Initial commit

.github/workflows/ci.yaml

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+name: CI
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+env:
+  UV_SYSTEM_PYTHON: 1
+
+jobs:
+  uv-example:
+    name: python
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run tests
+        run: uv run pytest tests

.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Virtual environments
+.venv
+
+# Project files
+.idea/

.python-version

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+3.13

context/graph.py

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+import networkx as nx
+import time
+
+
+class Graph:
+    def __init__(self, concept_ids, hierarchy):
+        """
+        :param concept_ids: list of concept ids to create a hierarchy from
+        :param hierarchy: full hierarchy edge list (e.g. SNOMED's
+        CONCEPT_ANCESTOR.csv)
+        """
+        self.graph = nx.DiGraph()
+        start = time.time()
+
+
+
+        delta = time.time() - start
+        print(f"Processed data in {delta:.2f} seconds")
+
+    def add_edge(self, u, v):
+        self.graph.add_edge(u, v)
+
+    def remove_edge(self, u, v):
+        self.graph.remove_edge(u, v)
+
+    def has_edge(self, u, v):
+        return self.graph.has_edge(u, v)
+
+    def get_neighbors(self, u):
+        return list(self.graph.successors(u))

examples/example_usage.py

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+from context.graph import Graph
+import networkx as nx
+import polars as pl
+
+concept_ids = [1, 2, 3, 4]
+hierarchy = pl.read_csv("~/Desktop/snomed_vocabulary/CONCEPT_ANCESTOR.csv")
+
+g = Graph(concept_ids, hierarchy)
+

hello.py

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+def main():
+    print("Hello from context!")
+
+
+if __name__ == "__main__":
+    main()

pyproject.toml

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+[project]
+name = "context"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.13"
+dependencies = [
+    "networkx>=3.4.2",
+    "numpy>=2.2.0",
+    "polars>=1.17.1",
+]
+
+[dependency-groups]
+dev = [
+    "pytest>=8.3.4",
+]

tests/__init__.py

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+"""Requests test package initialisation."""
+
+import warnings

tests/test_edge-list.py

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+from context.graph import Graph
+import networkx as nx
+
+
+def test_addition():
+    assert (1 + 1) == 2
+
+
+def test_directed_graph():
+    concept_ids = [1, 2, 3, 4]
+    hierarchy = [(1, 2), (2, 3), (3, 4)]
+    g = Graph(concept_ids, hierarchy)
+    assert isinstance(g.graph, nx.DiGraph), "Graph is not a directed graph"