event based temporal SEIR algorithm (#1415)

* event based temporal SEIR algorithm

* fix the event queue so it is actually a min heap and return algorithm result

* add proper test

* add python interface

* improve the repr for AlgorithmResult

* more repr cleanup

* get rid of the Options in AlgorithmResult by only returning vertices that actually have results

* basic python test

* add python docs

* fix the docs ignores

* this should not be a doc comment

* bring back the AlgorithmResult docs hack

* fix formatting and actually include in docs

* no doctests for python!

* bring back missing import

.gitignore

@@ -7,24 +7,20 @@ massif.*
 **/.env/
 comparison-benchmark/python/data/*
 .vscode
-docs/source/_rustdoc/*
-docs/nx.html
-docs/graph.html
-docs/build/*
 .DS_Store
 docs/logs/*
 .python-version
 .ipynb_checkpoints
-docs/source/_rustdoc/*
-docs/build/*
-docs/logs/*
 _autosummary
 examples/docker/lotr/lotr
 examples/py/enron/emails.csv
 examples/py/enron/lib/
+docs/source/_rustdoc/
+docs/logs/
 /docs/lib/
 /docs/build/
-docs/source/
+docs/nx.html
+docs/graph.html
 .env
 
 # Byte-compiled / optimized / DLL files

docs/source/reference/algorithms/dynamics.rst

@@ -0,0 +1,4 @@
+Dynamics
+********
+
+.. autofunction:: raphtory.algorithms.temporal_SEIR

docs/source/reference/algorithms/index.rst

@@ -9,6 +9,7 @@ Algorithms
    centrality
    community_detection
    cores
+   dynamics
    metrics
    motifs
    pathing

python/src/graphql.rs

@@ -13,12 +13,11 @@ use raphtory_core::{
     },
     vectors::{embeddings::openai_embedding, EmbeddingFunction},
 };
-use raphtory_graphql::{url_decode_graph, url_encode_graph, RaphtoryServer};
+use raphtory_graphql::{url_encode_graph, RaphtoryServer};
 use reqwest::Client;
 use serde_json::{json, Map, Number, Value};
 use std::{
     collections::HashMap,
-    future::Future,
     path::PathBuf,
     thread,
     thread::{sleep, JoinHandle},

python/src/lib.rs

@@ -100,6 +100,7 @@ fn raphtory(py: Python<'_>, m: &PyModule) -> PyResult<()> {
         hits,
         balance,
         label_propagation,
+        temporal_SEIR,
     );
     m.add_submodule(algorithm_module)?;
 

python/tests/test_algorithms.py

@@ -311,7 +311,6 @@ def test_single_source_shortest_path():
     assert res_one.get_all_with_names() == {
         "1": ["1"],
         "2": ["1", "2"],
-        "3": None,
         "4": ["1", "4"],
     }
     assert (
@@ -461,3 +460,21 @@ def test_label_propagation_algorithm():
     assert len(result) == len(expected)
     for group in expected:
         assert group in result
+
+
+def test_temporal_SEIR():
+    g = Graph()
+    g.add_edge(1, 1, 2)
+    g.add_edge(2, 2, 3)
+    g.add_edge(3, 3, 4)
+    g.add_edge(4, 4, 5)
+    # Should be seeded with 2 vertices
+    res = algorithms.temporal_SEIR(g, 2, 1.0, 0, rng_seed=1)
+    seeded = [v for v in res.get_all_values() if v.infected == 0]
+    assert len(seeded) == 2
+
+    res = algorithms.temporal_SEIR(g, [1], 1.0, 0, rng_seed=1).sort_by_value(reverse=False)
+    for i, (n, v) in enumerate(res):
+        assert n == g.node(i+1)
+        assert v.infected == i
+

raphtory/Cargo.toml

@@ -80,6 +80,7 @@ quickcheck_macros = "1"
 tempfile = "3.2"
 tokio = { version = "1.27.0", features = ["full"]} # for vector testing
 dotenv = "0.15.0" # for vector testing
+streaming-stats = "0.2"
 
 [features]
 default = []