Merge pull request #580 from graphistry/dev/comm_layout

Dev/comm layout
graphistry · Aug 3, 2024 · 56d83db · 56d83db
2 parents a9945bf + b46df4c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,21 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Development]
 
+## [0.34.3 - 2024-08-03]
+
+### Added
+
+* Layout `modularity_weighted_layout` that uses edge weights to more strongly emphasize community structure
+
+### Docs
+
+* Tutorial for `modularity_weighted_layout`
+
+### Infra
+
+* Upgrade tests to`docker compose` from `docker-compose` 
+* Remove deprecated `version` to address warnings
+
 ## [0.34.2 - 2024-07-22]
 
 ### Fixed

diff --git a/README.md b/README.md
@@ -1513,6 +1513,22 @@ g.ring_categorical_layout(
 )
 ```
 
+### Layout: Modularity weighted
+
+Weight edges by community membership to emphasize community structure. See [(Notebook tutorial)](https://github.com/graphistry/pygraphistry/blob/master/demos/more_examples/graphistry_features/layout_modularity_weighted.ipynb)
+
+```python
+g.modularity_weighted_layout().plot() 
+g.modularity_weighted_layout('my_community_col').plot()
+g.modularity_weighted_layout(
+  community_alg='louvain',
+  engine='cudf',
+  same_community_weight=2.0,
+  cross_community_weight=0.3,
+  edge_influence=2.0
+).plot()
+```
+
 ### Plugin: igraph
 
 With `pip install graphistry[igraph]`, you can also use [`igraph` layouts](https://igraph.org/python/doc/api/igraph.Graph.html#layout):

diff --git a/demos/more_examples/graphistry_features/layout_modularity_weighted.ipynb b/demos/more_examples/graphistry_features/layout_modularity_weighted.ipynb
@@ -0,0 +1,210 @@
+{
+  "nbformat": 4,
+  "nbformat_minor": 0,
+  "metadata": {
+    "colab": {
+      "provenance": []
+    },
+    "kernelspec": {
+      "name": "python3",
+      "display_name": "Python 3"
+    },
+    "language_info": {
+      "name": "python"
+    }
+  },
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "source": [
+        "### Modularity weighted layout\n",
+        "\n",
+        "When community labels are known, modularity weighting helps force the layout to better hightlight the community structure. The layout algorithm will weight edges based on whether they are same-community vs cross-community. If no community labels are provided, default to using Louivain."
+      ],
+      "metadata": {
+        "id": "UEQyPUiIK6VS"
+      }
+    },
+    {
+      "cell_type": "code",
+      "execution_count": 1,
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/"
+        },
+        "id": "Z9i0f7MrH4V9",
+        "outputId": "5aa22d94-64e1-4bed-a579-e5333c0c19aa"
+      },
+      "outputs": [
+        {
+          "output_type": "stream",
+          "name": "stdout",
+          "text": [
+            "\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m75.0/75.0 kB\u001b[0m \u001b[31m2.5 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
+            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m263.0/263.0 kB\u001b[0m \u001b[31m9.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
+            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m3.1/3.1 MB\u001b[0m \u001b[31m28.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
+            "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m332.3/332.3 kB\u001b[0m \u001b[31m8.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
+            "\u001b[?25h"
+          ]
+        }
+      ],
+      "source": [
+        "! pip install -q graphistry igraph"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "import graphistry\n",
+        "import pandas as pd\n",
+        "graphistry.register(api=3, username=FILL_ME_IN, password=FILL_ME_IN)"
+      ],
+      "metadata": {
+        "id": "Nk2xIrpUH5ud"
+      },
+      "execution_count": 24,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "df = pd.read_csv('https://raw.githubusercontent.com/graphistry/pygraphistry/master/demos/data/transactions.csv')\n",
+        "g = graphistry.edges(df, 'Destination', 'Source')"
+      ],
+      "metadata": {
+        "id": "LWZoFxJ2IYMS"
+      },
+      "execution_count": 4,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# Before\n",
+        "g.compute_igraph('community_multilevel', directed=False).plot()"
+      ],
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 561
+        },
+        "id": "ffGGHcs_KPKH",
+        "outputId": "769c30cc-99cd-4f43-d059-06ade9446c8d"
+      },
+      "execution_count": 27,
+      "outputs": [
+        {
+          "output_type": "stream",
+          "name": "stderr",
+          "text": [
+            "WARNING:graphistry.plugins.igraph:edge index g._edge not set so using edge index as ID; set g._edge via g.edges(), or change merge_if_existing to FalseWARNING:graphistry.plugins.igraph:edge index g._edge __edge_index__ missing as attribute in ig; using ig edge order for IDs"
+          ]
+        },
+        {
+          "output_type": "execute_result",
+          "data": {
+            "text/plain": [
+              "<IPython.core.display.HTML object>"
+            ],
+            "text/html": [
+              "\n",
+              "            <iframe id=\"582bf801-1b1e-489a-82f6-ab125dfac968\" src=\"https://hub.graphistry.com/graph/graph.html?dataset=0d6a30dfaa094e8a8b328615444dfd95&type=arrow&viztoken=4d1bfb2c-ca98-4d37-868e-43529b4146c6&usertag=7b512218-pygraphistry-0.34.2&splashAfter=1722670549&info=true\"\n",
+              "                    allowfullscreen=\"true\" webkitallowfullscreen=\"true\" mozallowfullscreen=\"true\"\n",
+              "                    oallowfullscreen=\"true\" msallowfullscreen=\"true\"\n",
+              "                    style=\"width:100%; height:500px; border: 1px solid #DDD; overflow: hidden\"\n",
+              "                    \n",
+              "            >\n",
+              "            </iframe>\n",
+              "        \n",
+              "            <script>\n",
+              "                try {\n",
+              "                  $(\"#582bf801-1b1e-489a-82f6-ab125dfac968\").bind('mousewheel', function(e) { e.preventDefault(); });\n",
+              "                } catch (e) { console.error('exn catching scroll', e); }\n",
+              "            </script>\n",
+              "        "
+            ]
+          },
+          "metadata": {},
+          "execution_count": 27
+        }
+      ]
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# After\n",
+        "g2 = g.modularity_weighted_layout(g)"
+      ],
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/"
+        },
+        "id": "ltw6qybCi0xA",
+        "outputId": "ef5ea3ea-5b3d-429e-c979-ce13ea80797f"
+      },
+      "execution_count": 19,
+      "outputs": [
+        {
+          "output_type": "stream",
+          "name": "stderr",
+          "text": [
+            "WARNING:graphistry.plugins.igraph:edge index g._edge not set so using edge index as ID; set g._edge via g.edges(), or change merge_if_existing to FalseWARNING:graphistry.plugins.igraph:edge index g._edge __edge_index__ missing as attribute in ig; using ig edge order for IDs"
+          ]
+        }
+      ]
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "g2.plot()"
+      ],
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 543
+        },
+        "id": "rqBkXQDWdOE7",
+        "outputId": "f2eee36e-ddd5-4d21-fcec-32761476aa55"
+      },
+      "execution_count": 21,
+      "outputs": [
+        {
+          "output_type": "execute_result",
+          "data": {
+            "text/plain": [
+              "<IPython.core.display.HTML object>"
+            ],
+            "text/html": [
+              "\n",
+              "            <iframe id=\"afae5f89-0caf-4aa5-b1af-b5dabdd43e79\" src=\"https://hub.graphistry.com/graph/graph.html?dataset=e64d74fbd26541169ac8b670ed57a19a&type=arrow&viztoken=5e9461fa-ad1d-4ccd-8632-43f15e379f62&usertag=7b512218-pygraphistry-0.34.2&splashAfter=1722667198&info=true&edgeInfluence=2.0\"\n",
+              "                    allowfullscreen=\"true\" webkitallowfullscreen=\"true\" mozallowfullscreen=\"true\"\n",
+              "                    oallowfullscreen=\"true\" msallowfullscreen=\"true\"\n",
+              "                    style=\"width:100%; height:500px; border: 1px solid #DDD; overflow: hidden\"\n",
+              "                    \n",
+              "            >\n",
+              "            </iframe>\n",
+              "        \n",
+              "            <script>\n",
+              "                try {\n",
+              "                  $(\"#afae5f89-0caf-4aa5-b1af-b5dabdd43e79\").bind('mousewheel', function(e) { e.preventDefault(); });\n",
+              "                } catch (e) { console.error('exn catching scroll', e); }\n",
+              "            </script>\n",
+              "        "
+            ]
+          },
+          "metadata": {},
+          "execution_count": 21
+        }
+      ]
+    },
+    {
+      "cell_type": "code",
+      "source": [],
+      "metadata": {
+        "id": "oFTINwvZfsuH"
+      },
+      "execution_count": null,
+      "outputs": []
+    }
+  ]
+}
diff --git a/docker/dc.sh b/docker/dc.sh
@@ -1,8 +1,8 @@
 #!/bin/bash
 set -ex
 
-# Alias for docker-compose
+# Alias for docker compose
 
 COMPOSE_DOCKER_CLI_BUILD=1 \
 DOCKER_BUILDKIT=1 \
-    docker-compose $@
+    docker compose $@
diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
@@ -1,5 +1,3 @@
-version: "3.5"
-
 networks:
   grph_net:
     name: grph_net

diff --git a/docker/test-cpu-local-neo4j-only.sh b/docker/test-cpu-local-neo4j-only.sh
@@ -9,7 +9,7 @@ WITH_SUDO=${WITH_SUDO:-}
 
 COMPOSE_DOCKER_CLI_BUILD=1 \
 DOCKER_BUILDKIT=1 \
-docker-compose build \
+docker compose build \
     --build-arg PYTHON_VERSION=${PYTHON_VERSION} \
     --build-arg SENTENCE_TRANSFORMER="${SENTENCE_TRANSFOMER}" \
     --build-arg PIP_DEPS="-e .[test,bolt]" \

diff --git a/docker/test-cpu-local.sh b/docker/test-cpu-local.sh
@@ -31,7 +31,7 @@ then
     echo "WITH_BUILD (transformer: $SENTENCE_TRANSFORMER)"
     COMPOSE_DOCKER_CLI_BUILD=1 \
     DOCKER_BUILDKIT=1 \
-    docker-compose build \
+    docker compose build \
         --build-arg PYTHON_VERSION=${PYTHON_VERSION} \
         --build-arg PIP_DEPS="${PIP_DEPS}" \
         --build-arg SENTENCE_TRANSFORMER="${SENTENCE_TRANSFOMER}" \

diff --git a/docker/test-gpu-local.sh b/docker/test-gpu-local.sh
@@ -27,7 +27,7 @@ fi
 
 COMPOSE_DOCKER_CLI_BUILD=1 \
 DOCKER_BUILDKIT=1 \
-docker-compose build \
+docker compose build \
     --build-arg PIP_DEPS="${PIP_DEPS}" \
     test-gpu
 

diff --git a/docs/source/graphistry.layout.modularity_weighted.rst b/docs/source/graphistry.layout.modularity_weighted.rst
@@ -0,0 +1,19 @@
+:orphan:
+
+.. ^ FIXME
+
+graphistry.layout.modularity_weighted package
+=============================================
+
+Submodules
+----------
+
+Module contents
+---------------
+
+.. automodule:: graphistry.layout.modularity_weighted
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
diff --git a/graphistry/layout/__init__.py b/graphistry/layout/__init__.py
@@ -1,5 +1,6 @@
 #from .utils import *
 #from .graph import *
 from .gib import group_in_a_box_layout
-from .sugiyama import SugiyamaLayout
+from .modularity_weighted import modularity_weighted_layout
 from .ring import time_ring, ring_categorical, ring_continuous
+from .sugiyama import SugiyamaLayout
diff --git a/graphistry/layout/modularity_weighted/__init__.py b/graphistry/layout/modularity_weighted/__init__.py
@@ -0,0 +1 @@
+from .modularity_weighted import modularity_weighted_layout
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		from .modularity_weighted import modularity_weighted_layout