Update some dependencies (#26)

But I'm keeping typeguard back at major version 2 for now, as
detailed below.

* Update dependencies

* Keep typeguard back so typechecked works in notebooks

This seems to have stopped working in major version 3 (based on
my testing in this project). The current major version of typeguard
is 4. The issue looks like:

agronholm/typeguard#364

This should probably only be a temporary solution. There are other
libraries I could use. But also, it's not obvious that the added
clarity of presentation from defining the top-level functions in
the notebooks that use them, rather than in modules as I would
ordinarily do, is justified, even in the absence of this issue. So
it may be worthwhile to revisit that design decision for codegraph.
But for now I'm keeping that as it is and holding back typeguard.

This commit also updates typing-extensions to the next patch
version.

* Re-run notebooks

Pipfile

@@ -9,11 +9,12 @@ ipykernel = "*"
 pygit2 = "*"
 pyyaml = "*"
 requests = "*"
-typeguard = "*"
+typeguard = ">=2.13.3,<3"
 
 [dev-packages]
 jupyterlab = "*"
 nbdime = "*"
+jupyter-collaboration = "*"
 
 [requires]
 python_version = "3.11"

builtin_types.ipynb

@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "c7c6edec",
    "metadata": {},
@@ -29,6 +30,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "24294bbf",
    "metadata": {},
@@ -94,6 +96,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "9cbabfef",
    "metadata": {},
@@ -164,6 +167,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "207c86c9",
    "metadata": {},
@@ -1312,7 +1316,7 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x7f21e43d3d50>"
+       "<graphviz.graphs.Digraph at 0x7fd5c43e2b10>"
       ]
      },
      "metadata": {},
@@ -1337,6 +1341,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "24f24590",
    "metadata": {},
@@ -2485,7 +2490,7 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.sources.Source at 0x7f21e75f6950>"
+       "<graphviz.sources.Source at 0x7fd5c434ad90>"
       ]
      },
      "metadata": {},
@@ -2510,6 +2515,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "71307bf9",
    "metadata": {},
@@ -3658,7 +3664,7 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.sources.Source at 0x7f21e64e0990>"
+       "<graphviz.sources.Source at 0x7fd5c4399690>"
       ]
      },
      "metadata": {},

exceptions.ipynb

@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "040bed61-ea7e-4dd2-bdd0-08fc5a5e2d60",
    "metadata": {},
@@ -11,6 +12,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "bc326a09-3a49-4394-a5a0-bb0173416fc5",
    "metadata": {},
@@ -42,6 +44,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "d9dc6090-2225-4095-9dad-d6844ff3f5ec",
    "metadata": {},
@@ -433,6 +436,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "a01abdfa-4f00-4c85-9e45-f074ddcb9902",
    "metadata": {},

fibonacci.ipynb

@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "d41c8419",
    "metadata": {},
@@ -283,7 +284,7 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x7f25744ae850>"
+       "<graphviz.graphs.Digraph at 0x7f9a2de98750>"
       ]
      },
      "execution_count": 5,
@@ -296,6 +297,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "756b8104-0956-4764-82d6-2bba07d92f86",
    "metadata": {},