[Cleanup] Gathering graph utilities around BasicGraph/MoleculeGraph

Before this change, we have many graph-related functions with various
pre-requisites on graphs, plus lots of conversions from pyg to networkx.

This change:

- introduces two classes BasicGraph and MoleculeGraph, depending on
	which invariants hold on the graph;
- attaches the relevant methods to BasicGraph/MoleculeGraph instead of
	pyg;
- makes sure that we have only one single conversion from pyg to networkx.

examples/pipeline.ipynb

@@ -19,14 +19,11 @@
    "metadata": {},
    "outputs": [
     {
-     "ename": "ModuleNotFoundError",
-     "evalue": "No module named 'torch_geometric'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mtorch_geometric\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdatasets\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mpyg_dataset\u001b[39;00m\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mtorch_geometric\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdata\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mpyg_data\u001b[39;00m\n\u001b[1;32m      3\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mqek\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdata\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdataset\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mqek_dataset\u001b[39;00m\n",
-      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'torch_geometric'"
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/tmp/ipykernel_782556/4114388664.py:9: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
+      "  from tqdm.autonotebook import tqdm\n"
      ]
     }
    ],
@@ -67,17 +64,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import qek.data.datatools as qek_datatools\n",
-    "from qek.utils import compute_register, is_disk_graph"
+    "import qek.data.datatools as qek_datatools"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -101,7 +90,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "093a63f828d44786afb3c91f8c9dd78f",
+       "model_id": "8dfa40146d2a40b4b26b378debf4d231",
        "version_major": 2,
        "version_minor": 0
       },
@@ -114,13 +103,13 @@
     }
    ],
    "source": [
-    "list_of_graph = []\n",
+    "list_of_graphs = []\n",
     "RADIUS = 5.001\n",
     "EPS = 0.01\n",
-    "for graph in tqdm(og_ptcfm):\n",
-    "    graph_with_pos = qek_datatools.add_graph_coord(graph=graph, blockade_radius=RADIUS)\n",
-    "    if is_disk_graph(graph_with_pos, radius=RADIUS+EPS):\n",
-    "        list_of_graph.append((graph_with_pos, graph.y.item()))"
+    "for data in tqdm(og_ptcfm):\n",
+    "    graph = qek_datatools.MoleculeGraph(data=data, blockade_radius=RADIUS)\n",
+    "    if graph.is_disk_graph(radius=RADIUS+EPS):\n",
+    "        list_of_graphs.append((graph, data.y.item()))"
    ]
   },
   {
@@ -143,9 +132,9 @@
     "# Create a sequence:\n",
     "\n",
     "def create_sequence_from_graph(graph:pyg_data.Data, device=pl.devices.Device)-> pl.Sequence:\n",
-    "    if not qek_datatools.check_compatibility_graph_device(graph, device):\n",
+    "    if not graph.is_embeddable(device):\n",
     "        raise ValueError(f\"The graph is not compatible with {device}\")\n",
-    "    reg = compute_register(data_graph=graph)\n",
+    "    reg = graph.compute_register()\n",
     "    seq = pl.Sequence(register=reg, device=device)\n",
     "    Omega_max = 1.0 * 2 * np.pi\n",
     "    t_max = 660\n",
@@ -161,7 +150,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -182,19 +171,22 @@
       "The graph is not compatible with AnalogDevice\n",
       "The graph is not compatible with AnalogDevice\n",
       "The graph is not compatible with AnalogDevice\n",
-      "The graph is not compatible with AnalogDevice\n"
+      "The graph is not compatible with AnalogDevice\n",
+      "We may embed 279/294 graphs\n"
      ]
     }
    ],
    "source": [
     "dataset_sequence = []\n",
     "\n",
-    "for graph, target in list_of_graph:\n",
-    "    # Some graph are not compatible with the AnalogDevice device\n",
+    "for graph, target in list_of_graphs:\n",
+    "    # Not all graphs are compatible with AnalogDevice\n",
     "    try:\n",
     "        dataset_sequence.append((create_sequence_from_graph(graph, device=pl.AnalogDevice), target))\n",
     "    except ValueError as err:\n",
-    "        print(f\"{err}\")"
+    "        print(f\"{err}\")\n",
+    "\n",
+    "print(f\"We may embed {len(dataset_sequence)}/{len(list_of_graphs)} graphs\")"
    ]
   },
   {