Merge pull request #5 from AFM-SPM/ns-rse/1-import-notebooks

Explicitly loading packages in the notebooks themselves
AFM-SPM · Oct 11, 2023 · 7d6d605 · 7d6d605
2 parents d730e62 + a3f8a8d
commit 7d6d605
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Showing 3 changed files with 79 additions and 11 deletions.
diff --git a/content/00-Walkthrough-minicircle.ipynb b/content/00-Walkthrough-minicircle.ipynb
@@ -36,6 +36,27 @@
     "## Getting Started\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "386691b8-2247-4895-b9b5-4bade440b7d9",
+   "metadata": {},
+   "source": [
+    "## Install requirements\n",
+    "\n",
+    "A few libraries need manually loading  before you can run this Notebook"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "367a5181-ab9e-45df-81b7-0ba00096d1d8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%pip install pgfinder==0.0.3\n",
+    "%pip install ipywidgets matplotlib nupy"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "9fe935a6-591d-45fb-a65b-83087e320842",

diff --git a/content/02-Summary-statistics-and-plots.ipynb b/content/02-Summary-statistics-and-plots.ipynb
@@ -35,13 +35,47 @@
     "\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "799b696d-c8f1-4f3a-a79e-ad531304f3d9",
+   "metadata": {},
+   "source": [
+    "# Setup"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c54b6944-c942-4b4c-852b-1e425f559703",
+   "metadata": {},
+   "source": [
+    "## Install requirements\n",
+    "\n",
+    "A few libraries need isntalling before you can run this Notebook. This will take a short while as the packages are downloaded and installed."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9fe4ea7c-31b1-45e7-9f41-741834f8d947",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%pip install ipywidgets\n",
+    "%pip install matplotlib\n",
+    "%pip install pandas\n",
+    "%pip install seaborn\n",
+    "%pip install topostats"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
    "id": "e9925511-9e30-4c69-86cf-531cda8fea10",
    "metadata": {},
    "source": [
-    "## Load Libraries"
+    "## Load Libraries\n",
+    "\n",
+    "The required libraries and modules are now `import`ed."
    ]
   },
   {

diff --git a/content/03-Plotting-scans.ipynb b/content/03-Plotting-scans.ipynb
@@ -30,17 +30,30 @@
    "source": [
     "# Setup\n",
     "\n",
-    "The first step required is to import some Python libraries to load and plot the data. You should run this Notebook\n",
-    "within a Conda/Virtual Environment into which you have installed TopoStats, ideally with the necessary Notebook\n",
-    "extensions. The following command will install TopoStats from [PyPI](https://pypi.org/project/topostats/) with the\n",
-    "requirements for running Notebooks.\n",
-    "\n",
-    "```python\n",
-    "pip install topostats[notebooks]\n",
-    "```\n",
+    "The first step required is to install some Python libraries required to load and plot the data."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "817fb4bb-843a-4fe7-867b-737c752281b3",
+   "metadata": {},
+   "source": [
+    "## Install requirements\n",
     "\n",
-    "You should have successfully processed images using `run_topostats` at least once, this will have saved processed scans\n",
-    "to disk that we will load."
+    "A few libraries need isntalling before you can run this Notebook. This will take a short while as the packages are downloaded and installed."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "02f3611a-d520-4ff7-a709-1f56569162ae",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%pip install ipywidgets\n",
+    "%pip install matplotlib\n",
+    "%pip install numpy\n",
+    "%pip install topostats"
    ]
   },
   {