diff options
Diffstat (limited to 'tex/src')
| -rw-r--r-- | tex/src/figure-data-lineage.tex | 28 | ||||
| -rw-r--r-- | tex/src/figure-download.tex | 8 | ||||
| -rw-r--r-- | tex/src/figure-mk20tab3.tex | 50 | ||||
| -rw-r--r-- | tex/src/preamble-style.tex | 11 | ||||
| -rw-r--r-- | tex/src/references.tex | 59 |
5 files changed, 130 insertions, 26 deletions
diff --git a/tex/src/figure-data-lineage.tex b/tex/src/figure-data-lineage.tex index aa2a397..010a0be 100644 --- a/tex/src/figure-data-lineage.tex +++ b/tex/src/figure-data-lineage.tex @@ -136,14 +136,14 @@ %% input-2.dat \ifdefined\inputtwo - \node (input2) [node-terminal, at={(-2.93cm,1.1cm)}] {input2.dat}; + \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,1.1cm)}] {}; + \node (input2-west) [node-point, at={(-4.33cm,1.9cm)}] {}; \draw [->,rounded corners] (INPUTS.west) -| (input2-west) |- (input2); \fi @@ -155,31 +155,14 @@ %% out1b.dat \ifdefined\outoneb - \node (out1b) [node-terminal, at={(-0.13cm,1.1cm)}] {out-1b.dat}; + \node (out1b) [node-terminal, at={(-0.13cm,1.1cm)}] {menke20-table-3.txt}; \draw [->] (out1b) -- (a1tex); \fi %% outonebdep \ifdefined\outonebdep \node (out1b-west) [node-point, at={(-1.53cm,1.1cm)}] {}; - \node (out1a) [node-terminal, at={(-0.13cm,2.7cm)}] {out-1a.dat}; - \node (a1conf1) [node-nonterminal, at={(-0.13cm,4.6cm)}] {param-1.conf}; - \draw [->] (input2) -- (out1b); - \draw [->] (out1a) -- (out1b); - \draw [->,rounded corners] (a1conf1.west) -| (out1b-west) |- (out1b); - \fi - - %% input1.dat - \ifdefined\inputone - \node (input1) [node-terminal, at={(-2.93cm,1.9cm)}] {input1.dat}; - \draw [->,rounded corners,] (input1.north) |- (out1a); - \fi - - %% input1 dependencies - \ifdefined\inputonedep - \node (input1-east) [node-point, at={(-1.53cm,1.9cm)}] {}; - \node (input1-west) [node-point, at={(-4.33cm,1.9cm)}] {}; - \draw [->,rounded corners] (INPUTS.west) -| (input1-west) |- (input1); + \draw [->, rounded corners] (input2) |- (out1b); \fi %% analysis2.tex @@ -227,14 +210,13 @@ \node (out2a-west) [node-point, at={(1.27cm,1.9cm)}] {}; \draw [->,rounded corners] (a2conf1.west) -| (out2a-west) |- (out2a); \draw [->,rounded corners] (a2conf2.west) -| (out2a-west) |- (out2a); - \draw [->] (input1) -- (out2a); + %\draw [->] (input1) -- (out2a); \fi %% Dependencies of out-3a \ifdefined\outthreeadep \node (out3a-west) [node-point, at={(4.07cm,2.7cm)}] {}; \node (a3conf1) [node-nonterminal, at={(5.47cm,4.6cm)}] {param-3.conf}; - \draw [->] (out1a) -- (out3a); \draw [rounded corners] (a3conf1.west) -| (out3a-west) |- (out3a); \fi \end{tikzpicture} diff --git a/tex/src/figure-download.tex b/tex/src/figure-download.tex new file mode 100644 index 0000000..b9da02f --- /dev/null +++ b/tex/src/figure-download.tex @@ -0,0 +1,8 @@ +\begin{tcolorbox} + \footnotesize + \texttt{\mkcomment{Write download URL into the paper (through a LaTeX macro).}} + + \texttt{\mktarget{\$(mtexdir)/download.tex}: \$(\mkvar{indir})/menke20.xlsx} + + \texttt{\mktab{}\mkprog{echo} "\textbackslash{}newcommand{\textbackslash{}menketwentyurl}\{\mktarget{\$(MK20URL)}\}" > \$@} +\end{tcolorbox} diff --git a/tex/src/figure-mk20tab3.tex b/tex/src/figure-mk20tab3.tex new file mode 100644 index 0000000..ebeac0e --- /dev/null +++ b/tex/src/figure-mk20tab3.tex @@ -0,0 +1,50 @@ +\begin{tcolorbox} + \footnotesize + \texttt{\mkcomment{Define and build the directory hosting the final table.}} + + \texttt{\mkvar{a1dir} = \$(\mkvar{BDIR})/analysis-1} + + \texttt{\mktarget{\$(a1dir)}:} + + \texttt{\mktab{}\mkprog{mkdir} \$@} + + \vspace{1.5em} + \texttt{\mkcomment{Define and build the main target.}} + + \texttt{\mkvar{mk20tab3} = \$(\mkvar{a1dir})/menke20-table-3.txt} + + \texttt{\mktarget{\$(mk20tab3)}: \$(\mkvar{indir})/menke20.xlsx | \$(\mkvar{a1dir})} + + \texttt{\recipecomment{Call XLSX I/O to convert all the spreadsheets into different CSV files.}} + + \texttt{\recipecomment{We only want the `table-3' spreadsheet, but XLSX I/O doesn't allow setting its}} + + \texttt{\recipecomment{output filename. For simplicity, let's assume its written in `table-3.csv'.}} + + \texttt{\mktab{}\mkprog{xlsxio\_xlsx2csv} \$<} + + \vspace{0.5em} + \texttt{\recipecomment{Use GNU AWK to keep the desired columns in space-separated, fixed-width format.}} + + \texttt{\recipecomment{With `FPAT' commas within double quotes are not counted as columns.}} + + \texttt{\mktab{}\mkprog{awk} 'NR>1\{printf("\%-10d\%-10d\%-10d \%s\textbackslash{}n", \$\$2, \$\$3, \$\$(NF-1)*\$\$NF, \$\$1)\}' \textbackslash} + + \texttt{\mktab{}{ }{ }{ }{ }FPAT='([\^{},]+)|("[\^{}"]+")' table-3.csv > \$@} + + \vspace{0.5em} + \texttt{\recipecomment{Delete the temporary CSV file.}} + + \texttt{\mktab{}\mkprog{rm} table-3.csv} + + \vspace{1.5em} + \texttt{\mkcomment{Main LaTeX macro file}} + + \texttt{\mktarget{\$(mtexdir)/analysis1.tex}: \$(\mkvar{mk20tab3)}} + + \texttt{\recipecomment{Count the total number of papers in their study to report in this paper.}} + + \texttt{\mktab{}v=\$\$(\mkprog{awk} '\!/\^{}\#/\{c+=\$\$2\} END\{print c\}' \$(\mkvar{mk20tab3)})} + + \texttt{\mktab{}\mkprog{echo} "\textbackslash{}newcommand\{\textbackslash{}menkenumpapers\}\{\$\$v\}" > \$@} +\end{tcolorbox} diff --git a/tex/src/preamble-style.tex b/tex/src/preamble-style.tex index 9556f54..e20c73c 100644 --- a/tex/src/preamble-style.tex +++ b/tex/src/preamble-style.tex @@ -135,11 +135,16 @@ \renewcommand\footrulewidth{0.0pt} } +%% For creating color boxes +\usepackage[many]{tcolorbox} + %% Custom macros \newcommand{\inlinecode}[1]{\textcolor{blue!35!black}{\texttt{#1}}} %% Example Makefile macros -\newcommand{\mkcomment}[1]{\textcolor{red!35!white}{#1}} +\newcommand{\mkcomment}[1]{\textcolor{red!70!white}{\# #1}} +\newcommand{\mkvar}[1]{\textcolor{orange!40!black}{#1}} \newcommand{\mktarget}[1]{\textcolor{blue!40!black}{#1}} -\newcommand{\mkprereq}[1]{\textcolor{green!30!black}{#1}} -\newcommand{\mktab}[1]{\textcolor{black!25!white}{\_\_\_TAB\_\_\_}} +\newcommand{\mkprog}[1]{\textcolor{green!30!black}{#1}} +\newcommand{\mktab}[1]{\textcolor{black!30!white}{\_\_\_TAB\_\_\_}} +\newcommand{\recipecomment}[1]{{ }{ }{ }{ }{ }{ }{ }{ }{ }\mkcomment{#1}} diff --git a/tex/src/references.tex b/tex/src/references.tex index 2a67584..f4dee1d 100644 --- a/tex/src/references.tex +++ b/tex/src/references.tex @@ -12,6 +12,24 @@ +@ARTICLE{konkol20, + author = {{Konkol}, Markus and {N{\"u}st}, Daniel and {Goulier}, Laura}, + title = "{Publishing computational research -- A review of infrastructures for reproducible and transparent scholarly communication}", + journal = {arXiv}, + year = 2020, + month = jan, + pages = {2001.00484}, +archivePrefix = {arXiv}, + eprint = {2001.00484}, + primaryClass = {cs.DL}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv200100484K}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + + + @ARTICLE{infante20, author = {{Infante-Sainz}, Ra{\'u}l and {Trujillo}, Ignacio and {Rom{\'a}n}, Javier}, @@ -49,6 +67,47 @@ archivePrefix = {arXiv}, +@ARTICLE{miksa19a, + author = {Tomasz Miksa and Paul Walk and Peter Neish}, + title = {RDA DMP Common Standard for Machine-actionable Data Management Plans}, + year = {2019}, + journal = {RDA}, + pages = {doi:10.15497/rda00039}, + doi = {10.15497/rda00039}, +} + + + + + +@ARTICLE{miksa19b, + author = {Tomasz Miksa and Stephanie Simms and Daniel Mietchen and Sarah Jones}, + title = {Ten principles for machine-actionable data management plans}, + year = {2019}, + journal = {PLoS Computational Biology}, + volume = {15}, + pages = {e1006750}, + doi = {10.1371/journal.pcbi.1006750}, +} + + + + + +@ARTICLE{dicosmo19, + author = {Roberto {Di Cosmo} and Francois Pellegrini}, + title = {Encouraging a wider usage of software derived from research}, + year = {2019}, + journal = {\doihref{https://www.ouvrirlascience.fr/wp-content/uploads/2020/02/Opportunity-Note_software-derived-from-research_EN.pdf}{Ouvrir la science}}, + volume = {}, + pages = {}, + doi = {}, +} + + + + + @ARTICLE{perignon19, author = {Christophe P\'erignon and Kamel Gadouche and Christophe Hurlin and Roxane Silberman and Eric Debonnel}, title = {Certify reproducibility with confidential data}, |