Convert bookdown site to Quarto (#21)

Author: jmwingenroth

.github/workflows/publish.yml

@@ -0,0 +1,25 @@
+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
+
+      - name: Render and Publish
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -4,3 +4,6 @@
 .Ruserdata
 
 .DS_Store
+_book/
+
+/.quarto/

01-files.Rmd 01-files.qmd01-files.Rmd renamed to 01-files.qmd

@@ -1,9 +1,3 @@
----
-editor_options: 
-  markdown: 
-    wrap: 72
----
-
 # File Structure
 
 This section details emLab's organizational stucture for Google
@@ -44,7 +38,7 @@ Google Docs/Sheets/Slides. Everything else is stored at GRIT.
 
 ### General Structure
 
-```         
+```
 Google Drive
   |__ My Drive
   |   |__ ... whatever files you have on your personal Google Drive ...
@@ -71,7 +65,7 @@ The emLab Google Shared Drive is organized into three main folders:
 
 ### Project Folder Structure
 
-```         
+```
 Google Drive
   |__ Shared drives
       |__ emLab
@@ -113,7 +107,7 @@ the Google Shared Drive, except it also has folders for `data`.
 
 ### General Structure
 
-```         
+```
 |__ emLab
   |__ central-emlab-resources
   |__ communications
@@ -134,15 +128,15 @@ The emLab GRIT data directory is organized into five main folders:
 
 -   `data`: includes the centralized emLab data directory of the
     commonly used datasets we work with across projects (see Sections
-    \@ref(emlab-data-directory-overview) and \@ref(emlab-data-directory)
+    @sec-emlab-data-directory-overview and @sec-emlab-data-directory
     for more on this)
 
 -   `projects`: includes data and files on past (archive) and current
     projects
 
 ### Project Folder Structure
 
-```         
+```
 |__ emLab
   |__ projects
     |__ archived-projects
@@ -160,8 +154,7 @@ Each project folder on GRIT must contain the following 6 folders:
 
 -   `data`: This data folder will contain a `data_overview` spreadsheet
     and all of the intermediate datasets as well as output datasets
-    associated with the project (see Section
-    \@ref(project-data-directory) for more on this). Be sure to also add
+    associated with the project (see @sec-project-data-directory for more on this). Be sure to also add
     a copy of your final datasets to the `emlab/data`data directory.
 
 -   `deliverables`: final reports, paper manuscripts, other final
@@ -201,7 +194,7 @@ multiple projects. More detail is provided in the subsequent sections.
 **All** data used in a project should live in this project-specific
 repository. To help keep track of project data, we highly recommend
 creating and maintaining a `data_overview` Google sheet on the Google
-Shared Drive (see Section \@ref(project-data-directory) for more
+Shared Drive (see @sec-project-data-directory for more
 information). This overview spreadsheet will provide a centralized
 summary of the data inputs and outputs for a project, and also allow
 teams to keep track of the status of adding the data to the `emlab/data`
@@ -214,10 +207,10 @@ To illustrate how each of these subfolders might be used, consider the
 following. A team may receive data from partners, extract data from
 external sources, compile survey responses, create a new dataset from a
 literature review, or use results from previous projects as input. These
-data are termed “raw data” and should never be directly modified - **all
+data are termed "raw data" and should never be directly modified - **all
 of the errors, mistakes, and gremlins should be kept in the original
 versions**. Instead, they should be processed / cleaned, and then
-exported as “clean data” that is actually used in analyses. The script
+exported as "clean data" that is actually used in analyses. The script
 used to do the processing / cleaning then acts as a reproducable record
 of everything that was done to the raw data.
 
@@ -237,7 +230,7 @@ input for analyses within this project. The `output` folder will then
 contain the stock assessment results that might be relevant to other
 projects.
 
-```         
+```
 |__ emLab
   |__ projects
     |__ current-rojects
@@ -257,14 +250,14 @@ emLab projects once the project is complete. To do this, any `output`
 data (and `raw` data if it is not already there) should be moved to the
 `emlab/data` folder, as described below.
 
-#### `emlab/data` {#emlab-data-directory-overview}
+#### `emlab/data` {#sec-emlab-data-directory-overview}
 
 As a general rule, this folder contains all data *used* and *produced*
 by emLab projects. The idea is to make it easier for people to find data
 that has been used in previous projects, as well as to use previous
 results as inputs for new projects. In other words, it is the place to
 store data that could be used commonly across multiple projects. Please
-see Section \@ref(#emlab-data-directory) for an overview of metadata
+see @sec-emlab-data-directory for an overview of metadata
 that should be included with each dataset.
 
 To illustrate types of data that should be in the `emlab/data` folder,
@@ -282,7 +275,7 @@ data. **All datasets in this folder should be contained within their own
 folders that include at minimum the data and metadata files.** For
 example, a file structure for the two datasets mentioned above might be:
 
-```         
+```
 |__ emLab
   |__ data
     |__ upsides
@@ -302,7 +295,7 @@ relatively straightforward with the metadata file and a single csv file.
 However, the folder containing the RAM database is more complicated as
 this is a dataset that is re-released every so often as a new version.
 Specific guidelines for organizing different types of data within the
-`emlab/data` folder are discussed in detail in Section \@ref(data).
+`emlab/data` folder are discussed in detail in @sec-data.
 
 ## GitHub Structure
 
@@ -367,15 +360,15 @@ As such, you go to GitHub and create the following four repositories:
 
 You'll clone the Blue Future repo into your comuter, using the usual:
 
-```         
+```
 git clone https://github.com/emlab-ucsb/BlueFuture.git
 ```
 
 Now, instead of cloning the repos for each paper and the app into their
 own folder, you'll navigate into your local BlueFuture folder. Then,
 instead of cloning them there, you can just do:
 
-```         
+```
 git submodule add https://github.com/emlab-ucsb/Paper1.git
 ```