Github Action: Lint Notebooks

Author: github-action

module_notebooks/00-environment-setup.ipynb

@@ -175,12 +175,6 @@
   }
  ],
  "metadata": {
-  "environment": {
-   "kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
-   "name": "workbench-notebooks.m129",
-   "type": "gcloud",
-   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m129"
-  },
   "kernelspec": {
    "display_name": "nigms-pangenomics (Local)",
    "language": "python",

module_notebooks/02-building-graphs-with-pggb.ipynb

@@ -728,7 +728,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -891,12 +891,6 @@
   }
  ],
  "metadata": {
-  "environment": {
-   "kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
-   "name": "workbench-notebooks.m129",
-   "type": "gcloud",
-   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m129"
-  },
   "kernelspec": {
    "display_name": "nigms-pangenomics (Local)",
    "language": "python",

module_notebooks/05-indexing-graphs-with-vg.ipynb

@@ -120,7 +120,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -168,7 +168,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -187,7 +187,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -215,24 +215,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[vg autoindex] Executing command: vg autoindex --workflow giraffe -g graphs/yprp.chrVIII.pggb.vg -p graphs/yprp.chrVIII.pggb\n",
-      "[IndexRegistry]: Checking for haplotype lines in GFA.\n",
-      "[IndexRegistry]: Constructing VG graph from GFA input.\n",
-      "[IndexRegistry]: Constructing XG graph from VG graph.\n",
-      "[IndexRegistry]: Constructing a greedy path cover GBWT\n",
-      "[IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation.\n",
-      "[IndexRegistry]: Constructing distance index for Giraffe.\n",
-      "[IndexRegistry]: Constructing minimizer index.\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "!vg autoindex --workflow giraffe -g graphs/yprp.chrVIII.pggb.vg -p graphs/yprp.chrVIII.pggb"
    ]
@@ -259,30 +244,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "-rw-r--r-- 1 jupyter jupyter  815936 Apr 29 16:46 graphs/yprp.chrVIII.pggb.dist\n",
-      "-rw-r--r-- 1 jupyter jupyter  772909 Apr 28 21:33 graphs/yprp.chrVIII.pggb.fa\n",
-      "-rw-r--r-- 1 jupyter jupyter   20480 Apr 28 21:33 graphs/yprp.chrVIII.pggb.fa.ndb\n",
-      "-rw-r--r-- 1 jupyter jupyter 1317154 Apr 28 21:33 graphs/yprp.chrVIII.pggb.fa.nhr\n",
-      "-rw-r--r-- 1 jupyter jupyter  231148 Apr 28 21:33 graphs/yprp.chrVIII.pggb.fa.nin\n",
-      "-rw-r--r-- 1 jupyter jupyter     577 Apr 28 21:33 graphs/yprp.chrVIII.pggb.fa.njs\n",
-      "-rw-r--r-- 1 jupyter jupyter  231032 Apr 28 21:33 graphs/yprp.chrVIII.pggb.fa.not\n",
-      "-rw-r--r-- 1 jupyter jupyter  221019 Apr 28 21:33 graphs/yprp.chrVIII.pggb.fa.nsq\n",
-      "-rw-r--r-- 1 jupyter jupyter   16384 Apr 28 21:33 graphs/yprp.chrVIII.pggb.fa.ntf\n",
-      "-rw-r--r-- 1 jupyter jupyter   77012 Apr 28 21:33 graphs/yprp.chrVIII.pggb.fa.nto\n",
-      "-rw-r--r-- 1 jupyter jupyter 1538338 Apr 28 20:18 graphs/yprp.chrVIII.pggb.gfa\n",
-      "-rw-r--r-- 1 jupyter jupyter  794240 Apr 29 16:46 graphs/yprp.chrVIII.pggb.giraffe.gbz\n",
-      "-rw-r--r-- 1 jupyter jupyter 8706216 Apr 29 16:46 graphs/yprp.chrVIII.pggb.min\n",
-      "-rw-r--r-- 1 jupyter jupyter 1538338 Apr 29 03:33 graphs/yprp.chrVIII.pggb.vg\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "#This will list some of our original graphs as well.\n",
     "\n",
@@ -361,21 +325,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "nodes\t19252\n",
-      "edges\t25908\n",
-      "19252\n",
-      "25908\n",
-      "length\t622372\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "!vg stats -z -N -E -l graphs/yprp.chrVIII.pggb.vg"
    ]
@@ -440,32 +392,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "\n",
-       "        <iframe\n",
-       "            width=\"800\"\n",
-       "            height=\"400\"\n",
-       "            src=\"../html/flashcard_graphstats.html\"\n",
-       "            frameborder=\"0\"\n",
-       "            allowfullscreen\n",
-       "            \n",
-       "        ></iframe>\n",
-       "        "
-      ],
-      "text/plain": [
-       "<IPython.lib.display.IFrame at 0x7fd23bc45be0>"
-      ]
-     },
-     "execution_count": 10,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "from IPython.display import IFrame\n",
     "IFrame('../html/flashcard_graphstats.html', width=800, height=400)"
@@ -494,12 +423,6 @@
   }
  ],
  "metadata": {
-  "environment": {
-   "kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
-   "name": "workbench-notebooks.m129",
-   "type": "gcloud",
-   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m129"
-  },
   "kernelspec": {
    "display_name": "nigms-pangenomics (Local)",
    "language": "python",