adding some tests for taxonomy

tests/test_taxonomy.py

@@ -0,0 +1,57 @@
+import pytest
+import requests
+import tempfile
+from pathlib import Path
+from Bio.Phylo import BaseTree
+from nbt.Taxon import Taxon
+from taxonomy import read_bold_taxonomy, read_ncbi_taxonomy, get_tip_by_processid
+
+
+@pytest.fixture
+def bold_tree():
+    bold_file = Path(__file__).parent.parent / "examples" / "bold.xlsx"
+    return read_bold_taxonomy(bold_file)
+
+
+@pytest.fixture
+def ncbi_tree():
+    ncbi_url = "http://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz"
+
+    with tempfile.NamedTemporaryFile(suffix='.tar.gz', delete=False) as temp_file:
+        response = requests.get(ncbi_url)
+        response.raise_for_status()  # Raise an exception for bad status codes
+        temp_file.write(response.content)
+        temp_file_path = temp_file.name
+
+    try:
+        return read_ncbi_taxonomy(temp_file_path)
+    finally:
+        Path(temp_file_path).unlink()  # Delete the temporary file
+
+
+def test_get_tip_by_processid(bold_tree):
+    process_id = "BGENL1996-24"
+    tip = get_tip_by_processid(process_id, bold_tree)
+
+    assert isinstance(tip, Taxon)
+    assert tip.name == "Eremochlorita tessellata"
+    assert tip.taxonomic_rank == "species"
+
+
+def test_bold_tree_ancestry(bold_tree):
+    process_id = "BGENL1996-24"
+    tip = get_tip_by_processid(process_id, bold_tree)
+
+    class_ancestor = next(node for node in bold_tree.get_path(tip) if node.taxonomic_rank == "class")
+    assert class_ancestor.name == "Insecta"
+
+
+def test_ncbi_tree_structure(ncbi_tree):
+    insecta_node = next(node for node in ncbi_tree.get_nonterminals()
+                        if node.name == "Insecta" and node.taxonomic_rank == "class")
+
+    assert insecta_node is not None
+    assert insecta_node.guids['taxon'] == "50557"
+
+    terminal_descendants = list(insecta_node.get_terminals())
+    assert len(terminal_descendants) > 0