dev/stable docs using mike

.github/workflows/docs-dev.yml

@@ -26,10 +26,13 @@ jobs:
         # First configure git correctly
         # Then use the alias of the current dev version to delete it based on its identifier
         # Then deploy the new version so that there is only one dev version at a time
+        # Only make dev the default if no stable version exists yet, so stable stays the default once published
         run: |
           git config user.name github-actions
           git config user.email [email protected]
           git fetch origin gh-pages --depth=1
           mike delete --push $(mike list | grep dev | awk '{print $1}' | tr -d '()')
           mike deploy --push --update-aliases "${{ env.package_version }}-dev" dev
-          mike set-default --push --allow-empty dev
+          if ! mike list stable > /dev/null 2>&1; then
+            mike set-default --push dev
+          fi

.github/workflows/docs-stable.yml

@@ -20,6 +20,9 @@ jobs:
           python -c 'import pathpyG; print(f"package_version={pathpyG.__version__}")' >> "$GITHUB_ENV"
 
       - name: Publish docs
+        env:
+          # Pin "Open in Colab" links to the commit these docs are built from	
+          DOCS_GIT_REF: ${{ github.sha }}
         run: |
           git config user.name github-actions
           git config user.email [email protected]

docs/getting_started.md

@@ -30,9 +30,6 @@ uv pip install pathpyg[cu129]
 
 You can install the latest stable release of PathpyG via pip:
 
-!!! warning "TODO"
-    This is not yet available. We will release the first stable version soon.
-
 ```bash
 pip install pathpyg
 ```

docs/overrides/home.html

@@ -1,4 +1,4 @@
-{% extends "base.html" %}
+{% extends "main.html" %}
 
 {% block tabs %}
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/OwlCarousel2/2.3.4/assets/owl.carousel.min.css">

docs/overrides/main.html

@@ -1,21 +1,26 @@
 {% extends "base.html" %}
 
 <!-- You can include an announcement bar with the block "announce" -->
+{% block announce -%}
+  {%- if config.extra.docs_version.endswith("-dev") %}
+    You're viewing the development docs. Features documented here may not be in a released version of pathpyG yet.
+  {%- endif %}
+{%- endblock %}
 
 <!-- Includes a download button in the Jupyter tutorials -->
 {% block content %}
 {% if page.nb_url %}
     <a href="{{ page.nb_url }}" title="Download Notebook" class="md-content__button md-icon">
         {% include ".icons/material/download.svg" %}
     </a>
-    <a href="{{ page.edit_url | replace('https://github.com/pathpy/pathpyG/edit/', 'https://colab.research.google.com/github/pathpy/pathpyG/blob/') }}" title="Open in Google Colab" class="md-content__button md-icon">
+    <a href="https://colab.research.google.com/github/pathpy/pathpyG/blob/{{ config.extra.git_ref }}/docs/{{ page.file.src_uri }}" title="Open in Google Colab" class="md-content__button md-icon">
       {% include ".icons/simple/googlecolab.svg" %}
     </a>
 {% endif %}
 {{ super() }}
 {% endblock %}
 
-<!-- Adds a warning to the top of the page if the page is not the dev or the stable version -->
+<!-- Adds a warning to the top of the page if the page is not the stable version -->
 {% block outdated %}
   You're not viewing the latest version.
   <a href="{{ '../' ~ base_url }}">

docs/tutorial/archive/_scalability_analysis.ipynb

@@ -36,7 +36,7 @@
     "    res['temp_net_events'] = g.data.edge_index.size(1)\n",
     "\n",
     "    start_time = time.time()\n",
-    "    eg = pp.algorithms.lift_order_temporal(g, delta=exp['delta'])\n",
+    "    eg = pp.core.event_graph.EventGraph.build_edge_index(g, delta=exp['delta'])\n",
     "    eg.to(exp['device'])\n",
     "    res['lift_event_graph_time'] = time.time() - start_time\n",
     "    res['event_graph_edges'] = eg.size(1)\n",
@@ -1392,13 +1392,13 @@
      "evalue": "",
      "output_type": "error",
      "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[4], line 13\u001b[0m\n\u001b[1;32m     11\u001b[0m exp[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmax_order\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m k\n\u001b[1;32m     12\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 13\u001b[0m     res \u001b[38;5;241m=\u001b[39m \u001b[43mtest_mo_scalability\u001b[49m\u001b[43m(\u001b[49m\u001b[43mg\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mexp\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     14\u001b[0m     printer\u001b[38;5;241m.\u001b[39mpprint(res)\n\u001b[1;32m     15\u001b[0m     results_rm[delta][k] \u001b[38;5;241m=\u001b[39m res\n",
-      "Cell \u001b[0;32mIn[2], line 16\u001b[0m, in \u001b[0;36mtest_mo_scalability\u001b[0;34m(g, exp)\u001b[0m\n\u001b[1;32m     13\u001b[0m res[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mevent_graph_edges\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m eg\u001b[38;5;241m.\u001b[39msize(\u001b[38;5;241m1\u001b[39m)\n\u001b[1;32m     15\u001b[0m start_time \u001b[38;5;241m=\u001b[39m time\u001b[38;5;241m.\u001b[39mtime()\n\u001b[0;32m---> 16\u001b[0m m \u001b[38;5;241m=\u001b[39m \u001b[43mpp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mMultiOrderModel\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfrom_temporal_graph\u001b[49m\u001b[43m(\u001b[49m\u001b[43mg\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdelta\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mexp\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mdelta\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmax_order\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mexp\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mmax_order\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     17\u001b[0m res[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmo_time\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m time\u001b[38;5;241m.\u001b[39mtime() \u001b[38;5;241m-\u001b[39m start_time\n\u001b[1;32m     18\u001b[0m res[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmax_order_nodes\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m m\u001b[38;5;241m.\u001b[39mlayers[exp[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmax_order\u001b[39m\u001b[38;5;124m'\u001b[39m]]\u001b[38;5;241m.\u001b[39mN\n",
-      "File \u001b[0;32m/workspaces/pathpyG/src/pathpyG/core/multi_order_model.py:108\u001b[0m, in \u001b[0;36mMultiOrderModel.from_temporal_graph\u001b[0;34m(g, delta, max_order, weight, cached)\u001b[0m\n\u001b[1;32m    106\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m max_order \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[1;32m    107\u001b[0m     node_sequence \u001b[38;5;241m=\u001b[39m torch\u001b[38;5;241m.\u001b[39mcat([node_sequence[edge_index[\u001b[38;5;241m0\u001b[39m]], node_sequence[edge_index[\u001b[38;5;241m1\u001b[39m]][:, \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m:]], dim\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m)\n\u001b[0;32m--> 108\u001b[0m     edge_index \u001b[38;5;241m=\u001b[39m \u001b[43mlift_order_temporal\u001b[49m\u001b[43m(\u001b[49m\u001b[43mg\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdelta\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    109\u001b[0m     edge_weight \u001b[38;5;241m=\u001b[39m aggregate_node_attributes(edge_index, edge_weight, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msrc\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m    111\u001b[0m     \u001b[38;5;66;03m# Aggregate\u001b[39;00m\n",
-      "File \u001b[0;32m/workspaces/pathpyG/src/pathpyG/algorithms/temporal.py:39\u001b[0m, in \u001b[0;36mlift_order_temporal\u001b[0;34m(g, delta)\u001b[0m\n\u001b[1;32m     36\u001b[0m dst_node_mask \u001b[38;5;241m=\u001b[39m torch\u001b[38;5;241m.\u001b[39misin(edge_index[\u001b[38;5;241m0\u001b[39m], edge_index[\u001b[38;5;241m1\u001b[39m, src_edge_idx])\n\u001b[1;32m     37\u001b[0m dst_edge_idx \u001b[38;5;241m=\u001b[39m indices[dst_time_mask \u001b[38;5;241m&\u001b[39m dst_node_mask]\n\u001b[0;32m---> 39\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[43mdst_edge_idx\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msize\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m)\u001b[49m \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m \u001b[38;5;129;01mand\u001b[39;00m src_edge_idx\u001b[38;5;241m.\u001b[39msize(\u001b[38;5;241m0\u001b[39m) \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m     40\u001b[0m \n\u001b[1;32m     41\u001b[0m     \u001b[38;5;66;03m# compute second-order edges between src and dst idx for all edges where dst in src_edges matches src in dst_edges\u001b[39;00m\n\u001b[1;32m     42\u001b[0m     x \u001b[38;5;241m=\u001b[39m torch\u001b[38;5;241m.\u001b[39mcartesian_prod(src_edge_idx, dst_edge_idx)\u001b[38;5;241m.\u001b[39mt()\n\u001b[1;32m     43\u001b[0m     \u001b[38;5;66;03m# print(x.size(1))\u001b[39;00m\n",
-      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
+      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
+      "\u001B[0;31mKeyboardInterrupt\u001B[0m                         Traceback (most recent call last)",
+      "Cell \u001B[0;32mIn[4], line 13\u001B[0m\n\u001B[1;32m     11\u001B[0m exp[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mmax_order\u001B[39m\u001B[38;5;124m'\u001B[39m] \u001B[38;5;241m=\u001B[39m k\n\u001B[1;32m     12\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m---> 13\u001B[0m     res \u001B[38;5;241m=\u001B[39m \u001B[43mtest_mo_scalability\u001B[49m\u001B[43m(\u001B[49m\u001B[43mg\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mexp\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m     14\u001B[0m     printer\u001B[38;5;241m.\u001B[39mpprint(res)\n\u001B[1;32m     15\u001B[0m     results_rm[delta][k] \u001B[38;5;241m=\u001B[39m res\n",
+      "Cell \u001B[0;32mIn[2], line 16\u001B[0m, in \u001B[0;36mtest_mo_scalability\u001B[0;34m(g, exp)\u001B[0m\n\u001B[1;32m     13\u001B[0m res[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mevent_graph_edges\u001B[39m\u001B[38;5;124m'\u001B[39m] \u001B[38;5;241m=\u001B[39m eg\u001B[38;5;241m.\u001B[39msize(\u001B[38;5;241m1\u001B[39m)\n\u001B[1;32m     15\u001B[0m start_time \u001B[38;5;241m=\u001B[39m time\u001B[38;5;241m.\u001B[39mtime()\n\u001B[0;32m---> 16\u001B[0m m \u001B[38;5;241m=\u001B[39m \u001B[43mpp\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mMultiOrderModel\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mfrom_temporal_graph\u001B[49m\u001B[43m(\u001B[49m\u001B[43mg\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mdelta\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mexp\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[38;5;124;43mdelta\u001B[39;49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[43m]\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mmax_order\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mexp\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[38;5;124;43mmax_order\u001B[39;49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[43m]\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m     17\u001B[0m res[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mmo_time\u001B[39m\u001B[38;5;124m'\u001B[39m] \u001B[38;5;241m=\u001B[39m time\u001B[38;5;241m.\u001B[39mtime() \u001B[38;5;241m-\u001B[39m start_time\n\u001B[1;32m     18\u001B[0m res[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mmax_order_nodes\u001B[39m\u001B[38;5;124m'\u001B[39m] \u001B[38;5;241m=\u001B[39m m\u001B[38;5;241m.\u001B[39mlayers[exp[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mmax_order\u001B[39m\u001B[38;5;124m'\u001B[39m]]\u001B[38;5;241m.\u001B[39mN\n",
+      "File \u001B[0;32m/workspaces/pathpyG/src/pathpyG/core/multi_order_model.py:108\u001B[0m, in \u001B[0;36mMultiOrderModel.from_temporal_graph\u001B[0;34m(g, delta, max_order, weight, cached)\u001B[0m\n\u001B[1;32m    106\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m max_order \u001B[38;5;241m>\u001B[39m \u001B[38;5;241m1\u001B[39m:\n\u001B[1;32m    107\u001B[0m     node_sequence \u001B[38;5;241m=\u001B[39m torch\u001B[38;5;241m.\u001B[39mcat([node_sequence[edge_index[\u001B[38;5;241m0\u001B[39m]], node_sequence[edge_index[\u001B[38;5;241m1\u001B[39m]][:, \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m1\u001B[39m:]], dim\u001B[38;5;241m=\u001B[39m\u001B[38;5;241m1\u001B[39m)\n\u001B[0;32m--> 108\u001B[0m     edge_index \u001B[38;5;241m=\u001B[39m \u001B[43mlift_order_temporal\u001B[49m\u001B[43m(\u001B[49m\u001B[43mg\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mdelta\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m    109\u001B[0m     edge_weight \u001B[38;5;241m=\u001B[39m aggregate_node_attributes(edge_index, edge_weight, \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124msrc\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m    111\u001B[0m     \u001B[38;5;66;03m# Aggregate\u001B[39;00m\n",
+      "File \u001B[0;32m/workspaces/pathpyG/src/pathpyG/algorithms/temporal.py:39\u001B[0m, in \u001B[0;36mlift_order_temporal\u001B[0;34m(g, delta)\u001B[0m\n\u001B[1;32m     36\u001B[0m dst_node_mask \u001B[38;5;241m=\u001B[39m torch\u001B[38;5;241m.\u001B[39misin(edge_index[\u001B[38;5;241m0\u001B[39m], edge_index[\u001B[38;5;241m1\u001B[39m, src_edge_idx])\n\u001B[1;32m     37\u001B[0m dst_edge_idx \u001B[38;5;241m=\u001B[39m indices[dst_time_mask \u001B[38;5;241m&\u001B[39m dst_node_mask]\n\u001B[0;32m---> 39\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[43mdst_edge_idx\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43msize\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;241;43m0\u001B[39;49m\u001B[43m)\u001B[49m \u001B[38;5;241m>\u001B[39m \u001B[38;5;241m0\u001B[39m \u001B[38;5;129;01mand\u001B[39;00m src_edge_idx\u001B[38;5;241m.\u001B[39msize(\u001B[38;5;241m0\u001B[39m) \u001B[38;5;241m>\u001B[39m \u001B[38;5;241m0\u001B[39m:\n\u001B[1;32m     40\u001B[0m \n\u001B[1;32m     41\u001B[0m     \u001B[38;5;66;03m# compute second-order edges between src and dst idx for all edges where dst in src_edges matches src in dst_edges\u001B[39;00m\n\u001B[1;32m     42\u001B[0m     x \u001B[38;5;241m=\u001B[39m torch\u001B[38;5;241m.\u001B[39mcartesian_prod(src_edge_idx, dst_edge_idx)\u001B[38;5;241m.\u001B[39mt()\n\u001B[1;32m     43\u001B[0m     \u001B[38;5;66;03m# print(x.size(1))\u001B[39;00m\n",
+      "\u001B[0;31mKeyboardInterrupt\u001B[0m: "
      ]
     }
    ],