From 79b61f69a4a313a7de08aeded417111def5afbb5 Mon Sep 17 00:00:00 2001
From: howardbaek <howardbaek.fh@gmail.com>
Date: Thu, 7 Sep 2023 14:45:27 -0700
Subject: [PATCH 01/82] Testing git on terminal

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 04db84a6e..e7fb81296 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 ## Open-source Tools for Training Resources - OTTR
 
-Go to [ottrproject.org](https://www.ottrproject.org/) to get started! :tada:
+Testing git Go to [ottrproject.org](https://www.ottrproject.org/) to get started! :tada:
 
 The purpose of this course template and guide is to make course publishing maintenance across multiple different platforms _less painful_.
 

From f84d7bf57f573a336d8f1ff0445375e06ecd2244 Mon Sep 17 00:00:00 2001
From: howardbaek <howardbaek.fh@gmail.com>
Date: Thu, 7 Sep 2023 14:48:30 -0700
Subject: [PATCH 02/82] Revert changes

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e7fb81296..04db84a6e 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 ## Open-source Tools for Training Resources - OTTR
 
-Testing git Go to [ottrproject.org](https://www.ottrproject.org/) to get started! :tada:
+Go to [ottrproject.org](https://www.ottrproject.org/) to get started! :tada:
 
 The purpose of this course template and guide is to make course publishing maintenance across multiple different platforms _less painful_.
 

From 46dd84c504af505dbf042be994cdb1f23bdee3ef Mon Sep 17 00:00:00 2001
From: howardbaek <howardbaek.fh@gmail.com>
Date: Thu, 7 Sep 2023 15:09:34 -0700
Subject: [PATCH 03/82] Initial pass at URL checker

---
 .github/workflows/check-url.yml | 42 +++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 .github/workflows/check-url.yml

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
new file mode 100644
index 000000000..f21558d2e
--- /dev/null
+++ b/.github/workflows/check-url.yml
@@ -0,0 +1,42 @@
+name: Periodic URL Check
+
+on:
+  schedule:
+    # At 00:00 on Sundays
+    - cron: '0 0 * * 0'
+
+jobs:
+
+  yaml-check:
+    name: Load user automation choices
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Delete branch locally and remotely
+        run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
+
+      # Make the branch fresh
+      - name: Make the branch fresh
+        run: |
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
+
+          branch_name='preview-${{ github.event.pull_request.number }}'
+          echo branch doesnt exist
+          git checkout -b $branch_name || echo branch exists
+          git push --set-upstream origin $branch_name
+       shell: bash
+
+  url-check:
+    name: Check URLs
+    needs: yaml-check
+    if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}
+    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
+    with:
+      check_type: urls
+      error_min: 0
+      gh_pat: secrets.GH_PAT

From 274775042e9fd9ff7460c626b3dae6e7dad74566 Mon Sep 17 00:00:00 2001
From: howardbaek <howardbaek.fh@gmail.com>
Date: Thu, 7 Sep 2023 15:12:06 -0700
Subject: [PATCH 04/82] Test URL checker by running every 2 mint

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

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index f21558d2e..1f128be32 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -2,8 +2,8 @@ name: Periodic URL Check
 
 on:
   schedule:
-    # At 00:00 on Sundays
-    - cron: '0 0 * * 0'
+    # At every 2nd minute
+    - cron: '*/2 * * * *'
 
 jobs:
 

From df7515696c2de0364dac75074a1544aef2a6e31e Mon Sep 17 00:00:00 2001
From: howardbaek <howardbaek.fh@gmail.com>
Date: Thu, 7 Sep 2023 15:18:18 -0700
Subject: [PATCH 05/82] Fix syntax

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 1f128be32..6986b2cb5 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -31,7 +31,7 @@ jobs:
           git push --set-upstream origin $branch_name
        shell: bash
 
-  url-check:
+   url-check:
     name: Check URLs
     needs: yaml-check
     if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}

From 2a74a4f56951c1e285656dadc63cdee31fba54db Mon Sep 17 00:00:00 2001
From: howardbaek <howardbaek.fh@gmail.com>
Date: Thu, 7 Sep 2023 15:25:21 -0700
Subject: [PATCH 06/82] Syntax

---
 .github/workflows/check-url.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 6986b2cb5..7894ea803 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -6,7 +6,6 @@ on:
     - cron: '*/2 * * * *'
 
 jobs:
-
   yaml-check:
     name: Load user automation choices
     runs-on: ubuntu-latest
@@ -17,8 +16,6 @@ jobs:
           fetch-depth: 0
       - name: Delete branch locally and remotely
         run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
-
-      # Make the branch fresh
       - name: Make the branch fresh
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE
@@ -30,8 +27,7 @@ jobs:
           git checkout -b $branch_name || echo branch exists
           git push --set-upstream origin $branch_name
        shell: bash
-
-   url-check:
+  url-check:
     name: Check URLs
     needs: yaml-check
     if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}

From 4be79895606d37a1cde18c7d31fdd758556d8bd9 Mon Sep 17 00:00:00 2001
From: howardbaek <howardbaek.fh@gmail.com>
Date: Thu, 7 Sep 2023 15:28:59 -0700
Subject: [PATCH 07/82] chatgpt?

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

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 7894ea803..6dfc7436d 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -35,4 +35,5 @@ jobs:
     with:
       check_type: urls
       error_min: 0
-      gh_pat: secrets.GH_PAT
+      gh_pat: ${{ secrets.GH_PAT }}
+

From 80ec10d55043fae8a7b18cd116cd195a1d7936e5 Mon Sep 17 00:00:00 2001
From: Howard Baek <50791792+howardbaek@users.noreply.github.com>
Date: Tue, 12 Sep 2023 13:36:50 -0500
Subject: [PATCH 08/82] Fix spacing

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 6dfc7436d..73bdc3674 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -26,7 +26,7 @@ jobs:
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
           git push --set-upstream origin $branch_name
-       shell: bash
+  shell: bash
   url-check:
     name: Check URLs
     needs: yaml-check

From 3f8d0e51eedd8e214919ebca506e5f7bfd05e35c Mon Sep 17 00:00:00 2001
From: Howard Baek <50791792+howardbaek@users.noreply.github.com>
Date: Tue, 12 Sep 2023 13:45:43 -0500
Subject: [PATCH 09/82] Remove "shell:bash"

---
 .github/workflows/check-url.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 73bdc3674..df72527ae 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -26,7 +26,6 @@ jobs:
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
           git push --set-upstream origin $branch_name
-  shell: bash
   url-check:
     name: Check URLs
     needs: yaml-check
@@ -35,5 +34,5 @@ jobs:
     with:
       check_type: urls
       error_min: 0
-      gh_pat: ${{ secrets.GH_PAT }}
+      gh_pat: secrets.GH_PAT
 

From 407e83d872ae6b502509d0291c5198fdb6d350af Mon Sep 17 00:00:00 2001
From: Howard Baek <50791792+howardbaek@users.noreply.github.com>
Date: Tue, 12 Sep 2023 13:50:20 -0500
Subject: [PATCH 10/82] Please work

---
 .github/workflows/check-url.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index df72527ae..3d61e997b 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -26,6 +26,7 @@ jobs:
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
           git push --set-upstream origin $branch_name
+        shell: bash
   url-check:
     name: Check URLs
     needs: yaml-check

From d60a9d8f5169de7b325ef26a7a82f3f72d624a92 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 14:05:28 -0400
Subject: [PATCH 11/82] Add spacing and indents

---
 .github/workflows/check-url.yml | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 3d61e997b..1f803a411 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -6,7 +6,7 @@ on:
     - cron: '*/2 * * * *'
 
 jobs:
-  yaml-check:
+  set-up:
     name: Load user automation choices
     runs-on: ubuntu-latest
     steps:
@@ -14,8 +14,10 @@ jobs:
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
+
       - name: Delete branch locally and remotely
         run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
+
       - name: Make the branch fresh
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE
@@ -27,13 +29,15 @@ jobs:
           git checkout -b $branch_name || echo branch exists
           git push --set-upstream origin $branch_name
         shell: bash
+
   url-check:
     name: Check URLs
-    needs: yaml-check
+    needs: set-up
     if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}
-    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
-    with:
-      check_type: urls
-      error_min: 0
-      gh_pat: secrets.GH_PAT
 
+    - name: Run the checks
+      uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
+      with:
+        check_type: urls
+        error_min: 0
+        gh_pat: secrets.GH_PAT

From 30b104d01b5aafb1b58a0857ffb2197051767d7a Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 14:10:20 -0400
Subject: [PATCH 12/82] Fix indentation

---
 .github/workflows/check-url.yml | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 1f803a411..7337be851 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -28,16 +28,10 @@ jobs:
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
           git push --set-upstream origin $branch_name
-        shell: bash
 
-  url-check:
-    name: Check URLs
-    needs: set-up
-    if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}
-
-    - name: Run the checks
-      uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
-      with:
-        check_type: urls
-        error_min: 0
-        gh_pat: secrets.GH_PAT
+      - name: Run the checks
+        uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
+        with:
+          check_type: urls
+          error_min: 0
+          gh_pat: secrets.GH_PAT

From 4f356051aab92ee4d278c2c24e373c292e659d72 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 14:14:55 -0400
Subject: [PATCH 13/82] Tryna find this indentation

---
 .github/workflows/check-url.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 7337be851..288e7d1a5 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -15,9 +15,6 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Delete branch locally and remotely
-        run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
-
       - name: Make the branch fresh
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE

From e154c6bf9846161a0e270252363be9db1b9bdcef Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 14:18:58 -0400
Subject: [PATCH 14/82] Add config option

---
 .github/workflows/check-url.yml | 18 +++++++++++-------
 config_automation.yml           |  2 ++
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 288e7d1a5..ec4d31a85 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -2,7 +2,6 @@ name: Periodic URL Check
 
 on:
   schedule:
-    # At every 2nd minute
     - cron: '*/2 * * * *'
 
 jobs:
@@ -25,10 +24,15 @@ jobs:
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
           git push --set-upstream origin $branch_name
+    outputs:
+      toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"
 
-      - name: Run the checks
-        uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
-        with:
-          check_type: urls
-          error_min: 0
-          gh_pat: secrets.GH_PAT
+  url-check:
+    name: Check URLs
+    needs: set-up
+    if: ${{needs.yaml-check.outputs.toggle_url_check_periodically == 'yes'}}
+    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
+    with:
+      check_type: urls
+      error_min: 0
+      gh_pat: secrets.GH_PAT
diff --git a/config_automation.yml b/config_automation.yml
index 1c9d38a5d..1a1a57761 100644
--- a/config_automation.yml
+++ b/config_automation.yml
@@ -12,6 +12,8 @@ spell-check: yes
 style-code: yes
 # Test build the docker image if any docker-relevant files have been changed
 docker-test: no
+# Should URLs be tested periodically?
+url-check-periodically: yes
 
 ##### Renderings run upon merge to main branch #####
 # Rendering each platform's content

From fa7970075982d4dacc4d5f2be26c27a5950a8d12 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 14:20:25 -0400
Subject: [PATCH 15/82] Add workflow dispatch button too

---
 .github/workflows/check-url.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index ec4d31a85..c35068542 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -1,6 +1,7 @@
 name: Periodic URL Check
 
 on:
+  workflow_dispatch:
   schedule:
     - cron: '*/2 * * * *'
 

From 77ab7e796c19a4f32cc87a8a5820a1efd9824765 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 14:23:14 -0400
Subject: [PATCH 16/82] temporarily have a pull_request trigger

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index c35068542..da9dc6d6a 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -1,7 +1,7 @@
 name: Periodic URL Check
 
 on:
-  workflow_dispatch:
+  pull_request:
   schedule:
     - cron: '*/2 * * * *'
 

From 1a4c12ad1d6131a051d4f32d204a848e0e076ae0 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 14:25:30 -0400
Subject: [PATCH 17/82] Add URL config

---
 .github/workflows/check-url.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index da9dc6d6a..830d31e77 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -15,6 +15,11 @@ jobs:
         with:
           fetch-depth: 0
 
+      - name: Load environment from YAML
+        uses: doughepi/yaml-env-action@v1.0.0
+        with:
+            files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
+
       - name: Make the branch fresh
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE

From a4e0f1fab2f71c300f57236d64e902797256aefd Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 14:29:24 -0400
Subject: [PATCH 18/82] Add a delete step

---
 .github/workflows/check-url.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 830d31e77..b28c7a3c8 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -20,6 +20,10 @@ jobs:
         with:
             files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
 
+      # Delete the branch if this has been run before
+      - name: Delete branch locally and remotely
+        run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
+
       - name: Make the branch fresh
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE

From fa608e5fc6bf92082869efcefac9fa83f8773f11 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 14:37:53 -0400
Subject: [PATCH 19/82] Fix spec

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index b28c7a3c8..46506ffb2 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -40,7 +40,7 @@ jobs:
   url-check:
     name: Check URLs
     needs: set-up
-    if: ${{needs.yaml-check.outputs.toggle_url_check_periodically == 'yes'}}
+    if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
     uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
     with:
       check_type: urls

From 7decb8e02b53a746b0f7a5cc7977128d5ea21ec6 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 14:42:26 -0400
Subject: [PATCH 20/82] Update for branch problem

---
 .github/workflows/check-url.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 46506ffb2..fec351c57 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -15,6 +15,7 @@ jobs:
         with:
           fetch-depth: 0
 
+        # Use the yaml-env-action action.
       - name: Load environment from YAML
         uses: doughepi/yaml-env-action@v1.0.0
         with:
@@ -24,6 +25,7 @@ jobs:
       - name: Delete branch locally and remotely
         run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
 
+      # Make the branch fresh
       - name: Make the branch fresh
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE
@@ -34,6 +36,8 @@ jobs:
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
           git push --set-upstream origin $branch_name
+        shell: bash
+        
     outputs:
       toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"
 

From 65df96d186a6e12ee27e9f8a55e95d9f9f9c7a6f Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:08:50 -0400
Subject: [PATCH 21/82] Add issue creating infrastructure

---
 .github/ISSUE_TEMPLATE/url-error.md |  8 +++++
 .github/workflows/check-url.yml     | 46 +++++++++++++++++++++++++----
 2 files changed, 48 insertions(+), 6 deletions(-)
 create mode 100644 .github/ISSUE_TEMPLATE/url-error.md

diff --git a/.github/ISSUE_TEMPLATE/url-error.md b/.github/ISSUE_TEMPLATE/url-error.md
new file mode 100644
index 000000000..f2d35479b
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/url-error.md
@@ -0,0 +1,8 @@
+---
+title: Broken URLs found in the course!
+labels: url-error
+---
+URL's in this course were just checked and some broken URLs were found.
+
+**Number of errors:** {{ env.ERROR_NUM }}  
+**Number of errors:** {{ env.FILE_PATH }}
diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index fec351c57..0cee1582f 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -37,7 +37,7 @@ jobs:
           git checkout -b $branch_name || echo branch exists
           git push --set-upstream origin $branch_name
         shell: bash
-        
+
     outputs:
       toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"
 
@@ -45,8 +45,42 @@ jobs:
     name: Check URLs
     needs: set-up
     if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
-    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
-    with:
-      check_type: urls
-      error_min: 0
-      gh_pat: secrets.GH_PAT
+
+    - name: Run the check
+      uses: jhudsl/ottr-reports@main
+      id: check_results
+      continue-on-error: true
+      with:
+        check_type: urls
+        error_min: 1
+
+    - name: Declare file path and time
+      id: check-report
+      run: |
+        branch_name='preview-${{ github.event.pull_request.number }}'
+        echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
+        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/$branch_name/${{ steps.check_results.outputs.report_path }}" >> $GITHUB_OUTPUT
+        error_num=$(cat ${{ steps.check_results.outputs.report_path }} | wc -l)
+        error_num="$((error_num-1))"
+        echo "error_num=$error_num" >> $GITHUB_OUTPUT
+        error_list=$(cat ${{ steps.check_results.outputs.report_path }}
+        echo "error_list=$error_list" >> $GITHUB_OUTPUT
+      shell: bash
+
+    - name: If too many URL errors, then make an issue
+      if: ${{ steps.check-report.outputs.error_num <= 1 }}
+    - uses: JasonEtco/create-an-issue@v2
+      with:
+        filename: .github/ISSUE_TEMPLATE/url-error.md
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        ERROR_LIST: ${{ steps.check_results.outputs.error_list }}
+        ERROR_NUM: ${{ steps.check-report.outputs.error_num }}
+
+    - name: Stop if failure
+      if: steps.check_results.outcome == 'failure'
+      run: exit 1
+
+    - name: If no URL errors than delete the branch we made
+      if: ${{ steps.check-report.outputs.error_num <= 1 }}
+      run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"

From 6aa1c3a84b138116b76349564bec86e15b90d6b9 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:09:20 -0400
Subject: [PATCH 22/82] Add issue template

---
 .github/ISSUE_TEMPLATE/url-error.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/ISSUE_TEMPLATE/url-error.md b/.github/ISSUE_TEMPLATE/url-error.md
index f2d35479b..1d225b6f1 100644
--- a/.github/ISSUE_TEMPLATE/url-error.md
+++ b/.github/ISSUE_TEMPLATE/url-error.md
@@ -5,4 +5,4 @@ labels: url-error
 URL's in this course were just checked and some broken URLs were found.
 
 **Number of errors:** {{ env.ERROR_NUM }}  
-**Number of errors:** {{ env.FILE_PATH }}
+**File_where errors are:** {{ env.FILE_PATH }}

From e747bbc34c43626d26f532d0ad5cbc72039d0c27 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:12:36 -0400
Subject: [PATCH 23/82] Add steps:

---
 .github/ISSUE_TEMPLATE/url-error.md | 2 +-
 .github/workflows/check-url.yml     | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/ISSUE_TEMPLATE/url-error.md b/.github/ISSUE_TEMPLATE/url-error.md
index 1d225b6f1..0e7f7546e 100644
--- a/.github/ISSUE_TEMPLATE/url-error.md
+++ b/.github/ISSUE_TEMPLATE/url-error.md
@@ -5,4 +5,4 @@ labels: url-error
 URL's in this course were just checked and some broken URLs were found.
 
 **Number of errors:** {{ env.ERROR_NUM }}  
-**File_where errors are:** {{ env.FILE_PATH }}
+**File where errors are:** {{ env.FILE_PATH }}
diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 0cee1582f..865600526 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -46,6 +46,7 @@ jobs:
     needs: set-up
     if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
 
+    steps:
     - name: Run the check
       uses: jhudsl/ottr-reports@main
       id: check_results

From 6242dc02899630e2e56121b3cbadb18b3aae81d2 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:15:09 -0400
Subject: [PATCH 24/82] Declare docker

---
 .github/workflows/check-url.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 865600526..88ed4f267 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -43,7 +43,9 @@ jobs:
 
   url-check:
     name: Check URLs
-    needs: set-up
+    runs-on: ubuntu-latest
+    container:
+      image: jhudsl/base_ottr:main
     if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
 
     steps:

From 4a8942e339e322e259e5445f8071da19d7e21076 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:17:09 -0400
Subject: [PATCH 25/82] get rid of dash

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 88ed4f267..1c115c020 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -72,7 +72,7 @@ jobs:
 
     - name: If too many URL errors, then make an issue
       if: ${{ steps.check-report.outputs.error_num <= 1 }}
-    - uses: JasonEtco/create-an-issue@v2
+      uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md
       env:

From 2df94c596232d5b45a80185cd9568a9fc21b363d Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:19:06 -0400
Subject: [PATCH 26/82] Move if

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 1c115c020..0c406243d 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -43,10 +43,10 @@ jobs:
 
   url-check:
     name: Check URLs
+    if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
     runs-on: ubuntu-latest
     container:
       image: jhudsl/base_ottr:main
-    if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
 
     steps:
     - name: Run the check

From 2b947cc079ab82bee828515e60d1f3839bcacc7f Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:21:01 -0400
Subject: [PATCH 27/82] Add a needs argument

---
 .github/workflows/check-url.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 0c406243d..613a71305 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -43,6 +43,7 @@ jobs:
 
   url-check:
     name: Check URLs
+    needs: set-up
     if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
     runs-on: ubuntu-latest
     container:

From b84b2d5a08fe200f3ea629e9c888668f70e2b0bf Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:28:41 -0400
Subject: [PATCH 28/82] Add an option for it branch exists

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 613a71305..43a585792 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -35,7 +35,7 @@ jobs:
           branch_name='preview-${{ github.event.pull_request.number }}'
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
-          git push --set-upstream origin $branch_name
+          git push --set-upstream origin $branch_name || echo echo branch exists remotely
         shell: bash
 
     outputs:

From 26b840f160a3e6f2711486a9fed47b80ffa06bfb Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:30:54 -0400
Subject: [PATCH 29/82] missing paranthesis

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 43a585792..02a219269 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -67,7 +67,7 @@ jobs:
         error_num=$(cat ${{ steps.check_results.outputs.report_path }} | wc -l)
         error_num="$((error_num-1))"
         echo "error_num=$error_num" >> $GITHUB_OUTPUT
-        error_list=$(cat ${{ steps.check_results.outputs.report_path }}
+        error_list=$(cat ${{ steps.check_results.outputs.report_path }})
         echo "error_list=$error_list" >> $GITHUB_OUTPUT
       shell: bash
 

From 46ca8986368440931b27d404d8d916eda118fe99 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:36:18 -0400
Subject: [PATCH 30/82] Make sure its checked out

---
 .github/workflows/check-url.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 02a219269..abf70c2ae 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -50,6 +50,11 @@ jobs:
       image: jhudsl/base_ottr:main
 
     steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
     - name: Run the check
       uses: jhudsl/ottr-reports@main
       id: check_results

From 38091e74427fa7e7dbf5a8c23ba3a80defdb7861 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:42:34 -0400
Subject: [PATCH 31/82] Try mapfile?

---
 .github/workflows/check-url.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index abf70c2ae..62b81c5aa 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -66,13 +66,11 @@ jobs:
     - name: Declare file path and time
       id: check-report
       run: |
-        branch_name='preview-${{ github.event.pull_request.number }}'
         echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
-        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/$branch_name/${{ steps.check_results.outputs.report_path }}" >> $GITHUB_OUTPUT
         error_num=$(cat ${{ steps.check_results.outputs.report_path }} | wc -l)
         error_num="$((error_num-1))"
         echo "error_num=$error_num" >> $GITHUB_OUTPUT
-        error_list=$(cat ${{ steps.check_results.outputs.report_path }})
+        error_list=$(mapfile -t myArray < ${{ steps.check_results.outputs.report_path }})
         echo "error_list=$error_list" >> $GITHUB_OUTPUT
       shell: bash
 

From 8dec79625ee1664caa44151720515f39b5f00018 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:44:53 -0400
Subject: [PATCH 32/82] Add a file

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

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 9316682a7..99b1bcd40 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -38,7 +38,7 @@ jobs:
           branch_name='preview-${{ github.event.pull_request.number }}'
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
-          git push --set-upstream origin $branch_name
+          git push --set-upstream origin $branch_name || echo echo branch exists remotely
         shell: bash
 
     outputs:

From a1fa04a122c1d5be509bb5fb7438ca72f5cde2c3 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:53:10 -0400
Subject: [PATCH 33/82] Didn't fix template issue

---
 .github/ISSUE_TEMPLATE/url-error.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/ISSUE_TEMPLATE/url-error.md b/.github/ISSUE_TEMPLATE/url-error.md
index 0e7f7546e..e740ccbb8 100644
--- a/.github/ISSUE_TEMPLATE/url-error.md
+++ b/.github/ISSUE_TEMPLATE/url-error.md
@@ -5,4 +5,4 @@ labels: url-error
 URL's in this course were just checked and some broken URLs were found.
 
 **Number of errors:** {{ env.ERROR_NUM }}  
-**File where errors are:** {{ env.FILE_PATH }}
+**File where errors are:** {{ env.ERROR_LIST }}

From 3a4dac523e0848257b90272a37efffdfc5543f12 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 20 Sep 2023 15:58:27 -0400
Subject: [PATCH 34/82] Put file link

---
 .github/ISSUE_TEMPLATE/url-error.md |  2 +-
 .github/workflows/check-url.yml     | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/ISSUE_TEMPLATE/url-error.md b/.github/ISSUE_TEMPLATE/url-error.md
index e740ccbb8..fe1319662 100644
--- a/.github/ISSUE_TEMPLATE/url-error.md
+++ b/.github/ISSUE_TEMPLATE/url-error.md
@@ -5,4 +5,4 @@ labels: url-error
 URL's in this course were just checked and some broken URLs were found.
 
 **Number of errors:** {{ env.ERROR_NUM }}  
-**File where errors are:** {{ env.ERROR_LIST }}
+**File where errors are:** [url checks file here]({{ env.FILE_URL }})
diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 62b81c5aa..0eba2c748 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -66,12 +66,10 @@ jobs:
     - name: Declare file path and time
       id: check-report
       run: |
-        echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
         error_num=$(cat ${{ steps.check_results.outputs.report_path }} | wc -l)
         error_num="$((error_num-1))"
         echo "error_num=$error_num" >> $GITHUB_OUTPUT
-        error_list=$(mapfile -t myArray < ${{ steps.check_results.outputs.report_path }})
-        echo "error_list=$error_list" >> $GITHUB_OUTPUT
+        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/$branch_name/${{ steps.check_results.outputs.report_path }}" >> $GITHUB_OUTPUT
       shell: bash
 
     - name: If too many URL errors, then make an issue
@@ -81,7 +79,7 @@ jobs:
         filename: .github/ISSUE_TEMPLATE/url-error.md
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        ERROR_LIST: ${{ steps.check_results.outputs.error_list }}
+        FILE_URL: ${{ steps.check_results.outputs.error_url }}
         ERROR_NUM: ${{ steps.check-report.outputs.error_num }}
 
     - name: Stop if failure
@@ -90,4 +88,6 @@ jobs:
 
     - name: If no URL errors than delete the branch we made
       if: ${{ steps.check-report.outputs.error_num <= 1 }}
-      run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
+      run: |
+        git config --system --add safe.directory "$GITHUB_WORKSPACE"
+        git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"

From 7cd6c56d287866f95b6b965fa007e5a4fdd4d5e1 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 21 Sep 2023 08:09:24 -0400
Subject: [PATCH 35/82] Fix link

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 0eba2c748..888a509e8 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -79,7 +79,7 @@ jobs:
         filename: .github/ISSUE_TEMPLATE/url-error.md
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        FILE_URL: ${{ steps.check_results.outputs.error_url }}
+        FILE_URL: ${{ steps.check-report.outputs.error_url }}
         ERROR_NUM: ${{ steps.check-report.outputs.error_num }}
 
     - name: Stop if failure

From 05563a1c5dd06bd42b219915a1d9c5460c126f6e Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 21 Sep 2023 08:14:49 -0400
Subject: [PATCH 36/82] Fix less than or greater than

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 888a509e8..fd978538c 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -73,7 +73,7 @@ jobs:
       shell: bash
 
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num <= 1 }}
+      if: ${{ steps.check-report.outputs.error_num > 1 }}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md

From da60ae3ef1f213303f7e3c6fe9b7928637b9bb7b Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 21 Sep 2023 08:30:52 -0400
Subject: [PATCH 37/82] Add in a spelling error to check if this works

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 04db84a6e..82b4460d0 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,7 @@
 ## Open-source Tools for Training Resources - OTTR
 
+spling rror
+
 Go to [ottrproject.org](https://www.ottrproject.org/) to get started! :tada:
 
 The purpose of this course template and guide is to make course publishing maintenance across multiple different platforms _less painful_.
@@ -30,4 +32,3 @@ _This template and guide helps you_:
 - Check out our [course on using Leanpub](https://hutchdatascience.org/Using_Leanpub/index.html) for help publishing on this platform.
 - Please take a look at the [code of conduct](./code_of_conduct.md).
 - If you encounter any problems or have ideas for improvements to this template repository or this getting started guide, please [file an issue here](https://github.com/jhudsl/OTTR_Template/issues/new/choose)! Your feedback is very much appreciated.
-

From 2a9b34b78c3e7d94b9969bff98f2c37293d9a16d Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 21 Sep 2023 08:33:56 -0400
Subject: [PATCH 38/82] Add spelling errors to test part 2

---
 01-intro.Rmd | 2 ++
 README.md    | 2 --
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/01-intro.Rmd b/01-intro.Rmd
index 886eb5281..598959894 100644
--- a/01-intro.Rmd
+++ b/01-intro.Rmd
@@ -5,6 +5,8 @@ ottrpal::set_knitr_image_path()
 
 # Introduction
 
+spling rror
+baiusbdfius
 
 ## Motivation
 
diff --git a/README.md b/README.md
index 82b4460d0..44ebd89d1 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,5 @@
 ## Open-source Tools for Training Resources - OTTR
 
-spling rror
-
 Go to [ottrproject.org](https://www.ottrproject.org/) to get started! :tada:
 
 The purpose of this course template and guide is to make course publishing maintenance across multiple different platforms _less painful_.

From 91e68e3cbe0bf308ee83e3db97e64a484a31fd5d Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 21 Sep 2023 08:40:53 -0400
Subject: [PATCH 39/82] Try to fix

---
 .github/workflows/check-url.yml | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index fd978538c..d55e51cf0 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -72,8 +72,17 @@ jobs:
         echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/$branch_name/${{ steps.check_results.outputs.report_path }}" >> $GITHUB_OUTPUT
       shell: bash
 
+    - name: Stop if failure
+      if: steps.check_results.outcome == 'failure'
+      run: exit 1
+
+    - name: Print out error variables
+      run: |
+        echo ${{ steps.check-report.outputs.error_url }}
+        echo ${{ steps.check-report.outputs.error_num }}
+
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num > 1 }}
+      if: ${{ steps.check-report.outputs.error_num => 1 }}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md
@@ -82,12 +91,8 @@ jobs:
         FILE_URL: ${{ steps.check-report.outputs.error_url }}
         ERROR_NUM: ${{ steps.check-report.outputs.error_num }}
 
-    - name: Stop if failure
-      if: steps.check_results.outcome == 'failure'
-      run: exit 1
-
     - name: If no URL errors than delete the branch we made
-      if: ${{ steps.check-report.outputs.error_num <= 1 }}
+      if: ${{ steps.check-report.outputs.error_num < 1 }}
       run: |
         git config --system --add safe.directory "$GITHUB_WORKSPACE"
         git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"

From 418686c88c59c120659ddd0769adaf445d6d1c6e Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 21 Sep 2023 08:44:58 -0400
Subject: [PATCH 40/82] Reverse order or < and =

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index d55e51cf0..ebfd0b418 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -82,7 +82,7 @@ jobs:
         echo ${{ steps.check-report.outputs.error_num }}
 
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num => 1 }}
+      if: ${{ steps.check-report.outputs.error_num >= 1 }}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md

From 6ed286dbff64d934ab180b7e5485b97bf1f4de7e Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 21 Sep 2023 08:50:01 -0400
Subject: [PATCH 41/82] Change branch name

---
 .github/workflows/check-url.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index ebfd0b418..1cc48ed0e 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -23,7 +23,7 @@ jobs:
 
       # Delete the branch if this has been run before
       - name: Delete branch locally and remotely
-        run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
+        run: git push origin --delete preview-spell-error || echo "No branch to delete"
 
       # Make the branch fresh
       - name: Make the branch fresh
@@ -32,10 +32,9 @@ jobs:
           git config --global user.email "itcrtrainingnetwork@gmail.com"
           git config --global user.name "jhudsl-robot"
 
-          branch_name='preview-${{ github.event.pull_request.number }}'
           echo branch doesnt exist
-          git checkout -b $branch_name || echo branch exists
-          git push --set-upstream origin $branch_name || echo echo branch exists remotely
+          git checkout -b preview-spell-error || echo branch exists
+          git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
         shell: bash
 
     outputs:
@@ -69,7 +68,7 @@ jobs:
         error_num=$(cat ${{ steps.check_results.outputs.report_path }} | wc -l)
         error_num="$((error_num-1))"
         echo "error_num=$error_num" >> $GITHUB_OUTPUT
-        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/$branch_name/${{ steps.check_results.outputs.report_path }}" >> $GITHUB_OUTPUT
+        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/preview-spell-error/${{ steps.check_results.outputs.report_path }}" >> $GITHUB_OUTPUT
       shell: bash
 
     - name: Stop if failure
@@ -95,4 +94,4 @@ jobs:
       if: ${{ steps.check-report.outputs.error_num < 1 }}
       run: |
         git config --system --add safe.directory "$GITHUB_WORKSPACE"
-        git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
+        git push origin --delete preview-spell-error || echo "No branch to delete"

From 500506c456288dcd372042b6a20ed550731683c1 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 21 Sep 2023 09:05:43 -0400
Subject: [PATCH 42/82] Make sure branch is checked out

---
 .github/workflows/check-url.yml | 36 ++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 1cc48ed0e..f95d7f5cb 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -21,22 +21,6 @@ jobs:
         with:
             files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
 
-      # Delete the branch if this has been run before
-      - name: Delete branch locally and remotely
-        run: git push origin --delete preview-spell-error || echo "No branch to delete"
-
-      # Make the branch fresh
-      - name: Make the branch fresh
-        run: |
-          git config --global --add safe.directory $GITHUB_WORKSPACE
-          git config --global user.email "itcrtrainingnetwork@gmail.com"
-          git config --global user.name "jhudsl-robot"
-
-          echo branch doesnt exist
-          git checkout -b preview-spell-error || echo branch exists
-          git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
-        shell: bash
-
     outputs:
       toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"
 
@@ -54,6 +38,22 @@ jobs:
       with:
         fetch-depth: 0
 
+    # Delete the branch if this has been run before
+    - name: Delete branch locally and remotely
+      run: git push origin --delete preview-spell-error || echo "No branch to delete"
+
+    # Make the branch fresh
+    - name: Make the branch fresh
+      run: |
+        git config --global --add safe.directory $GITHUB_WORKSPACE
+        git config --global user.email "itcrtrainingnetwork@gmail.com"
+        git config --global user.name "jhudsl-robot"
+
+        echo branch doesnt exist
+        git checkout -b preview-spell-error || echo branch exists
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+      shell: bash
+
     - name: Run the check
       uses: jhudsl/ottr-reports@main
       id: check_results
@@ -65,10 +65,10 @@ jobs:
     - name: Declare file path and time
       id: check-report
       run: |
-        error_num=$(cat ${{ steps.check_results.outputs.report_path }} | wc -l)
+        error_num=$(cat check_reports/url_checks.tsv | wc -l)
         error_num="$((error_num-1))"
         echo "error_num=$error_num" >> $GITHUB_OUTPUT
-        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/preview-spell-error/${{ steps.check_results.outputs.report_path }}" >> $GITHUB_OUTPUT
+        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/preview-spell-error/check_reports/url_checks.tsv" >> $GITHUB_OUTPUT
       shell: bash
 
     - name: Stop if failure

From c3f6ac84446967643b72a564f6437b19277dbc95 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 21 Sep 2023 09:12:29 -0400
Subject: [PATCH 43/82] Look for an issue

---
 .github/workflows/check-url.yml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index f95d7f5cb..d6a09da9c 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -80,8 +80,16 @@ jobs:
         echo ${{ steps.check-report.outputs.error_url }}
         echo ${{ steps.check-report.outputs.error_num }}
 
+    - name: Check if Issue Exists
+      uses: nickderobertis/check-if-issue-exists-action@master
+      id: check_if_issue_exists
+      with:
+        repo: ${GITHUB_REPOSITORY}
+        token: ${{ secrets.GITHUB_TOKEN }}
+        title: Broken URLs found in the course!
+
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num >= 1 }}
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.check_if_issue_exists.outputs.exists == 'false'}}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md

From 641875a852b37e0136bcb96d99650f8b13ab1c52 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 21 Sep 2023 09:28:59 -0400
Subject: [PATCH 44/82] Trying a different issue finder

---
 .github/workflows/check-url.yml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index d6a09da9c..6918eb538 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -80,16 +80,17 @@ jobs:
         echo ${{ steps.check-report.outputs.error_url }}
         echo ${{ steps.check-report.outputs.error_num }}
 
-    - name: Check if Issue Exists
-      uses: nickderobertis/check-if-issue-exists-action@master
-      id: check_if_issue_exists
+    - name: Find issues
+      uses: actions-cool/issues-helper@v3
+      id: find-issue
       with:
-        repo: ${GITHUB_REPOSITORY}
+        actions: 'find-issues'
         token: ${{ secrets.GITHUB_TOKEN }}
-        title: Broken URLs found in the course!
+        issue-state: 'open'
+        title-includes: 'Broken URLs found in the course!'
 
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.check_if_issue_exists.outputs.exists == 'false'}}
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.exists == 'false'}}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md

From 3c24629588eadb5651140ce4c0180b021ad0181e Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 22 Sep 2023 08:27:54 -0400
Subject: [PATCH 45/82] Gonna make my own issue finder

---
 .github/workflows/check-url.yml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 6918eb538..96e496b95 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -81,13 +81,6 @@ jobs:
         echo ${{ steps.check-report.outputs.error_num }}
 
     - name: Find issues
-      uses: actions-cool/issues-helper@v3
-      id: find-issue
-      with:
-        actions: 'find-issues'
-        token: ${{ secrets.GITHUB_TOKEN }}
-        issue-state: 'open'
-        title-includes: 'Broken URLs found in the course!'
 
     - name: If too many URL errors, then make an issue
       if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.exists == 'false'}}

From 590933f492104f532a63bcfc024e55883934fc01 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 22 Sep 2023 10:53:33 -0400
Subject: [PATCH 46/82] Add find issue bits

---
 .github/workflows/check-url.yml |  7 +++++-
 scripts/find_issue.R            | 44 +++++++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+), 1 deletion(-)
 create mode 100644 scripts/find_issue.R

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 96e496b95..c516c317f 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -81,9 +81,14 @@ jobs:
         echo ${{ steps.check-report.outputs.error_num }}
 
     - name: Find issues
+      id: find-issue
+      run: |
+        issue_exists=$(Rscript --vanilla scripts/find_issue.R --repo "$GITHUB_REPOSITORY" --git_pat "$GH_PAT")
+        echo URL issue exists: $issue_exists
+        echo "issue_exists=$issue_exists" >> $GITHUB_OUTPUT
 
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.exists == 'false'}}
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_exists == 'FALSE'}}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md
diff --git a/scripts/find_issue.R b/scripts/find_issue.R
new file mode 100644
index 000000000..c242ffdbc
--- /dev/null
+++ b/scripts/find_issue.R
@@ -0,0 +1,44 @@
+#!/usr/bin/env Rscript
+
+# Written by Candace Savonen Sept 2021
+
+if (!("optparse" %in% installed.packages())){
+  install.packages("optparse")
+}
+
+library(optparse)
+
+option_list <- list(
+  optparse::make_option(
+    c("--repo"),
+    type = "character",
+    default = NULL,
+    help = "GitHub repository name, e.g. jhudsl/OTTR_Template",
+  ),
+  optparse::make_option(
+    c("--git_pat"),
+    type = "character",
+    default = NULL,
+    help = "GitHub personal access token",
+  )
+)
+
+# Read the arguments passed
+opt_parser <- optparse::OptionParser(option_list = option_list)
+opt <- optparse::parse_args(opt_parser)
+
+repo <- opt$repo
+git_pat <- opt$git_pat
+
+if (!is.character(repo)) {
+  repo <- as.character(repo)
+}
+
+install.packages('githubr')
+
+issue_titles <- get_issues(opt$repo)$title, git_pat = opt$git_pat)
+
+issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
+
+# Print out the result
+write(issue_exists, stdout())

From feb31b876be8742c663093c108cda82082286567 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 22 Sep 2023 11:04:12 -0400
Subject: [PATCH 47/82] Add CRAN mirror

---
 scripts/find_issue.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index c242ffdbc..a6f4e3574 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -34,7 +34,7 @@ if (!is.character(repo)) {
   repo <- as.character(repo)
 }
 
-install.packages('githubr')
+install.packages('githubr', repos='http://cran.us.r-project.org')
 
 issue_titles <- get_issues(opt$repo)$title, git_pat = opt$git_pat)
 

From 1e50a2d9c0e748de212854e87bb17583dad4e21d Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 22 Sep 2023 11:25:58 -0400
Subject: [PATCH 48/82] Fix syntax

---
 scripts/find_issue.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index a6f4e3574..d00fefcec 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -36,7 +36,7 @@ if (!is.character(repo)) {
 
 install.packages('githubr', repos='http://cran.us.r-project.org')
 
-issue_titles <- get_issues(opt$repo)$title, git_pat = opt$git_pat)
+issue_titles <- get_issues(opt$repo, git_pat = opt$git_pat)$title
 
 issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
 

From e08c9e103e0ae96f3c836d4b97c4a84d76bd3fd3 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 22 Sep 2023 13:07:49 -0400
Subject: [PATCH 49/82] Delete spelling errors

---
 01-intro.Rmd | 2 --
 1 file changed, 2 deletions(-)

diff --git a/01-intro.Rmd b/01-intro.Rmd
index 598959894..886eb5281 100644
--- a/01-intro.Rmd
+++ b/01-intro.Rmd
@@ -5,8 +5,6 @@ ottrpal::set_knitr_image_path()
 
 # Introduction
 
-spling rror
-baiusbdfius
 
 ## Motivation
 

From a3e2dd93cd308ac6b5b2f838033a5f6816156979 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Tue, 24 Oct 2023 08:28:53 -0400
Subject: [PATCH 50/82] Add a missing githubr::

---
 scripts/find_issue.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index d00fefcec..7551a179b 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -36,7 +36,7 @@ if (!is.character(repo)) {
 
 install.packages('githubr', repos='http://cran.us.r-project.org')
 
-issue_titles <- get_issues(opt$repo, git_pat = opt$git_pat)$title
+issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
 
 issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
 

From 3df3e40b966f38eaffea634d1b8bfa3cbeff8344 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Tue, 24 Oct 2023 10:01:54 -0400
Subject: [PATCH 51/82] Install from github

---
 scripts/find_issue.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 7551a179b..8d7cc34b6 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -34,7 +34,7 @@ if (!is.character(repo)) {
   repo <- as.character(repo)
 }
 
-install.packages('githubr', repos='http://cran.us.r-project.org')
+remotes::install_github("fhdsl/githubr", auth_token = opt$git_pat)
 
 issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
 

From c640fe33b75cf3498e270c5f8043e455c7ec2eca Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Tue, 24 Oct 2023 10:09:39 -0400
Subject: [PATCH 52/82] Fix GH_PAT

---
 .github/workflows/check-url.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index c516c317f..2329561c2 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -82,6 +82,8 @@ jobs:
 
     - name: Find issues
       id: find-issue
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
       run: |
         issue_exists=$(Rscript --vanilla scripts/find_issue.R --repo "$GITHUB_REPOSITORY" --git_pat "$GH_PAT")
         echo URL issue exists: $issue_exists

From ebc0d47ffac742e8082d4c012525007e202c1c8f Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Tue, 24 Oct 2023 10:18:39 -0400
Subject: [PATCH 53/82] Install from CRAN again

---
 scripts/find_issue.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 8d7cc34b6..7551a179b 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -34,7 +34,7 @@ if (!is.character(repo)) {
   repo <- as.character(repo)
 }
 
-remotes::install_github("fhdsl/githubr", auth_token = opt$git_pat)
+install.packages('githubr', repos='http://cran.us.r-project.org')
 
 issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
 

From 1580cc847a27e623382b485aa3c1e048a3c09f81 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Tue, 24 Oct 2023 11:03:22 -0400
Subject: [PATCH 54/82] Install from github but use devtools

---
 scripts/find_issue.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 7551a179b..f9661da57 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -34,7 +34,8 @@ if (!is.character(repo)) {
   repo <- as.character(repo)
 }
 
-install.packages('githubr', repos='http://cran.us.r-project.org')
+# install.packages('githubr', repos='http://cran.us.r-project.org')
+devtools::install_github("fhdsl/githubr", auth_token = opt$git_pat)
 
 issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
 

From cde9b610a2436f12cc4c8b26a62614ad35461bad Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Tue, 24 Oct 2023 11:12:13 -0400
Subject: [PATCH 55/82] dependencies = TRUE

---
 scripts/find_issue.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index f9661da57..2baf95e5d 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -35,11 +35,11 @@ if (!is.character(repo)) {
 }
 
 # install.packages('githubr', repos='http://cran.us.r-project.org')
-devtools::install_github("fhdsl/githubr", auth_token = opt$git_pat)
+devtools::install_github("fhdsl/githubr", auth_token = opt$git_pat, dependencies = TRUE)
 
 issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
 
 issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
 
 # Print out the result
-write(issue_exists, stdout())
+write(as.character(issue_exists), stdout())

From 0d97f4a622dfa68d11cd67d908ef3b990fd13310 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Tue, 24 Oct 2023 14:04:22 -0400
Subject: [PATCH 56/82] Install from CRAN instead

---
 scripts/find_issue.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 2baf95e5d..9f3b3ee3d 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -34,8 +34,8 @@ if (!is.character(repo)) {
   repo <- as.character(repo)
 }
 
-# install.packages('githubr', repos='http://cran.us.r-project.org')
-devtools::install_github("fhdsl/githubr", auth_token = opt$git_pat, dependencies = TRUE)
+install.packages('githubr', repos='http://cran.us.r-project.org')
+# devtools::install_github("fhdsl/githubr", auth_token = opt$git_pat, dependencies = TRUE)
 
 issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
 

From 77848065a7af1251ebe64844e61b7afde4ec2abe Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 25 Oct 2023 08:38:51 -0400
Subject: [PATCH 57/82] Test variables

---
 .github/workflows/check-url.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 2329561c2..ba7705f41 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -85,7 +85,9 @@ jobs:
       env:
         GH_PAT: ${{ secrets.GH_PAT }}
       run: |
-        issue_exists=$(Rscript --vanilla scripts/find_issue.R --repo "$GITHUB_REPOSITORY" --git_pat "$GH_PAT")
+        echo "$GH_PAT"
+        echo "$GITHUB_REPOSITORY"
+        issue_exists=$(Rscript --vanilla scripts/find_issue.R --repo $GITHUB_REPOSITORY --git_pat $GH_PAT)
         echo URL issue exists: $issue_exists
         echo "issue_exists=$issue_exists" >> $GITHUB_OUTPUT
 

From a04720a9963ce1333319708b3996992dcc3c1c00 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 2 Nov 2023 13:44:28 -0400
Subject: [PATCH 58/82] Retrigger a run for GHA

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

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index ba7705f41..6320efa5f 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -20,7 +20,6 @@ jobs:
         uses: doughepi/yaml-env-action@v1.0.0
         with:
             files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
-
     outputs:
       toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"
 

From 891d5bed829b08667c4837c408a9e4ac5c07722f Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 2 Nov 2023 13:53:35 -0400
Subject: [PATCH 59/82] Print out session info

---
 scripts/find_issue.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 9f3b3ee3d..2cad65957 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -42,4 +42,4 @@ issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
 issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
 
 # Print out the result
-write(as.character(issue_exists), stdout())
+write(sessionInfo(), stdout())

From 918083df3264c942f73984b8788f164a9de5b3ba Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 2 Nov 2023 13:54:24 -0400
Subject: [PATCH 60/82] Actually what I did won't work!

---
 scripts/find_issue.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 2cad65957..fe0a8ff61 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -23,6 +23,9 @@ option_list <- list(
   )
 )
 
+# Print out the result
+write(sessionInfo(), stdout())
+
 # Read the arguments passed
 opt_parser <- optparse::OptionParser(option_list = option_list)
 opt <- optparse::parse_args(opt_parser)
@@ -42,4 +45,4 @@ issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
 issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
 
 # Print out the result
-write(sessionInfo(), stdout())
+write(as.character(issue_exists), stdout())

From 3b2dc08332282f6220e329b486e06c29bfff05dc Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 2 Nov 2023 13:57:17 -0400
Subject: [PATCH 61/82] use cat() instead

---
 scripts/find_issue.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index fe0a8ff61..21dd39004 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -24,7 +24,7 @@ option_list <- list(
 )
 
 # Print out the result
-write(sessionInfo(), stdout())
+cat(sessionInfo())
 
 # Read the arguments passed
 opt_parser <- optparse::OptionParser(option_list = option_list)

From 3dde5185e39c9c880fb535de6d85bccec3ccd246 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 2 Nov 2023 14:37:09 -0400
Subject: [PATCH 62/82] unlist

---
 scripts/find_issue.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 21dd39004..cd300a1a0 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -24,7 +24,7 @@ option_list <- list(
 )
 
 # Print out the result
-cat(sessionInfo())
+unlist(sessionInfo())
 
 # Read the arguments passed
 opt_parser <- optparse::OptionParser(option_list = option_list)

From cc733bad1af05f9ad95abf194a54cb2a1792833f Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 2 Nov 2023 14:40:58 -0400
Subject: [PATCH 63/82] I need cat() too

---
 scripts/find_issue.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index cd300a1a0..3053c6f1b 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -24,7 +24,7 @@ option_list <- list(
 )
 
 # Print out the result
-unlist(sessionInfo())
+cat(unlist(sessionInfo()))
 
 # Read the arguments passed
 opt_parser <- optparse::OptionParser(option_list = option_list)

From 7d6e766e93f83230fb9fa47c234d21b1f78ceccc Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 2 Nov 2023 14:45:40 -0400
Subject: [PATCH 64/82] Why is GHA not printing this out? Try message()

---
 scripts/find_issue.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 3053c6f1b..366ddd8cd 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -24,7 +24,7 @@ option_list <- list(
 )
 
 # Print out the result
-cat(unlist(sessionInfo()))
+message(unlist(sessionInfo()))
 
 # Read the arguments passed
 opt_parser <- optparse::OptionParser(option_list = option_list)

From 4c489387ea3c521f439b0eb64cb536262bcc28c7 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 2 Nov 2023 14:54:18 -0400
Subject: [PATCH 65/82] Save session info to a file and archive upload it

---
 .github/workflows/check-url.yml | 8 ++++++++
 scripts/find_issue.R            | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 6320efa5f..680c28f23 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -90,6 +90,14 @@ jobs:
         echo URL issue exists: $issue_exists
         echo "issue_exists=$issue_exists" >> $GITHUB_OUTPUT
 
+    # We want to retrieve this file after this runs so we can see what spell check errors were detected
+    - name: Archive session info 
+      uses: actions/upload-artifact@v3
+      # These arguments underneath `with` are generally action specific so we have to check the documentation: https://github.com/marketplace/actions/upload-a-build-artifact
+      with:
+        name: session_info.txt
+        path: session_info.txt
+
     - name: If too many URL errors, then make an issue
       if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_exists == 'FALSE'}}
       uses: JasonEtco/create-an-issue@v2
diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 366ddd8cd..1baface59 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -24,7 +24,7 @@ option_list <- list(
 )
 
 # Print out the result
-message(unlist(sessionInfo()))
+write(unlist(sessionInfo()), "session_info.txt")
 
 # Read the arguments passed
 opt_parser <- optparse::OptionParser(option_list = option_list)

From 8403a7e200a22a688765122d90642d3aced6aa05 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 2 Nov 2023 14:56:19 -0400
Subject: [PATCH 66/82] Shut off the other things so this step completes

---
 scripts/find_issue.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 1baface59..195914376 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -40,9 +40,9 @@ if (!is.character(repo)) {
 install.packages('githubr', repos='http://cran.us.r-project.org')
 # devtools::install_github("fhdsl/githubr", auth_token = opt$git_pat, dependencies = TRUE)
 
-issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
+# issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
 
-issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
+#issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
 
 # Print out the result
 write(as.character(issue_exists), stdout())

From 8a51b458dc6496047e1bd581d0394b1a0386d892 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 2 Nov 2023 15:00:00 -0400
Subject: [PATCH 67/82] Comment out one more step

---
 scripts/find_issue.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 195914376..cf287a7e1 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -37,7 +37,7 @@ if (!is.character(repo)) {
   repo <- as.character(repo)
 }
 
-install.packages('githubr', repos='http://cran.us.r-project.org')
+# install.packages('githubr', repos='http://cran.us.r-project.org')
 # devtools::install_github("fhdsl/githubr", auth_token = opt$git_pat, dependencies = TRUE)
 
 # issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
@@ -45,4 +45,4 @@ install.packages('githubr', repos='http://cran.us.r-project.org')
 #issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
 
 # Print out the result
-write(as.character(issue_exists), stdout())
+# write(as.character(issue_exists), stdout())

From d76574b097df294f99271c07442e9427fbda0671 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 08:17:17 -0500
Subject: [PATCH 68/82] Order dictionary.txt

---
 OTTR_template.Rproj      | 17 ++++++++++++++++
 resources/dictionary.txt | 42 ++++++++++++++++++++++++++++++++++++----
 2 files changed, 55 insertions(+), 4 deletions(-)
 create mode 100644 OTTR_template.Rproj

diff --git a/OTTR_template.Rproj b/OTTR_template.Rproj
new file mode 100644
index 000000000..628359e14
--- /dev/null
+++ b/OTTR_template.Rproj
@@ -0,0 +1,17 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+
+BuildType: Website
diff --git a/resources/dictionary.txt b/resources/dictionary.txt
index e3afe6f18..1520d003f 100644
--- a/resources/dictionary.txt
+++ b/resources/dictionary.txt
@@ -1,33 +1,67 @@
 AnVIL
+Audiographer
+Audiography
+automagic
 BIPOC
 Bloomberg
 Bookdown
+chapt
 Coursera
+creativecommons
 css
 Datatrail
 DataTrail
+DISCOVERABLE
 Dockerfile
 Dockerhub
 dropdown
+enforceability
+faq
 favicon
+FirstName
+Funder
+fyi
 GDSCN
-GitHub
-Github
+Generis
 GH
+Github
+GitHub
+https
+ies
+iframe
+immunities
 impactful
 ITCR
 itcrtraining
 ITN
-fyi
+LastName
 Leanpub
+Licensor
+LICENSOR
 Markua
 mentorship
+MERCHANTABILITY
+Muschelli
 NCI
 NHGRI
+OTTR
 ottrpal
+ottrproject
 Pandoc
+png
+pre
+reproducibility
+rmarkdown
+RMarkdown
+Savonen
+sexualized
+socio
+synched
+tada
 UE
 UE5
-reproducibility
 underserved
+Videographer
+Videography
+WIPO	
 www

From 7baf79ba494123ffe80ea142a1b997e6f7ce9b7b Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 08:18:02 -0500
Subject: [PATCH 69/82] Add broken URL

---
 01-intro.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/01-intro.Rmd b/01-intro.Rmd
index 886eb5281..ced897ddb 100644
--- a/01-intro.Rmd
+++ b/01-intro.Rmd
@@ -4,7 +4,7 @@ ottrpal::set_knitr_image_path()
 ```
 
 # Introduction
-
+https://ahuidshiushiufhs.com
 
 ## Motivation
 

From 45eb1a191a1286ca77cfb9b0fe460005e5b669ea Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 08:22:12 -0500
Subject: [PATCH 70/82] Make it so blank is the logic

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

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 680c28f23..bef6d6697 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -91,7 +91,7 @@ jobs:
         echo "issue_exists=$issue_exists" >> $GITHUB_OUTPUT
 
     # We want to retrieve this file after this runs so we can see what spell check errors were detected
-    - name: Archive session info 
+    - name: Archive session info
       uses: actions/upload-artifact@v3
       # These arguments underneath `with` are generally action specific so we have to check the documentation: https://github.com/marketplace/actions/upload-a-build-artifact
       with:
@@ -99,7 +99,7 @@ jobs:
         path: session_info.txt
 
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_exists == 'FALSE'}}
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_exists == ''}}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md

From f8d555e1b2d88e9b610947e769eb3549969a8a56 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 08:25:03 -0500
Subject: [PATCH 71/82] Just retrigger the check

---
 01-intro.Rmd | 1 +
 1 file changed, 1 insertion(+)

diff --git a/01-intro.Rmd b/01-intro.Rmd
index ced897ddb..622874d63 100644
--- a/01-intro.Rmd
+++ b/01-intro.Rmd
@@ -6,6 +6,7 @@ ottrpal::set_knitr_image_path()
 # Introduction
 https://ahuidshiushiufhs.com
 
+
 ## Motivation
 
 

From a2ffbceb76cdfbade44332387833622680e79f3f Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 08:31:55 -0500
Subject: [PATCH 72/82] Try again

---
 .github/workflows/check-url.yml | 2 +-
 scripts/find_issue.R            | 9 ++++-----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index bef6d6697..44d54e8e3 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -99,7 +99,7 @@ jobs:
         path: session_info.txt
 
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_exists == ''}}
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_exists == TRUE}}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md
diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index cf287a7e1..4214162a6 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -37,12 +37,11 @@ if (!is.character(repo)) {
   repo <- as.character(repo)
 }
 
-# install.packages('githubr', repos='http://cran.us.r-project.org')
-# devtools::install_github("fhdsl/githubr", auth_token = opt$git_pat, dependencies = TRUE)
+install.packages('githubr', repos='http://cran.us.r-project.org')
 
-# issue_titles <- githubr::get_issues(opt$repo, git_pat = opt$git_pat)$title
+issue_titles <- githubr::get_issues(repo, git_pat = git_pat)$title
 
-#issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
+issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
 
 # Print out the result
-# write(as.character(issue_exists), stdout())
+write(as.character(issue_exists), stdout())

From 18ee7b48f092d013db24410d5a685c64f9a99d9c Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 08:35:29 -0500
Subject: [PATCH 73/82] fix true

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 44d54e8e3..f6198dfd6 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -99,7 +99,7 @@ jobs:
         path: session_info.txt
 
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_exists == TRUE}}
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_exists == 'true'}}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md

From dc6c371fdbe0c0474a8bacaf713c2d66bbf2ab23 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 08:42:46 -0500
Subject: [PATCH 74/82] drop quotes

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index f6198dfd6..983a435cc 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -99,7 +99,7 @@ jobs:
         path: session_info.txt
 
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_exists == 'true'}}
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_exists == true}}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md

From b85042a5fee26bf1b876ff3b52dcacb3f22538fd Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 08:51:09 -0500
Subject: [PATCH 75/82] Let's try this

---
 scripts/find_issue.R | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 4214162a6..f3783e719 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -23,9 +23,6 @@ option_list <- list(
   )
 )
 
-# Print out the result
-write(unlist(sessionInfo()), "session_info.txt")
-
 # Read the arguments passed
 opt_parser <- optparse::OptionParser(option_list = option_list)
 opt <- optparse::parse_args(opt_parser)
@@ -37,9 +34,11 @@ if (!is.character(repo)) {
   repo <- as.character(repo)
 }
 
-install.packages('githubr', repos='http://cran.us.r-project.org')
+install.packages('gh', repos='http://cran.us.r-project.org')
 
-issue_titles <- githubr::get_issues(repo, git_pat = git_pat)$title
+my_issues <- gh::gh("GET https://api.github.com/repos/{repo}/issues", repo = repo_name, .token = git_pat, per_page = "max")
+my_issues <- unlist(my_issues)
+issue_titles <- my_issues[which(names(my_issues) == "title")]
 
 issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
 

From e364016f60694bea10e412d8a47e963f0d2f0c6e Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 08:54:07 -0500
Subject: [PATCH 76/82] repo_name -> repo

---
 scripts/find_issue.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index f3783e719..4f25b6038 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -36,7 +36,7 @@ if (!is.character(repo)) {
 
 install.packages('gh', repos='http://cran.us.r-project.org')
 
-my_issues <- gh::gh("GET https://api.github.com/repos/{repo}/issues", repo = repo_name, .token = git_pat, per_page = "max")
+my_issues <- gh::gh("GET https://api.github.com/repos/{repo}/issues", repo = repo, .token = git_pat, per_page = "max")
 my_issues <- unlist(my_issues)
 issue_titles <- my_issues[which(names(my_issues) == "title")]
 

From 3093c4c4cbfd674b287ae6f251e674abb4376c3f Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 08:59:43 -0500
Subject: [PATCH 77/82] change per_page

---
 scripts/find_issue.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 4f25b6038..7a3f753f7 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -36,7 +36,10 @@ if (!is.character(repo)) {
 
 install.packages('gh', repos='http://cran.us.r-project.org')
 
-my_issues <- gh::gh("GET https://api.github.com/repos/{repo}/issues", repo = repo, .token = git_pat, per_page = "max")
+my_issues <- gh::gh("GET https://api.github.com/repos/{repo}/issues", 
+                    repo = repo, 
+                    .token = git_pat, 
+                    per_page = 100)
 my_issues <- unlist(my_issues)
 issue_titles <- my_issues[which(names(my_issues) == "title")]
 

From 526c91712e7873779b2c3bb96984ed725e40ade6 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 09:09:06 -0500
Subject: [PATCH 78/82] mysterious error

---
 .github/workflows/check-url.yml | 12 ++----------
 scripts/find_issue.R            | 10 +++++-----
 2 files changed, 7 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 983a435cc..9e1c790ea 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -88,18 +88,10 @@ jobs:
         echo "$GITHUB_REPOSITORY"
         issue_exists=$(Rscript --vanilla scripts/find_issue.R --repo $GITHUB_REPOSITORY --git_pat $GH_PAT)
         echo URL issue exists: $issue_exists
-        echo "issue_exists=$issue_exists" >> $GITHUB_OUTPUT
-
-    # We want to retrieve this file after this runs so we can see what spell check errors were detected
-    - name: Archive session info
-      uses: actions/upload-artifact@v3
-      # These arguments underneath `with` are generally action specific so we have to check the documentation: https://github.com/marketplace/actions/upload-a-build-artifact
-      with:
-        name: session_info.txt
-        path: session_info.txt
+        echo "issue_existence=$issue_exists" >> $GITHUB_OUTPUT
 
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_exists == true}}
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_existence >= 1}}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md
diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 7a3f753f7..d9646a36a 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -36,14 +36,14 @@ if (!is.character(repo)) {
 
 install.packages('gh', repos='http://cran.us.r-project.org')
 
-my_issues <- gh::gh("GET https://api.github.com/repos/{repo}/issues", 
-                    repo = repo, 
-                    .token = git_pat, 
-                    per_page = 100)
+my_issues <- gh::gh("GET https://api.github.com/repos/{repo}/issues",
+                    repo = repo,
+                    .token = git_pat)
+
 my_issues <- unlist(my_issues)
 issue_titles <- my_issues[which(names(my_issues) == "title")]
 
 issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
 
 # Print out the result
-write(as.character(issue_exists), stdout())
+write(length(issue_exists), stdout())

From 2405c61b1f48ece8c8308e088a4a56882fd3f184 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 09:17:03 -0500
Subject: [PATCH 79/82] Print out clues

---
 scripts/find_issue.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index d9646a36a..4178fde8e 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -40,6 +40,9 @@ my_issues <- gh::gh("GET https://api.github.com/repos/{repo}/issues",
                     repo = repo,
                     .token = git_pat)
 
+# Print out the result
+write(my_issues, stdout())
+
 my_issues <- unlist(my_issues)
 issue_titles <- my_issues[which(names(my_issues) == "title")]
 

From 5107f2d4726e88db999a19c28af52d25aa432a40 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 09:24:33 -0500
Subject: [PATCH 80/82] Update script

---
 scripts/find_issue.R | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/scripts/find_issue.R b/scripts/find_issue.R
index 4178fde8e..9661a569b 100644
--- a/scripts/find_issue.R
+++ b/scripts/find_issue.R
@@ -34,19 +34,22 @@ if (!is.character(repo)) {
   repo <- as.character(repo)
 }
 
-install.packages('gh', repos='http://cran.us.r-project.org')
-
-my_issues <- gh::gh("GET https://api.github.com/repos/{repo}/issues",
-                    repo = repo,
-                    .token = git_pat)
+# Github api get
+result <- httr::GET(
+  paste0("https://api.github.com/repos/", repo, "/issues"),
+  httr::add_headers(Authorization = paste0("Bearer ", git_pat)),
+  httr::accept_json()
+)
 
-# Print out the result
-write(my_issues, stdout())
+if (httr::status_code(result) != 200) {
+  httr::stop_for_status(result)
+}
 
-my_issues <- unlist(my_issues)
-issue_titles <- my_issues[which(names(my_issues) == "title")]
+# Process and return results
+result_content <- httr::content(result, "text")
+result_list <- jsonlite::fromJSON(result_content)
 
-issue_exists <- any(grep('Broken URLs found in the course!', issue_titles))
+issue_exists <- length(grep('Broken URLs found in the course!', result_list$title))
 
 # Print out the result
-write(length(issue_exists), stdout())
+write(issue_exists, stdout())

From 92a64fa8896484bb31457879a408eee59e7b69e7 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 09:30:04 -0500
Subject: [PATCH 81/82] Fix logic

---
 .github/workflows/check-url.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 9e1c790ea..cc930205d 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -91,7 +91,7 @@ jobs:
         echo "issue_existence=$issue_exists" >> $GITHUB_OUTPUT
 
     - name: If too many URL errors, then make an issue
-      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_existence >= 1}}
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_existence == 0}}
       uses: JasonEtco/create-an-issue@v2
       with:
         filename: .github/ISSUE_TEMPLATE/url-error.md

From 3bf5ac4f0b2e34246f1d6600276ef18f73f46aee Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 29 Feb 2024 09:36:12 -0500
Subject: [PATCH 82/82] fix so runs once a month

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

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index cc930205d..493ea2bef 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -1,9 +1,9 @@
 name: Periodic URL Check
 
 on:
-  pull_request:
+  workflow_dispatch:
   schedule:
-    - cron: '*/2 * * * *'
+    - cron: '0 0 1 * *'
 
 jobs:
   set-up: