From f79f64e92fdf735c24433abb1a5efd758738fa25 Mon Sep 17 00:00:00 2001
From: Adam Taranto <adam.p.taranto@gmail.com>
Date: Mon, 14 Oct 2024 14:09:57 +1100
Subject: [PATCH] init tests

---
 src/python/tests/test_add.py | 160 +++++++++++++++++++++++++++++++++++
 1 file changed, 160 insertions(+)
 create mode 100644 src/python/tests/test_add.py

diff --git a/src/python/tests/test_add.py b/src/python/tests/test_add.py
new file mode 100644
index 0000000..c0406b6
--- /dev/null
+++ b/src/python/tests/test_add.py
@@ -0,0 +1,160 @@
+import pytest
+
+from oxli import KmerCountTable
+
+
+def test_add_basic():
+    """Test basic addition of two KmerCountTables."""
+    table1 = KmerCountTable(5)
+    table2 = KmerCountTable(5)
+
+    table1.consume("ATGCATGCA")
+    table2.consume("ATGCATGCA")
+
+    counts_added, new_keys = table1.add(table2)
+
+    assert counts_added == 5  # 5 kmers in "ATGCATGCA"
+    assert new_keys == 0  # No new keys added
+    assert table1.sum_counts == 10  # Each kmer counted twice
+
+
+def test_add_different_content():
+    """Test addition of KmerCountTables with different content."""
+    table1 = KmerCountTable(5)
+    table2 = KmerCountTable(5)
+
+    table1.consume("ATGCATGCA")
+    table2.consume("TGCATGCATGG")
+
+    counts_added, new_keys = table1.add(table2)
+
+    assert len(table1) == 3
+    assert counts_added == 7
+    assert new_keys == 1  # One new kmer: "CATGG" "3442404512935954368"
+    assert table1.sum_counts == 12
+
+
+def test_add_different_ksize():
+    """Test addition of KmerCountTables with different ksizes."""
+    table1 = KmerCountTable(5)
+    table2 = KmerCountTable(6)
+
+    with pytest.raises(ValueError):
+        table1.add(table2)
+
+
+def test_add_empty_tables():
+    """Test addition of empty KmerCountTables."""
+    table1 = KmerCountTable(5)
+    table2 = KmerCountTable(5)
+
+    counts_added, new_keys = table1.add(table2)
+
+    assert counts_added == 0
+    assert new_keys == 0
+    assert table1.sum_counts == 0
+
+
+def test_add_to_empty_table():
+    """Test addition to an empty KmerCountTable."""
+    table1 = KmerCountTable(5)
+    table2 = KmerCountTable(5)
+
+    table2.consume("ATGCATGCA")
+
+    counts_added, new_keys = table1.add(table2)
+
+    assert len(table1) == 2
+    assert counts_added == 5
+    assert new_keys == 2  # All keys are new
+    assert table1.sum_counts == 5
+
+
+def test_add_consumed_attribute():
+    """Test that the 'consumed' attribute is correctly updated."""
+    table1 = KmerCountTable(5)
+    table2 = KmerCountTable(5)
+
+    table1.consume("ATGCA")
+    table2.consume("TGCAT")
+
+    initial_consumed = table1.consumed
+    table1.add(table2)
+
+    assert table1.consumed == initial_consumed + table2.consumed
+
+
+@pytest.mark.parametrize(
+    "store_kmers1,store_kmers2",
+    [(True, True), (True, False), (False, True), (False, False)],
+)
+def test_add_store_kmers_combinations(store_kmers1, store_kmers2, capfd):
+    """Test addition with different combinations of store_kmers option."""
+    table1 = KmerCountTable(5, store_kmers=store_kmers1)
+    table2 = KmerCountTable(5, store_kmers=store_kmers2)
+
+    table1.consume("ATGCA")
+    table2.consume("GGCAT")
+
+    counts_added, new_keys = table1.add(table2)
+
+    assert counts_added == 1
+    assert new_keys == 1
+
+    captured = capfd.readouterr()
+    if store_kmers1 and not store_kmers2:
+        assert "Warning: Incoming table does not store k-mers" in captured.err
+
+    if store_kmers1 and store_kmers2:
+        assert table1.dump_kmers(sortkeys=True) == [("ATGCA", 1), ("ATGCC", 1)]
+
+
+def test_add_large_tables():
+    """Test addition of large KmerCountTables to check performance."""
+    table1 = KmerCountTable(5)
+    table2 = KmerCountTable(5)
+
+    long_seq = "ATGC" * 100000  # 400,000 base pairs
+    table1.consume(long_seq)
+    table2.consume(long_seq)
+
+    counts_added, new_keys = table1.add(table2)
+
+    assert counts_added == 399996  # (400000 - 5 + 1) kmers
+    assert new_keys == 0
+    assert table1.sum_counts == 799992  # Each kmer counted twice
+
+
+def test_add_multiple_times():
+    """Test adding multiple KmerCountTables."""
+    table1 = KmerCountTable(5)
+    table2 = KmerCountTable(5)
+    table3 = KmerCountTable(5)
+
+    table1.consume("ATGCA")
+    table2.consume("TGCAT")
+    table3.consume("GCATG")
+
+    table1.add(table2)
+    counts_added, new_keys = table1.add(table3)
+
+    assert counts_added == 1
+    assert new_keys == 1
+    assert table1.sum_counts == 3
+
+
+def test_add_self():
+    """Test adding a KmerCountTable to itself."""
+    table = KmerCountTable(5)
+    table.consume("ATGCATGCA")
+
+    with pytest.raises(ValueError, match="Cannot add KmerCountTable to itself."):
+        table.add(table)
+
+    # Ensure the original table is unchanged
+    assert table.sum_counts() == 5  # 5 kmers in "ATGCATGCA"
+
+
+# Run the tests
+if __name__ == "__main__":
+    pytest.main([__file__])