Add tests for hictkpy::BinTable

test/test_bin_table.py

@@ -0,0 +1,77 @@
+# Copyright (C) 2024 Roberto Rossini <roberros@uio.no>
+#
+# SPDX-License-Identifier: MIT
+
+
+import pytest
+
+import hictkpy
+
+from .helpers import numpy_avail, pandas_avail, pyarrow_avail
+
+
+class TestClass:
+    def test_accessors(self):
+        chroms = {"chr1": 1000, "chr2": 500}
+        bins = hictkpy.BinTable(chroms, 100)
+
+        assert len(bins.chromosomes()) == 2
+        assert bins.bin_size() == 100
+        assert len(bins) == 15
+
+    def test_getters(self):
+        chroms = {"chr1": 1000, "chr2": 500}
+        bins = hictkpy.BinTable(chroms, 100)
+
+        assert bins.get(1).chrom == "chr1"
+        assert bins.get(1).start == 100
+        assert bins.get(1).end == 200
+        with pytest.raises(Exception):
+            bins.get(9999)
+
+        assert bins.get_id("chr1", 153) == 1
+        with pytest.raises(Exception):
+            bins.get_id("abc", 100)
+
+    @pytest.mark.skipif(not numpy_avail(), reason="numpy is not available")
+    def test_vectorized_getters(self):
+        import numpy as np
+
+        chroms = {"chr1": 1000, "chr2": 500}
+        bins = hictkpy.BinTable(chroms, 100)
+
+        assert len(bins.get(np.array([1, 1]))) == 2
+        assert len(bins.get_ids(np.array(["chr1", "chr1"]), np.array([1, 1]))) == 2
+
+    @pytest.mark.skipif(not pandas_avail() or not pyarrow_avail(), reason="pandas is not available")
+    def test_merge(self):
+        import pandas as pd
+
+        chroms = {"chr1": 1000, "chr2": 500}
+        bins = hictkpy.BinTable(chroms, 100)
+
+        expected = pd.DataFrame(
+            {
+                "chrom1": pd.Categorical(["chr1", "chr2"], categories=["chr1", "chr2"]),
+                "start1": [0, 0],
+                "end1": [100, 100],
+                "chrom2": pd.Categorical(["chr1", "chr2"], categories=["chr1", "chr2"]),
+                "start2": [0, 0],
+                "end2": [100, 100],
+            }
+        )
+
+        bin_ids = pd.DataFrame({"bin1_id": [0, 10], "bin2_id": [0, 10]})
+
+        assert (expected == bins.merge(bin_ids).drop(columns=["bin1_id", "bin2_id"])).all().all()
+
+    def test_to_df(self):
+        chroms = {"chr1": 1000, "chr2": 500}
+        bins = hictkpy.BinTable(chroms, 100)
+
+        assert len(bins.to_df()) == len(bins)
+        assert len(bins.to_df("chr1")) == 10
+        assert len(bins.to_df("chr2:0-200")) == 2
+        assert len(bins.to_df("chr2\t0\t200", "BED")) == 2
+        with pytest.raises(RuntimeError):
+            bins.to_df("chr0")