From 03457584521859b085b3fa699936304dcee42fa7 Mon Sep 17 00:00:00 2001
From: Shannon Rankin <59101864+shannonrankin@users.noreply.github.com>
Date: Thu, 24 Oct 2024 13:34:39 -0700
Subject: [PATCH] Modify Open Science

Remove Open Science from output (except from Optional Pages), and refer to Open Science repo. The pages were retained, and the section info commented out from the _quarto.yml, so it can be easily reverted if necessary. However, the Open Science repo will be updated, whereas this will not be. In the future, should remove/delete these pages.
---
 _quarto.yml             | 18 +++++++++---------
 content/OpenScience.qmd |  4 ++--
 index.qmd               |  2 +-
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/_quarto.yml b/_quarto.yml
index f813e9b..7453270 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -63,15 +63,15 @@ website:
           - content/OpenScience.qmd
           - content/PublicationsPresentations.qmd
           - content/Resources.qmd
-      - section: "NMFS Open Science Directions"
-        contents:
-          - content/NMFS_OpenSciDirections/Getting-Started.qmd
-          - content/NMFS_OpenSciDirections/organize.qmd
-          - content/NMFS_OpenSciDirections/add-content.qmd
-          - content/NMFS_OpenSciDirections/rendering.qmd
-          - content/NMFS_OpenSciDirections/rmarkdown.Rmd
-          - content/NMFS_OpenSciDirections/code.qmd
-          - content/NMFS_OpenSciDirections/acknowledgements.qmd 
+      # - section: "NMFS Open Science Directions"  #Removed but did not yet delete
+      #   contents:
+      #     - content/NMFS_OpenSciDirections/Getting-Started.qmd
+      #     - content/NMFS_OpenSciDirections/organize.qmd
+      #     - content/NMFS_OpenSciDirections/add-content.qmd
+      #     - content/NMFS_OpenSciDirections/rendering.qmd
+      #     - content/NMFS_OpenSciDirections/rmarkdown.Rmd
+      #     - content/NMFS_OpenSciDirections/code.qmd
+      #     - content/NMFS_OpenSciDirections/acknowledgements.qmd 
         
 format:
   html:
diff --git a/content/OpenScience.qmd b/content/OpenScience.qmd
index ac8cc07..e9aa3fa 100644
--- a/content/OpenScience.qmd
+++ b/content/OpenScience.qmd
@@ -2,6 +2,6 @@
 title: Open Science
 ---
 
-This section is optional but is a great place for all of your open science related resources and tools. You can include information here for our Openscapes work, stack exchange, GitHub, co working guides, etc.
+This section is optional but we recommend creating this place to point to the [Open Science repository](https://sael-swfsc.github.io/OpenScience/). 
 
-[SAEL Example](https://sael-swfsc.github.io/SAEL-lab-manual/content/OpenScience_Getting-Started.html)
+[SAEL Example](https://sael-swfsc.github.io/SAEL-lab-manual/content/OpenScience.html)
diff --git a/index.qmd b/index.qmd
index 3bb06e9..9783143 100644
--- a/index.qmd
+++ b/index.qmd
@@ -88,7 +88,7 @@ This template will create a Quarto website that each lab can copy and edit with
 
         ![](content/images/website.png)
 
-8.  Your lab manual is now created! Go [here](https://sael-swfsc.github.io/OpenScience/content/GithubDesktop.html) for more directions on how to start editing you manual using GitHub Desktop and R Studio (start at step 4)
+8.  Your lab manual is now created! Go [here](https://sael-swfsc.github.io/OpenScience/content/labManual.html) for more information on building your lab manual.
 
 ## Example Manuals