From 810bf421d4f5a07ed4ee1611e226709ae606f303 Mon Sep 17 00:00:00 2001
From: John Turner <turnerjp@nigms.nih.gov>
Date: Mon, 18 Nov 2024 17:03:13 +0000
Subject: [PATCH 1/2] fix the workflows so they pull the correct version.

---
 .github/workflows/check-links.yaml   | 7 ++-----
 .github/workflows/notebook-lint.yaml | 2 +-
 reusable-workflow-repo               | 1 -
 3 files changed, 3 insertions(+), 7 deletions(-)
 delete mode 160000 reusable-workflow-repo

diff --git a/.github/workflows/check-links.yaml b/.github/workflows/check-links.yaml
index 8869a77..166bb1c 100644
--- a/.github/workflows/check-links.yaml
+++ b/.github/workflows/check-links.yaml
@@ -4,13 +4,10 @@ on:
   pull_request:
   workflow_dispatch:
 
-env:
-  workflow_ref: main
 
 jobs:
   link_check:
     name: 'Link Check'
-    uses: NIGMS/NIGMS-Sandbox/.github/workflows/check-links.yaml@${{env.workflow_ref}}
+    uses: NIGMS/NIGMS-Sandbox/.github/workflows/check-links.yaml@main
     with:
-      repo_link_ignore_list: ""
-      workflow_ref: ${{env.workflow_ref}}
\ No newline at end of file
+      repo_link_ignore_list: ""
\ No newline at end of file
diff --git a/.github/workflows/notebook-lint.yaml b/.github/workflows/notebook-lint.yaml
index 2038a72..507ba19 100644
--- a/.github/workflows/notebook-lint.yaml
+++ b/.github/workflows/notebook-lint.yaml
@@ -11,4 +11,4 @@ jobs:
     name: 'Linting'
     uses: NIGMS/NIGMS-Sandbox/.github/workflows/notebook-lint.yaml@main
     with:
-      directory: .
+      directory: .
\ No newline at end of file
diff --git a/reusable-workflow-repo b/reusable-workflow-repo
deleted file mode 160000
index c4c1c85..0000000
--- a/reusable-workflow-repo
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit c4c1c8516d686f25a3d8d91004d897f86b1b7346

From dbb241e85188e9315f6ba7bff2300f70b61851a8 Mon Sep 17 00:00:00 2001
From: github-action <cbiit-github-action@github.com>
Date: Mon, 18 Nov 2024 17:03:44 +0000
Subject: [PATCH 2/2] Github Action: Lint Notebooks

---
 tutorial_1-bismark.ipynb | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/tutorial_1-bismark.ipynb b/tutorial_1-bismark.ipynb
index b5965d8..3561f4c 100644
--- a/tutorial_1-bismark.ipynb
+++ b/tutorial_1-bismark.ipynb
@@ -818,11 +818,7 @@
    ]
   }
  ],
- "metadata": {
-  "language_info": {
-   "name": "python"
-  }
- },
+ "metadata": {},
  "nbformat": 4,
  "nbformat_minor": 5
 }