update

NIGMS · Jul 11, 2024 · 86781a1 · 86781a1
1 parent 4ee37fd
commit 86781a1
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Showing 2 changed files with 4 additions and 34 deletions.
diff --git a/.github/workflows/lint.py b/.github/workflows/lint.py
@@ -37,7 +37,7 @@ def delete_checkpoints_dirs(root_dir):
 
 if __name__ == "__main__":
     # Change this to the directory containing your notebooks
-    notebook_dir = '.'
+    notebook_dir = '../../'
 
     for root, dirs, files in os.walk(notebook_dir):
         for file in files:

diff --git a/tutorial_1-bismark.ipynb b/tutorial_1-bismark.ipynb
@@ -643,22 +643,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "24117698-6013-4a55-bd91-dea1a7f8c61e",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'igv_notebook' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[4], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m b2 \u001b[38;5;241m=\u001b[39m \u001b[43migv_notebook\u001b[49m\u001b[38;5;241m.\u001b[39mBrowser(\n\u001b[1;32m      2\u001b[0m     {\n\u001b[1;32m      3\u001b[0m        \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgenome\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmm39\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m      4\u001b[0m        \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mlocus\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mchr6:4,733,000-4,749,000\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m      5\u001b[0m     }\n\u001b[1;32m      6\u001b[0m )\n\u001b[1;32m      7\u001b[0m b2\u001b[38;5;241m.\u001b[39mload_track({\n\u001b[1;32m      8\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mSRX271141\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m      9\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpath\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mTutorial_1/bismark/SRX271141.sort.bam\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     12\u001b[0m     \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtype\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124malignment\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m     13\u001b[0m })\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'igv_notebook' is not defined"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "b2 = igv_notebook.Browser(\n",
     "    {\n",
@@ -830,25 +818,7 @@
    ]
   }
  ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.3"
-  }
- },
+ "metadata": {},
  "nbformat": 4,
  "nbformat_minor": 5
 }