ennbo 0.0.7__tar.gz

ennbo-0.0.7/.cursorrules

@@ -0,0 +1,54 @@
+# FIRST RULE OF CURSOR - MANDATORY: READ THIS FIRST
+MANDATORY FIRST ACTION: When the user sends their first request in a conversation, you MUST immediately read style.md using the read_file tool BEFORE performing any other action (no searches, no code reading, no tool calls of any kind). This is the absolute first step - do not answer the question, do not search, do not read other files. Read style.md first, then proceed with the user's request.
+
+
+--
+
+### Cursor Rule: Claims vs Hypotheses
+
+- Label uncertain reasoning as Hypothesis; only use Claim with explicit evidence.
+- Claims must cite evidence (code refs, logs, metrics). Otherwise, downgrade to Hypothesis.
+- For each Hypothesis, include:
+  - Hypothesis: concise, falsifiable statement.
+  - Predictions: measurable outcomes if true.
+  - Test: minimal experiment (setup, variables, metrics, pass/fail).
+  - Confounders: likely alternatives and controls.
+- Language:
+  - Hypothesis: “suggests”, “may”, “indicates”.
+  - Claim (with evidence): “shows”, “demonstrates”, “causes”.
+- Trigger this rule when explaining performance differences, algorithm behavior, or proposing changes.
+- Whenever you see an error happen more two or more times in a row, stop, state the problem clearly, then hypothesize the cause.  Then test to determine the cause. Once the cause is determined, fix the problem.
+
+--
+
+When running python code, you'll need to set PYTHONPATH
+
+--
+
+When your write code, always make sure `pytest -sv tests` and `ruff check` pass.
+Iterate until they do.
+
+--
+
+# Debugging process rule
+
+When debugging: run the broken code first to observe the actual failure, write a test that reproduces that exact failure, then fix it. Don't guess—observe empirically. Replicate the exact code path that fails in the test, not a simplified version. The broken code is the source of truth; observe it directly before fixing.
+--
+
+
+Acronyms we can use to make communication more efficient:
+DRY: Don't Repeat Yourself. The user would like you to look for opportunities to factor out common code.
+DCC: Don't Change Code. Repond to the user's query, but don't change *any* code.
+DCT: Don't Change Tests.  Repond to the user's query, but don't change any tests. You may change non-test code, though.
+OCT: *Only* Change Tests. Repond to the user's query, but don't change any non-test code. You may change test code, though.
+RR: Restate my request clearly. Lmk if you have any questions. DCC
+
+--
+
+# Cursor Roles
+The Tester: The Tester writes unit tests but does not implement the code being tested. Tests for unimplemented code should be failing tests.
+The Implementor: The Implementor writes code but does not write or change tests.
+
+--
+
+After every 5th request, `cat .cursorrules`

ennbo-0.0.7/.cursorrules~

@@ -0,0 +1,51 @@
+# FIRST RULE OF CURSOR - MANDATORY: READ THIS FIRST
+MANDATORY FIRST ACTION: When the user sends their first request in a conversation, you MUST immediately read style.md using the read_file tool BEFORE performing any other action (no searches, no code reading, no tool calls of any kind). This is the absolute first step - do not answer the question, do not search, do not read other files. Read style.md first, then proceed with the user's request.
+
+
+--
+
+### Cursor Rule: Claims vs Hypotheses
+
+- Label uncertain reasoning as Hypothesis; only use Claim with explicit evidence.
+- Claims must cite evidence (code refs, logs, metrics). Otherwise, downgrade to Hypothesis.
+- For each Hypothesis, include:
+  - Hypothesis: concise, falsifiable statement.
+  - Predictions: measurable outcomes if true.
+  - Test: minimal experiment (setup, variables, metrics, pass/fail).
+  - Confounders: likely alternatives and controls.
+- Language:
+  - Hypothesis: “suggests”, “may”, “indicates”.
+  - Claim (with evidence): “shows”, “demonstrates”, “causes”.
+- Trigger this rule when explaining performance differences, algorithm behavior, or proposing changes.
+- Whenever you see an error happen more two or more times in a row, stop, state the problem clearly, then hypothesize the cause.  Then test to determine the cause. Once the cause is determined, fix the problem.
+
+--
+
+When running python code, you'll need to set PYTHONPATH
+
+--
+
+When your write code, always make sure `pytest -sv tests` and `ruff check` pass.
+Iterate until they do.
+
+--
+
+# Debugging process rule
+
+When debugging: run the broken code first to observe the actual failure, write a test that reproduces that exact failure, then fix it. Don't guess—observe empirically. Replicate the exact code path that fails in the test, not a simplified version. The broken code is the source of truth; observe it directly before fixing.
+--
+
+
+Acronyms we can use to make communication more efficient:
+DRY: Don't Repeat Yourself. The user would like you to look for opportunities to factor out common code.
+DCC: Don't Change Code. Repond to the user's query, but don't change *any* code.
+DCT: Don't Change Tests.  Repond to the user's query, but don't change any tests. You may change non-test code, though.
+OCT: *Only* Change Tests. Repond to the user's query, but don't change any non-test code. You may change test code, though.
+RR: Restate my request clearly. Lmk if you have any questions. DCC
+
+--
+
+# Cursor Roles
+The Tester: The Tester writes unit tests but does not implement the code being tested. Tests for unimplemented code should be failing tests.
+The Implementor: The Implementor writes code but does not write or change tests.
+

ennbo-0.0.7/.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-json
+      - id: check-added-large-files
+        args: ["--maxkb=500"]
+
+  # Forbid committing binary files and run custom checks
+  - repo: local
+    hooks:
+      - id: forbid-binary
+        name: Forbid committing binary files
+        entry: bash -c 'echo \"Binary files are not allowed in this repository.\"; exit 1'
+        language: system
+        types: [binary]
+
+      - id: find-forgotten-py
+        name: Find forgotten Python files via git status
+        entry: admin/find_forgotten_py.sh
+        language: system
+        pass_filenames: false
+        always_run: true
+
+  # Linting, formatting, and import sorting via Ruff
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.0
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+      - id: ruff-format

ennbo-0.0.7/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 yubo research
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

ennbo-0.0.7/PKG-INFO

@@ -0,0 +1,75 @@
+Metadata-Version: 2.4
+Name: ennbo
+Version: 0.0.7
+Summary: Epistemic Nearest Neighbors
+Project-URL: Homepage, https://github.com/yubo-research/enn
+Project-URL: Source, https://github.com/yubo-research/enn
+Author-email: YUBO Lab <david.sweet@yu.edu>
+License: MIT License
+        
+        Copyright (c) 2025 yubo research
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+License-File: LICENSE
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+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: numpy==1.26.4
+Requires-Dist: scipy==1.15.3
+Requires-Dist: torch==2.5.1
+Description-Content-Type: text/markdown
+
+# Epistemic Nearest Neighbors
+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/core.py) [1]
+- TuRBO-ENN optimizer, class [`TurboOptimizer`](https://github.com/yubo-research/enn/blob/main/src/enn/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.
+
+[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  
+[2] **Eriksson, D., Pearce, M., Gardner, J. R., Turner, R., & Poloczek, M. (2020).** Scalable Global Optimization via Local Bayesian Optimization. *Advances in Neural Information Processing Systems, 32*.  
+   https://arxiv.org/abs/1910.01739  
+[3] **Rashidi, B., Johnstonbaugh, K., & Gao, C. (2024).** Cylindrical Thompson Sampling for High-Dimensional Bayesian Optimization. *Proceedings of The 27th International Conference on Artificial Intelligence and Statistics* (pp. 3502–3510). PMLR.  
+   https://proceedings.mlr.press/v238/rashidi24a.html  
+
+
+## Installation
+`pip install ennbo`
+
+## Demonstration
+[`demo_enn.ipynb`](https://github.com/yubo-research/enn/tree/main/examples) - Shows how to use [`EpistemicNearestNeighbors`](https://github.com/yubo-research/enn/blob/main/src/enn/core.py) to build and query an ENN model.  
+[`demo_turbo_enn.ipynb`](https://github.com/yubo-research/enn/tree/main/examples) - Shows how to use [`TurboOptimizer`](https://github.com/yubo-research/enn/blob/main/src/enn/turbo_optimizer.py) to optimize the Ackley function.
+
+
+

ennbo-0.0.7/README.md

@@ -0,0 +1,30 @@
+# Epistemic Nearest Neighbors
+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/core.py) [1]
+- TuRBO-ENN optimizer, class [`TurboOptimizer`](https://github.com/yubo-research/enn/blob/main/src/enn/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.
+
+[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  
+[2] **Eriksson, D., Pearce, M., Gardner, J. R., Turner, R., & Poloczek, M. (2020).** Scalable Global Optimization via Local Bayesian Optimization. *Advances in Neural Information Processing Systems, 32*.  
+   https://arxiv.org/abs/1910.01739  
+[3] **Rashidi, B., Johnstonbaugh, K., & Gao, C. (2024).** Cylindrical Thompson Sampling for High-Dimensional Bayesian Optimization. *Proceedings of The 27th International Conference on Artificial Intelligence and Statistics* (pp. 3502–3510). PMLR.  
+   https://proceedings.mlr.press/v238/rashidi24a.html  
+
+
+## Installation
+`pip install ennbo`
+
+## Demonstration
+[`demo_enn.ipynb`](https://github.com/yubo-research/enn/tree/main/examples) - Shows how to use [`EpistemicNearestNeighbors`](https://github.com/yubo-research/enn/blob/main/src/enn/core.py) to build and query an ENN model.  
+[`demo_turbo_enn.ipynb`](https://github.com/yubo-research/enn/tree/main/examples) - Shows how to use [`TurboOptimizer`](https://github.com/yubo-research/enn/blob/main/src/enn/turbo_optimizer.py) to optimize the Ackley function.
+
+
+

ennbo-0.0.7/admin/find_forgotten_py.sh

@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Run from repo root so paths from git status are correct
+REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+cd "$REPO_ROOT"
+
+echo "Scanning for untracked or modified Python files (git status)..."
+
+status_output="$(git status --porcelain --untracked-files=all)"
+
+if [[ -z "$status_output" ]]; then
+  echo "Working tree clean. No forgotten .py files."
+  exit 0
+fi
+
+# Select only:
+# - untracked files ("??")
+# - or files with unstaged changes (second status column non-space)
+# We parse the raw porcelain line as:
+#   XY <space> PATH
+# where X is index status, Y is work-tree status.
+py_files="$(
+  printf '%s\n' "$status_output" |
+    awk '{
+      line = $0
+      x = substr(line, 1, 1)
+      y = substr(line, 2, 1)
+      path = substr(line, 4)
+      if ((x == "?" && y == "?") || y != " ")
+        print path
+    }' |
+    grep -E '\.py$' || true
+)"
+
+if [[ -z "$py_files" ]]; then
+  echo "No forgotten .py files detected."
+  exit 0
+fi
+
+echo "Potential forgotten Python files:"
+printf "%s\n" "$py_files"
+exit 1