Add pytest suite with stubbed ispec connection

bcmproteomics/tests/test_ispec.py

@@ -0,0 +1,54 @@
+"""Pytest suite for bcmproteomics ispec module."""
+
+import pandas as pd
+
+from bcmproteomics import ispec
+
+
+class FakeConnection:
+    """Minimal connection stub returned by patched ``filedb_connect``."""
+
+    def __init__(self):
+        self.closed = False
+
+    def close(self):
+        self.closed = True
+
+
+def test_get_funcats_uses_stubbed_connection(monkeypatch):
+    """Ensure ``get_funcats`` relies on the patched connection and stays offline."""
+
+    fake_conn = FakeConnection()
+    captured = {}
+
+    def fake_filedb_connect(params=None):
+        captured["called"] = True
+        return fake_conn
+
+    def fake_read_sql(sql, conn, index_col=None):
+        captured["sql"] = sql
+        captured["conn"] = conn
+        captured["index_col"] = index_col
+        return pd.DataFrame(
+            {
+                "gene_u2gPeptiBAQAveCount": [1.0],
+                "gene_GeneSymbol": ["ABC"],
+                "gene_GeneDescription": ["Example"],
+                "gene_FunCats": ["Category"],
+            },
+            index=pd.Index([123], name="gene_GeneID"),
+        )
+
+    monkeypatch.setattr(ispec, "filedb_connect", fake_filedb_connect)
+    monkeypatch.setattr(ispec.pd, "read_sql", fake_read_sql)
+
+    result = ispec.get_funcats([123])
+
+    assert captured["called"] is True
+    assert captured["conn"] is fake_conn
+    assert captured["index_col"] == "gene_GeneID"
+    assert captured["sql"].startswith("Select gene_GeneID")
+    assert "123" in captured["sql"]
+    assert "GeneSymbol" in result.columns
+    assert result.index.name == "GeneID"
+    assert fake_conn.closed is True

requirements.txt

@@ -6,3 +6,4 @@ scikit-learn
 statsmodels
 seaborn
 click
+pytest