Minimal refactor tests

tests/conftest.py

@@ -0,0 +1,52 @@
+import os
+from pathlib import Path
+
+import pytest
+import torch
+
+TEST_DIR = Path(__file__).parent
+ENV_PDB_DIR = os.environ.get("ENV_PDB_DIR")
+PDB_BASE_DIR = Path(ENV_PDB_DIR) if ENV_PDB_DIR else TEST_DIR / "test_files"
+
+
+@pytest.fixture
+def device():
+    return torch.device("cuda" if torch.cuda.is_available() else "cpu")
+
+@pytest.fixture(scope="session")
+def pdb_base_dir():
+    """Wrapper of constant PDB_BASE_DIR.
+    """
+    return PDB_BASE_DIR
+
+
+def _resolve_pdb_path(pdb_id):
+    """Resolves a PDB path, skipping if missing."""
+    path = PDB_BASE_DIR / pdb_id / f"{pdb_id}_final.pdb"
+    if not path.exists():
+        pytest.skip(f"PDB file not found: {path}")
+    return str(path)
+
+
+@pytest.fixture
+def pdb_6eey():
+    """6eey - standard PDB that passes all quality checks."""
+    return _resolve_pdb_path("6eey")
+
+
+@pytest.fixture
+def pdb_2b5w():
+    """2b5w - fails COM distance check."""
+    return _resolve_pdb_path("2b5w")
+
+
+@pytest.fixture
+def pdb_8dzt():
+    """8dzt - fails water clash check at 2% threshold with 2A distance."""
+    return _resolve_pdb_path("8dzt")
+
+
+@pytest.fixture
+def pdb_1deu():
+    """1deu - has insertion codes (52 residues with ins_code='P')."""
+    return _resolve_pdb_path("1deu")

tests/test_dataset.py

@@ -19,8 +19,6 @@
 All test cases created with assistance from Claude Code.
 """
 
-from pathlib import Path
-
 import numpy as np
 import pytest
 import torch
@@ -44,39 +42,6 @@
 )
 
 
-@pytest.fixture
-def pdb_base_dir():
-    """Base directory for PDB files."""
-    return Path("/sb/wankowicz_lab/data/srivasv/pdb_redo_data")
-
-
-@pytest.fixture
-def pdb_6eey(pdb_base_dir):
-    """Path to 6eey PDB file - should pass all quality checks."""
-    path = pdb_base_dir / "6eey" / "6eey_final.pdb"
-    if not path.exists():
-        pytest.skip(f"PDB file not found: {path}")
-    return str(path)
-
-
-@pytest.fixture
-def pdb_2b5w(pdb_base_dir):
-    """Path to 2b5w PDB file - should fail COM distance check."""
-    path = pdb_base_dir / "2b5w" / "2b5w_final.pdb"
-    if not path.exists():
-        pytest.skip(f"PDB file not found: {path}")
-    return str(path)
-
-
-@pytest.fixture
-def pdb_8dzt(pdb_base_dir):
-    """Path to 8dzt PDB file - should fail water clash check at 2% threshold."""
-    path = pdb_base_dir / "8dzt" / "8dzt_final.pdb"
-    if not path.exists():
-        pytest.skip(f"PDB file not found: {path}")
-    return str(path)
-
-
 @pytest.fixture
 def tmp_processed_dir(tmp_path):
     """Temporary directory for processed files."""

tests/test_encoder.py

@@ -20,11 +20,6 @@
 
 # ============== Fixtures ==============
 
-@pytest.fixture
-def device():
-    return torch.device("cuda" if torch.cuda.is_available() else "cpu")
-
-
 @pytest.fixture
 def sample_homogeneous_data():
     """Sample Data for testing ProteinGVPEncoder directly."""

tests/test_flow.py

@@ -19,11 +19,6 @@
 from src.gvp_encoder import GVPEncoder, ProteinGVPEncoder, make_encoder_data
 
 
-@pytest.fixture
-def device():
-    return torch.device("cuda" if torch.cuda.is_available() else "cpu")
-
-
 @pytest.fixture
 def simple_hetero_data(device):
     """Minimal HeteroData with protein and water nodes."""

tests/test_forward.py

@@ -77,11 +77,6 @@ def __exit__(self, exc_type, exc, tb):
         return False  # don't suppress exceptions
 
 
-@pytest.fixture
-def device():
-    return torch.device("cuda" if torch.cuda.is_available() else "cpu")
-
-
 def make_batched_hetero(
     device,
     n_graphs=2,