Remove most usages of put_{vector,vector_list}; deprecate get_set

miplearn/components/objective.py

@@ -3,7 +3,7 @@
 #  Released under the modified BSD license. See COPYING.md for more details.
 
 import logging
-from typing import List, Dict, Any, TYPE_CHECKING, Tuple, Optional
+from typing import List, Dict, Any, TYPE_CHECKING, Tuple, Optional, cast
 
 import numpy as np
 from overrides import overrides
@@ -77,10 +77,11 @@ class ObjectiveValueComponent(Component):
         _: Optional[Instance],
         sample: Sample,
     ) -> Tuple[Dict[str, List[List[float]]], Dict[str, List[List[float]]]]:
-        lp_instance_features = sample.get_vector("lp_instance_features")
-        if lp_instance_features is None:
-            lp_instance_features = sample.get_vector("static_instance_features")
-        assert lp_instance_features is not None
+        lp_instance_features_np = sample.get_array("lp_instance_features")
+        if lp_instance_features_np is None:
+            lp_instance_features_np = sample.get_array("static_instance_features")
+        assert lp_instance_features_np is not None
+        lp_instance_features = cast(List[float], lp_instance_features_np.tolist())
 
         # Features
         x: Dict[str, List[List[float]]] = {

miplearn/components/primal.py

@@ -142,13 +142,13 @@ class PrimalSolutionComponent(Component):
     ) -> Tuple[Dict[Category, List[List[float]]], Dict[Category, List[List[float]]]]:
         x: Dict = {}
         y: Dict = {}
-        instance_features = sample.get_vector("static_instance_features")
+        instance_features = sample.get_array("static_instance_features")
         mip_var_values = sample.get_array("mip_var_values")
-        var_features = sample.get_vector_list("lp_var_features")
+        var_features = sample.get_array("lp_var_features")
         var_names = sample.get_array("static_var_names")
         var_categories = sample.get_array("static_var_categories")
         if var_features is None:
-            var_features = sample.get_vector_list("static_var_features")
+            var_features = sample.get_array("static_var_features")
         assert instance_features is not None
         assert var_features is not None
         assert var_names is not None

miplearn/components/static_lazy.py

@@ -207,14 +207,14 @@ class StaticLazyConstraintsComponent(Component):
         x: Dict[ConstraintCategory, List[List[float]]] = {}
         y: Dict[ConstraintCategory, List[List[float]]] = {}
         cids: Dict[ConstraintCategory, List[ConstraintName]] = {}
-        instance_features = sample.get_vector("static_instance_features")
-        constr_features = sample.get_vector_list("lp_constr_features")
+        instance_features = sample.get_array("static_instance_features")
+        constr_features = sample.get_array("lp_constr_features")
         constr_names = sample.get_array("static_constr_names")
-        constr_categories = sample.get_vector("static_constr_categories")
+        constr_categories = sample.get_array("static_constr_categories")
         constr_lazy = sample.get_array("static_constr_lazy")
         lazy_enforced = sample.get_set("mip_constr_lazy_enforced")
         if constr_features is None:
-            constr_features = sample.get_vector_list("static_constr_features")
+            constr_features = sample.get_array("static_constr_features")
 
         assert instance_features is not None
         assert constr_features is not None
@@ -227,7 +227,7 @@ class StaticLazyConstraintsComponent(Component):
             if not constr_lazy[cidx]:
                 continue
             category = constr_categories[cidx]
-            if category is None:
+            if len(category) == 0:
                 continue
             if category not in x:
                 x[category] = []

miplearn/features/sample.py

@@ -38,15 +38,6 @@ VectorList = Union[
 class Sample(ABC):
     """Abstract dictionary-like class that stores training data."""
 
-    @abstractmethod
-    def get_bytes(self, key: str) -> Optional[Bytes]:
-        warnings.warn("Deprecated", DeprecationWarning)
-        return None
-
-    @abstractmethod
-    def put_bytes(self, key: str, value: Bytes) -> None:
-        warnings.warn("Deprecated", DeprecationWarning)
-
     @abstractmethod
     def get_scalar(self, key: str) -> Optional[Any]:
         pass
@@ -64,15 +55,6 @@ class Sample(ABC):
     def put_vector(self, key: str, value: Vector) -> None:
         warnings.warn("Deprecated", DeprecationWarning)
 
-    @abstractmethod
-    def get_vector_list(self, key: str) -> Optional[Any]:
-        warnings.warn("Deprecated", DeprecationWarning)
-        return None
-
-    @abstractmethod
-    def put_vector_list(self, key: str, value: VectorList) -> None:
-        warnings.warn("Deprecated", DeprecationWarning)
-
     @abstractmethod
     def put_array(self, key: str, value: Optional[np.ndarray]) -> None:
         pass
@@ -90,6 +72,7 @@ class Sample(ABC):
         pass
 
     def get_set(self, key: str) -> Set:
+        warnings.warn("Deprecated", DeprecationWarning)
         v = self.get_vector(key)
         if v:
             return set(v)
@@ -97,6 +80,7 @@ class Sample(ABC):
             return set()
 
     def put_set(self, key: str, value: Set) -> None:
+        warnings.warn("Deprecated", DeprecationWarning)
         v = list(value)
         self.put_vector(key, v)
 
@@ -114,15 +98,6 @@ class Sample(ABC):
         for v in value:
             self._assert_is_scalar(v)
 
-    def _assert_is_vector_list(self, value: Any) -> None:
-        assert isinstance(
-            value, (list, np.ndarray)
-        ), f"list or numpy array expected; found instead: {value} ({value.__class__})"
-        for v in value:
-            if v is None:
-                continue
-            self._assert_is_vector(v)
-
     def _assert_supported(self, value: np.ndarray) -> None:
         assert isinstance(value, np.ndarray)
         assert value.dtype.kind in "biufS", f"Unsupported dtype: {value.dtype}"
@@ -145,10 +120,6 @@ class MemorySample(Sample):
         self._data: Dict[str, Any] = data
         self._check_data = check_data
 
-    @overrides
-    def get_bytes(self, key: str) -> Optional[Bytes]:
-        return self._get(key)
-
     @overrides
     def get_scalar(self, key: str) -> Optional[Any]:
         return self._get(key)
@@ -157,17 +128,6 @@ class MemorySample(Sample):
     def get_vector(self, key: str) -> Optional[Any]:
         return self._get(key)
 
-    @overrides
-    def get_vector_list(self, key: str) -> Optional[Any]:
-        return self._get(key)
-
-    @overrides
-    def put_bytes(self, key: str, value: Bytes) -> None:
-        assert isinstance(
-            value, (bytes, bytearray)
-        ), f"bytes expected; found: {value}"  # type: ignore
-        self._put(key, value)
-
     @overrides
     def put_scalar(self, key: str, value: Scalar) -> None:
         if value is None:
@@ -184,12 +144,6 @@ class MemorySample(Sample):
             self._assert_is_vector(value)
         self._put(key, value)
 
-    @overrides
-    def put_vector_list(self, key: str, value: VectorList) -> None:
-        if self._check_data:
-            self._assert_is_vector_list(value)
-        self._put(key, value)
-
     def _get(self, key: str) -> Optional[Any]:
         if key in self._data:
             return self._data[key]
@@ -239,16 +193,6 @@ class Hdf5Sample(Sample):
         self.file = h5py.File(filename, mode, libver="latest")
         self._check_data = check_data
 
-    @overrides
-    def get_bytes(self, key: str) -> Optional[Bytes]:
-        if key not in self.file:
-            return None
-        ds = self.file[key]
-        assert (
-            len(ds.shape) == 1
-        ), f"1-dimensional array expected; found shape {ds.shape}"
-        return ds[()].tobytes()
-
     @overrides
     def get_scalar(self, key: str) -> Optional[Any]:
         if key not in self.file:
@@ -277,26 +221,6 @@ class Hdf5Sample(Sample):
         else:
             return ds[:].tolist()
 
-    @overrides
-    def get_vector_list(self, key: str) -> Optional[Any]:
-        if key not in self.file:
-            return None
-        ds = self.file[key]
-        lens = self.get_vector(f"{key}_lengths")
-        if h5py.check_string_dtype(ds.dtype):
-            padded = ds.asstr()[:].tolist()
-        else:
-            padded = ds[:].tolist()
-        return _crop(padded, lens)
-
-    @overrides
-    def put_bytes(self, key: str, value: Bytes) -> None:
-        if self._check_data:
-            assert isinstance(
-                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:
@@ -328,29 +252,6 @@ class Hdf5Sample(Sample):
 
         self._put(key, value, compress=True)
 
-    @overrides
-    def put_vector_list(self, key: str, value: VectorList) -> None:
-        if self._check_data:
-            self._assert_is_vector_list(value)
-        padded, lens = _pad(value)
-        self.put_vector(f"{key}_lengths", lens)
-        data = None
-        for v in value:
-            if v is None or len(v) == 0:
-                continue
-            if isinstance(v[0], str):
-                data = np.array(padded, dtype="S")
-            elif isinstance(v[0], float):
-                data = np.array(padded, dtype=np.dtype("f2"))
-            elif isinstance(v[0], bool):
-                data = np.array(padded, dtype=bool)
-            else:
-                data = np.array(padded)
-            break
-        if data is None:
-            data = np.array(padded)
-        self._put(key, data, compress=True)
-
     def _put(self, key: str, value: Any, compress: bool = False) -> Dataset:
         if key in self.file:
             del self.file[key]
@@ -394,44 +295,3 @@ class Hdf5Sample(Sample):
         assert col is not None
         assert data is not None
         return coo_matrix((data, (row, col)))
-
-
-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)
-
-    # Find appropriate constant to pad the vectors
-    constant: Union[int, float, str] = 0
-    for v in veclist:
-        if v is None or len(v) == 0:
-            continue
-        if isinstance(v[0], int):
-            constant = 0
-        elif isinstance(v[0], float):
-            constant = 0.0
-        elif isinstance(v[0], str):
-            constant = ""
-        else:
-            assert False, f"unsupported data type: {v[0]}"
-
-    # Pad vectors
-    for (i, vi) in enumerate(veclist):
-        if vi is None:
-            vi = veclist[i] = []
-        assert isinstance(vi, list), f"list expected; found: {vi}"
-        for k in range(len(vi), maxlen):
-            vi.append(constant)
-
-    return veclist, lens
-
-
-def _crop(veclist: VectorList, lens: List[int]) -> VectorList:
-    result: VectorList = cast(VectorList, [])
-    for (i, v) in enumerate(veclist):
-        if lens[i] < 0:
-            result.append(None)  # type: ignore
-        else:
-            assert isinstance(v, list)
-            result.append(v[: lens[i]])
-    return result

miplearn/instance/file.py

@@ -111,14 +111,14 @@ class FileInstance(Instance):
     def load(self) -> None:
         if self.instance is not None:
             return
-        self.instance = pickle.loads(self.h5.get_bytes("pickled"))
+        self.instance = pickle.loads(self.h5.get_array("pickled").tobytes())
         assert isinstance(self.instance, Instance)
 
     @classmethod
     def save(cls, instance: Instance, filename: str) -> None:
         h5 = Hdf5Sample(filename, mode="w")
-        instance_pkl = pickle.dumps(instance)
-        h5.put_bytes("pickled", instance_pkl)
+        instance_pkl = np.frombuffer(pickle.dumps(instance), dtype=np.int8)
+        h5.put_array("pickled", instance_pkl)
 
     @overrides
     def create_sample(self) -> Sample:

tests/components/test_objective.py

@@ -13,6 +13,7 @@ from miplearn.components.objective import ObjectiveValueComponent
 from miplearn.features.sample import Sample, MemorySample
 from miplearn.solvers.learning import LearningSolver
 from miplearn.solvers.pyomo.gurobi import GurobiPyomoSolver
+from miplearn.solvers.tests import assert_equals
 
 
 @pytest.fixture
@@ -21,7 +22,7 @@ def sample() -> Sample:
         {
             "mip_lower_bound": 1.0,
             "mip_upper_bound": 2.0,
-            "lp_instance_features": [1.0, 2.0, 3.0],
+            "lp_instance_features": np.array([1.0, 2.0, 3.0]),
         },
     )
     return sample
@@ -29,18 +30,18 @@ def sample() -> Sample:
 
 def test_sample_xy(sample: Sample) -> None:
     x_expected = {
-        "Lower bound": [[1.0, 2.0, 3.0]],
-        "Upper bound": [[1.0, 2.0, 3.0]],
+        "Lower bound": np.array([[1.0, 2.0, 3.0]]),
+        "Upper bound": np.array([[1.0, 2.0, 3.0]]),
     }
     y_expected = {
-        "Lower bound": [[1.0]],
-        "Upper bound": [[2.0]],
+        "Lower bound": np.array([[1.0]]),
+        "Upper bound": np.array([[2.0]]),
     }
     xy = ObjectiveValueComponent().sample_xy(None, sample)
     assert xy is not None
     x_actual, y_actual = xy
-    assert x_actual == x_expected
-    assert y_actual == y_expected
+    assert_equals(x_actual, x_expected)
+    assert_equals(y_actual, y_expected)
 
 
 def test_fit_xy() -> None:

tests/components/test_static_lazy.py

@@ -36,13 +36,15 @@ def sample() -> Sample:
             "static_constr_names": np.array(["c1", "c2", "c3", "c4", "c5"], dtype="S"),
             "static_instance_features": [5.0],
             "mip_constr_lazy_enforced": {b"c1", b"c2", b"c4"},
-            "lp_constr_features": [
-                [1.0, 1.0],
-                [1.0, 2.0],
-                [1.0, 3.0],
-                [1.0, 4.0, 0.0],
-                None,
-            ],
+            "lp_constr_features": np.array(
+                [
+                    [1.0, 1.0, 0.0],
+                    [1.0, 2.0, 0.0],
+                    [1.0, 3.0, 0.0],
+                    [1.0, 4.0, 0.0],
+                    [0.0, 0.0, 0.0],
+                ]
+            ),
             "static_constr_lazy_count": 4,
         },
     )
@@ -216,7 +218,7 @@ def test_fit_xy() -> None:
 
 def test_sample_xy(sample: Sample) -> None:
     x_expected = {
-        b"type-a": [[5.0, 1.0, 1.0], [5.0, 1.0, 2.0], [5.0, 1.0, 3.0]],
+        b"type-a": [[5.0, 1.0, 1.0, 0.0], [5.0, 1.0, 2.0, 0.0], [5.0, 1.0, 3.0, 0.0]],
         b"type-b": [[5.0, 1.0, 4.0, 0.0]],
     }
     y_expected = {

tests/features/test_extractor.py

@@ -61,7 +61,7 @@ def test_knapsack() -> None:
         np.array(["default", "default", "default", "default", ""], dtype="S"),
     )
     assert_equals(
-        sample.get_vector_list("static_var_features"),
+        sample.get_array("static_var_features"),
         np.array(
             [
                 [23.0, 505.0, 1.0, 0.32899, 0.0, 505.0, 1.0],
@@ -155,7 +155,7 @@ def test_knapsack() -> None:
         np.array([1.0, 0.923077, 1.0, 0.0, 67.0]),
     )
     assert_equals(
-        sample.get_vector_list("lp_var_features"),
+        sample.get_array("lp_var_features"),
         np.array(
             [
                 [

tests/instance/test_file.py

@@ -18,7 +18,7 @@ def test_usage() -> None:
     filename = tempfile.mktemp()
     FileInstance.save(original, filename)
     sample = Hdf5Sample(filename, check_data=True)
-    assert len(sample.get_bytes("pickled")) > 0
+    assert len(sample.get_array("pickled")) > 0
 
     # Solve instance from disk
     solver = LearningSolver(solver=GurobiSolver())