Add some basic smoke tests

These just check that the basic functions are working

Author: hyanwong

tests/test_smoke.py

@@ -0,0 +1,182 @@
+import msprime
+import pytest
+
+import tskit_arg_visualizer as argviz
+
+
+def _example_d3arg():
+    ts = msprime.sim_ancestry(
+        samples=4,
+        sequence_length=100,
+        recombination_rate=1e-2,
+        record_full_arg=True,
+        ploidy=1,
+        random_seed=123,
+    )
+    return ts, argviz.D3ARG.from_ts(ts)
+
+
+class TestRenderingSmoke:
+    def test_draw_returns_drawinfo_without_opening_browser(self, monkeypatch):
+        _, d3arg = _example_d3arg()
+
+        # Keep test non-interactive while still exercising HTML generation path.
+        monkeypatch.setattr(argviz, "display", lambda *_args, **_kwargs: None)
+
+        info = d3arg.draw(
+            width=320,
+            height=240,
+            tree_highlighting=False,
+            show_mutations=False,
+            is_notebook=True,
+        )
+
+        assert isinstance(info, argviz.DrawInfo)
+        # Width/height may be adjusted internally (e.g., axis/title spacing),
+        # so only assert broad sanity constraints here.
+        assert float(info.width) >= 320
+        assert float(info.height) >= 240
+        assert info.uid.startswith("arg_")
+
+        included_nodes = info.included.nodes
+        assert isinstance(included_nodes, list)
+        assert len(included_nodes) > 0
+        assert set(included_nodes).issubset(set(d3arg.nodes["id"]))
+
+    def test_draw_nodes_returns_drawinfo_without_opening_browser(self, monkeypatch):
+        _, d3arg = _example_d3arg()
+
+        monkeypatch.setattr(argviz, "display", lambda *_args, **_kwargs: None)
+
+        info = d3arg.draw_nodes(
+            seed_nodes=[d3arg.sample_order[0]],
+            depth=1,
+            width=320,
+            height=240,
+            tree_highlighting=False,
+            show_mutations=False,
+            is_notebook=True,
+        )
+
+        assert isinstance(info, argviz.DrawInfo)
+        assert float(info.width) >= 320
+        assert float(info.height) >= 240
+        assert info.uid.startswith("arg_")
+
+        included_nodes = info.included.nodes
+        assert isinstance(included_nodes, list)
+        assert len(included_nodes) > 0
+        assert set(included_nodes).issubset(set(d3arg.nodes["id"]))
+
+    def test_draw_genome_bar_smoke_notebook_mode(self, monkeypatch):
+        _, d3arg = _example_d3arg()
+
+        monkeypatch.setattr(argviz, "display", lambda *_args, **_kwargs: None)
+
+        result = d3arg.draw_genome_bar(
+            width=320,
+            show_mutations=True,
+            is_notebook=True,
+        )
+        assert result is None
+
+
+class TestGraphSubsetSmoke:
+    def test_from_ts_and_subset_graph_smoke(self):
+        ts, d3arg = _example_d3arg()
+
+        assert d3arg.num_samples == ts.num_samples
+        assert not d3arg.nodes.empty
+        assert not d3arg.edges.empty
+
+        subset = d3arg.subset_graph(seed_nodes=[d3arg.sample_order[0]], depth=1)
+        assert not subset.nodes.empty
+        assert not subset.edges.empty
+
+        node_ids = set(subset.nodes["id"].tolist())
+        assert set(subset.edges["source"]).issubset(node_ids)
+        assert set(subset.edges["target"]).issubset(node_ids)
+        assert set(subset.mutations["edge"]).issubset(set(subset.edges["id"]))
+
+
+class TestSecondaryPositionUtilities:
+    def test_extract_x_positions_from_json_smoke(self):
+        arg_no_labels = {
+            "width": 500,
+            "y_axis": {"include_labels": False},
+            "data": {
+                "nodes": [
+                    {"id": 1, "x": 50},
+                    {"id": 2, "x": 450},
+                ]
+            },
+        }
+        pos_no_labels = argviz.extract_x_positions_from_json(arg_no_labels)
+        assert pos_no_labels[1] == pytest.approx(0.0)
+        assert pos_no_labels[2] == pytest.approx(1.0)
+
+        arg_with_labels = {
+            "width": 500,
+            "y_axis": {"include_labels": True},
+            "data": {
+                "nodes": [
+                    {"id": 1, "x": 150},
+                    {"id": 2, "x": 450},
+                ]
+            },
+        }
+        pos_with_labels = argviz.extract_x_positions_from_json(arg_with_labels)
+        assert pos_with_labels[1] == pytest.approx(0.0)
+        assert pos_with_labels[2] == pytest.approx(1.0)
+
+    def test_calculate_evenly_distributed_positions_smoke(self):
+        positions = argviz.calculate_evenly_distributed_positions(
+            num_elements=5, start=0, end=1, round_to=3
+        )
+        assert len(positions) == 5
+        assert positions[0] == 0
+        assert positions[-1] == 1
+        assert positions == sorted(positions)
+
+        midpoint = argviz.calculate_evenly_distributed_positions(
+            num_elements=1, start=10, end=20, round_to=3
+        )
+        assert midpoint == [15.0]
+
+    def test_convert_time_to_position_monotonic_in_time_scale(self):
+        y_shift = 7
+        height = 200
+        y_for_recent = argviz.convert_time_to_position(
+            t=0,
+            min_time=0,
+            max_time=10,
+            scale="time",
+            unique_times=[0, 5, 10],
+            h_spacing=0.5,
+            height=height,
+            y_shift=y_shift,
+        )
+        y_for_ancient = argviz.convert_time_to_position(
+            t=10,
+            min_time=0,
+            max_time=10,
+            scale="time",
+            unique_times=[0, 5, 10],
+            h_spacing=0.5,
+            height=height,
+            y_shift=y_shift,
+        )
+        assert y_for_ancient < y_for_recent
+
+    def test_convert_time_to_position_rank_requires_known_time(self):
+        with pytest.raises(RuntimeError):
+            argviz.convert_time_to_position(
+                t=3,
+                min_time=0,
+                max_time=10,
+                scale="rank",
+                unique_times=[0, 1, 2],
+                h_spacing=0.5,
+                height=100,
+                y_shift=0,
+            )