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docs/source/dataclustering.rst

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+DataClustering module
+=====================
+.. automodule:: pygenstability.DataClustering
+   :members:

tests/test_dataclustering.py

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+"""Test dataclustering module."""
+import pytest
+from pathlib import Path
+import yaml
+
+from pygenstability import DataClustering
+
+from dictdiffer import diff
+
+from .utils import _to_list
+
+DATA = Path(__file__).absolute().parent / "data"
+
+
+def test_DataClustering(X):
+    """Test the DataClustering class"""
+    # default
+    clustering = DataClustering()
+    res = clustering.fit(X)
+    results = _to_list({"labels": res.labels_, "results": res.results_})
+    yaml.dump(results, open(DATA / "test_dataclustering_default.yaml", "w"))
+    expected_results = yaml.safe_load(open(DATA / "test_dataclustering_default.yaml", "r"))
+    assert len(list(diff(expected_results, results, tolerance=1e-5))) == 0
+
+    # with knn
+    clustering = DataClustering(graph_method="knn-mst")
+    res = clustering.fit(X)
+    results = _to_list({"labels": res.labels_, "results": res.results_})
+    yaml.dump(results, open(DATA / "test_dataclustering_knn.yaml", "w"))
+    expected_results = yaml.safe_load(open(DATA / "test_dataclustering_knn.yaml", "r"))
+    assert len(list(diff(expected_results, results, tolerance=1e-5))) == 0
+
+    # precomputed
+    clustering = DataClustering(graph_method="precomputed")
+    with pytest.raises(AssertionError):
+        res = clustering.fit(X)
+
+    # precompute it as default
+    clustering.method = "cknn-mst"
+    X = clustering.get_graph(X)
+    clustering.method = "precomputed"
+
+    res = clustering.fit(X)
+    results = _to_list({"labels": res.labels_, "results": res.results_})
+    expected_results = yaml.safe_load(open(DATA / "test_dataclustering_default.yaml", "r"))
+    assert len(list(diff(expected_results, results, tolerance=1e-5))) == 0
+
+    # scales selection
+    scales = clustering.scale_selection()
+    assert len(scales) == 4
+
+    # test plots
+    clustering.plot_scan(live=False)
+    clustering.plot_robust_partitions(x_coord=X[:, 0], y_coord=X[:, 1], show=False)
+    clustering.plot_robust_partitions(x_coord=X[:, 0], y_coord=X[:, 1], show=True)
+    clustering.plot_sankey(live=False)
+
+    clustering.results_ = None
+    assert clustering.plot_scan() == None