Initial commit

.github/workflows/publish.yml

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+on:
+  workflow_dispatch:
+  push:
+    branches: main
+
+name: Quarto Publish
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          version: pre-release
+          tinytex: true
+
+
+      - name: Render and Publish
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

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+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+
+/.quarto/
+/_manuscript
+
+/agujournal2019.cls
+/trackchanges.sty
+.Rproj.user
+.Rhistory
+.Rdata
+.httr-oauth
+.DS_Store

README.md

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+## A Quarto Manuscript Template
+
+This is a template repo for generating a manuscript from Quarto that accompanies the tutorial at: [Quarto Manuscripts: RStudio](https://quarto.org/docs/manuscripts/authoring/rstudio.html)
+

_extensions/quarto-journals/agu/_extension.yml

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+title: AGU Journals Template
+author: Charles Teague
+version: 0.1.0
+contributes:
+  formats:
+    common:
+      knitr:
+        opts_chunk:
+          echo: false
+      number-sections: true
+      csl: american-geophysical-union.csl
+      filters:
+        - agu.lua
+    pdf:
+      documentclass: agujournal2019
+      classoptions: draft
+      header-includes: |
+        \usepackage{url} %this package should fix any errors with URLs in refs.
+        \usepackage{lineno}
+        \usepackage[inline]{trackchanges} %for better track changes. finalnew option will compile document with changes incorporated.
+        \usepackage{soul}
+        \linenumbers
+      template-partials:
+        - "partials/title.tex"
+        - "partials/_authors.tex"
+        - "partials/before-body.tex"
+        - "partials/_affiliations.tex"
+        - "partials/_corresponding-author.tex"
+      format-resources:
+        - agujournal2019.cls
+        - trackchanges.sty
+    html:
+      toc: true

_extensions/quarto-journals/agu/agu.lua

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+
+
+if quarto.doc.is_format("pdf") then
+return { 
+  {
+    Div = function(div)
+      if div.identifier == 'refs' then
+        div.content:insert(pandoc.RawBlock('latex', '\\vspace{1em}'))
+        return div
+      end
+    end
+  }
+}
+end