Merge branch 'main' into bbs/icons

.github/spellignore.txt

@@ -20,21 +20,26 @@ CarpentriesLibrary
 CarpentriesSoftware
 Center
 CHAOSS
+citable
 codebase
+CodeMeta
 CodeRefinery
+comp-lvls-se
 Coursera
 CRSP
 CSE
+curation
 cybersecurity
 DALIA
 DaLiJe
 de
+deRSE
 DFG
 DigComp
 DigCompEdu
 DigCompOrg
 DigiFlex
-digitalization
+digitalisation
 DigitalSkillsGap
 distributable
 DMP
@@ -46,12 +51,14 @@ EduTrain
 edX
 EMBL
 EMBL-EBI
+eng
 ENCCS
 EOR
 Erlangen-Nürnberg
 ERuDIte
 EuroCC
 EuroHPC
+examplemaster
 exascale
 ExCALIBUR
 EXCELERATE
@@ -62,7 +69,8 @@ findability
 findable
 FIXME
 Forschung
-FORTRAN
+Friedrich
+Fortran
 franca
 funders
 FutureUniversity
@@ -104,6 +112,7 @@ MOOCs
 MPI
 multicore
 multithreading
+neuro-symbolic
 NFDI
 NFDI4Ing
 numpy
@@ -125,6 +134,7 @@ RDM
 RDM-RSE
 repos
 reproducibility
+ReproHack
 researchology
 researchonomy
 reusability
@@ -133,6 +143,7 @@ RSE's
 rse-specialisations
 RTPs
 scipy
+SeniorCC
 SRU
 SSI
 sth
@@ -143,7 +154,9 @@ swrepo
 swrepos
 SWREPOS
 SysOps
+tbl
 TeSS
+teams-se
 TrainingMaterial
 UofO
 un-deRSE

.github/workflows/compile.yml

@@ -11,24 +11,19 @@ jobs:
       - name: Install pandoc
         run: |
           sudo apt-get update && sudo apt-get install -y --no-install-recommends \
-            texlive pandoc texlive-bibtex-extra texlive-fonts-recommended \
-            texlive-xetex lmodern biber latexmk python3 python3-yaml \
+            texlive texlive-latex-extra pandoc latexmk \
+            texlive-bibtex-extra biber \
+            texlive-fonts-recommended texlive-fonts-extra lmodern fonts-linuxlibertine \
+            python3 python3-yaml \
             xz-utils make gpg-agent
           python3 -m pip install -r ${{ env.DIR }}/requirements.txt
-      - name: Configure LaTeX environment
-        working-directory: ${{ env.DIR }}
-        run: |
-          mkdir -p "${HOME}/texmf"
-          tlmgr init-usertree
-          tlmgr option repository https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/tlnet-final/
-          tlmgr install academicons
       - name: pandoc compile
         working-directory: ${{ env.DIR }}
         run: make all
       - name: move
         run: mkdir -p github_artifacts && mv ${{ env.DIR }}/*.pdf ./github_artifacts/
       - name: Upload pdf as artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: PDF files
           path: ./github_artifacts
@@ -39,7 +34,7 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           path: github_artifacts
       - name: move

.github/workflows/spellcheck.yml

@@ -18,15 +18,23 @@ jobs:
             # strip citations and references
             sed -ri 's/\[@[A-Za-z0-9_ ;@-]+\]//g' $file
             sed -ri 's/[^#\[][@#][A-Za-z0-9_ ;@-]+:[A-Za-z0-9_ ;@-]+}*//g' $file
+            sed -ri 's/@[A-Za-z0-9_]+//g' $file
             # strip words that escape the spellchecker allowlist
-            sed -i 's/Dr.-Ing.//g; s/Ph.D.//g; s/M.Sc.//g; s/B.Sc.//g; ' $file
+            sed -i 's/Dr.-Ing.//g; s/Ph.D.//g; s/M.Sc.//g; s/B.Sc.//g; s/Fortran//g;' $file
             # latex commands
             grep -P -oh -e "(?<=[\\\\\{])[A-Za-z]+" $file | sort | uniq >> .github/spellignore.txt
             # RSE compositions
             grep -P -oh -e "[\w-]*RSE[\w-]*" $file | sort | uniq >> .github/spellignore.txt
             # remove header
             sed -i '1,/---/{/^---$/,/^---$/d}' $file
           done
+      - name: "populate spellignore with author names"
+        uses: mikefarah/yq@master
+        with:
+          cmd: |
+            yq '.authors[] | .lastName' contributors.yml | sed 's/ /\n/g; /null/d' >> .github/spellignore.txt
+            yq '.authors[] | .firstName' contributors.yml | sed 's/ /\n/g; /null/d' >> .github/spellignore.txt
+            yq '.authors[] | .suffixName' contributors.yml | sed 's/ /\n/g; /null/d' >> .github/spellignore.txt
       - uses: eschercloudai/[email protected]
         with:
           files-to-check: "competencies.md|call_to_action.md|survey.md|institutionalised_education.md|intro.md"

Makefile

@@ -2,24 +2,17 @@
 
 MAKE_PDFA := true
 
-ifeq ($(MAKE_PDFA),true)
-  template_opts=--with-pdfx
-  xelatex_opts=-shell-escape
-else
-  template_opts=
-  xelatex_opts=
-endif
-
 objects := intro.pdf competencies.pdf institutionalised_education.pdf survey.pdf call_to_action.pdf
 
 all: $(objects)
 
-%.pdf: %.md bibliography.bib contributors.yml preamble.sty build/template.tex
+%.pdf: %.md bibliography.bib contributors.yml preamble.sty build/template.tex glossary.tex filter.py
 	@mkdir -p build
-	@rm -f build/pdfa.xmpi build/creationdate.lua build/creationdate.timestamp
+	@rm -f build/pdfa.xmpi
 	cp --update preamble.sty build/
 	cp --update bibliography.bib build/
-	python3 filter.py --input="$<" --output="build/$<" --contributors="contributors.yml"
+	cp --update glossary.tex build/
+	python3 filter.py --input="${<}" --output="build/${<}" --contributors="contributors.yml"
 	pandoc \
 	    --standalone \
 	    --number-sections \
@@ -28,23 +21,30 @@ all: $(objects)
 	    --biblatex \
 	    --toc \
 	    --template="build/template.tex" \
+	    -M pdfa-$(MAKE_PDFA)=1 \
 	    -M date="`date "+%B %e, %Y"`" \
 	    -M datexmp="`date "+%F"`" \
+	    -M linkcolor=darkgray \
 	    -V hyperrefoptions=pdfa \
 	    -V colorlinks=true \
 	    -V papersize=a4 \
 	    -o "build/${@:.pdf=}.tex" \
 	    "build/$<"
+	@sed -i '/\\author{}/d' "build/${@:.pdf=}.tex"
+	if grep -q "\\makeglossaries" "${<}"; then \
+		cd build; \
+		pdflatex --jobname="${@:.pdf=}" "${@:.pdf=}.tex"; \
+		makeglossaries "${@:.pdf=}"; \
+	fi
 	latexmk \
-	    -e '$$'"hash_calc_ignore_pattern{'timestamp'} = '^';" \
-	    -xelatex -bibtex -halt-on-error $(xelatex_opts) \
+	    -pdflatex -bibtex -halt-on-error \
 	    -jobname="${@:.pdf=}" -cd "build/${@:.pdf=}.tex"
-	@mv "build/${@}" ${@}
+	@mv "build/${@}" "${@}"
 
 build/template.tex: template.py
 	@mkdir -p build
 	pandoc --print-default-template=latex > "${@}"
-	python3 "${<}" $(template_opts) "${@}"
+	python3 "${<}" "${@}"
 
 clean:
 	rm -f $(objects)

README.md

@@ -5,12 +5,15 @@ Output of the de-RSE 2023 Conference Workshop on "Teaching and Learning Research
 Since the original idea grew in size and scope we had to split the paper in different subpapers highlighting different aspects
 
 Get the latest version of the respective PDF files here:
-* "Teaching and Learning Research Software Engineering" ([intro.pdf](https://github.com/CaptainSifff/paper_teaching-learning-RSE/blob/build/intro.pdf))
+
 * "Foundational competencies and responsibilities of an RSE" ([competencies.pdf](https://github.com/CaptainSifff/paper_teaching-learning-RSE/blob/build/competencies.pdf))
 * "Institutionalized Organisation of RSE Education" ([institutionalised_education.pdf](https://github.com/CaptainSifff/paper_teaching-learning-RSE/blob/build/institutionalised_education.pdf))
 * "A Survey of Initiatives Providing Educative Material in the RSE Space" ([survey.pdf](https://github.com/CaptainSifff/paper_teaching-learning-RSE/blob/build/survey.pdf))
 * "Educating RSEs in Germany - What Needs to Be Done" ([call_to_action.pdf](https://github.com/CaptainSifff/paper_teaching-learning-RSE/blob/build/call_to_action.pdf))
 
+Older:
+* "Teaching and Learning Research Software Engineering" ([intro.pdf](https://github.com/CaptainSifff/paper_teaching-learning-RSE/blob/build/intro.pdf))
+
 ## How to contribute - Some of our rules
 
 This paper is intended as a collaborative effort and we are looking for input from you.
@@ -21,6 +24,10 @@ This paper is intended as a collaborative effort and we are looking for input fr
 
 **We use British English**
 
+**We have regular meetings, out meeting notes can be found here: https://pad.gwdg.de/s/pVBQ3Sh7Z#**
+
+**If you want to get notified of our calls, and participate in the discussion by E-Mail, we have a Mailing-List: https://lists.uni-wuerzburg.de/mailman/listinfo/teachingrse**
+
 - competencies.md will be published on arxiv. LaTeX tags/code is fine in here.
 - survey.md will move to a website, hence this file has to be Markdown
 - We utilise tags to categorise issues and PRs to the respective paper.
@@ -70,3 +77,8 @@ All people that have participated in discussions with us,
 e.g. at deRSE23 or undeRSE23 are at least eligible for contributor status.
 If you have participated regularly at our weekly working meetings you are eligible for
 authorship.
+
+The first paper,
+_Foundational Competencies and Responsibilities of a Research Software Engineer_,
+is now available as a pre-print: https://arxiv.org/abs/2311.11457
+Feedback is welcome as an issue on this repository.