misc cleanup (#54)

* misc cleanup

* fix: typo

* fix: `test_shortest_path`

Author: aMahanna

README.md

@@ -1,7 +1,5 @@
 # nx-arangodb
 
-<a href="https://colab.research.google.com/github/arangodb/nx-arangodb/blob/main/docs/nx_arangodb.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>
-
 
 <div style="display: flex; align-items: center; gap: 10px;">
     <img src="https://avatars.githubusercontent.com/u/388785?s=200&v=4" alt="NetworkX" style="height: 60px;">
@@ -12,10 +10,10 @@
 
 <br>
 
+<a href="https://colab.research.google.com/github/arangodb/nx-arangodb/blob/main/docs/nx_arangodb.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>
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 [![CodeQL](https://github.com/arangodb/nx-arangodb/actions/workflows/analyzee.yaml/badge.svg)](https://github.com/arangodb/nx-arangodb/actions/workflows/analyzee.yaml)
 [![Docs](https://github.com/arangodb/nx-arangodb/actions/workflows/docs.yaml/badge.svg)](https://github.com/arangodb/nx-arangodb/actions/workflows/docs.yaml)
-[![Last commit](https://img.shields.io/github/last-commit/arangodb/nx-arangodb)](https://github.com/arangodb/nx-arangodb/commits/main)
 
 [![PyPI version badge](https://img.shields.io/pypi/v/nx-arangodb?color=3775A9&style=for-the-badge&logo=pypi&logoColor=FFD43B)](https://pypi.org/project/nx-arangodb/)
 [![Python versions badge](https://img.shields.io/badge/3.10%2B-3776AB?style=for-the-badge&logo=python&logoColor=FFD43B&label=Python)](https://pypi.org/project/nx-arangodb/)
@@ -31,9 +29,7 @@ https://github.com/user-attachments/assets/e5f56574-d3ef-452c-ab21-b47b3d5d5900
 
 ## What is this?
 
-This is a [backend to NetworkX](https://networkx.org/documentation/stable/reference/backends.html) that offers [ArangoDB](https://github.com/arangodb/arangodb) as a [Persistence Layer to NetworkX Graphs](https://arangodb.com/introducing-the-arangodb-networkx-persistence-layer/).
-
-`nx-arangodb` allows you to:
+This is a [backend to NetworkX](https://networkx.org/documentation/stable/reference/backends.html) that offers [ArangoDB](https://github.com/arangodb/arangodb) as a [Persistence Layer to NetworkX Graphs](https://arangodb.com/introducing-the-arangodb-networkx-persistence-layer/):
 1. Persist NetworkX Graphs to ArangoDB.
 2. Reload NetworkX Graphs from ArangoDB.
 2. Perform CRUD on ArangoDB Graphs via NetworkX.
@@ -42,11 +38,10 @@ This is a [backend to NetworkX](https://networkx.org/documentation/stable/refere
 Benefits of having ArangoDB as a backend to NetworkX include:
 1. No need to re-create the graph every time you start a new session.
 2. Access to GPU-accelerated graph analytics ([nx-cugraph](https://docs.rapids.ai/api/cugraph/nightly/nx_cugraph/nx_cugraph/)).
-2. Access to a database query language ([Arango Query Language](https://arangodb.com/sql-aql-comparison/)).
-3. Access to a visual interface for graph exploration ([ArangoDB Web UI](https://docs.arangodb.com/3.11/components/web-interface/graphs/)).
-4. Access to cross-collaboration on the same graph ([ArangoDB Cloud](https://dashboard.arangodb.cloud/)).
-
-6. Access to efficient distribution of graph data ([ArangoDB SmartGraphs](https://docs.arangodb.com/3.11/graphs/smartgraphs/)).
+3. Access to a database query language ([Arango Query Language](https://arangodb.com/sql-aql-comparison/)).
+4. Access to a visual interface for graph exploration ([ArangoDB Web UI](https://docs.arangodb.com/stable/components/web-interface/graphs/)).
+5. Access to cross-collaboration on the same graph ([ArangoDB Cloud](https://docs.arangodb.com/stable/get-started/set-up-a-cloud-instance/)).
+6. Access to efficient distribution of graph data ([ArangoDB SmartGraphs](https://docs.arangodb.com/stable/graphs/smartgraphs/)).
 
 <p align="center">
     <img src="./docs/_static/nxadb.png" style="height: 200px;">
@@ -55,7 +50,7 @@ Benefits of having ArangoDB as a backend to NetworkX include:
 
 ## Does this replace NetworkX?
 
-No. This is a plugin to NetworkX, which means that you can use NetworkX as you normally would, but with the added benefit of persisting your graphs to a database.
+Not really. This is a plugin to NetworkX, which means that you can use NetworkX as you normally would, but with the added benefit of persisting your graphs to a database.
 
 ```python
 import os
@@ -111,7 +106,7 @@ pip install nx-cugraph-cu12 --extra-index-url https://pypi.nvidia.com
 pip install nx-arangodb
 ```
 
-## What are the easiests ways to set up ArangoDB?
+## How can I set up ArangoDB?
 
 **1) Local Instance via Docker**
 
@@ -149,7 +144,7 @@ os.environ["DATABASE_NAME"] = credentials["dbName"]
 # ...
 ```
 
-## How does Algorithm Dispatching work?
+## How does algorithm dispatching work?
 
 `nx-arangodb` will automatically dispatch algorithm calls to either CPU or GPU based on if `nx-cugraph` is installed. We rely on a rust-based library called [phenolrs](https://github.com/arangoml/phenolrs) to retrieve ArangoDB Graphs as fast as possible.
 

_nx_arangodb/__init__.py

@@ -26,8 +26,8 @@
     "project": "nx-arangodb",
     "package": "nx_arangodb",
     "url": "https://github.com/arangodb/nx-arangodb",
-    "short_summary": "Remote storage backend.",
-    # "description": "TODO",
+    "short_summary": "ArangoDB storage backend to NetworkX.",
+    "description": "Persist, maintain, and reload NetworkX graphs with ArangoDB.",
     "functions": {
         # BEGIN: functions
         "shortest_path",
@@ -81,7 +81,6 @@ def get_info():
         "db_name": None,
         "read_parallelism": None,
         "read_batch_size": None,
-        "write_batch_size": None,
         "use_gpu": True,
     }
 

nx_arangodb/algorithms/shortest_paths/generic.py

@@ -54,7 +54,7 @@ def shortest_path(
         "weight": weight,
     }
 
-    result = list(G.aql(query, bind_vars=bind_vars))
+    result = list(G.query(query, bind_vars=bind_vars))
 
     if not result:
         raise nx.NodeNotFound(f"Either source {source} or target {target} is not in G")

nx_arangodb/classes/dict/node.py

@@ -19,6 +19,7 @@
     doc_delete,
     doc_insert,
     doc_update,
+    edges_delete,
     get_arangodb_graph,
     get_node_id,
     get_node_type_and_id,
@@ -303,21 +304,7 @@ def __delitem__(self, key: str) -> None:
         if not self.graph.has_vertex(node_id):
             raise KeyError(key)
 
-        # TODO: wrap in edges_delete() method
-        remove_statements = "\n".join(
-            f"REMOVE e IN `{edge_def['edge_collection']}` OPTIONS {{ignoreErrors: true}}"  # noqa
-            for edge_def in self.graph.edge_definitions()
-        )
-
-        query = f"""
-            FOR v, e IN 1..1 ANY @src_node_id GRAPH @graph_name
-                {remove_statements}
-        """
-
-        bind_vars = {"src_node_id": node_id, "graph_name": self.graph.name}
-
-        aql(self.db, query, bind_vars)
-        #####
+        edges_delete(self.db, self.graph, node_id)
 
         doc_delete(self.db, node_id)
 

nx_arangodb/classes/digraph.py

@@ -66,6 +66,13 @@ def __init__(
             self.remove_node = self.remove_node_override
             self.reverse = self.reverse_override
 
+            assert isinstance(self._succ, AdjListOuterDict)
+            assert isinstance(self._pred, AdjListOuterDict)
+            self._succ.mirror = self._pred
+            self._pred.mirror = self._succ
+            self._succ.traversal_direction = TraversalDirection.OUTBOUND
+            self._pred.traversal_direction = TraversalDirection.INBOUND
+
         if (
             not self.is_multigraph()
             and incoming_graph_data is not None
@@ -78,6 +85,8 @@ def __init__(
     #######################
 
     # TODO?
+    # If we want to continue with "Experimental Views" we need to implement the
+    # InEdgeView and OutEdgeView classes.
     # @cached_property
     # def in_edges(self):
     # pass

nx_arangodb/classes/function.py

@@ -578,6 +578,24 @@ def doc_delete(db: StandardDatabase, id: str, **kwargs: Any) -> None:
     db.delete_document(id, silent=True, **kwargs)
 
 
+def edges_delete(
+    db: StandardDatabase, graph: Graph, src_node_id: str, **kwargs: Any
+) -> None:
+    remove_statements = "\n".join(
+        f"REMOVE e IN `{edge_def['edge_collection']}` OPTIONS {{ignoreErrors: true}}"  # noqa
+        for edge_def in graph.edge_definitions()
+    )
+
+    query = f"""
+        FOR v, e IN 1..1 ANY @src_node_id GRAPH @graph_name
+            {remove_statements}
+    """
+
+    bind_vars = {"src_node_id": src_node_id, "graph_name": graph.name}
+
+    aql(db, query, bind_vars)
+
+
 def doc_insert(
     db: StandardDatabase,
     collection: str,