025}
+
+% to compile a camera-ready version, add the [final] option, e.g.:
+%     \usepackage[final]{agents4science_2025}
+
+% to avoid loading the natbib package, add option nonatbib:
+%    \usepackage[nonatbib]{agents4science_2025}
+
+% For workshops, the authors should use the workshop options and add the name of the workshop. 
+% The "\workshoptitle" command is used to set the workshop title.
+%
+% \usepackage[sglblindworkshop]{agents4science_2025}
+% \workshoptitle{WORKSHOP TITLE}
+
+
+\usepackage[utf8]{inputenc} % allow utf-8 input
+\usepackage[T1]{fontenc}    % use 8-bit T1 fonts
+\usepackage{hyperref}       % hyperlinks
+\usepackage{url}            % simple URL typesetting
+\usepackage{booktabs}       % professional-quality tables
+\usepackage{amsfonts}       % blackboard math symbols
+\usepackage{nicefrac}       % compact symbols for 1/2, etc.
+\usepackage{microtype}      % microtypography
+\usepackage{xcolor}         % colors
+
+% Note: For the workshop paper template, both \title{} and \workshoptitle{} are required.
+% \title{} is the paper title and \workshoptitle{} is the workshop title for the footnote. 
+\title{Formatting Instructions For Agents4Science 2025}
+
+
+% The \author macro works with any number of authors. There are two commands
+% used to separate the names and addresses of multiple authors: \And and \AND.
+%
+% Using \And between authors leaves it to LaTeX to determine where to break the
+% lines. Using \AND forces a line break at that point. So, if LaTeX puts 3 of 4
+% authors names on the first line, and the last on the second line, try using
+% \AND instead of \And before the third author name.
+
+
+\author{%
+  David S.~Hippocampus\thanks{Use footnote for providing further information
+    about author (webpage, alternative address)---\emph{not} for acknowledging
+    funding agencies.} \\
+  Department of Computer Science\\
+  Cranberry-Lemon University\\
+  Pittsburgh, PA 15213 \\
+  \texttt{hippo@cs.cranberry-lemon.edu} \\
+  % examples of more authors
+  % \And
+  % Coauthor \\
+  % Affiliation \\
+  % Address \\
+  % \texttt{email} \\
+  % \AND
+  % Coauthor \\
+  % Affiliation \\
+  % Address \\
+  % \texttt{email} \\
+  % \And
+  % Coauthor \\
+  % Affiliation \\
+  % Address \\
+  % \texttt{email} \\
+  % \And
+  % Coauthor \\
+  % Affiliation \\
+  % Address \\
+  % \texttt{email} \\
+}
+
+
+\begin{document}
+
+
+\maketitle
+
+
+\begin{abstract}
+  The abstract paragraph should be indented \nicefrac{1}{2}~inch (3~picas) on
+  both the left- and right-hand margins. Use 10~point type, with a vertical
+  spacing (leading) of 11~points.  The word \textbf{Abstract} must be centered,
+  bold, and in point size 12. Two line spaces precede the abstract. The abstract
+  must be limited to one paragraph.
+\end{abstract}
+
+
+\section{Submission of papers to Agents4Science 2025}
+
+
+Please read the instructions below carefully and follow them faithfully.
+
+
+\subsection{Style}
+
+
+Papers to be submitted to Agents4Science 2025 must be prepared according to the
+instructions presented here. Papers may only be up to {\bf eight} pages long,
+including figures.
+Additional pages \emph{containing references, checklist, and the optional technical appendices} do not count as content pages.
+Papers that exceed the page limit will not be
+reviewed, or in any other way considered for presentation at the conference.
+
+
+Authors are required to use the Agents4Science \LaTeX{} style files obtainable at the
+conference website as indicated below. Please make sure you use the current files
+and not previous versions. Tweaking the style files may be grounds for
+rejection.
+
+
+\subsection{Retrieval of style files}
+
+
+The style files for Agents4Science and other conference information are available on
+the website at
+\begin{center}
+  \url{https://agents4science.stanford.edu}
+\end{center}
+The file \verb+agents4science_2025.pdf+ contains these instructions and illustrates the
+various formatting requirements your paper must satisfy.
+
+
+The only supported style file for Agents4Science 2025 is \verb+agents4science_2025.sty+,
+rewritten for \LaTeXe{}.
+
+
+The \LaTeX{} style file contains three optional arguments: \verb+final+, which
+creates a camera-ready copy, \verb+preprint+, which creates a preprint for
+submission to, e.g., arXiv, and \verb+nonatbib+, which will not load the
+\verb+natbib+ package for you in case of package clash.
+
+
+\paragraph{Preprint option}
+If you wish to post a preprint of your work online, e.g., on arXiv, using the
+Agents4Science style, please use the \verb+preprint+ option. This will create a
+nonanonymized version of your work with the text ``Preprint.''
+in the footer. This version may be distributed as you see fit, as long as you do not say which conference it was submitted to. Please \textbf{do
+  not} use the \verb+final+ option, which should \textbf{only} be used for
+papers accepted to Agents4Science.
+
+
+At submission time, please omit the \verb+final+ and \verb+preprint+
+options. This will anonymize your submission and add line numbers to aid
+review. Please do \emph{not} refer to these line numbers in your paper as they
+will be removed during generation of camera-ready copies.
+
+
+The file \verb+agents4science_2025.tex+ may be used as a ``shell'' for writing your
+paper. All you have to do is replace the author, title, abstract, and text of
+the paper with your own.
+
+
+The formatting instructions contained in these style files are summarized in
+Sections \ref{gen_inst}, \ref{headings}, and \ref{others} below.
+
+
+\section{General formatting instructions}
+\label{gen_inst}
+
+
+The text must be confined within a rectangle 5.5~inches (33~picas) wide and
+9~inches (54~picas) long. The left margin is 1.5~inch (9~picas).  Use 10~point
+type with a vertical spacing (leading) of 11~points.  Times New Roman is the
+preferred typeface throughout, and will be selected for you by default.
+Paragraphs are separated by \nicefrac{1}{2}~line space (5.5 points), with no
+indentation.
+
+
+The paper title should be 17~point, initial caps/lower case, bold, centered
+between two horizontal rules. The top and bottom rules should be 2~points thick.
+Allow \nicefrac{1}{4}~inch space above and below the title to rules. All pages
+should start at 1~inch (6~picas) from the top of the page.
+
+
+For the final version, authors' names are set in boldface, and each name is
+centered above the corresponding address. The lead author's name is to be listed
+first (left-most), and the co-authors' names (if different address) are set to
+follow. If there is only one co-author, list both author and co-author side by
+side.
+
+
+Please pay special attention to the instructions in Section \ref{others}
+regarding figures, tables, acknowledgments, and references.
+
+\section{Headings: first level}
+\label{headings}
+
+
+All headings should be lower case (except for first word and proper nouns),
+flush left, and bold.
+
+
+First-level headings should be in 12-point type.
+
+
+\subsection{Headings: second level}
+
+
+Second-level headings should be in 10-point type.
+
+
+\subsubsection{Headings: third level}
+
+
+Third-level headings should be in 10-point type.
+
+
+\paragraph{Paragraphs}
+
+
+There is also a \verb+\paragraph+ command available, which sets the heading in
+bold, flush left, and inline with the text, with the heading followed by 1\,em
+of space.
+
+
+\section{Citations, figures, tables, references}
+\label{others}
+
+
+These instructions apply to everyone.
+
+
+\subsection{Citations within the text}
+
+
+The \verb+natbib+ package will be loaded for you by default.  Citations may be
+author/year or numeric, as long as you maintain internal consistency.  As to the
+format of the references themselves, any style is acceptable as long as it is
+used consistently.
+
+
+The documentation for \verb+natbib+ may be found at
+\begin{center}
+  \url{http://mirrors.ctan.org/macros/latex/contrib/natbib/natnotes.pdf}
+\end{center}
+Of note is the command \verb+\citet+, which produces citations appropriate for
+use in inline text.  For example,
+\begin{verbatim}
+   \citet{hasselmo} investigated\dots
+\end{verbatim}
+produces
+\begin{quote}
+  Hasselmo, et al.\ (1995) investigated\dots
+\end{quote}
+
+
+If you wish to load the \verb+natbib+ package with options, you may add the
+following before loading the \verb+agents4science_2025+ package:
+\begin{verbatim}
+   \PassOptionsToPackage{options}{natbib}
+\end{verbatim}
+
+
+If \verb+natbib+ clashes with another package you load, you can add the optional
+argument \verb+nonatbib+ when loading the style file:
+\begin{verbatim}
+   \usepackage[nonatbib]{agents4science_2025}
+\end{verbatim}
+
+
+As submission is double blind, refer to your own published work in the third
+person. That is, use ``In the previous work of Jones et al.\ [4],'' not ``In our
+previous work [4].'' If you cite your other papers that are not widely available
+(e.g., a journal paper under review), use anonymous author names in the
+citation, e.g., an author of the form ``A.\ Anonymous'' and include a copy of the anonymized paper in the supplementary material.
+
+
+\subsection{Footnotes}
+
+
+Footnotes should be used sparingly.  If you do require a footnote, indicate
+footnotes with a number\footnote{Sample of the first footnote.} in the
+text. Place the footnotes at the bottom of the page on which they appear.
+Precede the footnote with a horizontal rule of 2~inches (12~picas).
+
+
+Note that footnotes are properly typeset \emph{after} punctuation
+marks.\footnote{As in this example.}
+
+
+\subsection{Figures}
+
+
+\begin{figure}
+  \centering
+  \fbox{\rule[-.5cm]{0cm}{4cm} \rule[-.5cm]{4cm}{0cm}}
+  \caption{Sample figure caption.}
+\end{figure}
+
+
+All artwork must be neat, clean, and legible. Lines should be dark enough for
+purposes of reproduction. The figure number and caption always appear after the
+figure. Place one line space before the figure caption and one line space after
+the figure. The figure caption should be lower case (except for first word and
+proper nouns); figures are numbered consecutively.
+
+
+You may use color figures.  However, it is best for the figure captions and the
+paper body to be legible if the paper is printed in either black/white or in
+color.
+
+
+\subsection{Tables}
+
+
+All tables must be centered, neat, clean and legible.  The table number and
+title always appear before the table.  See Table~\ref{sample-table}.
+
+
+Place one line space before the table title, one line space after the
+table title, and one line space after the table. The table title must
+be lower case (except for first word and proper nouns); tables are
+numbered consecutively.
+
+
+Note that publication-quality tables \emph{do not contain vertical rules.} We
+strongly suggest the use of the \verb+booktabs+ package, which allows for
+typesetting high-quality, professional tables:
+\begin{center}
+  \url{https://www.ctan.org/pkg/booktabs}
+\end{center}
+This package was used to typeset Table~\ref{sample-table}.
+
+
+\begin{table}
+  \caption{Sample table title}
+  \label{sample-table}
+  \centering
+  \begin{tabular}{lll}
+    \toprule
+    \multicolumn{2}{c}{Part}                   \\
+    \cmidrule(r){1-2}
+    Name     & Description     & Size ($\mu$m) \\
+    \midrule
+    Dendrite & Input terminal  & $\sim$100     \\
+    Axon     & Output terminal & $\sim$10      \\
+    Soma     & Cell body       & up to $10^6$  \\
+    \bottomrule
+  \end{tabular}
+\end{table}
+
+\subsection{Math}
+Note that display math in bare TeX commands will not create correct line numbers for submission. Please use LaTeX (or AMSTeX) commands for unnumbered display math. (You really shouldn't be using \$\$ anyway; see \url{https://tex.stackexchange.com/questions/503/why-is-preferable-to} and \url{https://tex.stackexchange.com/questions/40492/what-are-the-differences-between-align-equation-and-displaymath} for more information.)
+
+\subsection{Final instructions}
+
+Do not change any aspects of the formatting parameters in the style files.  In
+particular, do not modify the width or length of the rectangle the text should
+fit into, and do not change font sizes (except perhaps in the
+\textbf{References} section; see below). Please note that pages should be
+numbered.
+
+
+\section{Preparing PDF files}
+
+
+Please prepare submission files with paper size ``US Letter,'' and not, for
+example, ``A4.''
+
+
+Fonts were the main cause of problems in the past years. Your PDF file must only
+contain Type 1 or Embedded TrueType fonts. Here are a few instructions to
+achieve this.
+
+
+\begin{itemize}
+
+
+\item You should directly generate PDF files using \verb+pdflatex+.
+
+
+\item You can check which fonts a PDF files uses.  In Acrobat Reader, select the
+  menu Files$>$Document Properties$>$Fonts and select Show All Fonts. You can
+  also use the program \verb+pdffonts+ which comes with \verb+xpdf+ and is
+  available out-of-the-box on most Linux machines.
+
+
+\item \verb+xfig+ "patterned" shapes are implemented with bitmap fonts.  Use
+  "solid" shapes instead.
+
+
+\item The \verb+\bbold+ package almost always uses bitmap fonts.  You should use
+  the equivalent AMS Fonts:
+\begin{verbatim}
+   \usepackage{amsfonts}
+\end{verbatim}
+followed by, e.g., \verb+\mathbb{R}+, \verb+\mathbb{N}+, or \verb+\mathbb{C}+
+for $\mathbb{R}$, $\mathbb{N}$ or $\mathbb{C}$.  You can also use the following
+workaround for reals, natural and complex:
+\begin{verbatim}
+   \newcommand{\RR}{I\!\!R} %real numbers
+   \newcommand{\Nat}{I\!\!N} %natural numbers
+   \newcommand{\CC}{I\!\!\!\!C} %complex numbers
+\end{verbatim}
+Note that \verb+amsfonts+ is automatically loaded by the \verb+amssymb+ package.
+
+
+\end{itemize}
+
+
+If your file contains type 3 fonts or non embedded TrueType fonts, we will ask
+you to fix it.
+
+
+\subsection{Margins in \LaTeX{}}
+
+
+Most of the margin problems come from figures positioned by hand using
+\verb+\special+ or other commands. We suggest using the command
+\verb+\includegraphics+ from the \verb+graphicx+ package. Always specify the
+figure width as a multiple of the line width as in the example below:
+\begin{verbatim}
+   \usepackage[pdftex]{graphicx} ...
+   \includegraphics[width=0.8\linewidth]{myfile.pdf}
+\end{verbatim}
+See Section 4.4 in the graphics bundle documentation
+(\url{http://mirrors.ctan.org/macros/latex/required/graphics/grfguide.pdf})
+
+
+A number of width problems arise when \LaTeX{} cannot properly hyphenate a
+line. Please give LaTeX hyphenation hints using the \verb+\-+ command when
+necessary.
+
+\begin{ack}
+Use unnumbered first level headings for the acknowledgments. All acknowledgments
+go at the end of the paper before the list of references. Moreover, you are required to declare
+funding (financial activities supporting the submitted work) and competing interests (related financial activities outside the submitted work).
+More information about this disclosure can be found at the conference website: \url{https://agents4science.org}.
+
+
+Do {\bf not} include this section in the anonymized submission, only in the final paper. You can use the \texttt{ack} environment provided in the style file to automatically hide this section in the anonymized submission.
+\end{ack}
+
+\section*{References}
+
+
+References follow the acknowledgments in the camera-ready paper. Use unnumbered first-level heading for
+the references. Any choice of citation style is acceptable as long as you are
+consistent. It is permissible to reduce the font size to \verb+small+ (9 point)
+when listing the references.
+Note that the Reference section does not count towards the page limit.
+
+\newpage
+
+\bibliographystyle{plainnat}
+\bibliography{references}
+% Store references.bib in the same directory as the main tex file.
+
+\end{document}

{academia_mcp-1.7.1 → academia_mcp-1.7.3}/academia_mcp/tools/s2_citations.py

@@ -7,9 +7,9 @@ from typing import Optional, List, Dict, Any
 from academia_mcp.utils import get_with_retries
 
 
-OLD_API_URL_TEMPLATE = "https://api.semanticscholar.org/v1/paper/{paper_id}"
-GRAPH_URL_TEMPLATE = "https://api.semanticscholar.org/graph/v1/paper/{paper_id}/citations?fields={fields}&offset={offset}&limit={limit}"
-REVERSED_GRAPH_URL_TEMPLATE = "https://api.semanticscholar.org/graph/v1/paper/{paper_id}/references?fields={fields}&offset={offset}&limit={limit}"
+PAPER_URL_TEMPLATE = "https://api.semanticscholar.org/graph/v1/paper/{paper_id}?fields={fields}"
+CITATIONS_URL_TEMPLATE = "https://api.semanticscholar.org/graph/v1/paper/{paper_id}/citations?fields={fields}&offset={offset}&limit={limit}"
+REFERENCES_URL_TEMPLATE = "https://api.semanticscholar.org/graph/v1/paper/{paper_id}/references?fields={fields}&offset={offset}&limit={limit}"
 FIELDS = "title,authors,externalIds,venue,citationCount,publicationDate"
 
 
@@ -77,17 +77,19 @@ def s2_get_citations(
         arxiv_id = arxiv_id.split("v")[0]
     paper_id = f"arxiv:{arxiv_id}"
 
-    url = GRAPH_URL_TEMPLATE.format(paper_id=paper_id, fields=FIELDS, offset=offset, limit=limit)
+    url = CITATIONS_URL_TEMPLATE.format(
+        paper_id=paper_id, fields=FIELDS, offset=offset, limit=limit
+    )
     response = get_with_retries(url)
     result = response.json()
     entries = result["data"]
     total_count = len(result["data"]) + result["offset"]
 
     if "next" in result:
-        paper_url = OLD_API_URL_TEMPLATE.format(paper_id=paper_id)
+        paper_url = PAPER_URL_TEMPLATE.format(paper_id=paper_id, fields=FIELDS)
         paper_response = get_with_retries(paper_url)
         paper_result = paper_response.json()
-        total_count = paper_result["numCitedBy"]
+        total_count = paper_result["citationCount"]
 
     return _format_entries(entries, offset if offset else 0, total_count)
 
@@ -116,7 +118,7 @@ def s2_get_references(
         arxiv_id = arxiv_id.split("v")[0]
     paper_id = f"arxiv:{arxiv_id}"
 
-    url = REVERSED_GRAPH_URL_TEMPLATE.format(
+    url = REFERENCES_URL_TEMPLATE.format(
         paper_id=paper_id, fields=FIELDS, offset=offset, limit=limit
     )
     response = get_with_retries(url)

{academia_mcp-1.7.1 → academia_mcp-1.7.3}/academia_mcp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: academia-mcp
-Version: 1.7.1
+Version: 1.7.3
 Summary: MCP server that provides different tools to search for scientific publications
 Author-email: Ilya Gusev <phoenixilya@gmail.com>
 Project-URL: Homepage, https://github.com/IlyaGusev/academia_mcp

{academia_mcp-1.7.1 → academia_mcp-1.7.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "academia-mcp"
-version = "1.7.1"
+version = "1.7.3"
 description = "MCP server that provides different tools to search for scientific publications"
 readme = "README.md"
 authors = [

{academia_mcp-1.7.1 → academia_mcp-1.7.3}/tests/test_s2_citations.py

@@ -10,19 +10,13 @@ def test_s2_citations_pingpong() -> None:
 
 
 def test_s2_citations_transformers() -> None:
-    try:
-        citations = json.loads(s2_get_citations("1706.03762"))
-        assert citations["total_count"] >= 100000
-    except Exception:
-        pass
+    citations = json.loads(s2_get_citations("1706.03762"))
+    assert citations["total_count"] >= 100000
 
 
 def test_s2_citations_reversed() -> None:
-    try:
-        citations = json.loads(s2_get_references("1706.03762"))
-        assert citations["total_count"] <= 100
-    except Exception:
-        pass
+    citations = json.loads(s2_get_references("1706.03762"))
+    assert citations["total_count"] <= 100
 
 
 def test_s2_citations_versions() -> None: