Upgrade directives with nbdev_migrate

Additionally, 03_example_graphs.ipynb had to be modified to not to
loose information, as originally the page description spanned two
lines (and nbdev_migrate lost the contents of the second line).

Also, _Reachability_labels_for_version_control_graphs.ipynb and
_Reachability_queries_in_large_graphs.ipynb were kept as is.  Those
files serve as original source to be put in nbdev-managed notebooks.

Author: jnareb

01_tools.ipynb

@@ -1,10 +1,15 @@
 {
  "cells": [
   {
-   "cell_type": "markdown",
+   "cell_type": "raw",
    "metadata": {},
    "source": [
-    "# Graphs in Python"
+    "---\n",
+    "output-file: tools.html\n",
+    "title: Graphs in Python\n",
+    "\n",
+    "---\n",
+    "\n"
    ]
   },
   {

02_related.ipynb

@@ -1,10 +1,15 @@
 {
  "cells": [
   {
-   "cell_type": "markdown",
+   "cell_type": "raw",
    "metadata": {},
    "source": [
-    "# Related works: various reachability labelings"
+    "---\n",
+    "output-file: related.html\n",
+    "title: 'Related works: various reachability labelings'\n",
+    "\n",
+    "---\n",
+    "\n"
    ]
   },
   {

03_example_graphs.ipynb

@@ -1,12 +1,14 @@
 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "raw",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "#default_exp example_graphs"
+    "---\n",
+    "description: Various functions to generate examples of directed graphs (DAGs), mainly graphs from various [related works](02_related.ipynb)\n",
+    "output-file: example_graphs.html\n",
+    "title: Example directed graphs\n",
+    "---"
    ]
   },
   {
@@ -15,18 +17,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%load_ext autoreload\n",
-    "%autoreload 2"
+    "#| default_exp example_graphs"
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "# Example directed graphs\n",
-    "\n",
-    "> Various functions to generate examples of directed graphs (DAGs),\n",
-    "> mainly graphs from various [related works](02_related.ipynb)"
+    "%load_ext autoreload\n",
+    "%autoreload 2"
    ]
   },
   {
@@ -35,7 +36,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#hide\n",
+    "#| include: false\n",
     "from nbdev.showdoc import *"
    ]
   },
@@ -45,7 +46,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#export\n",
+    "#| export\n",
     "import networkx as nx"
    ]
   },
@@ -85,7 +86,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#export\n",
+    "#| export\n",
     "def crown_DAG():\n",
     "    \"\"\"Returns crown DAG known as S_3^0 graph\n",
     "\n",
@@ -289,7 +290,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#export\n",
+    "#| export\n",
     "def small_DAG_FELINE():\n",
     "    \"\"\"Create small DAG (example in Figure 2 in FELINE paper)\n",
     "\n",
@@ -490,7 +491,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#export\n",
+    "#| export\n",
     "def tree_DAG():\n",
     "    \"\"\"Create tree DAG ('didactic example' in Figure 6 in FELINE paper)\n",
     "\n",
@@ -717,7 +718,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#export\n",
+    "#| export\n",
     "def levels_DAG_FELINE():\n",
     "    \"\"\"Create graph from Figure 9 in FELINE paper, used to show levels-filter\n",
     "\n",
@@ -1024,7 +1025,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#export\n",
+    "#| export\n",
     "def RCH_graph():\n",
     "    \"\"\"Create RCH example graph (example in Figure 1 and 2 in PReaCH paper)\n",
     "\n",
@@ -1195,7 +1196,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#export\n",
+    "#| export\n",
     "def commit_graph_Stolee():\n",
     "    \"\"\"Create an example of Git commit graph\n",
     "\n",
@@ -1397,7 +1398,7 @@
     }
    ],
    "source": [
-    "#hide\n",
+    "#| include: false\n",
     "# this should be the last cell of the notebook\n",
     "from nbdev.export import notebook2script\n",
     "notebook2script()"
@@ -1406,9 +1407,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "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": "3.8.5"
   }
  },
  "nbformat": 4,

05_reachability_index.ipynb

@@ -1,11 +1,17 @@
 {
  "cells": [
   {
-   "cell_type": "markdown",
+   "cell_type": "raw",
    "metadata": {},
    "source": [
-    "# Reachability index\n",
-    "> Describe different types of reachability indices (labels), define negative-cut and positive-cut filters"
+    "---\n",
+    "description: Describe different types of reachability indices (labels), define negative-cut\n",
+    "  and positive-cut filters\n",
+    "output-file: reachability_index.html\n",
+    "title: Reachability index\n",
+    "\n",
+    "---\n",
+    "\n"
    ]
   },
   {

06_levels.ipynb

@@ -1,12 +1,25 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "description: Defining topological levels, and describing their characteristics\n",
+    "output-file: levels.html\n",
+    "title: Topological levels\n",
+    "\n",
+    "---\n",
+    "\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "#default_exp labelling.levels"
+    "#| default_exp labelling.levels"
    ]
   },
   {
@@ -28,14 +41,6 @@
     "%autoreload 2"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Topological levels\n",
-    "> Defining topological levels, and describing their characteristics"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -57,7 +62,11 @@
     "\n",
     "The backward topological level increases at least by one when going in the opposite direction to edges (going backwards).\n",
     "\n",
-    "> Note: This reachability label is _immutable_ with respect to the graph growth by adding nodes."
+    ":::{.callout-note}\n",
+    "\n",
+    "This reachability label is _immutable_ with respect to the graph growth by adding nodes.\n",
+    "\n",
+    ":::"
    ]
   },
   {
@@ -109,7 +118,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "> Note: the alternative notation for $l_u$ is $l(u)$, and for $L_u$ is $L(u)$.\n",
+    ":::{.callout-note}\n",
+    "\n",
+    "the alternative notation for $l_u$ is $l(u)$, and for $L_u$ is $L(u)$.\n",
+    "\n",
+    ":::\n",
     "\n",
     "In other words the following observation holds:\n",
     "\n",
@@ -155,8 +168,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#export\n",
-    "import networkx as nx\n"
+    "#| export\n",
+    "import networkx as nx"
    ]
   },
   {
@@ -172,7 +185,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#export\n",
+    "#| export\n",
     "def find_levels(DG, attr=None):\n",
     "  \"\"\"Find levels (generation number) of all vertices in graph G\n",
     "  \n",
@@ -231,7 +244,7 @@
     "    for node, level in lvl.items():\n",
     "      DG.nodes[node][attr] = level\n",
     "  \n",
-    "  return lvl\n"
+    "  return lvl"
    ]
   },
   {
@@ -422,7 +435,7 @@
     }
    ],
    "source": [
-    "#hide\n",
+    "#| include: false\n",
     "# this should be the last cell of the notebook\n",
     "from nbdev.export import notebook2script\n",
     "notebook2script()"