Merge pull request #606 from DeepRank/fix_inspect_function_trainer_gc…

…roci2

fix: OSError when retrieving source code for lambda functions

deeprank2/trainer.py

@@ -6,6 +6,7 @@
 from time import time
 from typing import Any
 
+import dill
 import h5py
 import numpy as np
 import torch
@@ -946,7 +947,11 @@ def _save_model(self) -> dict[str, Any]:
             for key in features_transform_to_save.values():
                 if key["transform"] is None:
                     continue
-                str_expr = inspect.getsource(key["transform"])
+                # Serialize the function
+                serialized_func = dill.dumps(key["transform"])
+                # Deserialize the function
+                deserialized_func = dill.loads(serialized_func)  # noqa: S301
+                str_expr = inspect.getsource(deserialized_func)
                 match = re.search(r"[\"|\']transform[\"|\']:.*(lambda.*).*,.*[\"|\']standardize[\"|\'].*", str_expr).group(1)
                 key["transform"] = match
 

deeprank2/utils/grid.py

@@ -7,7 +7,7 @@
 import h5py
 import numpy as np
 from numpy.typing import NDArray
-from scipy.signal import bspline
+from scipy.interpolate import BSpline
 
 from deeprank2.domain import gridstorage
 
@@ -190,9 +190,9 @@ def _get_mapped_feature_bsp_line(
 
         fx, fy, fz = position
         bsp_data = (
-            bspline((self.xgrid - fx) / self._settings.resolutions[0], order)
-            * bspline((self.ygrid - fy) / self._settings.resolutions[1], order)
-            * bspline((self.zgrid - fz) / self._settings.resolutions[2], order)
+            BSpline((self.xgrid - fx) / self._settings.resolutions[0], order)
+            * BSpline((self.ygrid - fy) / self._settings.resolutions[1], order)
+            * BSpline((self.zgrid - fz) / self._settings.resolutions[2], order)
         )
 
         return value * bsp_data

docs/conf.py

@@ -28,7 +28,7 @@
     "scipy",
     "h5py",
     "sklearn",
-    "scipy.signal",
+    "scipy.interpolate",
     "torch",
     "torch.utils",
     "torch.utils.data",

env/deeprank2-docker.yml

@@ -25,7 +25,7 @@ dependencies:
   - pytorch-spline-conv>=1.2.2
   - tables>=3.8.0
   - numpy>=1.21.5
-  - scipy>=1.11.2
+  - scipy>=1.13.1
   - h5py>=3.6.0
   - networkx>=2.6.3
   - matplotlib>=3.5.1

env/deeprank2.yml

@@ -25,7 +25,7 @@ dependencies:
   - pytorch-spline-conv>=1.2.2
   - tables>=3.8.0
   - numpy>=1.21.5
-  - scipy>=1.11.2
+  - scipy>=1.13.1
   - h5py>=3.6.0
   - networkx>=2.6.3
   - matplotlib>=3.5.1

pyproject.toml

@@ -65,6 +65,10 @@ exclude = ["tests", "tests*", "*tests.*", "*tests"]
 [tool.setuptools.package-data]
 "*" = ["*.xlsx", "*.param", "*.top", "*residue-classes"]
 
+[tool.pytest.ini_options]
+# pytest options: -ra: show summary info for all test outcomes
+addopts = "-ra"  
+
 [tool.ruff]
 line-length = 159