From 94a4b39793110e99a74f24e39226ea63a76239f8 Mon Sep 17 00:00:00 2001
From: Trevor Manz <trevor.j.manz@gmail.com>
Date: Mon, 10 Jun 2024 12:28:31 -0400
Subject: [PATCH] Fix name

---
 paper/{prepare-myst.ts => export-pdf.ts} | 28 +++++++++++++++++++++++-
 paper/myst.yml                           | 22 +++++++++----------
 2 files changed, 37 insertions(+), 13 deletions(-)
 rename paper/{prepare-myst.ts => export-pdf.ts} (68%)

diff --git a/paper/prepare-myst.ts b/paper/export-pdf.ts
similarity index 68%
rename from paper/prepare-myst.ts
rename to paper/export-pdf.ts
index cb318ff7..995b35a7 100644
--- a/paper/prepare-myst.ts
+++ b/paper/export-pdf.ts
@@ -5,6 +5,8 @@ let [frontMatter, raw] = Deno.readTextFileSync("paper.md")
 	.replace("---", "")
 	.split("---");
 
+let output = Deno.args[0] || "dist/paper.pdf";
+
 let data = parse(frontMatter);
 // biome-ignore lint/performance/noDelete: <explanation>
 delete data["affiliations"];
@@ -15,6 +17,19 @@ delete data["tags"];
 // biome-ignore lint/performance/noDelete: <explanation>
 delete data["date"];
 
+data["exports"] = {
+	format: "typst",
+	template: "lapreprint-typst",
+	output: output,
+};
+
+data["margin"] = [
+	{
+		"title": "Correspondence to",
+		"content": "Correspondence: [author-email]",
+	}
+]
+
 let markdown = raw
 	// Replace markdown images with myst images
 	.replace(/!\[(.*?)\]\((.*?)\)/g, (_, alt: string, filepath: string) => {
@@ -33,10 +48,21 @@ ${content}
 	.replace("# Overview", "# Project Overview");
 
 Deno.writeTextFileSync(
-	"main.md",
+	"tmp.md",
 	`\
 ---
 ${stringify(data)}
 ---
 ${markdown}`,
 );
+
+new Deno.Command("myst", { args: ["build", "--pdf", "tmp.md"] })
+	.output()
+	.then((data) => {
+		console.log(data)
+		console.log(`PDF saved to ${output}`);
+	})
+	.catch(console.error)
+	.finally(async () => {
+		await Deno.remove("tmp.md");
+	});
diff --git a/paper/myst.yml b/paper/myst.yml
index ad007eb5..8a9f9de2 100644
--- a/paper/myst.yml
+++ b/paper/myst.yml
@@ -1,34 +1,32 @@
 version: 1
 project:
-  title: 'anywidget: reusable widgets for interactive analysis and visualization in computational notebooks'
-  # Authors should have affiliations, emails and ORCIDs if available
   authors:
     - name: Trevor Manz
-      email: trevor_manz@g.harvard.edu
+      email: "trevor\_manz@g.harvard.edu"
       orcid: 0000-0001-7694-5164
       affiliations:
-        - Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
-      corresponding: true
+        - Department of Biomedical Informatics, Harvard Medical School
+      corresponding: "trevor\_manz@g.harvard.edu"
     - name: Nezar Abdennur
-      email: nezar.abdennur@umassmed.edu
+      email: "nezar.abdennur@umassmed.edu"
       orcid: 0000-0001-5814-0864
       affiliations:
-        - Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, USA
-        - Department of Systems Biology, UMass Chan Medical School, Worcester, MA, USA
+        - Department of Genomics and Computational Biology, UMass Chan Medical School
+        - Department of Systems Biology, UMass Chan Medical School
     - name: Nils Gehlenborg
-      email: nils@hms.harvard.edu
+      email: "nils@hms.harvard.edu"
       orcid: 0000-0003-0327-8297
       affiliations:
-        - Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
+        - Department of Biomedical Informatics, Harvard Medical School
   keywords:
     - Computational notebooks
     - Jupyter
     - Widgets
     - Python
+    - R
     - JavaScript
     - Data visualization
     - Interactive computing
-
   abbreviations:
     JCP: Jupyter Compatible Platform
     AFM: Anywidget Front-End Module
@@ -37,4 +35,4 @@ project:
   subject: Research Article
   open_access: true
   license: CC-BY-4.0
-  date: 2024-07-10
+  date: 2024-06-07