JOSS paper

.github/workflows/joss.yml

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+name: JOSS Paper
+on:
+    push:
+        paths:
+        - doc/paper/**
+        - .github/workflows/joss.yml
+    schedule:
+        - cron:  '17 3 * * 0'
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    paper:
+        runs-on: ubuntu-latest
+        name: Paper Draft
+        steps:
+            - name: Checkout
+              uses: actions/checkout@v5
+
+            - name: Build draft PDF
+              uses: openjournals/openjournals-draft-action@master
+              with:
+                journal: joss
+                paper-path: doc/paper/paper.md
+
+            - name: Upload
+              uses: actions/upload-artifact@v4
+              with:
+                name: paper
+                path: doc/paper/paper.pdf
+
+# vim: sw=4

doc/paper/.gitignore

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+.inara
+joss
+*.pdf
+*.tex
+latex.out

doc/paper/Makefile

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+OUTDIR?=latex.out
+TEXMK?=latexmk -verbose -pdflua -output-directory=$(OUTDIR)
+
+INARA_PATH := .inara
+TARGET_FOLDER := $$(pwd)/publishing-artifacts
+
+JOURNAL := joss
+INARA_DATA_PATH := $(INARA_PATH)/data
+OPENJOURNALS_PATH := $(INARA_PATH)/resources
+ARTICLE_INFO_FILE = $(OPENJOURNALS_PATH)/default-article-info.yaml
+
+all: paper
+.PHONY: all
+
+help: 			## Show this help
+	@echo -e "\nSpecify a command. The choices are:\n"
+	@grep -E '^[0-9a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "  \033[0;36m%-12s\033[m %s\n", $$1, $$2}'
+	@echo ""
+.PHONY: help
+
+%.pdf: %.tex
+	PYTHONWARNINGS=ignore $(TEXMK) $<
+	@cp $(OUTDIR)/$@ .
+
+paper: paper.md paper.bib		## Compile paper to PDF using JOSS tools
+	mkdir -p $(TARGET_FOLDER)
+	make -C $(INARA_PATH) -B resources/footer.csl
+	INARA_ARTIFACTS_PATH=$(TARGET_FOLDER)/ pandoc \
+	  --data-dir=$(INARA_DATA_PATH) \
+	  --defaults=$(INARA_DATA_PATH)/defaults/shared.yaml \
+	  --defaults=$(INARA_DATA_PATH)/defaults/pdf.yaml \
+	  --defaults=$(OPENJOURNALS_PATH)/$(JOURNAL)/defaults.yaml \
+	  --resource-path=$$(pwd):$(OPENJOURNALS_PATH) \
+	  --metadata=article-info-file=$(ARTICLE_INFO_FILE) \
+	  --variable=$(JOURNAL) \
+	  --output=$@.tex \
+	  $<
+	make paper.pdf
+.PHONY: paper
+
+inara:							## Download JOSS tools (inara) for compilation
+	@if [ ! -d "$(INARA_PATH)" ]; then \
+		git clone git@github.com:openjournals/inara.git $(INARA_PATH); \
+	else \
+		cd $(INARA_PATH) && git pull origin main; \
+	fi
+	mkdir -p joss
+	cp $(INARA_PATH)/resources/joss/logo.png joss/logo.png
+.PHONY: inara
+
+tidy: paper.bib			## Clean up bibliography (with bibtex-tidy)
+	@bibtex-tidy \
+		--modify \
+		--sort \
+		--sort-fields \
+		--drop-all-caps \
+		--merge last \
+		--numeric \
+		--strip-enclosing-braces \
+		--trailing-commas \
+		--blank-lines \
+		--remove-empty-fields \
+		--remove-dupe-fields \
+		--wrap \
+		$<
+.PHONY: tidy
+
+clean:						## Remove temporary files generated by JOSS tools
+	rm -rf $(TARGET_FOLDER)
+	rm -rf $(OUTDIR)
+.PHONY: clean
+
+purge: clean
+	rm -rf paper.pdf
+	rm -rf .inara
+.PHONY: purge
+

doc/paper/images/Makefile

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+OUTDIR?=latex.out
+TEXMK?=latexmk -verbose -pdf -output-directory=$(OUTDIR)
+PYTHON?=python -X dev
+
+all: figures
+
+help: 			## Show this help
+	@echo -e "\nSpecify a command. The choices are:\n"
+	@grep -E '^[0-9a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "  \033[0;36m%-12s\033[m %s\n", $$1, $$2}'
+	@echo ""
+.PHONY: help
+
+%.pdf: %.tex
+	PYTHONWARNINGS=ignore $(TEXMK) $<
+	@cp $(OUTDIR)/$@ .
+
+%.png: %.pdf
+	magick \
+		-density 600 \
+		$< \
+		-quality 100 \
+		-background white \
+		-alpha remove \
+		$@
+
+quadrature_rules.png:
+	magick \
+		quadrature_rule_vr_order_11_2d.png \
+		\( -size 900x`identify -format "%h" quadrature_rule_vr_order_11_2d.png` xc:white \) \
+		quadrature_rule_wv_order_11_2d.png \
+		+append \
+		-background white \
+		quadrature_rules.png
+
+figures: simplices quadratures ## Compile all figures
+	for img in simplices.png pkdo-2d.png quadrature_rules.png; do \
+		magick "$${img}" -trim +repage "$${img}"; \
+	done
+
+simplices: simplices.png
+quadratures: quadrature_rules.png

doc/paper/images/simplices.tex

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+\documentclass[tikz]{standalone}
+\usepackage{tikz}
+\usepackage{amsmath}
+
+\renewcommand\familydefault{\sfdefault}
+
+\begin{document}
+\large
+
+\begin{tikzpicture}[scale=2]
+\definecolor{VertexBlue}{HTML}{4C72B0};
+\definecolor{LineBlue}{HTML}{4C72B0};
+\definecolor{FaceBlue}{HTML}{D2DBEB};
+\definecolor{FaceDarkBlue}{HTML}{C0CDE3};
+
+% 1-simplex
+\begin{scope}[shift={(0, 0)}]
+\draw[LineBlue, ultra thick] (0, 1) -- (1.5, 1);
+\fill[VertexBlue] (0, 1) circle (2pt);
+\fill[VertexBlue] (1.5, 1) circle (2pt);
+\node at (0.75, -0.5) {1-simplex};
+\end{scope}
+
+% 2-simplex
+\begin{scope}[shift={(3, 0)}]
+\coordinate (A) at (0, 0);
+\coordinate (B) at (2, 0);
+\coordinate (C) at (0, 2);
+
+\fill[FaceBlue] (A) -- (B) -- (C) -- cycle;
+\draw[LineBlue, ultra thick] (A) -- (B) -- (C) -- cycle;
+\foreach \p in {A,B,C}
+    \fill[VertexBlue] (\p) circle (2pt);
+
+\node at (1, -0.5) {2-simplex};
+\end{scope}
+
+% 3-simplex
+\begin{scope}[shift={(6.5, 0)}]
+\coordinate (O) at (0, 0.5, 0);
+\coordinate (X) at (2, 0.5, 0);
+\coordinate (Y) at (0.75, 2, 0);
+\coordinate (Z) at (0.75, 0.0, 0.0);
+
+% faces
+\fill[FaceBlue] (O) -- (X) -- (Y) -- cycle;
+\fill[FaceBlue] (O) -- (X) -- (Z) -- cycle;
+\fill[FaceDarkBlue] (X) -- (Y) -- (Z) -- cycle;
+\fill[FaceBlue] (Y) -- (O) -- (Z) -- cycle;
+
+% edges
+\draw[LineBlue, ultra thick] (X) -- (Y) -- (O);
+\draw[LineBlue!60, ultra thick] (O) -- (X);
+\draw[LineBlue, ultra thick] (O) -- (Z);
+\draw[LineBlue, ultra thick] (X) -- (Z);
+\draw[LineBlue, ultra thick] (Y) -- (Z);
+
+% vertices
+\foreach \p in {O,X,Y,Z}
+    \fill[VertexBlue] (\p) circle (2pt);
+
+\node at (1, -0.5, 0) {3-simplex};
+\end{scope}
+\end{tikzpicture}
+
+\end{document}