ennbo 0.1.0__py3-none-any.whl → 0.1.7__py3-none-any.whl

enn/turbo/types/appendable_array.py

@@ -0,0 +1,85 @@
+from __future__ import annotations
+
+import numpy as np
+
+
+class AppendableArray:
+    def __init__(self, initial_capacity: int = 100) -> None:
+        self._initial_capacity = initial_capacity
+        self._buffer: np.ndarray | None = None
+        self._size = 0
+        self._num_cols: int | None = None
+
+    @property
+    def shape(self) -> tuple[int, int]:
+        if self._num_cols is None:
+            return (0, 0)
+        return (self._size, self._num_cols)
+
+    def _initialize_buffer(self, row: np.ndarray) -> None:
+        if row.ndim == 0:
+            self._num_cols = 1
+            row = row.reshape(1, 1)
+        elif row.ndim == 1:
+            self._num_cols = row.shape[0]
+            row = row[np.newaxis, :]
+        elif row.ndim == 2:
+            if row.shape[0] != 1:
+                raise ValueError(f"Expected row shape (1, D), got {row.shape}")
+            self._num_cols = row.shape[1]
+        else:
+            raise ValueError(f"Expected 0D, 1D or 2D array, got {row.ndim}D")
+
+        self._buffer = np.empty(
+            (self._initial_capacity, self._num_cols), dtype=row.dtype
+        )
+
+    def _validate_row(self, row: np.ndarray) -> np.ndarray:
+        if row.ndim == 0:
+            if self._num_cols != 1:
+                raise ValueError(f"Expected {self._num_cols} columns, got 1 (scalar)")
+            return row.reshape(1, 1)
+        if row.ndim == 1:
+            if row.shape[0] != self._num_cols:
+                raise ValueError(
+                    f"Expected {self._num_cols} columns, got {row.shape[0]}"
+                )
+            return row[np.newaxis, :]
+        if row.ndim == 2:
+            if row.shape != (1, self._num_cols):
+                raise ValueError(
+                    f"Expected shape (1, {self._num_cols}), got {row.shape}"
+                )
+            return row
+        raise ValueError(f"Expected 0D, 1D or 2D array, got {row.ndim}D")
+
+    def append(self, row: np.ndarray) -> None:
+        row = np.asarray(row)
+
+        if self._num_cols is None:
+            self._initialize_buffer(row)
+
+        row = self._validate_row(row)
+
+        assert self._buffer is not None
+        if self._size + 1 > self._buffer.shape[0]:
+            new_capacity = self._buffer.shape[0] * 2
+            new_buffer = np.empty(
+                (new_capacity, self._num_cols), dtype=self._buffer.dtype
+            )
+            new_buffer[: self._size] = self._buffer[: self._size]
+            self._buffer = new_buffer
+
+        self._buffer[self._size] = row
+        self._size += 1
+
+    def view(self) -> np.ndarray:
+        if self._buffer is None:
+            return np.empty((0, 0))
+        return self._buffer[: self._size]
+
+    def __len__(self) -> int:
+        return self._size
+
+    def __getitem__(self, key) -> np.ndarray:
+        return self.view()[key]

enn/turbo/types/gp_data_prep.py

@@ -0,0 +1,13 @@
+from __future__ import annotations
+from dataclasses import dataclass
+from typing import Any
+
+
+@dataclass
+class GPDataPrep:
+    train_x: Any
+    train_y: Any
+    is_multi: bool
+    y_mean: Any
+    y_std: Any
+    y_raw: Any

enn/turbo/types/gp_fit_result.py

@@ -0,0 +1,11 @@
+from __future__ import annotations
+from dataclasses import dataclass
+from typing import Any
+
+
+@dataclass
+class GPFitResult:
+    model: Any
+    likelihood: Any
+    y_mean: Any
+    y_std: Any

enn/turbo/types/obs_lists.py

@@ -0,0 +1,10 @@
+from __future__ import annotations
+from dataclasses import dataclass
+
+
+@dataclass
+class ObsLists:
+    x_obs: list
+    y_obs: list
+    y_tr: list
+    yvar_obs: list

enn/turbo/types/prepare_ask_result.py

@@ -0,0 +1,14 @@
+from __future__ import annotations
+from dataclasses import dataclass
+from typing import TYPE_CHECKING, Any
+
+if TYPE_CHECKING:
+    import numpy as np
+
+
+@dataclass
+class PrepareAskResult:
+    model: Any
+    y_mean: float | None
+    y_std: float | None
+    lengthscales: np.ndarray | None

enn/turbo/types/tell_inputs.py

@@ -0,0 +1,14 @@
+from __future__ import annotations
+from dataclasses import dataclass
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    import numpy as np
+
+
+@dataclass
+class TellInputs:
+    x: np.ndarray
+    y: np.ndarray
+    y_var: np.ndarray | None
+    num_metrics: int

{ennbo-0.1.0.dist-info → ennbo-0.1.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ennbo
-Version: 0.1.0
+Version: 0.1.7
 Summary: Epistemic Nearest Neighbors
 Project-URL: Homepage, https://github.com/yubo-research/enn
 Project-URL: Source, https://github.com/yubo-research/enn
@@ -36,12 +36,15 @@ Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Classifier: Topic :: Scientific/Engineering :: Mathematics
 Requires-Python: >=3.11
-Requires-Dist: faiss-cpu==1.9.0
-Requires-Dist: gpytorch==1.13
-Requires-Dist: nds==0.4.3
-Requires-Dist: numpy==1.26.4
-Requires-Dist: scipy==1.15.3
-Requires-Dist: torch==2.5.1
+Requires-Dist: faiss-cpu>=1.9.0
+Requires-Dist: gpytorch>=1.13
+Requires-Dist: numpy<2.0.0,>=1.26.4
+Requires-Dist: scipy>=1.15.3
+Requires-Dist: torch>=2.5.1
+Provides-Extra: dev
+Requires-Dist: nbmake>=1.5; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.4; extra == 'dev'
 Description-Content-Type: text/markdown
 
 # Epistemic Nearest Neighbors
@@ -50,12 +53,16 @@ A fast, alternative surrogate for Bayesian optimization
 ENN estimates a function's value and associated epistemic uncertainty using a K-Nearest Neighbors model. Queries take $O(N lnK)$ time, where $N$ is the number of observations available for KNN lookups. Compare to an exact GP, which takes $O(N^2)$ time. Additionally, measured running times are very small compared to GPs and other alternative surrogates. [1]
 
 ## Contents
-- ENN model, [`EpistemicNearestNeighbors`](https://github.com/yubo-research/enn/blob/main/src/enn/enn/enn.py) [1]
-- TuRBO-ENN optimizer, class [`TurboOptimizer`](https://github.com/yubo-research/enn/blob/main/src/enn/turbo/turbo_optimizer.py) has four modes
-	- `TURBO_ONE` - A clone of the TuRBO [2] reference [code](https://github.com/uber-research/TuRBO), reworked to have an `ask()`/`tell()` interface.
-	- `TURBO_ENN` - Same as TURBO_ONE, except uses ENN instead of GP and Pareto(mu, se) instead of Thompson sampling.
-	- `TURBO_ZERO` - Same as TURBO_ONE, except randomly-chosen RAASP [3] candidates are picked to be proposals. There is no surrogate.
-	- `LHD_ONLY` - Just creates an LHD design for every `ask()`. Good for a baseline and for testing.
+- ENN surrogate, [`EpistemicNearestNeighbors`](https://github.com/yubo-research/enn/blob/main/src/enn/enn/enn.py) [1]
+- TuRBO-ENN optimizer via [`create_optimizer`](https://github.com/yubo-research/enn/blob/main/src/enn/turbo/optimizer.py) with config factories
+	- `turbo_one_config()` - TuRBO [2], matching the reference implementation.
+	- `turbo_enn_config()` - Uses ENN instead of GP.
+	- `turbo_zero_config()` - No surrogate
+	- `lhd_only_config()` - LHD design on every `ask()`. Good for a baseline and for testing.
+The optimizer has an `ask()/tell()` interface. All `turbo_*()` methods follow TuRBO:
+  - Generate candidates with RAASP [3] sampling.
+  - Select a candidate with Thompson sampling (TuRBO-one), UCB (TuRBO-ENN), or randomly (TURBO-zero).
+
 
 [1] **Sweet, D., & Jadhav, S. A. (2025).** Taking the GP Out of the Loop. *arXiv preprint arXiv:2506.12818*.
    https://arxiv.org/abs/2506.12818
@@ -80,9 +87,10 @@ On my MacBook I can run into problems with dependencies and compatibilities.
 
 On MacOS try:
 ```
-micromamba env create -n ennbo -f conda-macos.yml
+micromamba env create -n ennbo -f admin/conda-macos.yml
 micromamba activate ennbo
 pip install --no-deps ennbo
+pytest -sv tests
 ```
 
 You may replace `micromamba` with `conda` and this will probably still work.

ennbo-0.1.7.dist-info/RECORD

@@ -0,0 +1,111 @@
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+enn/benchmarks/__init__.py,sha256=50yqq29luUZQmH618jLq006MwimJBYCvlR9PMSs97MM,79
+enn/benchmarks/ackley.py,sha256=LMx_8C4swL3oKbzm70S8wHe_fp7Z0JCbyoi4kx2E9YY,163
+enn/benchmarks/ackley_class.py,sha256=AwLwopw7bUQ0QaN1yFmVdNPZdL4948lqGfKIvyXk7Os,519
+enn/benchmarks/ackley_core.py,sha256=zIGlZuIkzfv2OLLU_R7hSSYnm0TCm7G7Nt7KlDXuu5k,328
+enn/benchmarks/double_ackley.py,sha256=IXZntZ1byJxIlFh3aj3Rzw_2cnjih8c9nyKTt_iM0P8,766
+enn/enn/candidates.py,sha256=axVT0bs0dt4ZEXmy_d540U1h0JJ-YIAqYFaUPaiXwa0,276
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enn/enn/__init__.py

@@ -1,4 +0,0 @@
-from .enn import EpistemicNearestNeighbors
-from .enn_fit import enn_fit
-
-__all__: list[str] = ["EpistemicNearestNeighbors", "enn_fit"]

enn/turbo/__init__.py

@@ -1,11 +0,0 @@
-from .turbo_mode import TurboMode
-from .turbo_optimizer import Telemetry, TurboOptimizer
-
-Turbo = TurboOptimizer
-
-__all__ = [
-    "TurboMode",
-    "TurboOptimizer",
-    "Turbo",
-    "Telemetry",
-]

enn/turbo/base_turbo_impl.py

@@ -1,98 +0,0 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING, Any, Callable
-
-if TYPE_CHECKING:
-    import numpy as np
-    from numpy.random import Generator
-
-from .turbo_config import TurboConfig
-
-
-class BaseTurboImpl:
-    def __init__(self, config: TurboConfig) -> None:
-        self._config = config
-
-    def get_x_center(
-        self,
-        x_obs_list: list,
-        y_obs_list: list,
-        rng: Generator,
-    ) -> np.ndarray | None:
-        import numpy as np
-
-        from .turbo_utils import argmax_random_tie
-
-        y_array = np.asarray(y_obs_list, dtype=float)
-        if y_array.size == 0:
-            return None
-        idx = argmax_random_tie(y_array, rng=rng)
-        x_array = np.asarray(x_obs_list, dtype=float)
-        return x_array[idx]
-
-    def needs_tr_list(self) -> bool:
-        return False
-
-    def create_trust_region(self, num_dim: int, num_arms: int) -> Any:
-        from .turbo_trust_region import TurboTrustRegion
-
-        return TurboTrustRegion(num_dim=num_dim, num_arms=num_arms)
-
-    def try_early_ask(
-        self,
-        num_arms: int,
-        x_obs_list: list,
-        draw_initial_fn: Callable[[int], np.ndarray],
-        get_init_lhd_points_fn: Callable[[int], np.ndarray | None],
-    ) -> np.ndarray | None:
-        return None
-
-    def handle_restart(
-        self,
-        x_obs_list: list,
-        y_obs_list: list,
-        yvar_obs_list: list,
-        init_idx: int,
-        num_init: int,
-    ) -> tuple[bool, int]:
-        return False, init_idx
-
-    def prepare_ask(
-        self,
-        x_obs_list: list,
-        y_obs_list: list,
-        yvar_obs_list: list,
-        num_dim: int,
-        gp_num_steps: int,
-        rng: Any | None = None,
-    ) -> tuple[Any, float | None, float | None, np.ndarray | None]:
-        return None, None, None, None
-
-    def select_candidates(
-        self,
-        x_cand: np.ndarray,
-        num_arms: int,
-        num_dim: int,
-        rng: Generator,
-        fallback_fn: Callable[[np.ndarray, int], np.ndarray],
-        from_unit_fn: Callable[[np.ndarray], np.ndarray],
-    ) -> np.ndarray:
-        raise NotImplementedError("Subclasses must implement select_candidates")
-
-    def update_trust_region(
-        self,
-        tr_state: Any,
-        y_obs_list: list,
-        x_center: np.ndarray | None = None,
-        k: int | None = None,
-    ) -> None:
-        import numpy as np
-
-        y_obs_array = np.asarray(y_obs_list, dtype=float)
-        tr_state.update(y_obs_array)
-
-    def estimate_y(self, x_unit: np.ndarray, y_observed: np.ndarray) -> np.ndarray:
-        return y_observed
-
-    def get_mu_sigma(self, x_unit: np.ndarray) -> tuple[np.ndarray, np.ndarray] | None:
-        return None

enn/turbo/lhd_only_impl.py

@@ -1,42 +0,0 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING, Any, Callable
-
-if TYPE_CHECKING:
-    import numpy as np
-    from numpy.random import Generator
-
-from .base_turbo_impl import BaseTurboImpl
-
-
-class LHDOnlyImpl(BaseTurboImpl):
-    def get_x_center(
-        self,
-        x_obs_list: list,
-        y_obs_list: list,
-        rng: Generator,
-    ) -> np.ndarray | None:
-        return None
-
-    def select_candidates(
-        self,
-        x_cand: np.ndarray,
-        num_arms: int,
-        num_dim: int,
-        rng: Generator,
-        fallback_fn: Callable[[np.ndarray, int], np.ndarray],
-        from_unit_fn: Callable[[np.ndarray], np.ndarray],
-    ) -> np.ndarray:
-        from .turbo_utils import latin_hypercube
-
-        unit = latin_hypercube(num_arms, num_dim, rng=rng)
-        return from_unit_fn(unit)
-
-    def update_trust_region(
-        self,
-        tr_state: Any,
-        y_obs_list: list,
-        x_center: np.ndarray | None = None,
-        k: int | None = None,
-    ) -> None:
-        pass

enn/turbo/turbo_config.py

@@ -1,28 +0,0 @@
-from __future__ import annotations
-
-from dataclasses import dataclass
-from typing import Literal
-
-
-@dataclass(frozen=True)
-class TurboConfig:
-    k: int | None = None
-    num_candidates: int | None = None
-    num_init: int | None = None
-    var_scale: float = 1.0
-
-    # Experimental
-    trailing_obs: int | None = None
-    num_fit_samples: int | None = None
-    num_fit_candidates: int | None = None
-    acq_type: Literal["thompson", "pareto", "ucb"] = "pareto"
-    local_only: bool = False
-
-    def __post_init__(self) -> None:
-        if self.acq_type not in ["thompson", "pareto", "ucb"]:
-            raise ValueError(
-                f"acq_type must be 'thompson', 'pareto', or 'ucb', got {self.acq_type!r}"
-            )
-        # Pareto acquisition is the only type that works well without hyperparameter fitting
-        if self.num_fit_samples is None and self.acq_type != "pareto":
-            raise ValueError(f"num_fit_samples required for acq_type={self.acq_type!r}")