update sn template to 12/2023 and support csl or natbib

.gitattributes

@@ -0,0 +1,3 @@
+_extensions/nature/csl/* linguist-vendored
+_extensions/nature/*.bst linguist-vendored
+_extensions/nature/sn-jnl.cls linguist-vendored

.gitignore

@@ -3,3 +3,12 @@
 .Rdata
 .httr-oauth
 .DS_Store
+/template_files/
+*.aux
+*.fdb_latexmk
+*.fls
+*.log
+/*.bst
+/*.cls
+template.*
+!template.{qmd,pdf}

.quartoignore

@@ -1,4 +1,5 @@
 *.pdf
 *.png
 *.rproj
-*.Rproj
+*.Rproj
+Makefile

Makefile

@@ -0,0 +1,90 @@
+.DEFAULT_GOAL := help
+
+ENV_PREFIX ?= .
+ENV_FILE := $(wildcard $(ENV_PREFIX)/.env)
+
+ifeq ($(strip $(ENV_FILE)),)
+$(info $(ENV_PREFIX)/.env file not found, skipping inclusion)
+else
+include $(ENV_PREFIX)/.env
+export
+endif
+
+GIT_SHA_SHORT = $(shell git rev-parse --short HEAD)
+GIT_REF = $(shell git rev-parse --abbrev-ref HEAD)
+
+#-------
+##@ help
+#-------
+
+# based on "https://gist.github.com/prwhite/8168133?permalink_comment_id=4260260#gistcomment-4260260"
+help: ## Display this help. (Default)
+	@grep -hE '^(##@|[A-Za-z0-9_ \-]*?:.*##).*$$' $(MAKEFILE_LIST) | \
+	awk 'BEGIN {FS = ":.*?## "}; /^##@/ {print "\n" substr($$0, 5)} /^[A-Za-z0-9_ \-]*?:.*##/ {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
+
+help-sort: ## Display alphabetized version of help (no section headings).
+	@grep -hE '^[A-Za-z0-9_ \-]*?:.*##.*$$' $(MAKEFILE_LIST) | sort | \
+	awk 'BEGIN {FS = ":.*?## "}; /^[A-Za-z0-9_ \-]*?:.*##/ {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
+
+HELP_TARGETS_PATTERN ?= test
+help-targets: ## Print commands for all targets matching a given pattern. eval "$(make help-targets HELP_TARGETS_PATTERN=render | sed 's/\x1b\[[0-9;]*m//g')"
+	@make help-sort | awk '{print $$1}' | grep '$(HELP_TARGETS_PATTERN)' | xargs -I {} printf "printf '___\n\n{}:\n\n'\nmake -n {}\nprintf '\n'\n"
+
+
+
+#--------------------------
+##@ download csl bibliography style files
+#--------------------------
+
+# list of citation style names to vendor
+CITATION_STYLES = \
+	nature-no-superscript \
+	springer-basic-author-date \
+	springer-basic-brackets-no-et-al \
+	springer-humanities-author-date \
+	springer-humanities-brackets \
+	springer-mathphys-author-date \
+	springer-mathphys-brackets \
+	springer-vancouver
+
+# base URL for downloading the citation styles
+BASE_URL = https://www.zotero.org/styles/
+
+CSL_PREFIX ?= _extensions/nature/csl
+
+download-csl-files: ## Download citation style files. Pass FORCE=1 to download even if file exists.
+	mkdir -p $(CSL_PREFIX)
+	@$(foreach style,$(CITATION_STYLES),\
+		if [ "$(FORCE)" = "1" ] || [ ! -f "$(CSL_PREFIX)/$(style).csl" ]; then \
+			echo "downloading: $(style).csl"; \
+			wget -O $(CSL_PREFIX)/$(style).csl $(BASE_URL)$(style); \
+		else \
+			echo "$(style).csl exists. skipping..."; \
+		fi;)
+
+#-----------------
+##@ render article
+#-----------------
+
+DOCUMENT_NAME ?= template
+
+render-latex: ## Render the article via LaTeX
+	quarto render $(DOCUMENT_NAME).qmd --to nature-pdf
+
+render: ## Render all article formats including pdf, html, and docx
+	quarto render $(DOCUMENT_NAME).qmd --to all
+
+clean: ## Clean compilation artifacts
+	rm sn-*.{bst,cls} || true
+
+clean-all: ## Clean all files including output files
+clean-all: clean
+	rm $(DOCUMENT_NAME).{tex,pdf,html,docx} || true
+	rm -r $(DOCUMENT_NAME)_files/
+
+#-------
+##@ regenerate preview
+#-------
+
+extract-preview: ## Extract the first page of the pdf as a png for the preview
+	pdftoppm -f 1 -l 1 -png $(DOCUMENT_NAME).pdf > $(DOCUMENT_NAME)_1.png

README.md

@@ -24,33 +24,77 @@ Then, add the format to your document options:
 ```yaml
 format:
   nature-pdf: default
-```    
+```
 
 ## Options
 
-- `journal`: the Nature subjournal
+- `journal.cite-style`: the name of the natbib style for the Nature subjournal
   - `default`: Default
   - `sn-nature`: Style for submissions to Nature Portfolio journals
   - `sn-basic`: Basic Springer Nature Reference Style/Chemistry Reference Style
-  - `sn-mathphys`: Math and Physical Sciences Reference Style
+  - `sn-mathphys-ay`: Math and Physical Sciences Reference Style (author-year)
+  - `sn-mathphys-num`: Math and Physical Sciences Reference Style (numbered)
   - `sn-aps`: American Physical Society (APS) Reference Style
   - `sn-vancouver`: Vancouver Reference Style
   - `sn-apa`: APA Reference Style 
   - `sn-chicago`: Chicago-based Humanities Reference Style
-- `classoptions`:
-  - `iicol`: double column layout, usually used with `journal: default`
-  - `Numbered`: Numbered reference style, usually used with `journal: sn-mathphys` or `journal: sn-vancouver`.
+- `classoption`:
+  - `iicol`: double column layout, usually used with `journal.cite-style: default`
+  - `Numbered`: Numbered reference style, usually used with `journal.cite-style: sn-vancouver`.
   - `referee`: double spaced for first submissions
   - `lineno`: print line numbers in the margin
 
+Since `cite-method: citeproc` is the
+[default](https://quarto.org/docs/authoring/footnotes-and-citations.html#sec-biblatex),
+to respect the natbib reference styles, you would need to set `cite-method: natbib`,
+such as:
+
+```yaml
+format:
+  nature-pdf:
+    journal: 
+      cite-style: sn-mathphys-num
+    cite-method: natbib
+```
+
+and restrict usage to [pandoc standard](https://pandoc.org/MANUAL.html#citation-syntax)
+references: `[@key01; @key02]`. This has the advantage that it will respect the styles
+officially included in the [Springer Nature template][springer-template].
+However it has the disadvantage that the citations will not be consistent with
+html and docx outputs. To achieve this, set
+
+```yaml
+csl: ./path/to/springer-basic-author-date.csl
+```
+
+to a path to a CSL file. Several are vendered in
+[_extensions/nature/csl/](./_extensions/nature/csl/).
+Additional CSL style files can be found in the
+[citation-style-language/styles](https://github.com/citation-style-language/styles)
+repository, the [recommended](https://citationstyles.org/authors/)
+[Zotero Style Repository](https://www.zotero.org/styles) for downloading these
+styles, and elsewhere[^1]. The `csl` parameter can be specified independent of the
+specification of `cite-method: citeproc` or `cite-method: natbib` but the former
+will lead to consistency of the pdf output with html and docx while the latter
+will use the csl file with citeproc for non-LaTeX outputs and natbib for the
+LaTeX-rendered pdf.
+
+[^1]: The vendored Citation Style Language (CSL) files are copyrighted by the [Citation Style Language project](https://citationstyles.org/). These files have not been modified and are redistributed as licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License ([CC BY-SA 3.0](https://creativecommons.org/licenses/by-sa/3.0/)).
+
 ## Example
 
 Here is the source code for a minimal sample document: [template.qmd](template.qmd).
 
 <!-- pdftools::pdf_convert('template.pdf',pages = 1) -->
-![[template.qmd](template.qmd)](template_1.png)
+<div style="width: 100%; text-align: left;">
+  <a href="template.pdf">
+    <img src="template_1.png" width="500" alt="link to template.pdf" style="max-width:100%;height:auto;">
+  </a>
+</div>
 
 ## License
 
-This modifies the Springer Nature journal article template package, available at <https://www.springernature.com/gp/authors/campaigns/latex-author-support/see-where-our-services-will-take-you/18782940>.
-The original template is licensed under the [LaTeX Project Public License 1.3c](https://www.latex-project.org/lppl/lppl-1-3c/). The template within is derived from this and makes modifications to separate into the full document into Quarto "partials". All modifications can be seen in this repo. 
+This modifies the [Springer Nature journal article template package][springer-template].
+The original template is licensed under the [LaTeX Project Public License 1.3c](https://www.latex-project.org/lppl/lppl-1-3c/). The template within is derived from this and makes modifications to separate into the full document into Quarto "partials". All modifications can be seen in this repo.
+
+[springer-template]: https://www.springernature.com/gp/authors/campaigns/latex-author-support/see-where-our-services-will-take-you/18782940

_extensions/nature/_extension.yml

@@ -1,5 +1,5 @@
 title: Nature Journal Template
-author: Christopher Kenny
+author: Christopher Kenny, Cameron Smith
 version: 1.0.0
 quarto-required: ">=1.4.0"
 contributes:
@@ -14,7 +14,8 @@ contributes:
         - sn-aps.bst
         - sn-basic.bst
         - sn-chicago.bst
-        - sn-mathphys.bst
+        - sn-mathphys-ay.bst
+        - sn-mathphys-num.bst
         - sn-nature.bst
         - sn-vancouver.bst
       template-partials:
@@ -23,4 +24,3 @@ contributes:
         - "partials/_author.tex"
         - "partials/_affiliation.tex"
         - "partials/before-body.tex"
-

_extensions/nature/csl/nature-no-superscript.csl

@@ -0,0 +1,127 @@
+<?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-GB">
+  <info>
+    <title>Nature (no superscript)</title>
+    <id>http://www.zotero.org/styles/nature-no-superscript</id>
+    <link href="http://www.zotero.org/styles/nature-no-superscript" rel="self"/>
+    <link href="http://www.nature.com/clpt/clptguidetoauthors.pdf" rel="documentation"/>
+    <author>
+      <name>Michael Berkowitz</name>
+      <email>[email protected]</email>
+    </author>
+    <category citation-format="numeric"/>
+    <category field="science"/>
+    <category field="generic-base"/>
+    <updated>2022-07-02T13:18:26+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="title">
+    <choose>
+      <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+        <text variable="title" font-style="italic"/>
+      </if>
+      <else-if type="chapter" match="any"/>
+      <else>
+        <text variable="title"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="author">
+    <names variable="author">
+      <name sort-separator=", " delimiter=", " and="symbol" initialize-with=". " delimiter-precedes-last="never" name-as-sort-order="all"/>
+      <label form="short" prefix=", "/>
+      <et-al font-style="italic"/>
+    </names>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if variable="volume" type="article" match="any"/>
+      <else-if variable="DOI">
+        <text variable="DOI" prefix="doi:"/>
+      </else-if>
+      <else-if variable="URL">
+        <text term="at"/>
+        <text variable="URL" prefix=" &lt;" suffix="&gt;"/>
+      </else-if>
+    </choose>
+  </macro>
+  <macro name="issuance">
+    <choose>
+      <if type="bill book graphic legal_case legislation motion_picture report song chapter paper-conference" match="any">
+        <group delimiter=", " prefix="(" suffix=").">
+          <text variable="publisher" form="long"/>
+          <date variable="issued">
+            <date-part name="year"/>
+          </date>
+        </group>
+      </if>
+      <else-if type="article">
+        <group delimiter=" ">
+          <choose>
+            <if variable="genre" match="any">
+              <text variable="genre" text-case="capitalize-first"/>
+            </if>
+            <else>
+              <text term="article" text-case="capitalize-first"/>
+            </else>
+          </choose>
+          <text term="at"/>
+          <choose>
+            <if variable="DOI" match="any">
+              <text variable="DOI" prefix="https://doi.org/"/>
+            </if>
+            <else>
+              <text variable="URL"/>
+            </else>
+          </choose>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else>
+        <date prefix="(" suffix=")." variable="issued">
+          <date-part name="year"/>
+        </date>
+      </else>
+    </choose>
+  </macro>
+  <macro name="editor">
+    <choose>
+      <if type="chapter paper-conference" match="any">
+        <names variable="editor" prefix="(" suffix=")">
+          <label form="short" suffix=" "/>
+          <name and="symbol" delimiter-precedes-last="never" initialize-with=". " name-as-sort-order="all"/>
+        </names>
+      </if>
+    </choose>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout prefix="(" suffix=")" delimiter=",">
+      <text variable="citation-number"/>
+    </layout>
+  </citation>
+  <bibliography et-al-min="6" et-al-use-first="1" second-field-align="flush" entry-spacing="0" line-spacing="2">
+    <layout>
+      <text variable="citation-number" suffix="."/>
+      <group delimiter=" ">
+        <text macro="author" suffix="."/>
+        <text macro="title" suffix="."/>
+        <choose>
+          <if type="chapter paper-conference" match="any">
+            <text term="in" form="long" plural="false"/>
+          </if>
+        </choose>
+        <text variable="container-title" font-style="italic" form="short"/>
+        <text macro="editor"/>
+        <group font-weight="bold">
+          <text variable="volume" suffix=","/>
+        </group>
+        <text variable="page"/>
+        <text macro="issuance"/>
+        <text macro="access"/>
+      </group>
+    </layout>
+  </bibliography>
+</style>