Plos

.github/workflows/paper.yml

@@ -21,16 +21,10 @@ jobs:
         run: pip install -r requirements.txt
 
       - name: Install LaTeX requirements for matplotlib
-        run: sudo apt update -y && sudo apt install -y texlive-latex-base texlive-latex-extra cm-super-minimal texlive-fonts-extra latexmk texlive-bibtex-extra biber texlive-lang-german
+        run: sudo apt update -y && sudo apt install -y build-essential texlive-latex-base texlive-latex-extra cm-super-minimal texlive-fonts-extra latexmk texlive-bibtex-extra biber texlive-lang-german
 
-      - name: Create contributor snippet
-        run: python contributors.py
-
-      - name: Create group composition plot
-        run: cd group_composition_plot && ./create_paper_plots.sh && cd -
-
       - name: Compile paper
-        run: latexmk -pdf --file-line-error --halt-on-error --interaction=nonstopmode --recorder paper.tex
+        run: make
 
       - name: move
         run: mkdir -p github_artifacts && mv ${{ env.DIR }}/*.pdf ./github_artifacts/ 

.gitignore

@@ -16,6 +16,8 @@
 *.dvi
 *.xdv
 *-converted-to.*
+norm.bib
+plos.bib
 # these rules might exclude image files for figures etc.
 # *.ps
 # *.eps

Makefile

@@ -2,13 +2,23 @@ all:	plots paper.pdf
 
 clean:
 		latexmk -c
-		rm paper.pdf
+		rm -f paper.pdf paper.bbl plos.bib norm.bib
 
-paper.pdf:	paper.tex positionpaper.bib contributors.tex
+paper.pdf:	paper.tex positionpaper.bib contributors.tex plos.bib
 		latexmk -pdflatex paper.tex
 
-contributors.tex:	contributors.tex.j2 contributors.yml
-		python3 contributors.py
+contributors.tex:	 contributors.yml contributors_plos.tex.j2
+		python3 contributors.py $< -t contributors_plos.tex.j2 -o $@
+
+# this step is to convert the input files to proper biblatex files
+# so we can turn them into bibtex files later on
+norm.bib:	positionpaper.bib bibliography.bib
+		biber --tool $^  --output-file $@
+
+plos.bib:	norm.bib
+		biber --tool $<  --output-file $@  \
+                  --configfile=biberconf.xml \
+                  --output-field-replace=location:address,journaltitle:journal
 
 plots::
 	$(MAKE) -C group_composition_plot

biberconf.xml

@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Got the date from https://gist.githubusercontent.com/mkouhia/f00fea7fc8d4effd9dfd/raw/500e9dbc6aa43a47e39c45ba230738ff4544709f/biblatex-to-bibtex.conf -->
+<config>
+  <output_fieldcase>lower</output_fieldcase>
+  <output_resolve>1</output_resolve>
+  <output_safechars>1</output_safechars>
+  <output_format>bibtex</output_format>
+  <sourcemap>
+    <maps datatype="bibtex">
+      <!-- Easy type conversions -->
+      <map>
+        <map_step map_type_source="report" map_type_target="techreport"/>
+        <map_step map_type_source="online" map_type_target="misc"/>
+        <map_step map_type_source="dataset" map_type_target="misc"/>
+      </map>
+      <!-- Date to year, month -->
+      <map>
+        <map_step map_field_source="date"
+        map_field_target="year" />
+      </map>
+      <map>
+        <map_step map_field_source="year"
+        map_match="(\d{4}|\d{2})-(\d{1,2})-(\d{1,2})"
+        map_final="1" />
+        <map_step map_field_source="year"
+        map_match="(\d{4}|\d{2})-(\d{1,2})-(\d{1,2})"
+        map_replace="$1" />
+        <map_step map_field_set="month" map_origfieldval="1" />
+        <map_step map_field_source="month"
+        map_match="(\d{4}|\d{2})-(\d{1,2})-(\d{1,2})"
+        map_replace="$2" />
+      </map>
+      <map>
+        <map_step map_field_source="year"
+        map_match="(\d{4}|\d{2})-(\d{1,2})" map_final="1" />
+        <map_step map_field_source="year"
+        map_match="(\d{4}|\d{2})-(\d{1,2})" map_replace="$1" />
+        <map_step map_field_set="month" map_origfieldval="1" />
+        <map_step map_field_source="month"
+        map_match="(\d{4}|\d{2})-(\d{1,2})" map_replace="$2" />
+      </map>
+    </maps>
+  </sourcemap>
+</config>

bibliography.bib

@@ -4725,7 +4725,7 @@ @online{SSIDataScience
 
 @online{SSIRSEandDS,
 organization = {Software Sustainability Institute },
-author = {Matthew Archer, Stephen Dowsland, Rosa Filgueira, R. Stuart Geiger, Alejandra Gonzalez-Beltran, Robert Haines, James Hetherington, Christopher Holdgraf, Sanaz Jabbari Bayandor, David Mawdsley, Heiko Mueller, Tom Redfern, Martin O'Reilly, Valentina Staneva, Mark Turner, Jake VanderPlas, Kirstie Whitaker},
+author = {Archer, Matthew and Dowsland, Stephen and Filgueira, Rosa and Geiger, R. Stuart and Gonzalez-Beltran, Alejandra and Haines, Robert and Hetherington, James and Holdgraf, Christopher and Bayandor, Sanaz Jabbari  and Mawdsley, David and Mueller, Heiko  and Redfern, Tom and O'Reilly, Martin and Staneva, Valentina and Turner, Mark and VanderPlas, Jake and Whitaker, Kirstie},
 title = {Research Software Engineers and Data Scientists: More in Common},
 url = {https://www.software.ac.uk/blog/2018-04-05-research-software-engineers-and-data-scientists-more-common},
 urldate = {2023-08-04}
@@ -5680,15 +5680,6 @@ @article{smith_SoftwareCitationPrinciples2016
   doi = {10.7717/peerj-cs.86}
 }
 
-@Article{goth_foundational_competencies_2024,
-  title={Foundational Competencies and Responsibilities of a Research Software Engineer},
-  author={Goth, Florian and Alves, Renato and Braun, Matthias and Castro, Leyla Jael and Chourdakis, Gerasimos and Christ, Simon and Cohen, Jeremy and Druskat, Stephan and Erxleben, Fredo and Grad, Jean-No{\"e}l and Hagdorn, Magnus and Hodges, Toby and Juckeland, Guido and Kempf, Dominic and Lamprecht, Anna-Lena and Linxweiler, Jan and L{\"o}ffler, Frank and Martone, Michele and Schwarzmeier, Moritz and Seibold, Heidi and Thiele, Jan Philipp and von Waldow, Harald and Wittke, Samantha},
-  year={2024},
-  journal={arXiv},
-  volume={2311.11457},
-  doi={10.48550/arXiv.2311.11457},
-}
-
 @InProceedings{haupt_hifis_consulting_2021,
   author       = {Haupt, Carina and Stoffers, Martin},
   title        = {Roles in Research Software Engineering ({RSE}) Consultancies},

contributors.py

@@ -2,35 +2,65 @@
 import jinja2
 import os
 import yaml
+import argparse
+from pathlib import Path
 
 
-with open("contributors.yml") as f:
-    data = yaml.safe_load(f)
+def main():
 
-# Sort by last name and contribution tier
-data["authors"] = list(sorted(sorted(data["authors"], key=lambda x: x["lastName"]), key=lambda x: x.get("tier", 2)))
+    parser = argparse.ArgumentParser()
+    parser.add_argument("contributors", type=Path,
+                        help="yml file containing the contributors")
+    parser.add_argument("-t", "--template", type=Path, required=True,
+                        help="name of template to use")
+    parser.add_argument("-o", "--output", type=Path,
+                        help="the name of the output file")
+    args = parser.parse_args()
 
-# Ensure that we have unique indices for the affiliations
-affiliations = list()
-for author in data["authors"]:
-    if 'affiliations' in author:
-        affiliations.extend(author["affiliations"])
-# make sure affiliations are not duplicated - here by checking for exact name string
-affiliations = list({aff['name']: aff for aff in affiliations}.values())
+    with args.contributors.open('r') as f:
+        data = yaml.safe_load(f)
 
-# create and add unique index and also a reverse lookup table
-data["affiliations"] = {i + 1: aff for i, aff in enumerate(affiliations)}
-aff_index_by_name    = {aff['name']: i for i, aff in data["affiliations"].items()}
+    # Sort by last name and contribution tier
+    data["authors"] = list(
+        sorted(
+            sorted(data["authors"], key=lambda x: x["lastName"]),
+            key=lambda x: x.get("tier", 2)))
 
-# attach index to authors
-for author in data["authors"]:
-    if 'affiliations' in author:
-        author["affiliations"] = [aff_index_by_name[aff['name']] for aff in author["affiliations"]]
+    # Ensure that we have unique indices for the affiliations
+    affiliations = []
+    for author in data["authors"]:
+        if 'affiliations' in author:
+            affiliations.extend(author["affiliations"])
+        if 'corresponding_author' in author and author['corresponding_author']:
+            data['corresponding_author'] = author['email']
+    # make sure affiliations are not duplicated - here by checking
+    # for exact name string
+    affiliations = list({aff['name']: aff for aff in affiliations}.values())
 
-env = jinja2.Environment(
-   loader=jinja2.FileSystemLoader(os.getcwd()),
-   keep_trailing_newline=True,
-)
+    # create and add unique index and also a reverse lookup table
+    data["affiliations"] = {i + 1: aff for i, aff in enumerate(affiliations)}
+    aff_index_by_name = {
+        aff['name']: i for i, aff in data["affiliations"].items()}
 
-with open("./contributors.tex", "w") as out:
-    out.write(env.get_template("contributors.tex.j2").render(data=data))
+    # attach index to authors
+    for author in data["authors"]:
+        if 'affiliations' in author:
+            author["affiliations"] = [
+                aff_index_by_name[
+                    aff['name']] for aff in author["affiliations"]]
+
+    env = jinja2.Environment(
+       loader=jinja2.FileSystemLoader(os.getcwd()),
+       keep_trailing_newline=True,
+    )
+
+    contribs = env.get_template(args.template.name).render(data=data)
+
+    if args.output is not None:
+        args.output.write_text(contribs)
+    else:
+        print(contribs)
+
+
+if __name__ == '__main__':
+    main()

contributors.yml

@@ -88,6 +88,7 @@ authors:
     firstName: Dominic
     lastName: Kempf
     initials: DK
+    corresponding_author: true
     affiliations:
       - name: Scientific Software Center, Heidelberg University, Germany
         ror: https://ror.org/038t36y30

contributors_plos.tex.j2

@@ -0,0 +1,22 @@
+% README: The file contributors.tex is automatically generated by running contributors.py.
+% Changed within will be OVERWRITTEN.
+% For changes to the tex template, change contributors.tex.j2.
+% For changes to the author information, change contributors.yml.
+%
+% Note: the zero-width character <200b> is in here on purpose (to not mess up authors without
+% affiliation)
+{%- for author in data.authors %}
+{{ author.author }}​{% if author.affiliations %}\textsuperscript{{ "{" }}{{ author.affiliations|join(",") }}{% if author.corresponding_author is defined and author.corresponding_author %}*{% endif %}{% if author.orcid is defined %}\texorpdfstring{\thinspace\orcidlink{ {{-author.orcid-}} }}{}{% endif %}{{ "}" }}{% endif %}
+{%- endfor %}
+\\
+\bigskip
+{%- for index, affiliation in data.affiliations.items() %}
+\textbf{{ "{" }}{{ index }}{{ "}" }} {{ affiliation.name }}{% if affiliation.ror is defined %}\texorpdfstring{\thinspace\rorlink{ {{-affiliation.ror-}} }} {}{% endif %}
+\\
+{%- endfor %}
+\bigskip
+{% if data.corresponding_author is defined %}
+
+* {{ data.corresponding_author }}
+{% endif %}
+