cob-unofficial:0.1.0

packages/preview/cob-unofficial/0.1.0/.gitignore

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+*.pdf

packages/preview/cob-unofficial/0.1.0/LICENSE

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+Permission to use, copy, modify, and/or distribute this software for
+any purpose with or without fee is hereby granted.
+
+THE SOFTWARE IS PROVIDED “AS IS” AND THE AUTHOR DISCLAIMS ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES
+OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE
+FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY
+DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN
+AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT
+OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

packages/preview/cob-unofficial/0.1.0/README.md

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+# Unofficial CoB (The Company of Biologists) template
+
+An unofficial template for The Company of Biologists (CoB) research articles.
+
+## Example
+
+See [template/report.typ](template/report.typ).
+
+![Example research article](inc/thumbnail.png)
+
+## Based on official CoB LaTeX template
+
+* [CoB Manuscript preparation](https://journals.biologists.com/dev/pages/manuscript-prep)
+* [CoB LaTeX template](https://journals.biologists.com/DocumentLibrary/DEV/DEV_latex_template.zip)

packages/preview/cob-unofficial/0.1.0/src/lib.typ

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+// Unofficial CoB (The Company of Biologists) template.
+
+#import "@preview/hallon:0.1.2"
+
+// Fonts.
+#let font-serif      = "Nimbus Roman"
+#let font-sans-serif = "Nimbus Sans"
+
+// titcolor specifies the "super" title colour.
+#let titcolor = rgb(64, 193, 234) // CoB cyan
+// linkblue specifies the colour of links.
+#let linkblue = rgb(66, 93, 178)
+
+// print-supertitle displays the "super" title (i.e. "RESEARCH") on the front
+// page.
+#let print-supertitle(supertitle) = {
+	set text(font: font-sans-serif, size: 8pt, fill: titcolor, tracking: 0.5pt)
+	//show text: smallcaps // TODO: figure out how to fix (need Cap version of font)?
+	show text: strong
+	show text: upper
+	block(supertitle)
+}
+
+// print-header-supertitle displays the "super" title (i.e. "RESEARCH") in the
+// page header.
+#let print-header-supertitle(supertitle) = {
+	set text(font: font-sans-serif, size: 5.6pt, fill: titcolor, tracking: 0.4pt)
+	//show text: smallcaps // TODO: figure out how to fix (need Cap version of font)?
+	show text: upper
+	supertitle
+}
+
+// print-title displays the title of the paper.
+#let print-title(title) = {
+	set text(font: font-sans-serif, size: 18pt)
+	block(title)
+}
+
+// print-authors displays the list of authors.
+#let print-authors(authors) = {
+	set text(font: font-sans-serif, size: 12pt)
+	show text: strong
+	block(authors.join(", ", last: " and "))
+}
+
+// print-availability displays an availability notice.
+#let print-availability(title, body) = {
+	set text(font: font-sans-serif, size: 7pt)
+	block(
+		above: 1.9em,
+		below: 0.8em,
+		text(font: font-sans-serif, size: 7.5pt, weight: "bold")[#title availability],
+	)
+	body
+}
+
+// data-availability displays a data availability notice.
+#let data-availability(body) = {
+	print-availability("Data", body)
+}
+
+// code-availability displays a code availability notice.
+#let code-availability(body) = {
+	print-availability("Code", body)
+}
+
+// template applies the CoB research paper format to the document.
+#let template(
+	supertitle:   "Research Article",
+	title:        "Paper Title",
+	authors:      ("John Doe", "Jane Rue"),
+	article-id:   "xxxxxx",
+	article-year: datetime.today().year(),
+	date:         datetime.today(),
+	body
+) = {
+	set page(
+		"us-letter",
+		margin: (
+			inside: 1.685cm,
+			outside: 1.77cm,
+			top: 2.38cm,
+		),
+		columns: 2,
+		header: context [
+			#if here().page() == 1 [
+				#set text(font: font-sans-serif, size: 7pt)
+				#rect(
+					stroke: (bottom: 0.5pt + black),
+					width: 100%,
+					inset: (x: 0pt, y: 1.02em),
+				)[
+					#stack(
+						dir: ltr,
+						[© #{article-year}. MANUSCRIPT SUBMITTED TO JOURNAL OF CELL SCIENCE (#{article-year}) 00, jcs#{article-id}. doi:#link("https://doi.org/10.1242/jcs."+article-id, "10.1242/jcs."+article-id)],
+						h(1fr),
+						box(
+							inset: (bottom: -0.175cm),
+							// TODO: use PDF version of logo when Typst 0.14.0 is released.
+							image("/inc/COB_Publisher_Logo.svg"),
+						),
+					)
+				]
+				#v(-0.3mm)
+			] else [
+				#rect(
+					stroke: (bottom: 0.5pt + black),
+					width: 100%,
+					inset: (x: 0pt, y: 0.7em)
+				)[
+					#stack(
+						dir: ltr,
+						print-header-supertitle(supertitle),
+						h(1fr),
+						text(font: font-serif, size: 7pt)[Journal of Cell Science (#{article-year}) 00, jcs#{article-id}. doi:#link("https://doi.org/10.1242/jcs."+article-id, "10.1242/jcs."+article-id)],
+					)
+
+				]
+			]
+		],
+		header-ascent: 30%,
+	)
+
+	// Set heading styles.
+	show heading.where(level: 1): it => {
+		set text(font: font-sans-serif, size: 8.5pt)
+		show text: upper
+		it
+	}
+	show heading.where(level: 2): it => {
+		set text(font: font-sans-serif, size: 8.5pt)
+		it
+	}
+	show heading.where(level: 3): it => {
+		//set text(font: font-serif, size: 9.4pt)
+		set text(weight: "regular") // disable bold
+		show text: emph
+		it
+	}
+
+	// Set default font and text size.
+	set text(font: font-serif, size: 9.4pt)
+
+	// Set line height and justification of paragraphs.
+	set par(
+		justify: true,
+		first-line-indent: 1.2em,
+		spacing: 0.5em,
+		leading: 0.5em, // adjust line height
+	)
+
+	//show ref: set text(fill: linkblue)
+	show link: set text(fill: linkblue)
+	show cite: set text(fill: linkblue)
+
+	// Set bibliography title.
+	set bibliography(title: "References")
+
+	// HACK to insert "Received date" before footnote entry list.
+	show footnote.entry: it => {
+		let loc = it.note.location()
+		if counter(footnote).at(loc).first() == 1 {
+			set text(size: 8pt)
+			block(
+				above: 0.5em,
+				strong[Received #date.display("[day] [month repr:long] [year]")]
+			)
+		}
+		it
+	}
+
+	// Style footnote links.
+	show footnote: set text(fill: linkblue)
+
+	// Style tables.
+	show figure.where(kind: table): block.with(above: 1em)
+	show figure.where(kind: table): set figure.caption(position: top, separator: ". ")
+	set table(
+		stroke: none,
+		inset: (x: 5pt, y: 2pt),
+	)
+	set table.hline(stroke: 0.3pt)
+
+	// Apply figure and subfigure styles.
+	show: hallon.style-figures
+
+	// Use short supplement for figures and subfigures (place after
+	// `hallon.style-subfig` show rule for supplement of "subfigure" kind to take
+	// effect).
+	show figure.where(kind: image): set figure(supplement: "Fig.")
+	show figure.where(kind: image): set figure.caption(separator: [. ])
+	show figure.where(kind: "subfigure"): set figure(supplement: "Fig.")
+
+	// https://rupress.org/jcb/pages/reference-guidelines
+	//
+	// - dependent style:   https://www.zotero.org/styles/the-journal-of-cell-biology
+	// - independent style: https://www.zotero.org/styles/the-rockefeller-university-press
+	set bibliography(style: "the-rockefeller-university-press.csl")
+
+	// Set space between columns.
+	set columns(gutter: 0.5cm)
+
+	// Display title and authors.
+	place(
+		top+left,
+		scope: "parent",
+		float: true,
+	)[
+		#v(0.6mm)
+		#print-supertitle(supertitle)
+		#v(2.6mm)
+		#print-title(title)
+		#v(0.4mm)
+		#print-authors(authors)
+		#v(0.78cm)
+	]
+
+	// Display body.
+	body
+}

packages/preview/cob-unofficial/0.1.0/src/the-journal-of-cell-biology.csl

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+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-US">
+  <info>
+    <title>The Journal of Cell Biology</title>
+    <id>http://www.zotero.org/styles/the-journal-of-cell-biology</id>
+    <link href="http://www.zotero.org/styles/the-journal-of-cell-biology" rel="self"/>
+    <link href="http://www.zotero.org/styles/the-rockefeller-university-press" rel="independent-parent"/>
+    <link href="http://jcb.rupress.org/" rel="documentation"/>
+    <category citation-format="author-date"/>
+    <category field="biology"/>
+    <issn>0021-9525</issn>
+    <eissn>1540-8140</eissn>
+    <updated>2013-04-25T00:05:05+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+</style>

packages/preview/cob-unofficial/0.1.0/src/the-rockefeller-university-press.csl

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+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
+  <info>
+    <title>The Rockefeller University Press</title>
+    <id>http://www.zotero.org/styles/the-rockefeller-university-press</id>
+    <link href="http://www.zotero.org/styles/the-rockefeller-university-press" rel="self"/>
+    <link href="http://jgp.rupress.org/site/misc/ifora.xhtml" rel="documentation"/>
+    <author>
+      <name>Charlie Kim</name>
+      <email>[email protected]</email>
+      <!-- Original credit to Rishi Parikh ([email protected]) for development of this style -->
+    </author>
+    <category citation-format="author-date"/>
+    <category field="biology"/>
+    <category field="medicine"/>
+    <summary>The Rockefeller University Press style</summary>
+    <updated>2013-09-27T22:18:36+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <macro name="editor">
+    <names variable="editor" delimiter=", ">
+      <name and="text" initialize-with="." delimiter=", "/>
+      <label form="long" prefix=", "/>
+    </names>
+  </macro>
+  <macro name="author">
+    <names variable="author">
+      <name name-as-sort-order="first" and="text" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
+      <label form="short" prefix=" " suffix=" "/>
+      <substitute>
+        <names variable="editor"/>
+        <text variable="title"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="author-short">
+    <names variable="author">
+      <name form="short" and="text" delimiter=", " initialize-with="."/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+        <text variable="title"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="title">
+    <text variable="title"/>
+  </macro>
+  <macro name="publisher">
+    <group delimiter=", " suffix=".">
+      <text variable="publisher"/>
+      <text variable="publisher-place"/>
+    </group>
+  </macro>
+  <macro name="year-date">
+    <date variable="issued">
+      <date-part name="year"/>
+    </date>
+  </macro>
+  <macro name="edition">
+    <choose>
+      <if is-numeric="edition">
+        <group delimiter=" ">
+          <number variable="edition" form="ordinal"/>
+          <text term="edition" form="short"/>
+        </group>
+      </if>
+      <else>
+        <text variable="edition" suffix="."/>
+      </else>
+    </choose>
+  </macro>
+  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" collapse="year-suffix">
+    <layout prefix="(" suffix=")" delimiter="; ">
+      <group delimiter=", ">
+        <text macro="author-short"/>
+        <text macro="year-date"/>
+        <text variable="locator"/>
+      </group>
+    </layout>
+  </citation>
+  <bibliography hanging-indent="true" et-al-min="99" et-al-use-first="98">
+    <sort>
+      <key macro="author"/>
+      <key variable="issued"/>
+    </sort>
+    <layout suffix=".">
+      <text macro="author" suffix="."/>
+      <date variable="issued" prefix=" " suffix=".">
+        <date-part name="year"/>
+      </date>
+      <choose>
+        <if type="bill book graphic legal_case legislation motion_picture report song thesis" match="any">
+          <group delimiter=". " prefix=" ">
+            <text macro="title"/>
+            <!-- based on the instructions for the Journal of Daire Science, the volume should also be included if present, see http://www.journalofdairyscience.org/webfiles/images/journals/jods/JDS_Instruct_for_Contributors_2012.pdf -->
+            <text variable="volume"/>
+            <text macro="edition"/>
+            <text macro="editor"/>
+            <text macro="publisher"/>
+            <text variable="number-of-pages" suffix=" pp"/>
+          </group>
+        </if>
+        <else-if type="chapter paper-conference" match="any">
+          <group delimiter=". " prefix=" ">
+            <text macro="title"/>
+            <group delimiter=" ">
+              <text term="in" text-case="capitalize-first" font-style="italic"/>
+              <text variable="container-title"/>
+            </group>
+            <text macro="editor"/>
+            <text macro="publisher"/>
+            <text variable="page"/>
+          </group>
+        </else-if>
+        <else>
+          <group delimiter=". " prefix=" ">
+            <text macro="title"/>
+            <text variable="container-title" form="short" font-style="italic"/>
+            <group delimiter=":">
+              <text variable="volume"/>
+              <text variable="page"/>
+            </group>
+            <text prefix="doi:" variable="DOI"/>
+          </group>
+        </else>
+      </choose>
+    </layout>
+  </bibliography>
+</style>