Sample: do not check data by default; minor fixes

miplearn/features/sample.py

@@ -110,10 +110,12 @@ class MemorySample(Sample):
     def __init__(
         self,
         data: Optional[Dict[str, Any]] = None,
+        check_data: bool = False,
     ) -> None:
         if data is None:
             data = {}
         self._data: Dict[str, Any] = data
+        self._check_data = check_data
 
     @overrides
     def get_bytes(self, key: str) -> Optional[Bytes]:
@@ -142,19 +144,22 @@ class MemorySample(Sample):
     def put_scalar(self, key: str, value: Scalar) -> None:
         if value is None:
             return
-        self._assert_is_scalar(value)
+        if self._check_data:
+            self._assert_is_scalar(value)
         self._put(key, value)
 
     @overrides
     def put_vector(self, key: str, value: Vector) -> None:
         if value is None:
             return
-        self._assert_is_vector(value)
+        if self._check_data:
+            self._assert_is_vector(value)
         self._put(key, value)
 
     @overrides
     def put_vector_list(self, key: str, value: VectorList) -> None:
-        self._assert_is_vector_list(value)
+        if self._check_data:
+            self._assert_is_vector_list(value)
         self._put(key, value)
 
     def _get(self, key: str) -> Optional[Any]:
@@ -175,8 +180,14 @@ class Hdf5Sample(Sample):
     are actually accessed, and therefore it is more scalable.
     """
 
-    def __init__(self, filename: str, mode: str = "r+") -> None:
+    def __init__(
+        self,
+        filename: str,
+        mode: str = "r+",
+        check_data: bool = False,
+    ) -> None:
         self.file = h5py.File(filename, mode, libver="latest")
+        self._check_data = check_data
 
     @overrides
     def get_bytes(self, key: str) -> Optional[Bytes]:
@@ -230,27 +241,30 @@ class Hdf5Sample(Sample):
 
     @overrides
     def put_bytes(self, key: str, value: Bytes) -> None:
-        assert isinstance(
+        if self._check_data:
-            value, (bytes, bytearray)
+            assert isinstance(
-        ), f"bytes expected; found: {value}"  # type: ignore
+                value, (bytes, bytearray)
+            ), f"bytes expected; found: {value}"  # type: ignore
         self._put(key, np.frombuffer(value, dtype="uint8"), compress=True)
 
     @overrides
     def put_scalar(self, key: str, value: Any) -> None:
         if value is None:
             return
-        self._assert_is_scalar(value)
+        if self._check_data:
+            self._assert_is_scalar(value)
         self._put(key, value)
 
     @overrides
     def put_vector(self, key: str, value: Vector) -> None:
         if value is None:
             return
-        self._assert_is_vector(value)
+        if self._check_data:
+            self._assert_is_vector(value)
 
         for v in value:
             # Convert strings to bytes
-            if isinstance(v, str):
+            if isinstance(v, str) or v is None:
                 value = np.array(
                     [u if u is not None else b"" for u in value],
                     dtype="S",
@@ -266,7 +280,8 @@ class Hdf5Sample(Sample):
 
     @overrides
     def put_vector_list(self, key: str, value: VectorList) -> None:
-        self._assert_is_vector_list(value)
+        if self._check_data:
+            self._assert_is_vector_list(value)
         padded, lens = _pad(value)
         self.put_vector(f"{key}_lengths", lens)
         data = None
@@ -297,7 +312,6 @@ class Hdf5Sample(Sample):
 
 
 def _pad(veclist: VectorList) -> Tuple[VectorList, List[int]]:
-    veclist = deepcopy(veclist)
     lens = [len(v) if v is not None else -1 for v in veclist]
     maxlen = max(lens)
 

tests/features/test_extractor.py

@@ -2,13 +2,20 @@
 #  Copyright (C) 2020-2021, UChicago Argonne, LLC. All rights reserved.
 #  Released under the modified BSD license. See COPYING.md for more details.
 
+import sys
+import time
+from typing import Any
+
 import numpy as np
+import gurobipy as gp
 
 from miplearn.features.extractor import FeaturesExtractor
-from miplearn.features.sample import Sample, MemorySample
+from miplearn.features.sample import MemorySample, Hdf5Sample
-from miplearn.solvers.internal import Variables, Constraints
+from miplearn.instance.base import Instance
 from miplearn.solvers.gurobi import GurobiSolver
+from miplearn.solvers.internal import Variables, Constraints
 from miplearn.solvers.tests import assert_equals
+import cProfile
 
 inf = float("inf")
 
@@ -166,3 +173,27 @@ def test_assert_equals() -> None:
     assert_equals(np.array([True, True]), [True, True])
     assert_equals((1.0,), (1.0,))
     assert_equals({"x": 10}, {"x": 10})
+
+
+class MpsInstance(Instance):
+    def __init__(self, filename: str) -> None:
+        super().__init__()
+        self.filename = filename
+
+    def to_model(self) -> Any:
+        return gp.read(self.filename)
+
+
+if __name__ == "__main__":
+    solver = GurobiSolver()
+    instance = MpsInstance(sys.argv[1])
+    solver.set_instance(instance)
+    solver.solve_lp(tee=True)
+    extractor = FeaturesExtractor(with_lhs=False)
+    sample = Hdf5Sample("tmp/prof.h5", mode="w")
+
+    def run():
+        extractor.extract_after_load_features(instance, solver, sample)
+        extractor.extract_after_lp_features(solver, sample)
+
+    cProfile.run("run()", filename="tmp/prof")