diff options
Diffstat (limited to 'tex/src')
| -rw-r--r-- | tex/src/figure-file-architecture.tex | 43 | ||||
| -rw-r--r-- | tex/src/references.tex | 28 |
2 files changed, 54 insertions, 17 deletions
diff --git a/tex/src/figure-file-architecture.tex b/tex/src/figure-file-architecture.tex index a4d4755..e08ee52 100644 --- a/tex/src/figure-file-architecture.tex +++ b/tex/src/figure-file-architecture.tex @@ -10,7 +10,7 @@ \footnotesize %% project/ - \node [dirbox, at={(0,4cm)}, minimum width=15cm, minimum height=9cm, + \node [dirbox, at={(0,4cm)}, minimum width=15cm, minimum height=9.9cm, label={[shift={(0,-5mm)}]\texttt{project/}}] {}; \ifdefined\fullfilearchitecture \node [node-nonterminal-thin, at={(-6.0cm,3.3cm)}] {COPYING}; @@ -31,7 +31,7 @@ \node [dirbox, at={(-4.35cm,2.1cm)}, minimum width=5.7cm, minimum height=5.3cm, label={[shift={(0,-5mm)}]\texttt{software/}}, fill=brown!20!white] {}; - %% reproduce/software/config + %% reproduce/software/config/ \node [dirbox, at={(-5.75cm,1.5cm)}, minimum width=2.6cm, minimum height=2.1cm, label={[shift={(0,-5mm)}]\texttt{config/}}, fill=brown!25!white] {}; \ifdefined\fullfilearchitecture @@ -42,7 +42,7 @@ \node [node-nonterminal-thin, at={(-5.75cm,-0.2cm)}] {checksums.conf}; \fi - %% reproduce/software/make + %% reproduce/software/make/ \node [dirbox, at={(-2.95cm,1.5cm)}, minimum width=2.6cm, minimum height=2.1cm, label={[shift={(0,-5mm)}]\texttt{make/}}, fill=brown!25!white] {}; \ifdefined\fullfilearchitecture @@ -53,15 +53,15 @@ \node [node-nonterminal-thin, at={(-2.95cm,-0.2cm)}] {python.mk}; \fi - %% reproduce/software/bash + %% reproduce/software/bash/ \node [dirbox, at={(-5.75cm,-0.8cm)}, minimum width=2.6cm, minimum height=1.6cm, - label={[shift={(0,-5mm)}]\texttt{bash/}}, fill=brown!25!white] {}; + label={[shift={(0,-5mm)}]\texttt{shell/}}, fill=brown!25!white] {}; \ifdefined\fullfilearchitecture - \node [node-nonterminal-thin, at={(-5.75cm,-1.5cm)}] {bashrc.sh}; - \node [node-nonterminal-thin, at={(-5.75cm,-2.0cm)}] {configure.sh}; + \node [node-nonterminal-thin, at={(-5.75cm,-1.5cm)}] {configure.sh}; + \node [node-nonterminal-thin, at={(-5.75cm,-2.0cm)}] {bashrc.sh}; \fi - %% reproduce/software/bibtex + %% reproduce/software/bibtex/ \node [dirbox, at={(-2.95cm,-0.8cm)}, minimum width=2.6cm, minimum height=2.1cm, label={[shift={(0,-5mm)}]\texttt{bibtex/}}, fill=brown!25!white] {}; \ifdefined\fullfilearchitecture @@ -74,7 +74,7 @@ \node [dirbox, at={(1.55cm,2.1cm)}, minimum width=5.7cm, minimum height=5.3cm, label={[shift={(0,-5mm)}]\texttt{analysis/}}, fill=brown!20!white] {}; - %% reproduce/analysis/config + %% reproduce/analysis/config/ \node [dirbox, at={(0.15cm,1.5cm)}, minimum width=2.6cm, minimum height=2.6cm, label={[shift={(0,-5mm)}]\texttt{config/}}, fill=brown!25!white] {}; \node [node-nonterminal-thin, at={(0.15cm,0.8cm)}] {INPUTS.conf}; @@ -82,7 +82,7 @@ \node [node-nonterminal-thin, at={(0.15cm,-0.2cm)}] {param-2a.conf}; \node [node-nonterminal-thin, at={(0.15cm,-0.7cm)}] {param-2b.conf}; - %% reproduce/analysis/make + %% reproduce/analysis/make/ \node [dirbox, at={(2.95cm,1.5cm)}, minimum width=2.6cm, minimum height=2.6cm, label={[shift={(0,-5mm)}]\texttt{make/}}, fill=brown!25!white] {}; \node [node-nonterminal-thin, at={(2.95cm,0.8cm)}] {top-prepare.mk}; @@ -90,14 +90,14 @@ \node [node-nonterminal-thin, at={(2.95cm,-0.2cm)}] {initialize.mk}; \node [node-nonterminal-thin, at={(2.95cm,-0.7cm)}] {analysis1.mk}; - %% reproduce/analysis/bash + %% reproduce/analysis/bash/ \node [dirbox, at={(0.15cm,-1.3cm)}, minimum width=2.6cm, minimum height=1.1cm, label={[shift={(0,-5mm)}]\texttt{bash/}}, fill=brown!25!white] {}; \ifdefined\fullfilearchitecture \node [node-nonterminal-thin, at={(0.15cm,-2.0cm)}] {process-A.sh}; \fi - %% reproduce/analysis/python + %% reproduce/analysis/python/ \node [dirbox, at={(2.95cm,-1.3cm)}, minimum width=2.6cm, minimum height=1.6cm, label={[shift={(0,-5mm)}]\texttt{python/}}, fill=brown!25!white] {}; \ifdefined\fullfilearchitecture @@ -109,7 +109,7 @@ \node [dirbox, at={(6cm,2.6cm)}, minimum width=2.7cm, minimum height=6cm, label={[shift={(0,-5mm)}]\texttt{tex/}}, fill=brown!15!white] {}; - %% tex/src + %% tex/src/ \node [dirbox, at={(6cm,2.1cm)}, minimum width=2.5cm, minimum height=1.6cm, label={[shift={(0,-5mm)}]\texttt{src/}}, fill=brown!20!white] {}; \node [node-nonterminal-thin, at={(6cm,1.4cm)}] {references.tex}; @@ -117,7 +117,7 @@ \node [node-nonterminal-thin, at={(6cm,0.9cm)}] {figure-1.tex}; \fi - %% tex/build + %% tex/build/ \ifdefined\fullfilearchitecture \node [dirbox, at={(6cm,0.1cm)}, minimum width=2.5cm, minimum height=1.3cm, label={[shift={(0,-5mm)}]\texttt{build/}}, dashed, , fill=brown!20!white] {}; @@ -125,7 +125,7 @@ \node [anchor=west, at={(4.7cm,-1.0cm)}] {\scriptsize\sf \LaTeX{} build directory.}; \fi - %% tex/tikz + %% tex/tikz/ \ifdefined\fullfilearchitecture \node [dirbox, at={(6cm,-1.6cm)}, minimum width=2.5cm, minimum height=1.6cm, label={[shift={(0,-5mm)}]\texttt{tikz/}}, dashed, fill=brown!20!white] {}; @@ -134,7 +134,7 @@ \node [anchor=west, at={(4.67cm,-3.0cm)}] {\scriptsize\sf by \LaTeX).}; \fi - %% .local + %% .local/ \ifdefined\fullfilearchitecture \node [dirbox, at={(-3.6cm,-3.6cm)}, minimum width=7cm, minimum height=1.2cm, label={[shift={(0,-5mm)}]\texttt{.local/}}, dashed, fill=brown!15!white] {}; @@ -144,7 +144,7 @@ {\scriptsize\sf Python or R, run `\texttt{.local/bin/python}' or `\texttt{.local/bin/R}'}; \fi - %% .build + %% .build/ \ifdefined\fullfilearchitecture \node [dirbox, at={(3.6cm,-3.6cm)}, minimum width=7cm, minimum height=1.2cm, label={[shift={(0,-5mm)}]\texttt{.build/}}, dashed, fill=brown!15!white] {}; @@ -153,4 +153,13 @@ \node [anchor=west, at={(0.1cm,-4.6cm)}] {\scriptsize\sf Enabling easy access to all of project's built components.}; \fi + + %% .git/ + \ifdefined\fullfilearchitecture + \node [dirbox, at={(0,-5cm)}, minimum width=14.2cm, minimum height=7mm, + label={[shift={(0,-5mm)}]\texttt{.git/}}, dashed, fill=brown!15!white] {}; + \node [anchor=north, at={(0cm,-5.3cm)}] + {\scriptsize\sf Full project temporal provenance (version controlled history) in Git.}; + \fi + \end{tikzpicture} diff --git a/tex/src/references.tex b/tex/src/references.tex index 68d59d3..305c3ab 100644 --- a/tex/src/references.tex +++ b/tex/src/references.tex @@ -35,6 +35,20 @@ archivePrefix = {arXiv}, +@ARTICLE{perignon19, + author = {Christophe P\'erignon and Kamel Gadouche and Christophe Hurlin and Roxane Silberman and Eric Debonnel}, + title = {Certify reproducibility with confidential data}, + year = {2019}, + journal = {Science}, + volume = {365}, + pages = {127}, + doi = {10.1126/science.aaw2825}, +} + + + + + @ARTICLE{munafo19, author = {Marcus Munaf\'o}, title = {Raising research quality will require collective action}, @@ -1537,6 +1551,20 @@ Reproducible Research in Image Processing}, +@ARTICLE{mcilroy78, + author = {M. D. McIlroy and E. N. Pinson and B. A. Tague}, + title = {UNIX Time-Sharing System: Forward}, + journal = {\doihref{https://archive.org/details/bstj57-6-1899/mode/2up}{Bell System Technical Journal}}, + year = {1978}, + volume = {57}, + pages = {6, ark:/13960/t0gt6xf72}, + doi = {}, +} + + + + + @ARTICLE{anscombe73, author = {{Anscombe}, F.J.}, title = {Graphs in Statistical Analysis}, |