From 51addce73291c1217bc95900de38a409b9419a2b Mon Sep 17 00:00:00 2001
From: carriewright11 <cwright2@fredhutch.org>
Date: Thu, 9 Jan 2025 13:32:29 -0500
Subject: [PATCH 1/9] adding icons to config

---
 config.yml       | 13 +++++++++++++
 course_setup.Rmd | 26 ++++++++++++++++++++++++++
 2 files changed, 39 insertions(+)
 create mode 100644 config.yml

diff --git a/config.yml b/config.yml
new file mode 100644
index 0000000..846476e
--- /dev/null
+++ b/config.yml
@@ -0,0 +1,13 @@
+default:
+  actions: "<img src='resources/icons/actions.png' alt='actions icon' class = icon>"
+  collab: "<img src='resources/icons/collaborator.png' alt='collaborator icon' class = icon>"
+  copy: "<img src='resources/icons/copy.png' alt='copy icon' class = icon>"
+  dev: "<img src='resources/icons/developer_settings.png' alt='developer settings icon' class = icon>"
+  edit: "<img src='resources/icons/edit.png' alt='edit icon' class = icon>"
+  pages: "<img src='resources/icons/pages.png' alt='pages icon' class = icon>"
+  PR: "<img src='resources/icons/pull_request.png' alt='pull request icon' class = icon>"
+  profile: "<img src='resources/icons/profile_photo.png' alt='profile photo icon' class = icon>"
+  token: "<img src='resources/icons/personal_tokens.png' alt='personal access token icon' class = icon>"
+  search: "<img src='resources/icons/search.png' alt='search icon' class = icon>"
+  secrets: "<img src='resources/icons/secrets_and_variables.png' alt='secrets and variables icon' class = icon>"
+  settings: "<img src='resources/icons/settings_gear.png' alt='settings gear icon' class = icon>"
diff --git a/course_setup.Rmd b/course_setup.Rmd
index 6276093..d1a6048 100644
--- a/course_setup.Rmd
+++ b/course_setup.Rmd
@@ -13,3 +13,29 @@ css: style.css
 <input type="checkbox">  In the upper right, _click on_: <div class = "github_button"><a href="https://github.com/new?template_name=OTTR_Template&template_owner=jhudsl"> Use this template</a></div>
 
 <input type="checkbox">  Set your repo to **Public**
+
+
+`r config::get("actions")`
+
+`r config::get("copy")`
+
+`r config::get("collab")`
+
+`r config::get("dev")`
+
+`r config::get("edit")`
+
+`r config::get("pages")`
+
+`r config::get("token")`
+
+`r config::get("profile")`
+
+`r config::get("PR")`
+
+`r config::get("search")`
+
+`r config::get("secrets")`
+
+`r config::get("settings")`
+

From d944037849bc042e4d635a442911a719b76ba289 Mon Sep 17 00:00:00 2001
From: Carrie Wright <23014755+carriewright11@users.noreply.github.com>
Date: Thu, 9 Jan 2025 14:27:21 -0500
Subject: [PATCH 2/9] Update pull_request.yml

trying to see if using ${{ secrets.GH_PAT }} to reference the PAT each time fixes the error we are getting which is causing the PR action to not work
---
 .github/workflows/pull_request.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index a53a3a7..ee7ac55 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -59,7 +59,7 @@ jobs:
     with:
       check_type: spelling
       error_min: 3
-      gh_pat: secrets.GH_PAT
+      gh_pat: ${{ secrets.GH_PAT }}
 
   url-check:
     name: Check URLs
@@ -69,7 +69,7 @@ jobs:
     with:
       check_type: urls
       error_min: 0
-      gh_pat: secrets.GH_PAT
+      gh_pat: ${{ secrets.GH_PAT }}
 
   render-preview:
     name: Render preview

From a0b587cd30495838d1f67efe07482d953ebc53ad Mon Sep 17 00:00:00 2001
From: carriewright11 <cwright2@fredhutch.org>
Date: Thu, 9 Jan 2025 14:37:33 -0500
Subject: [PATCH 3/9] going back

---
 .github/workflows/pull_request.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index ee7ac55..a53a3a7 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -59,7 +59,7 @@ jobs:
     with:
       check_type: spelling
       error_min: 3
-      gh_pat: ${{ secrets.GH_PAT }}
+      gh_pat: secrets.GH_PAT
 
   url-check:
     name: Check URLs
@@ -69,7 +69,7 @@ jobs:
     with:
       check_type: urls
       error_min: 0
-      gh_pat: ${{ secrets.GH_PAT }}
+      gh_pat: secrets.GH_PAT
 
   render-preview:
     name: Render preview

From 7fc1b1c8b009f1820f8c37baa547ca29e8298c32 Mon Sep 17 00:00:00 2001
From: carriewright11 <cwright2@fredhutch.org>
Date: Thu, 9 Jan 2025 14:41:40 -0500
Subject: [PATCH 4/9] trying another method for url check and spell check
 tokens

---
 .github/workflows/pull_request.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index a53a3a7..314fb62 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -59,7 +59,7 @@ jobs:
     with:
       check_type: spelling
       error_min: 3
-      gh_pat: secrets.GH_PAT
+      token: ${{ secrets.GH_PAT }}
 
   url-check:
     name: Check URLs
@@ -69,7 +69,7 @@ jobs:
     with:
       check_type: urls
       error_min: 0
-      gh_pat: secrets.GH_PAT
+      token: ${{ secrets.GH_PAT }}
 
   render-preview:
     name: Render preview

From 45e2a6433e25a7b9b118c436784278ec82031d77 Mon Sep 17 00:00:00 2001
From: carriewright11 <cwright2@fredhutch.org>
Date: Thu, 9 Jan 2025 14:45:29 -0500
Subject: [PATCH 5/9] trying another variation

---
 .github/workflows/pull_request.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 314fb62..d0ab8ee 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -59,7 +59,7 @@ jobs:
     with:
       check_type: spelling
       error_min: 3
-      token: ${{ secrets.GH_PAT }}
+      token: secrets.GH_PAT
 
   url-check:
     name: Check URLs
@@ -69,7 +69,7 @@ jobs:
     with:
       check_type: urls
       error_min: 0
-      token: ${{ secrets.GH_PAT }}
+      token: secrets.GH_PAT
 
   render-preview:
     name: Render preview

From cfa776b03d37474b65182e633710d074aa85eb3e Mon Sep 17 00:00:00 2001
From: Carrie Wright <23014755+carriewright11@users.noreply.github.com>
Date: Thu, 16 Jan 2025 12:22:06 -0500
Subject: [PATCH 6/9] Update .github/workflows/pull_request.yml

---
 .github/workflows/pull_request.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index d0ab8ee..64bd8f7 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -59,7 +59,8 @@ jobs:
     with:
       check_type: spelling
       error_min: 3
-      token: secrets.GH_PAT
+     secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
 
   url-check:
     name: Check URLs

From 83c5e9cb646e85d0a1fd8be92babbd922ff745d6 Mon Sep 17 00:00:00 2001
From: Carrie Wright <23014755+carriewright11@users.noreply.github.com>
Date: Thu, 16 Jan 2025 12:22:46 -0500
Subject: [PATCH 7/9] Update .github/workflows/pull_request.yml

---
 .github/workflows/pull_request.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 64bd8f7..3ed92ff 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -70,7 +70,8 @@ jobs:
     with:
       check_type: urls
       error_min: 0
-      token: secrets.GH_PAT
+    secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
 
   render-preview:
     name: Render preview

From a83c9561e44dae192ea9190f587289b52c7e6b5a Mon Sep 17 00:00:00 2001
From: Carrie Wright <23014755+carriewright11@users.noreply.github.com>
Date: Thu, 16 Jan 2025 12:23:06 -0500
Subject: [PATCH 8/9] Update .github/workflows/pull_request.yml

---
 .github/workflows/pull_request.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 3ed92ff..66b25e3 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -59,7 +59,8 @@ jobs:
     with:
       check_type: spelling
       error_min: 3
-     secrets:
+    secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
       gh_pat: ${{ secrets.GH_PAT }}
 
   url-check:

From d7ca4165064da459545e0de2ca415be2e212c3d4 Mon Sep 17 00:00:00 2001
From: Carrie Wright <23014755+carriewright11@users.noreply.github.com>
Date: Thu, 16 Jan 2025 12:23:24 -0500
Subject: [PATCH 9/9] Update .github/workflows/pull_request.yml

---
 .github/workflows/pull_request.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 66b25e3..6cc9be5 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -61,7 +61,6 @@ jobs:
       error_min: 3
     secrets:
       gh_pat: ${{ secrets.GH_PAT }}
-      gh_pat: ${{ secrets.GH_PAT }}
 
   url-check:
     name: Check URLs