Improve build scripts and arXiv compatibility

Author: AgenttiX

.github/workflows/main.yml

@@ -22,7 +22,7 @@ jobs:
           if-no-files-found: error
   gen_figures:
     runs-on: ubuntu-latest
-    timeout-minutes: 15
+    timeout-minutes: 20
     steps:
       - name: Setup Python
         uses: actions/setup-python@v5

Makefile

@@ -1,7 +1,7 @@
 all: clean pdf
 clean:
 	rm -f ./*.aux ./*.bbl ./*.bcf ./*.blg ./*.fdb_latexmk ./*.fls ./*.gz ./*.ilg ./*.ind ./*.lof ./*.log ./*.lot ./*.nlo ./*.nls ./*.out ./*.tdo ./*.toc ./*.xml \
-		./tex/*.dvi ./tex/*.log
+		./tex/*.dvi ./tex/*.log ./main.pdf
 pdf:
 	# Allow exit code 12. The double $$ is needed in a Makefile to refer to a shell variable instead of a make variable.
 	# https://stackoverflow.com/a/16315249

README.md

@@ -2,7 +2,7 @@
 
 My second master's thesis.
 
-Mika Mäki, 2021-2024
+Mika Mäki, 2021-2024, updated in 2025
 
 This thesis is a part of PTtools documentation, and will therefore be updated after its initial submission.
 You can find the latest version of the pdf in
@@ -19,7 +19,7 @@ The CC BY 4.0 license applies to this repository and the generated pdf files wit
 - Third-party figures in the odp and pdf slides and in the slide folders
 - The photo of my face in the odp and pdf slides
 - cft_meetup_presentation_2024/vlcsnap*.png figures
-- The figures in fig/lecture notes are CC-BY-4.0, but by [Hindmarsh et al., DOI: 10.21468/SciPostPhysLectNotes.24](https://scipost.org/10.21468/SciPostPhysLectNotes.24)
+- The figures in fig/lecture_notes are CC-BY-4.0, but by [Hindmarsh et al., DOI: 10.21468/SciPostPhysLectNotes.24](https://scipost.org/10.21468/SciPostPhysLectNotes.24)
 - The Python code in msc2_python/giese. This is originally developed by [Giese et al., DOI: 10.1088/1475-7516/2021/01/072](https://iopscience.iop.org/article/10.1088/1475-7516/2021/01/072)
 - The University of Helsinki LaTeX template files
   babelbst.tex, englbst.tex, finnbst.tex, swedbst.tex, tktl.bst, UH_TCM_MSc.cls, UH-logo.png

create_arxiv.sh

@@ -11,18 +11,25 @@ if command -v rsync &> /dev/null; then :; else
   sudo apt-get install rsync
 fi
 
+if [ ! -f main.bbl ]; then
+  echo "main.bbl was not found. Compiling the LaTeX files to create it."
+  make all
+fi
+
 echo "Removing existing arxiv folder and zip file."
 rm -rf arxiv arxiv.zip
 
 echo "Creating the arxiv folder and adding files."
 mkdir arxiv
 mkdir arxiv/anc
-# Rsync is used to enable excluding
-rsync -av --exclude=fig/*-converted-to.pdf --exclude=fig/lecture_notes --exclude=fig/tampere \
+# Rsync is used to enable excluding.
+rsync -av --exclude=fig/*-converted-to.pdf --exclude=fig/lecture_notes --exclude=fig/tampere --exclude=tex/other_models.tex \
   fig tex \
   .latexmkrc babelbst.tex englbst.tex finnbst.tex LICENSE main.bbl main.tex Makefile swedbst.tex tktl.bst UH-logo.png UH_TCM_MSc.cls \
   arxiv
-rsync -av --exclude msc2_python/logs --exclude msc2_python/tampere \
+# Ancillary files are placed in the anc directory.
+# https://info.arxiv.org/help/ancillary_files.html
+rsync -av --exclude='**/__pycache__' --exclude='*.pyc' --exclude=msc2_python/logs --exclude=msc2_python/tampere \
   msc2_python create_arxiv.sh arxiv/anc
 cp -r .github arxiv/anc/github
 

tex/phase_transitions.tex

@@ -307,7 +307,7 @@ \section{Field-fluid system}
 
 \begin{figure}[ht!]
 \centering
-\includegraphics[width=0.6\textwidth]{fig/potential.eps}
+\includegraphics[width=0.6\textwidth]{fig/potential.pdf}
 \caption{The thermal effective potential at different temperatures. Generated with PTtools utilities. See also \cite[fig. 4]{lecture_notes}.}
 \label{fig:potential}
 \end{figure}

tex/relativistic_combustion.tex

@@ -202,7 +202,7 @@ \section{Relativistic combustion}
 
 \begin{figure}[ht!]
 \centering
-\includegraphics[width=0.7\textwidth]{fig/vm_vp_plane.eps}
+\includegraphics[width=0.7\textwidth]{fig/vm_vp_plane.pdf}
 \caption{Relation between the fluid velocity just ahead of the wall $\tilde{v}_+$ and just behind the wall $\tilde{v}_-$. Generated with PTtools. See also \cite[fig. 13]{lecture_notes}.}
 \label{fig:vplus_vminus}
 \end{figure}

tex/results.tex

@@ -12,21 +12,21 @@
 
 \begin{figure}[ht!]
 \centering
-\includegraphics[width=\textwidth]{fig/const_cs_gw_v.eps}
+\includegraphics[width=\textwidth]{fig/const_cs_gw_v.pdf}
 \caption{Self-similar fluid profiles with four sound speed combinations, three different wall speeds $v_\text{wall}$ and two transition strengths $\alpha_n$}
 \label{fig:fluid_profiles}
 \end{figure}
 
 \begin{figure}[ht!]
 \centering
-\includegraphics[width=\textwidth]{fig/const_cs_gw.eps}
+\includegraphics[width=\textwidth]{fig/const_cs_gw.pdf}
 \caption{Gravitational wave power spectra computed with the sound shell model from the fluid profiles of fig. \ref{fig:fluid_profiles}}
 \label{fig:gw_spectra}
 \end{figure}
 
 \begin{figure}[ht!]
 \centering
-\includegraphics[width=\textwidth]{fig/const_cs_gw_omgw0.eps}
+\includegraphics[width=\textwidth]{fig/const_cs_gw_omgw0.pdf}
 \caption{Scaled gravitational wave power spectra today, $\Omega_{gw,0}$, of the gravitational wave power spectra of fig. \ref{fig:gw_spectra}}
 \label{fig:omgw0}
 \end{figure}
@@ -106,14 +106,14 @@
 
 \begin{figure}[ht!]
 \centering
-\includegraphics[width=\textwidth]{fig/giese_lisa_fig2_alpha_n.eps}
+\includegraphics[width=\textwidth]{fig/giese_lisa_fig2_alpha_n.pdf}
 \caption{Comparison of $\kappa$ values by \cite[fig. 2]{giese_2021} and PTtools}
 \label{fig:kappa_giese}
 \end{figure}
 
 \begin{figure}[ht!]
 \centering
-\includegraphics[width=\textwidth]{fig/giese_lisa_fig2_alpha_n_diff.eps}
+\includegraphics[width=\textwidth]{fig/giese_lisa_fig2_alpha_n_diff.pdf}
 \caption{Relative difference of the $\kappa$ values by \cite[fig. 2]{giese_2021} and PTtools}
 \label{fig:kappa_giese_diff}
 \end{figure}

tex/types_of_solutions.tex

@@ -72,7 +72,7 @@ \section{Types of solutions}
 
 \begin{figure}[ht!]
 \centering
-\includegraphics[width=\textwidth]{fig/relativistic_combustion.eps}
+\includegraphics[width=\textwidth]{fig/relativistic_combustion.pdf}
 \caption{Three different types of relativistic combustion. Generated with PTtools. See also \cites[fig. 14]{lecture_notes}[fig. 14]{mazumdar_review_2019}.}
 \label{fig:solution_types}
 \end{figure}