Merge branch 'u/morriscb/notebookCodeOceanCompat'

intro.md

@@ -59,6 +59,8 @@ Available notebooks:
 
 ## Release Notes
 * **[abc_atlas_access (v0.1.2)]**
+  * Add matplotlib magic.
+  * Fixed bugs in pathlib import in notebooks
   * Added script for selecting genes from expression matrices for use on
     CodeOcean.
 * **[abc_atlas_access (v0.1.1)]**

notebooks/10x_snRNASeq_tutorial_part_2a.ipynb

@@ -1,5 +1,21 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "IPython magic command to render matplotlib plots."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -15,11 +31,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
     "import pandas as pd\n",
     "from pathlib import Path\n",
     "import numpy as np\n",
@@ -42,7 +57,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -51,7 +66,7 @@
        "'releases/20240330/manifest.json'"
       ]
      },
-     "execution_count": 2,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -68,7 +83,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -89,7 +104,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -255,7 +270,7 @@
        "              WMB-10Xv3-TH               130454"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -281,7 +296,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -290,7 +305,7 @@
        "['WMB-10XMulti/log2', 'WMB-10XMulti/raw']"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -301,7 +316,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -319,7 +334,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -329,7 +344,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -420,7 +435,7 @@
        "ENSMUSG00000100241     Slc18a3"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -436,46 +451,46 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "WMB-10XMulti\n",
-      " - time taken:  0.1000140000000016\n",
+      " - time taken:  0.1458529999999989\n",
       "WMB-10Xv2-CTXsp\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "WMB-10Xv2-CTXsp-log2.h5ad: 100%|██████████| 1.74G/1.74G [01:09<00:00, 24.9MMB/s]   \n"
+      "WMB-10Xv2-CTXsp-log2.h5ad: 100%|███████████████████████████████████████████████████████████████████████████████████████| 1.74G/1.74G [01:08<00:00, 25.3MMB/s]\n"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      " - time taken:  2.0210620000000006\n",
+      " - time taken:  2.472235999999995\n",
       "WMB-10Xv2-HPF\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "WMB-10Xv2-HPF-log2.h5ad: 100%|██████████| 6.10G/6.10G [04:48<00:00, 21.2MMB/s]    \n"
+      "WMB-10Xv2-HPF-log2.h5ad: 100%|█████████████████████████████████████████████████████████████████████████████████████████| 6.10G/6.10G [04:05<00:00, 24.8MMB/s]\n"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      " - time taken:  6.7627419999999745\n",
-      "total time taken:  140.118578\n"
+      " - time taken:  9.844729000000001\n",
+      "total time taken:  114.037751\n"
      ]
     }
    ],
@@ -517,7 +532,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {