Merge pull request #15 from richelbilderbeek/version_0_6

Version 0 6

.github/workflows/check_bash_style.yaml

@@ -4,7 +4,7 @@ on:
   push:
   pull_request:
   schedule:
-  - cron: "0 0 16 * *"
+  - cron: "0 0 3 * *"
 
 
 jobs:
@@ -19,4 +19,4 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Check bash scripts for style
-        run: shellcheck *.sh scripts/*.sh
+        run: shellcheck scripts/*.sh

.github/workflows/count_words.yaml

@@ -22,6 +22,6 @@ jobs:
       - name: Count number of words
         run: texcount article.tex
 
-      - name: Count number of words, allow 5100
+      - name: Count number of words, allow 5004
         run: |
-          n_words=$(texcount article.tex | egrep "Words in text:.*" | cut -d ":" -f 2); if [ "$n_words" -gt 5100 ]; then print "ERROR: got $n_words words"; exit 42; fi
+          n_words=$(texcount article.tex | egrep "Words in text:.*" | cut -d ":" -f 2); if [ "$n_words" -gt 5004 ]; then print "ERROR: got $n_words words"; exit 42; fi

README.md

@@ -13,3 +13,12 @@
 
  * [PDFs](https://github.com/richelbilderbeek/chapter_paradata/releases/download/v0.5/article_pdfs.zip)
 
+## About the author
+
+Richèl J. C. Bilderbeek, Ph.D., has worked in computational biology 
+for more than a decade. 
+Currently, he works for the National Bioinformatics Infrastructure Sweden (NBIS) 
+in Uppsala, Sweden, as an application expert and trainer, 
+with a focus on reproducible research. 
+All his work can be found on GitHub 
+at https://github.com/richelbilderbeek and his YouTube channel. 

article.tex

@@ -62,7 +62,7 @@ \section{Introduction}
 paradata can be understood in general sense as 'data about processes’ (with e.g. survey paradata
 termed alternatively as records and audit trails) \cite{nicolaas2011survey},
 or in more specific sense in relation to data collection, as 'data about the data collection process' (\cite{choumert2019using}).
-This paper uses the latter as a working definition.
+This chapter uses the latter as a working definition.
 
 % \paragraph{Code is paradata}
 
@@ -99,7 +99,10 @@ \section{Introduction}
 its benefits.
 Finally, in computational fields, 
 it can help understand how scholarly knowledge is produced (\cite{huvila2022improving}).
-This paper discusses these general reasons applied to code.
+
+This chapter discusses these general reasons applied to code
+and its implications for knowledge management,
+including recommendations how to make code useful paradata in section \ref{sec:making-code-useful-paradata}.
 
 \begin{figure}[!htbp]
   \centering
@@ -161,7 +164,7 @@ \section{Genetic epidemiology}
 
 % \paragraph{Introduction}
 
-This paper uses genetic epidemiology as a specific example,
+This chapter uses genetic epidemiology as a specific example,
 to illustrate in which way code is paradata,
 and why this type of paradata is relevant.
 However, any field that uses computation 
@@ -180,7 +183,7 @@ \section{Genetic epidemiology}
 The trait is caused by the genetic make-up, or 'genotype'
 \iffalse
 (see Table \ref{tab:definitions} in the Supplementary Materials
-for the definitions of terms used in this paper)
+for the definitions of terms used in this chapter)
 \fi
 , of a person.
 The trait, also called 'phenotype', 
@@ -1011,7 +1014,7 @@ \section{Discussion}
 \section{Conclusions}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-This paper started with some suggestions to 
+This chapter started with some suggestions to 
 make paradata useful for data re(use):
 paradata should be extensive, comprehensively documented,
 with the creation of documentation and code going hand-in-hand,
@@ -1084,17 +1087,6 @@ \section{Data Accessibility}
 This article and its metadata can be found at 
 \url{https://github.com/richelbilderbeek/chapter_paradata}.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Author biography}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-Dr. Bilderbeek has worked in computational biology for more than a decade.
-Currently, he works for the National Bioinformatics Infrastructure Sweden (NBIS)
-in Uppsala, Sweden, 
-as an application expert and trainer, with a focus on reproducible research.
-All his work can be found on GitHub at \url{https://github.com/richelbilderbeek}
-and his YouTube channel.
-
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Bibliography
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -1120,13 +1112,13 @@ \section{Supplementary materials}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{This paper}
+\subsection{This chapter}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 This book chapter has been produced following all recommendations in it:
 it's \LaTeX code is hosted on GitHub 
 at \url{https://github.com/richelbilderbeek/chapter_paradata}.
-Due this, one can, among others, see the complete version history of this paper.
+Due this, one can, among others, see the complete version history of this chapter.
 This alone could allow research to be done on, for example,
 the effect of reviewers' feedback on a first manuscript.
 The website also supplies an alternative version of the same chapter
@@ -1159,7 +1151,7 @@ \section*{Definitions}
     Trait        & A phenotype                                                                  & The concentration of IL6RA in the blood                         \\
     \hline
   \end{tabular}
-  \caption{Terms used in this paper, and their definitions}
+  \caption{Terms used in this chapter, and their definitions}
   \label{tab:definitions}
 \end{table}
 
@@ -1186,7 +1178,7 @@ \section*{Recommendations}
                   & Standardise to link between container, paper and code repository \\
     \hline
   \end{tabular}
-  \caption{Recommendations described in this paper}
+  \caption{Recommendations described in this chapter}
   \label{tab:recommendations}
 \end{table}
 

header.tex

@@ -54,7 +54,7 @@
 \nonstopmode
 
 \title{
-  Making research code useful paradata
+Making research code useful paradata
 }
 \author{Richèl J.C. Bilderbeek}
 
@@ -76,7 +76,7 @@
 % \usepackage[hyphens]{url}
 
 % This is chapter number 7
-\setcounter{chapter}{6} % LaTeX adds one
+\setcounter{chapter}{1} % LaTeX adds one
 
 % This is the header of this article.
 % It contains the higher-level things, such as packages.

scripts/zip_tex_files.sh

@@ -6,4 +6,4 @@
 #
 #   ./scripts/zip_text_files.sh
 #
-zip tex_files.zip $(ls {article.*,header.*,figure_1.png,svmult.cls,svind.ist})
+zip tex_files.zip "$(ls {article.*,header.*,figure_1.png,svmult.cls,svind.ist})"