From 533407dccba817ce100ab6c0d69797fb6c18395c Mon Sep 17 00:00:00 2001
From: bmeluch <107661103+bmeluch@users.noreply.github.com>
Date: Thu, 13 Feb 2025 13:23:15 -0800
Subject: [PATCH 1/2] change colab script download links to point to main

---
 NOM_visualizations/R/NOM_R_notebook.ipynb                     | 4 ++--
 .../R/taxonomic_dist_soil_layer_R.ipynb                       | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/NOM_visualizations/R/NOM_R_notebook.ipynb b/NOM_visualizations/R/NOM_R_notebook.ipynb
index 07b19a6e..180a1c8d 100644
--- a/NOM_visualizations/R/NOM_R_notebook.ipynb
+++ b/NOM_visualizations/R/NOM_R_notebook.ipynb
@@ -16,7 +16,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {
     "metadata": {},
     "vscode": {
@@ -37,7 +37,7 @@
     "\n",
     "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") == \"\") source(\"../../utility_functions.R\")\n",
     "\n",
-    "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") != \"\") source(\"http://raw.githubusercontent.com/microbiomedata/nmdc_notebooks/refs/heads/90-modularize-r-api-wrapper-functions/utility_functions.R\")\n"
+    "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") != \"\") source(\"http://https://raw.githubusercontent.com/microbiomedata/nmdc_notebooks/refs/heads/main/utility_functions.R\")\n"
    ]
   },
   {
diff --git a/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb b/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb
index ceb074df..9e3639b8 100644
--- a/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb
+++ b/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb
@@ -12,7 +12,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "568d7112-ee43-41ce-aadb-39eaa9585dbd",
    "metadata": {
     "metadata": {},
@@ -31,7 +31,7 @@
     "\n",
     "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") == \"\") source(\"../../utility_functions.R\")\n",
     "\n",
-    "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") != \"\") source(\"http://raw.githubusercontent.com/microbiomedata/nmdc_notebooks/refs/heads/90-modularize-r-api-wrapper-functions/utility_functions.R\")"
+    "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") != \"\") source(\"http://https://raw.githubusercontent.com/microbiomedata/nmdc_notebooks/refs/heads/main/utility_functions.R\")"
    ]
   },
   {

From b4d7725fff6e43bcacae5b76f15e634eac955eb4 Mon Sep 17 00:00:00 2001
From: bmeluch <107661103+bmeluch@users.noreply.github.com>
Date: Thu, 13 Feb 2025 13:35:44 -0800
Subject: [PATCH 2/2] correct URL typo

---
 NOM_visualizations/R/NOM_R_notebook.ipynb                       | 2 +-
 .../R/taxonomic_dist_soil_layer_R.ipynb                         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/NOM_visualizations/R/NOM_R_notebook.ipynb b/NOM_visualizations/R/NOM_R_notebook.ipynb
index 180a1c8d..695354d7 100644
--- a/NOM_visualizations/R/NOM_R_notebook.ipynb
+++ b/NOM_visualizations/R/NOM_R_notebook.ipynb
@@ -37,7 +37,7 @@
     "\n",
     "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") == \"\") source(\"../../utility_functions.R\")\n",
     "\n",
-    "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") != \"\") source(\"http://https://raw.githubusercontent.com/microbiomedata/nmdc_notebooks/refs/heads/main/utility_functions.R\")\n"
+    "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") != \"\") source(\"http://raw.githubusercontent.com/microbiomedata/nmdc_notebooks/refs/heads/main/utility_functions.R\")\n"
    ]
   },
   {
diff --git a/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb b/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb
index 9e3639b8..9b734dd7 100644
--- a/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb
+++ b/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb
@@ -31,7 +31,7 @@
     "\n",
     "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") == \"\") source(\"../../utility_functions.R\")\n",
     "\n",
-    "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") != \"\") source(\"http://https://raw.githubusercontent.com/microbiomedata/nmdc_notebooks/refs/heads/main/utility_functions.R\")"
+    "if(Sys.getenv(\"COLAB_BACKEND_VERSION\") != \"\") source(\"http://raw.githubusercontent.com/microbiomedata/nmdc_notebooks/refs/heads/main/utility_functions.R\")"
    ]
   },
   {