Lint az py fixes

.github/workflows/deepretro_lint.yml

@@ -78,7 +78,7 @@ jobs:
 
       - name: Run ty check
         run: |
-          uv run --project deepretro --with ty ty check deepretro \
+          uv run --isolated --no-project --with ty ty check deepretro \
             --python-version 3.12 \
             --ignore unresolved-import \
             --ignore invalid-method-override \

.gitignore

@@ -18,3 +18,5 @@ coverage/
 docs/build/
 docs/_build/
 *.egg-info/
+deepretro/build/
+.worktrees/

deepretro/algorithms/stability_checker.py

@@ -70,6 +70,10 @@
 * `is_valid_smiles` — quick check that a SMILES string parses.
 """
 
+from __future__ import annotations
+
+from typing import Any
+
 from rdkit import Chem
 from rdkit.Chem import Descriptors
 from rdkit.Chem.rdMolDescriptors import (
@@ -82,8 +86,6 @@
     CalcNumBridgeheadAtoms,
 )
 
-from typing import Any
-
 # Helpers
 
 

deepretro/pyproject.toml

@@ -29,6 +29,10 @@ docs = [
     "sphinx-autodoc-typehints>=3.0",
     "myst-parser>=4.0",
 ]
+az = [
+    "aizynthfinder",
+    "pillow",
+]
 
 [project.urls]
 Repository = "https://github.com/deepforestsci/DeepRetro"

deepretro/tests/test_az.py

@@ -16,13 +16,23 @@
 from pathlib import Path
 
 import pytest
+from deepretro.utils.cache import CacheManager
 
 # Skip entire module if aizynthfinder is not installed
 aizynthfinder = pytest.importorskip("aizynthfinder")
 
 PROJECT_ROOT = Path(__file__).resolve().parents[2]
 AZ_MODULE_PATH = PROJECT_ROOT / "deepretro" / "utils" / "az.py"
 AZ_MODULE_NAME = "_deepretro_utils_az_under_test"
+_BASIC_ROUTE = [
+    {
+        "type": "mol",
+        "hide": False,
+        "smiles": "CCO",
+        "is_chemical": True,
+        "in_stock": True,
+    }
+]
 
 
 def _download_aizynth_models(models_dir: Path) -> None:
@@ -74,16 +84,6 @@ def az_module_with_models(az_module, az_models_dir):
     return az_module
 
 
-def _get_run_az_impl(az_module):
-    """Get the underlying run_az implementation (bypassing cache)."""
-    return getattr(az_module.run_az, "__wrapped__", az_module.run_az)
-
-
-def _get_run_az_with_img_impl(az_module):
-    """Get the underlying run_az_with_img implementation (bypassing cache)."""
-    return getattr(az_module.run_az_with_img, "__wrapped__", az_module.run_az_with_img)
-
-
 @pytest.mark.parametrize(
     ("smiles", "expected"),
     [
@@ -102,8 +102,7 @@ def test_is_basic_molecule_chemical_thresholds(az_module, smiles, expected):
 @pytest.mark.slow
 def test_run_az_returns_valid_result(az_module_with_models):
     """Test run_az with real AiZynthFinder returns (bool, list) with valid structure."""
-    run_az = _get_run_az_impl(az_module_with_models)
-    status, routes = run_az("C1CCCCC1", az_model="USPTO")
+    status, routes = az_module_with_models.run_az("C1CCCCC1", az_model="USPTO")
     assert isinstance(status, bool)
     assert isinstance(routes, list)
     # Routes may be empty or contain dicts with expected keys
@@ -115,9 +114,8 @@ def test_run_az_returns_valid_result(az_module_with_models):
 @pytest.mark.slow
 def test_run_az_uses_fallback_config_when_model_missing(az_module_with_models):
     """Test run_az falls back to AZ_MODEL_CONFIG_PATH when model-specific config missing."""
-    run_az = _get_run_az_impl(az_module_with_models)
     # MISSING_MODEL has no config in AZ_MODELS_PATH, so uses fallback
-    status, routes = run_az("C1CCCCC1", az_model="MISSING_MODEL")
+    status, routes = az_module_with_models.run_az("C1CCCCC1", az_model="MISSING_MODEL")
     assert isinstance(status, bool)
     assert isinstance(routes, list)
 
@@ -130,32 +128,46 @@ def test_run_az_raises_if_no_config_available(tmp_path, monkeypatch, az_module):
     monkeypatch.setattr(az_module, "AZ_MODEL_CONFIG_PATH", str(missing_fallback))
     monkeypatch.setattr(az_module, "BASIC_MOLECULES", [])
 
-    run_az = _get_run_az_impl(az_module)
     with pytest.raises(FileNotFoundError, match=re.escape(str(missing_fallback))):
-        run_az("CCCCC", az_model="MISSING_MODEL")
+        az_module.run_az("CCCCC", az_model="MISSING_MODEL")
 
 
 def test_run_az_short_circuits_for_feedstock_smiles(az_module_with_models):
     """Test run_az returns early for basic molecules without calling AiZynthFinder."""
-    run_az = _get_run_az_impl(az_module_with_models)
-    status, routes = run_az("CCO", az_model="USPTO")
+    status, routes = az_module_with_models.run_az("CCO", az_model="USPTO")
     assert status is True
-    assert routes == [
-        {
-            "type": "mol",
-            "hide": False,
-            "smiles": "CCO",
-            "is_chemical": True,
-            "in_stock": True,
-        }
-    ]
+    assert routes == _BASIC_ROUTE
 
 
+def test_run_az_has_no_cache_side_effect_without_cache(
+    az_module_with_models, tmp_path, monkeypatch
+):
+    """run_az should not create cache state unless the caller passes one in."""
+    cache_dir = tmp_path / "cache"
+    monkeypatch.setenv("DEEPRETRO_CACHE_DIR", str(cache_dir))
+
+    status, routes = az_module_with_models.run_az("CCO", az_model="USPTO")
+
+    assert status is True
+    assert routes == _BASIC_ROUTE
+    assert not cache_dir.exists()
+
+
+def test_run_az_uses_explicit_cache(az_module_with_models):
+    """run_az should reuse results only when an explicit cache is provided."""
+    cache = CacheManager()
+
+    first = az_module_with_models.run_az("CCO", az_model="USPTO", cache=cache)
+    second = az_module_with_models.run_az("CCO", az_model="USPTO", cache=cache)
+
+    assert first == second
+    assert cache.stats().hits == 1
+    assert cache.stats().misses == 1
+    assert cache.stats().num_entries == 1
 @pytest.mark.slow
 def test_run_az_with_img_returns_valid_result(az_module_with_models):
     """Test run_az_with_img with real AiZynthFinder returns (bool, list, images)."""
-    run_az_with_img = _get_run_az_with_img_impl(az_module_with_models)
-    status, routes, images = run_az_with_img("C1CCCCC1")
+    status, routes, images = az_module_with_models.run_az_with_img("C1CCCCC1")
     assert isinstance(status, bool)
     assert isinstance(routes, list)
     # images can be list of PIL Images or None
@@ -165,16 +177,21 @@ def test_run_az_with_img_returns_valid_result(az_module_with_models):
 
 def test_run_az_with_img_short_circuits_for_basic_molecules(az_module_with_models):
     """Test run_az_with_img returns early for basic molecules."""
-    run_az_with_img = _get_run_az_with_img_impl(az_module_with_models)
-    status, routes, images = run_az_with_img("CCO")
+    status, routes, images = az_module_with_models.run_az_with_img("CCO")
     assert status is True
-    assert routes == [
-        {
-            "type": "mol",
-            "hide": False,
-            "smiles": "CCO",
-            "is_chemical": True,
-            "in_stock": True,
-        }
-    ]
+    assert routes == _BASIC_ROUTE
     assert images is None
+
+
+def test_run_az_with_img_uses_explicit_cache(az_module_with_models):
+    """run_az_with_img should also cache only through the provided instance."""
+    cache = CacheManager()
+
+    first = az_module_with_models.run_az_with_img("CCO", cache=cache)
+    second = az_module_with_models.run_az_with_img("CCO", cache=cache)
+
+    assert first == second
+    assert first == (True, _BASIC_ROUTE, None)
+    assert cache.stats().hits == 1
+    assert cache.stats().misses == 1
+    assert cache.stats().num_entries == 1