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-rw-r--r--tex/src/figure-branching.tex6
-rw-r--r--tex/src/figure-data-lineage.tex18
-rw-r--r--tex/src/figure-tools-per-year.tex2
-rw-r--r--tex/src/preamble-project.tex37
-rw-r--r--tex/src/references.tex (renamed from tex/src/references.bib)42
5 files changed, 74 insertions, 31 deletions
diff --git a/tex/src/figure-branching.tex b/tex/src/figure-branching.tex
index 52a6303..7259f7d 100644
--- a/tex/src/figure-branching.tex
+++ b/tex/src/figure-branching.tex
@@ -120,9 +120,9 @@
\draw [->, black!40!white, rounded corners, line width=2mm]
(11cm,4.5cm) -- (12.5cm,5cm) -- (12.5cm,7.9cm);
\draw [black!40!white, line width=2mm] (9.5cm,6cm) -- (12.5cm,7cm);
- \draw [anchor=north, black!40!white] (12.7cm,4.8cm) node [scale=1.5]
- {\bf Derivative};
- \draw [anchor=north, black!40!white] (12.7cm,4.4cm) node [scale=1.5]
+ \draw [anchor=north, black!40!white] (12.6cm,4.8cm) node [scale=1.5]
+ {\bf Derived};
+ \draw [anchor=north, black!40!white] (12.6cm,4.4cm) node [scale=1.5]
{\bf project};
%% Maneage commits.
diff --git a/tex/src/figure-data-lineage.tex b/tex/src/figure-data-lineage.tex
index 146a833..fcc52d9 100644
--- a/tex/src/figure-data-lineage.tex
+++ b/tex/src/figure-data-lineage.tex
@@ -46,9 +46,9 @@
text centered,
font=\ttfamily,
text width=2.8cm,
+ minimum width=15cm,
minimum height=7.8cm,
draw=green!50!black!50,
- minimum width=\linewidth,
fill=black!10!green!2!white,
label={[shift={(0,-5mm)}]\texttt{top-make.mk}}] {};
@@ -62,7 +62,7 @@
\node (analysis2mk) [node-makefile, at={(2.67cm,-1.3cm)},
label={[shift={(0,-5mm)}]\texttt{demo-plot.mk}}] {};
\node [opacity=0.6] (analysis3mk) [node-makefile, at={(5.47cm,-1.3cm)},
- label={[shift={(0,-5mm)}, opacity=0.6]\texttt{another-step.mk}}] {};
+ label={[shift={(0,-5mm)}, opacity=0.6]\texttt{next-step.mk}}] {};
%% verify.mk
\node [at={(-5.3cm,-2.8cm)},
@@ -137,14 +137,16 @@
%% input-2.dat
\ifdefined\inputtwo
\node (input2) [node-terminal, at={(-2.93cm,1.9cm)}] {menke20.xlsx};
- \draw [->] (input2) -- (downloadtex);
\fi
%% INPUTS.conf
\ifdefined\inputsconf
\node (INPUTS) [node-nonterminal, at={(-2.93cm,4.6cm)}] {INPUTS.conf};
\node (input2-west) [node-point, at={(-4.33cm,1.9cm)}] {};
+ \node (downloadtex-west) [node-point, at={(-4.33cm,-0.8cm)}] {};
\draw [->,rounded corners] (INPUTS.west) -| (input2-west) |- (input2);
+ \draw [->,rounded corners] (INPUTS.west) -| (downloadtex-west)
+ |- (downloadtex);
\fi
%% analysis1.tex
@@ -155,7 +157,7 @@
%% out1b.dat
\ifdefined\outoneb
- \node (out1b) [node-terminal, at={(-0.13cm,1.1cm)}] {menke20-table-3.txt};
+ \node (out1b) [node-terminal, at={(-0.13cm,1.1cm)}] {table-3.txt};
\draw [->] (out1b) -- (a1tex);
\fi
@@ -173,9 +175,9 @@
%% out-2b.dat
\ifdefined\outtwob
- \node (menkedemoyear) [node-nonterminal, at={(2.67cm,4.6cm)}] {menke-demo-year.conf};
+ \node (menkedemoyear) [node-nonterminal, at={(2.67cm,4.6cm)}] {demo-year.conf};
\node (a2tex-west) [node-point, at={(1.27cm,-0.8cm)}] {};
- \node (out2b) [node-terminal, at={(2.67cm,0.3cm)}] {tools-per-year.txt};
+ \node (out2b) [node-terminal, at={(2.67cm,0.3cm)}] {columns.txt};
\draw [->] (out2b) -- (a2tex);
\draw [->,rounded corners] (menkedemoyear.west) -| (a2tex-west) |- (a2tex);
\fi
@@ -187,7 +189,7 @@
%% analysis3.tex
\ifdefined\analysisthreetex
- \node [opacity=0.6] (a3tex) [node-terminal, at={(5.47cm,-0.8cm)}] {another-step.tex};
+ \node [opacity=0.6] (a3tex) [node-terminal, at={(5.47cm,-0.8cm)}] {next-step.tex};
\draw [opacity=0.6, rounded corners, -, dashed] (a3tex) |- (initialize-south);
\fi
@@ -216,7 +218,7 @@
\ifdefined\outthreeadep
\node [opacity=0.6] (out3a-west) [node-point, at={(4.07cm,2.7cm)}] {};
\draw [opacity=0.6, ->,rounded corners, dashed] (input2) |- (out3a);
- \node [opacity=0.6] (a3conf1) [node-nonterminal, at={(5.47cm,4.6cm)}] {param-3.conf};
+ \node [opacity=0.6] (a3conf1) [node-nonterminal, at={(5.47cm,4.6cm)}] {param.conf};
\draw [opacity=0.6, rounded corners, dashed] (a3conf1.west) -| (out3a-west) |- (out3a);
\fi
\end{tikzpicture}
diff --git a/tex/src/figure-tools-per-year.tex b/tex/src/figure-tools-per-year.tex
index 75557ac..f82402f 100644
--- a/tex/src/figure-tools-per-year.tex
+++ b/tex/src/figure-tools-per-year.tex
@@ -1,4 +1,4 @@
-\begin{tikzpicture}
+\begin{tikzpicture}[scale=0.9]
\begin{axis}[
ymin=0,
ymax=100,
diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex
index c4d7feb..9b956cf 100644
--- a/tex/src/preamble-project.tex
+++ b/tex/src/preamble-project.tex
@@ -8,11 +8,9 @@
%% For the `\url' command.
\usepackage{url}
-% correct bad hyphenation here
-\hyphenation{op-tical net-works semi-conduc-tor}
-
-%% To use colors.
-\usepackage{xcolor}
+%% No need to load xcolor, its included by others below (it conflicts with
+%% the listings package.
+%\usepackage{xcolor}
%% To have links.
\usepackage[
@@ -25,3 +23,32 @@
%% To have typewriter font
\usepackage{courier}
+
+%% To have bold monospace
+%\usepackage[scaled=0.85]{beramono}
+\usepackage{inconsolata}
+
+%% To display codes.
+\usepackage{listings}
+\usepackage{etoolbox}
+\input{listings-bash.prf}
+\lstset{
+ frame=lines,
+ numbers=none,
+ language=bash,
+ commentstyle=\color{gray},
+ abovecaptionskip=0mm,
+ belowcaptionskip=0mm,
+ keywordstyle=\mdseries,
+ basicstyle=\small\ttfamily\color{blue!35!black},
+}
+\makeatletter
+\preto\lstlisting{\def\@captype{table}}
+\pretocmd\lst@makecaption{\noindent{\rule{\linewidth}{1pt}}}{}{}
+\makeatother
+
+
+
+
+%% Custom macros
+\newcommand{\inlinecode}[1]{\textcolor{blue!35!black}{\texttt{#1}}}
diff --git a/tex/src/references.bib b/tex/src/references.tex
index e19ec16..f355bba 100644
--- a/tex/src/references.bib
+++ b/tex/src/references.tex
@@ -1,10 +1,11 @@
-@ARTICLE{clement19,
- author = {Cl\'ement-Fontaine, M\'elanie and Di Cosmo, Roberto and Guerry, Bastien and MOREAU, Patrick and Pellegrini, Fran\c cois},
- title = {Encouraging a wider usage of software derived from research},
- year = {2019},
- journal = {Archives ouvertes HAL},
- volume = {},
- pages = {\href{https://hal.archives-ouvertes.fr/hal-02545142}{hal-02545142}},
+@ARTICLE{mesnard20,
+ author = {Olivier Mesnard and Lorena A. Barba},
+ title = {Reproducible Workflow on a Public Cloud for Computational Fluid Dynamics},
+ year = {2020},
+ journal = {Computing in Science \& Engineering},
+ volume = {22},
+ pages = {102-116},
+ doi = {10.1109/MCSE.2019.2941702},
}
@@ -73,7 +74,7 @@ archivePrefix = {arXiv},
month = "Feb",
volume = {491},
number = {4},
- pages = {5317},
+ pages = {5317-5329},
doi = {10.1093/mnras/stz3111},
archivePrefix = {arXiv},
eprint = {1911.01430},
@@ -100,13 +101,26 @@ archivePrefix = {arXiv},
+@ARTICLE{clement19,
+ author = {Cl\'ement-Fontaine, M\'elanie and Di Cosmo, Roberto and Guerry, Bastien and MOREAU, Patrick and Pellegrini, Fran\c cois},
+ title = {Encouraging a wider usage of software derived from research},
+ year = {2019},
+ journal = {Archives ouvertes HAL},
+ volume = {},
+ pages = {\href{https://hal.archives-ouvertes.fr/hal-02545142}{hal-02545142}},
+}
+
+
+
+
+
@ARTICLE{pimentel19,
author = {{Jo\~ao Felipe} Pimentel and Leonardo Murta and Vanessa Braganholo and Juliana Freire},
title = {A large-scale study about quality and reproducibility of jupyter notebooks},
year = {2019},
journal = {Proceedings of the 16th International Conference on Mining Software Repositories},
volume = {1},
- pages = {507},
+ pages = {507-517},
doi = {10.1109/MSR.2019.00077},
}
@@ -234,7 +248,7 @@ archivePrefix = {arXiv},
title = {Reproducibility and Replicability in Science},
journal = {The National Academies Press},
year = 2019,
- pages = {1},
+ pages = {1-256},
doi = {10.17226/25303},
}
@@ -316,7 +330,7 @@ author = "Adam Brinckman and Kyle Chard and Niall Gaffney and Mihael Hategan and
keywords = {Computer Science - Digital Libraries, Computer Science - Software Engineering},
year = "2019",
month = "May",
- pages = {39},
+ pages = {39-52},
archivePrefix = {arXiv},
eprint = {1905.11123},
primaryClass = {cs.DL},
@@ -742,7 +756,7 @@ archivePrefix = {arXiv},
journal = {International Journal on Digital Libraries},
volume = {18},
year = {2017},
- pages = {77},
+ pages = {77-92},
doi = {10.1007/s00799-016-0178-2},
}
@@ -982,7 +996,7 @@ archivePrefix = {arXiv},
month = sep,
volume = 220,
eid = {1},
- pages = {1},
+ pages = {1-33},
doi = {10.1088/0067-0049/220/1/1},
adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
@@ -1647,7 +1661,7 @@ Reproducible Research in Image Processing},
journal = {SEG Technical Program Expanded Abstracts},
year = {1992},
volume = {1},
- pages = {601},
+ pages = {601-604},
doi = {10.1190/1.1822162},
}
generated by cgit v1.2.1 (git 2.18.0) at 2024-12-26 06:04:04 +0000