academia-mcp 1.7.0__py3-none-any.whl → 1.7.2__py3-none-any.whl

academia_mcp/latex_templates/agents4science_2025/agents4science_2025.tex

@@ -449,242 +449,11 @@ 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.
-\medskip
-
-
-{
-\small
-
-
-[1] Alexander, J.A.\ \& Mozer, M.C.\ (1995) Template-based algorithms for
-connectionist rule extraction. In G.\ Tesauro, D.S.\ Touretzky and T.K.\ Leen
-(eds.), {\it Advances in Neural Information Processing Systems 7},
-pp.\ 609--616. Cambridge, MA: MIT Press.
-
-
-[2] Bower, J.M.\ \& Beeman, D.\ (1995) {\it The Book of GENESIS: Exploring
-  Realistic Neural Models with the GEneral NEural SImulation System.}  New York:
-TELOS/Springer--Verlag.
-
-
-[3] Hasselmo, M.E., Schnell, E.\ \& Barkai, E.\ (1995) Dynamics of learning and
-recall at excitatory recurrent synapses and cholinergic modulation in rat
-hippocampal region CA3. {\it Journal of Neuroscience} {\bf 15}(7):5249-5262.
-}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\appendix
-\section{Technical Appendices and Supplementary Material}
-Technical appendices with additional results, figures, graphs and proofs may be submitted with the paper submission before the full submission deadline, or as a separate PDF in the ZIP file below before the supplementary material deadline. There is no page limit for the technical appendices.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 \newpage
 
-\section*{Agents4Science AI Involvement Checklist}
-
-This checklist is designed to allow you to explain the role of AI in your research. This is important for understanding broadly how researchers use AI and how this impacts the quality and characteristics of the research. \textbf{Do not remove the checklist! Papers not including the checklist will be desk rejected.} You will give a score for each of the categories that define the role of AI in each part of the scientific process. The scores are as follows:
-
-\begin{itemize}
-    \item \involvementA{} \textbf{Human-generated}: Humans generated 95\% or more of the research, with AI being of minimal involvement.
-    \item \involvementB{} \textbf{Mostly human, assisted by AI}: The research was a collaboration between humans and AI models, but humans produced the majority (>50\%) of the research.
-    \item \involvementC{} \textbf{Mostly AI, assisted by human}: The research task was a collaboration between humans and AI models, but AI produced the majority (>50\%) of the research.
-    \item \involvementD{} \textbf{AI-generated}: AI performed over 95\% of the research. This may involve minimal human involvement, such as prompting or high-level guidance during the research process, but the majority of the ideas and work came from the AI.
-\end{itemize}
-
-These categories leave room for interpretation, so we ask that the authors also include a brief explanation elaborating on how AI was involved in the tasks for each category. Please keep your explanation to less than 150 words.
-
-IMPORTANT, please:
-\begin{itemize}
-    \item {\bf Delete this instruction block, but keep the section heading ``Agents4Science AI Involvement Checklist"},
-    \item  {\bf Keep the checklist subsection headings, questions/answers and guidelines below.}
-    \item {\bf Do not modify the questions and only use the provided macros for your answers}.
-\end{itemize} 
-
-\begin{enumerate}
-    \item \textbf{Hypothesis development}: Hypothesis development includes the process by which you came to explore this research topic and research question. This can involve the background research performed by either researchers or by AI. This can also involve whether the idea was proposed by researchers or by AI. 
-
-    Answer: \involvmentTODO{} % Answer with \involementA{}, \involementB{}, \involementC{}, or \involementD{}
-    
-    Explanation: \justificationTODO{}
-    \item \textbf{Experimental design and implementation}: This category includes design of experiments that are used to test the hypotheses, coding and implementation of computational methods, and the execution of these experiments. 
-
-    Answer: \involvmentTODO{} % Answer with \involementA{}, \involementB{}, \involementC{}, or \involementD{}
-    
-    Explanation: \justificationTODO{}
-    \item \textbf{Analysis of data and interpretation of results}: This category encompasses any process to organize and process data for the experiments in the paper. It also includes interpretations of the results of the study.
- 
-
-    Answer: \involvmentTODO{} % Answer with \involementA{}, \involementB{}, \involementC{}, or \involementD{}
-    
-    Explanation: \justificationTODO{}
-    \item \textbf{Writing}: This includes any processes for compiling results, methods, etc. into the final paper form. This can involve not only writing of the main text but also figure-making, improving layout of the manuscript, and formulation of narrative. 
-
-    Answer: \involvmentTODO{} % Answer with \involementA{}, \involementB{}, \involementC{}, or \involementD{}
-    
-    Explanation: \justificationTODO{}
-
-    \item \textbf{Observed AI Limitations}: What limitations have you found when using AI as a partner or lead author? 
-
-     
-    Description: \justificationTODO{}
-\end{enumerate}
-
 \bibliographystyle{plainnat}
 \bibliography{references}
 % Store references.bib in the same directory as the main tex file.
 
-\newpage
-
-\section*{Agents4Science Paper Checklist}
-
-%%% BEGIN INSTRUCTIONS %%%
-The checklist is designed to encourage best practices for responsible machine learning research, addressing issues of reproducibility, transparency, research ethics, and societal impact. Do not remove the checklist: {\bf Papers not including the checklist will be desk rejected.} The checklist should follow the references and follow the (optional) supplemental material. The checklist does NOT count towards the page limit. 
-
-Please read the checklist guidelines carefully for information on how to answer these questions. For each question in the checklist:
-\begin{itemize}
-    \item You should answer \answerYes{}, \answerNo{}, or \answerNA{}.
-    \item \answerNA{} means either that the question is Not Applicable for that particular paper or the relevant information is Not Available.
-    \item Please provide a short (1–2 sentence) justification right after your answer (even for NA). 
-\end{itemize}
-
-{\bf The checklist answers are an integral part of your paper submission.} They are visible to the reviewers and area chairs. You will be asked to also include it (after eventual revisions) with the final version of your paper, and its final version will be published with the paper.
-
-The reviewers of your paper will be asked to use the checklist as one of the factors in their evaluation. While "\answerYes{}" is generally preferable to "\answerNo{}", it is perfectly acceptable to answer "\answerNo{}" provided a proper justification is given. In general, answering "\answerNo{}" or "\answerNA{}" is not grounds for rejection. While the questions are phrased in a binary way, we acknowledge that the true answer is often more nuanced, so please just use your best judgment and write a justification to elaborate. All supporting evidence can appear either in the main paper or the supplemental material, provided in appendix. If you answer \answerYes{} to a question, in the justification please point to the section(s) where related material for the question can be found.
-
-IMPORTANT, please:
-\begin{itemize}
-    \item {\bf Delete this instruction block, but keep the section heading ``Agents4Science Paper Checklist"},
-    \item  {\bf Keep the checklist subsection headings, questions/answers and guidelines below.}
-    \item {\bf Do not modify the questions and only use the provided macros for your answers}.
-\end{itemize} 
-%%% END INSTRUCTIONS %%%
-
-
-\begin{enumerate}
-
-\item {\bf Claims}
-    \item[] Question: Do the main claims made in the abstract and introduction accurately reflect the paper's contributions and scope?
-    \item[] Answer: \answerTODO{} % Replace by \answerYes{}, \answerNo{}, or \answerNA{}.
-    \item[] Justification: \justificationTODO{}
-    \item[] Guidelines:
-    \begin{itemize}
-        \item The answer NA means that the abstract and introduction do not include the claims made in the paper.
-        \item The abstract and/or introduction should clearly state the claims made, including the contributions made in the paper and important assumptions and limitations. A No or NA answer to this question will not be perceived well by the reviewers. 
-        \item The claims made should match theoretical and experimental results, and reflect how much the results can be expected to generalize to other settings. 
-        \item It is fine to include aspirational goals as motivation as long as it is clear that these goals are not attained by the paper. 
-    \end{itemize}
-
-\item {\bf Limitations}
-    \item[] Question: Does the paper discuss the limitations of the work performed by the authors?
-    \item[] Answer: \answerTODO{} % Replace by \answerYes{}, \answerNo{}, or \answerNA{}.
-    \item[] Justification: \justificationTODO{}
-    \item[] Guidelines:
-    \begin{itemize}
-        \item The answer NA means that the paper has no limitation while the answer No means that the paper has limitations, but those are not discussed in the paper. 
-        \item The authors are encouraged to create a separate "Limitations" section in their paper.
-        \item The paper should point out any strong assumptions and how robust the results are to violations of these assumptions (e.g., independence assumptions, noiseless settings, model well-specification, asymptotic approximations only holding locally). The authors should reflect on how these assumptions might be violated in practice and what the implications would be.
-        \item The authors should reflect on the scope of the claims made, e.g., if the approach was only tested on a few datasets or with a few runs. In general, empirical results often depend on implicit assumptions, which should be articulated.
-        \item The authors should reflect on the factors that influence the performance of the approach. For example, a facial recognition algorithm may perform poorly when image resolution is low or images are taken in low lighting. 
-        \item The authors should discuss the computational efficiency of the proposed algorithms and how they scale with dataset size.
-        \item If applicable, the authors should discuss possible limitations of their approach to address problems of privacy and fairness.
-        \item While the authors might fear that complete honesty about limitations might be used by reviewers as grounds for rejection, a worse outcome might be that reviewers discover limitations that aren't acknowledged in the paper. Reviewers will be specifically instructed to not penalize honesty concerning limitations.
-    \end{itemize}
-
-\item {\bf Theory assumptions and proofs}
-    \item[] Question: For each theoretical result, does the paper provide the full set of assumptions and a complete (and correct) proof?
-    \item[] Answer: \answerTODO{} % Replace by \answerYes{}, \answerNo{}, or \answerNA{}.
-    \item[] Justification: \justificationTODO{}
-    \item[] Guidelines:
-    \begin{itemize}
-        \item The answer NA means that the paper does not include theoretical results. 
-        \item All the theorems, formulas, and proofs in the paper should be numbered and cross-referenced.
-        \item All assumptions should be clearly stated or referenced in the statement of any theorems.
-        \item The proofs can either appear in the main paper or the supplemental material, but if they appear in the supplemental material, the authors are encouraged to provide a short proof sketch to provide intuition. 
-    \end{itemize}
-
-    \item {\bf Experimental result reproducibility}
-    \item[] Question: Does the paper fully disclose all the information needed to reproduce the main experimental results of the paper to the extent that it affects the main claims and/or conclusions of the paper (regardless of whether the code and data are provided or not)?
-    \item[] Answer: \answerTODO{} % Replace by \answerYes{}, \answerNo{}, or \answerNA{}.
-    \item[] Justification: \justificationTODO{}
-    \item[] Guidelines:
-    \begin{itemize}
-        \item The answer NA means that the paper does not include experiments.
-        \item If the paper includes experiments, a No answer to this question will not be perceived well by the reviewers: Making the paper reproducible is important.
-        \item If the contribution is a dataset and/or model, the authors should describe the steps taken to make their results reproducible or verifiable. 
-        \item We recognize that reproducibility may be tricky in some cases, in which case authors are welcome to describe the particular way they provide for reproducibility. In the case of closed-source models, it may be that access to the model is limited in some way (e.g., to registered users), but it should be possible for other researchers to have some path to reproducing or verifying the results.
-    \end{itemize}
-
-\item {\bf Open access to data and code}
-    \item[] Question: Does the paper provide open access to the data and code, with sufficient instructions to faithfully reproduce the main experimental results, as described in supplemental material?
-    \item[] Answer: \answerTODO{} % Replace by \answerYes{}, \answerNo{}, or \answerNA{}.
-    \item[] Justification: \justificationTODO{}
-    \item[] Guidelines:
-    \begin{itemize}
-        \item The answer NA means that paper does not include experiments requiring code.
-        \item Please see the Agents4Science code and data submission guidelines on the conference website for more details.
-        \item While we encourage the release of code and data, we understand that this might not be possible, so “No” is an acceptable answer. Papers cannot be rejected simply for not including code, unless this is central to the contribution (e.g., for a new open-source benchmark).
-        \item The instructions should contain the exact command and environment needed to run to reproduce the results. 
-        \item At submission time, to preserve anonymity, the authors should release anonymized versions (if applicable).
-    \end{itemize}
-
-\item {\bf Experimental setting/details}
-    \item[] Question: Does the paper specify all the training and test details (e.g., data splits, hyperparameters, how they were chosen, type of optimizer, etc.) necessary to understand the results?
-    \item[] Answer: \answerTODO{} % Replace by \answerYes{}, \answerNo{}, or \answerNA{}.
-    \item[] Justification: \justificationTODO{}
-    \item[] Guidelines:
-    \begin{itemize}
-        \item The answer NA means that the paper does not include experiments.
-        \item The experimental setting should be presented in the core of the paper to a level of detail that is necessary to appreciate the results and make sense of them.
-        \item The full details can be provided either with the code, in appendix, or as supplemental material.
-    \end{itemize}
-
-\item {\bf Experiment statistical significance}
-    \item[] Question: Does the paper report error bars suitably and correctly defined or other appropriate information about the statistical significance of the experiments?
-    \item[] Answer: \answerTODO{} % Replace by \answerYes{}, \answerNo{}, or \answerNA{}.
-    \item[] Justification: \justificationTODO{}
-    \item[] Guidelines:
-    \begin{itemize}
-        \item The answer NA means that the paper does not include experiments.
-        \item The authors should answer "Yes" if the results are accompanied by error bars, confidence intervals, or statistical significance tests, at least for the experiments that support the main claims of the paper.
-        \item The factors of variability that the error bars are capturing should be clearly stated (for example, train/test split, initialization, or overall run with given experimental conditions).
-    \end{itemize}
-
-\item {\bf Experiments compute resources}
-    \item[] Question: For each experiment, does the paper provide sufficient information on the computer resources (type of compute workers, memory, time of execution) needed to reproduce the experiments?
-    \item[] Answer: \answerTODO{} % Replace by \answerYes{}, \answerNo{}, or \answerNA{}.
-    \item[] Justification: \justificationTODO{}
-    \item[] Guidelines:
-    \begin{itemize}
-        \item The answer NA means that the paper does not include experiments.
-        \item The paper should indicate the type of compute workers CPU or GPU, internal cluster, or cloud provider, including relevant memory and storage.
-        \item The paper should provide the amount of compute required for each of the individual experimental runs as well as estimate the total compute. 
-    \end{itemize}
-    
-\item {\bf Code of ethics}
-    \item[] Question: Does the research conducted in the paper conform, in every respect, with the Agents4Science Code of Ethics (see conference website)?
-    \item[] Answer: \answerTODO{} % Replace by \answerYes{}, \answerNo{}, or \answerNA{}.
-    \item[] Justification: \justificationTODO{}
-    \item[] Guidelines:
-    \begin{itemize}
-        \item The answer NA means that the authors have not reviewed the Agents4Science Code of Ethics.
-        \item If the authors answer No, they should explain the special circumstances that require a deviation from the Code of Ethics.
-    \end{itemize}
-
-
-\item {\bf Broader impacts}
-    \item[] Question: Does the paper discuss both potential positive societal impacts and negative societal impacts of the work performed?
-    \item[] Answer: \answerTODO{} % Replace by \answerYes{}, \answerNo{}, or \answerNA{}.
-    \item[] Justification: \justificationTODO{}
-    \item[] Guidelines:
-    \begin{itemize}
-        \item The answer NA means that there is no societal impact of the work performed.
-        \item If the authors answer NA or No, they should explain why their work has no societal impact or why the paper does not address societal impact.
-        \item Examples of negative societal impacts include potential malicious or unintended uses (e.g., disinformation, generating fake profiles, surveillance), fairness considerations, privacy considerations, and security considerations.
-        \item If there are negative societal impacts, the authors could also discuss possible mitigation strategies.
-    \end{itemize}
-
-
-\end{enumerate}
-
-
 \end{document}

academia_mcp/tools/latex.py

@@ -120,6 +120,7 @@ def compile_latex_from_str(
                     [
                         "pdflatex",
                         "-interaction=nonstopmode",
+                        "-file-line-error",
                         tex_filename,
                     ],
                     cwd=str(temp_dir_path),

{academia_mcp-1.7.0.dist-info → academia_mcp-1.7.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: academia-mcp
-Version: 1.7.0
+Version: 1.7.2
 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-1.7.0.dist-info → academia_mcp-1.7.2.dist-info}/RECORD

@@ -7,7 +7,7 @@ academia_mcp/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 academia_mcp/server.py,sha256=ZAd-sunkEkka6snOlzgLCMaIQCzstiXP1pFlo20oyvA,3195
 academia_mcp/utils.py,sha256=P9U3RjYzcztE0KxXvJSy5wSBaUg2CM9tpByljYrsrl4,4607
 academia_mcp/latex_templates/agents4science_2025/agents4science_2025.sty,sha256=hGcEPCYBJS4vdhWvN_yEaJC4GvT_yDroI94CfY2Oguk,12268
-academia_mcp/latex_templates/agents4science_2025/agents4science_2025.tex,sha256=k_nOyPv-OxGbFtKSou6nV6l413EfWvozE6zIx04s8iU,33924
+academia_mcp/latex_templates/agents4science_2025/agents4science_2025.tex,sha256=Tl1QkHXHRopw9VEfWrD3Layr5JP_0gIzVQjL4KXIWqc,15814
 academia_mcp/tools/__init__.py,sha256=nzMOzrIPVSXA3LQa02GPeX9SfAmg9f6_eZY97ALLNs4,1245
 academia_mcp/tools/anthology_search.py,sha256=rhFpJZqGLABgr0raDuH0CARBiAJNJtEI4dlMrKNHfDQ,7669
 academia_mcp/tools/arxiv_download.py,sha256=gBY0_Kz0yGtVkLMwn6GrAyfBjovZVgcSMuyy67p65Cw,10474
@@ -15,15 +15,15 @@ academia_mcp/tools/arxiv_search.py,sha256=pzM18qrF3QL03A53w003kE7hQi3s3QKtjgw0m7
 academia_mcp/tools/bitflip.py,sha256=eihmNk_C_8ZkBcjtJYH6MvZ0rItgIlvHHA0eGLxsvRs,12276
 academia_mcp/tools/document_qa.py,sha256=t9mygYQ7AFIAPiha1nZ-y043luQlkTCBdWb_SDnzEsE,2444
 academia_mcp/tools/hf_datasets_search.py,sha256=KiBkqT4rXjEN4oc1AWZOPnqN_Go90TQogY5-DUm3LQo,2854
-academia_mcp/tools/latex.py,sha256=bf8VZUgCByzBAMTZCeqrRrmakotext3d3DbtkiOTh1k,5892
+academia_mcp/tools/latex.py,sha256=llxxjBMHzDX4iNMeJSLuiP_sXT4umtYVyyhfZq2derM,5936
 academia_mcp/tools/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 academia_mcp/tools/review.py,sha256=LbebOHGs76qoSgWvTQ9Uj1fvmjc2eSBudX6n_zCINYI,10247
 academia_mcp/tools/s2_citations.py,sha256=dqrBp76RrX1zH2XzcMAoWBbvbtyhxLeF-xnqOKD_JiM,4852
 academia_mcp/tools/visit_webpage.py,sha256=OZdqDkVPIbANyFw5o5jIjU5Rr_dolxrGDs63Ud-GmRM,1966
 academia_mcp/tools/web_search.py,sha256=mobKm4iqKppn8pduZYMzWRo1MQBjkAqmMtrFLI5XY2Y,6296
-academia_mcp-1.7.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-academia_mcp-1.7.0.dist-info/METADATA,sha256=r1KjaW_Z7IhKjlej0EKOMuiydIKcGv6TKtJblMi0CKs,3714
-academia_mcp-1.7.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-academia_mcp-1.7.0.dist-info/entry_points.txt,sha256=gxkiKJ74w2FwJpSECpjA3XtCfI5ZfrM6N8cqnwsq4yY,51
-academia_mcp-1.7.0.dist-info/top_level.txt,sha256=CzGpRFsRRJRqWEb1e3SUlcfGqRzOxevZGaJWrtGF8W0,13
-academia_mcp-1.7.0.dist-info/RECORD,,
+academia_mcp-1.7.2.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+academia_mcp-1.7.2.dist-info/METADATA,sha256=OrWgykO5__PEKpBExYyOOfk7bGpbn02rO1thwtOfh-E,3714
+academia_mcp-1.7.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+academia_mcp-1.7.2.dist-info/entry_points.txt,sha256=gxkiKJ74w2FwJpSECpjA3XtCfI5ZfrM6N8cqnwsq4yY,51
+academia_mcp-1.7.2.dist-info/top_level.txt,sha256=CzGpRFsRRJRqWEb1e3SUlcfGqRzOxevZGaJWrtGF8W0,13
+academia_mcp-1.7.2.dist-info/RECORD,,