adcd 2.1.2__tar.gz

adcd-2.1.2/LICENSE

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+MIT License
+
+Copyright (c) 2026 Muhammad Afif Erdita
+
+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.

adcd-2.1.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: adcd
+Version: 2.1.2
+Summary: Anomaly-Driven Correction Discovery: Physics-Constrained Symbolic Regression for Evolutionary Scientific Discovery
+Author-email: Muhammad Afif Erdita <maeapip10@gmail.com>
+License: MIT
+Project-URL: Homepage, https://zenodo.org/records/20534940
+Project-URL: Repository, https://github.com/apiprdt/PhysicsPaper
+Project-URL: Bug Tracker, https://github.com/apiprdt/PhysicsPaper/issues
+Project-URL: DOI, https://doi.org/10.5281/zenodo.20534940
+Keywords: symbolic regression,physics,machine learning,scientific discovery,JAX
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.24
+Requires-Dist: scipy>=1.11
+Requires-Dist: sympy>=1.12
+Requires-Dist: jax>=0.4.20
+Requires-Dist: jaxlib>=0.4.20
+Requires-Dist: matplotlib>=3.7
+Provides-Extra: dev
+Requires-Dist: pytest>=7.4; extra == "dev"
+Requires-Dist: pytest-cov>=4.1; extra == "dev"
+Requires-Dist: flake8>=6.1; extra == "dev"
+Requires-Dist: black>=23.0; extra == "dev"
+Provides-Extra: llm
+Requires-Dist: google-generativeai>=0.3; extra == "llm"
+Provides-Extra: all
+Requires-Dist: adcd[dev,llm]; extra == "all"
+Dynamic: license-file
+
+# ADCD — Anomaly-Driven Correction Discovery
+
+[![DOI](https://zenodo.org/badge/20534940.svg)](https://doi.org/10.5281/zenodo.20534940)
+[![CI](https://github.com/apiprdt/PhysicsPaper/actions/workflows/ci.yml/badge.svg)](https://github.com/apiprdt/PhysicsPaper/actions/workflows/ci.yml)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+**Physics-Constrained Symbolic Regression for Evolutionary Scientific Discovery**
+
+ADCD is a symbolic regression framework that discovers *physical correction terms* rather than learning equations from scratch. Given a known classical law and anomalous observations, ADCD recovers the dimensionless correction Δ that reconciles theory with experiment — mirroring how physics actually evolves.
+
+> **82.8% (±7.7%) mean structural recovery** across 5 random seeds, with peak **94.4%** at the reference seed.  
+> **4/4 real-world structural class matches** (Mercury, Lamb Shift, Muon g-2, Blackbody).  
+> **77 automated unit tests** passing on Python 3.10 and 3.11.
+
+---
+
+## Key Features
+
+- **Correction-first paradigm** — starts from a known classical law, not a blank slate; designed for anomaly-driven theory refinement where the baseline is structurally correct
+- **Physics-gated search cascade** — AST complexity, dimensional homogeneity + transcendental guardrails, and asymptotic consistency (ARC) gates screen unphysical candidates *before* optimization
+- **JAX-traced L-BFGS-B optimizer** — parameter-scaled differentiable fitting with multi-restart log-uniform initialization
+- **BIC reranking** — selects the most parsimonious correction over purely numerical fits
+- **Residual feature intelligence** — statistical priors (monotonicity, curvature, oscillation, decay rate, symmetry) bias the template sampler toward the correct mathematical family
+- **Coarse empirical evaluation** — data-driven pre-filter ranks gate survivors before full JAX optimization
+- **Noise-robust** — 93.3% mean at 0% noise, 91.1% at 1%, 71.1% at 5%, 68.9% at 10%
+
+## Quick Start
+
+### Installation
+
+```bash
+pip install adcd
+```
+
+Or install from source:
+
+```bash
+git clone https://github.com/apiprdt/PhysicsPaper.git
+cd PhysicsPaper
+pip install -e ".[dev]"
+```
+
+### Usage
+
+Running ADCD is extremely simple using the high-level scientific API:
+
+```python
+import adcd
+
+# 1. Load a pre-defined benchmark scenario
+scenarios = adcd.get_all_scenarios()
+scenario = scenarios[0]  # Relativistic Kinetic Energy
+
+# 2. Run discovery in a single line!
+result = adcd.discover_correction(scenario, max_iterations=5, proposer="mock")
+
+print(f"Discovered correction: {result.best_expr}")
+print(f"Residual NMSE: {result.best_nmse_residual:.2e}")
+print(f"Parameters: {result.best_theta}")
+
+# 3. Export LaTeX or plot residuals
+print(result.export_latex())
+result.plot_residuals()
+```
+
+For custom experimental data, use `adcd.fit(...)`:
+
+```python
+import numpy as np
+import adcd
+
+x = np.linspace(1.0, 5.0, 100)
+X = {"x": x}
+y_classical = 2.0 * x
+y_observed  = 2.0 * x + 0.5 * x**2   # hidden x² correction
+
+result = adcd.fit(
+    X=X,
+    y_obs=y_observed,
+    y_classical=y_classical,
+    limit_variable="x",
+    limit_direction="0",
+    correction_mode="additive"
+)
+
+result.summary()
+```
+
+## Benchmark Results
+
+### Standard Benchmark (seed=42, Mock Proposer)
+
+Results from `run_correction_discovery.py --proposer mock` (reference seed=42, 4 iterations per scenario).
+
+| Scenario | Tier | 0% Noise | 1% Noise | 5% Noise | 10% Noise |
+|----------|------|:--------:|:--------:|:--------:|:---------:|
+| Relativistic KE | Textbook | ✓ | ✓ | ✓ | ✓ |
+| Yukawa Gravity | Textbook | ✓ | ✓ | ✓ | ✓ |
+| Anharmonic Spring | Textbook | ✓ | ✓ | ✓ | ✓ |
+| Screened Coulomb | Cross-Domain | ✓ | ✓ | ✗ | ✗ |
+| Net Radiation | Cross-Domain | ✓ | ✓ | ✓ | ✓ |
+| Nonlinear Drag | Cross-Domain | ✓ | ✓ | ✓ | ✓ |
+| Mystery-A (tanh²) | Synthetic | ✓ | ✓ | ✓ | ✓ |
+| Mystery-B (sinc) | Synthetic | ✓ | ✓ | ✓ | ✓ |
+| Mystery-C (log-quotient) | Synthetic | ✓ | ✓ | ✓ | ✓ |
+| **Overall** | | **100%** | **100%** | **88.9%** | **88.9%** |
+
+> **Note**: Screened Coulomb fails at ≥5% noise because exponential decay ($e^{-r/\lambda}$) and rational saturation ($r/(r+\lambda)$) are numerically indistinguishable at the tested SNR with limited dynamic range — an information-theoretic limit, not a framework deficiency.
+
+### Multi-Seed Reproducibility
+
+All results are reported across 5 independent random seeds (0, 7, 21, 42, 99):
+
+| Seed | Class Match Rate |
+|:----:|:----------------:|
+| 0 | 86.1% (31/36) |
+| 7 | 75.0% (27/36) |
+| 21 | 77.8% (28/36) |
+| 42 | 94.4% (34/36) |
+| 99 | 80.6% (29/36) |
+| **Mean** | **82.8% ± 7.7%** |
+
+Performance variation reflects stochastic template sampling in the MockProposer. Physics gates ensure that **when** the correct functional family is sampled, it consistently survives filtering and is selected by BIC reranking.
+
+### Real-World Physical Constants Benchmark
+
+Synthetic-real hybrid data using experimentally validated constants from JPL DE440, NIST, and CODATA:
+
+| Physical Scenario | Discovered Correction | Converged | Class Match | NMSE |
+|---|---|:---:|:---:|:---:|
+| Mercury Perihelion (GR) | `θ₀·vc²` | — | ✓ polynomial | 1.11e-05 |
+| Hydrogen Lamb Shift (QED) | `θ₀(n/θ₁)^(-θ₂)` | ✓ | ✓ power_law | 1.82e-18 |
+| Muon g-2 (Schwinger) | `θ₀(α/π)^θ₁` | ✓ | ✓ polynomial | 7.94e-07 |
+| Blackbody (Planck) | `-1 + e^(-f/θ₁)` | — | ✓ exponential | 2.59e-02 |
+
+All 4 scenarios achieve correct structural class identification. 2 scenarios (Lamb Shift, Muon g-2) achieve full convergence with NMSE < 10⁻⁶. Mercury and Blackbody achieve correct structural identification but quantitative convergence is limited by parametrization sensitivity and dynamic range, respectively.
+
+### PySR Comparison (fair profile: 100 iterations, maxsize 30, 60s timeout)
+
+| Method | 0% Noise | 1% Noise | 5% Noise | 10% Noise |
+|--------|:--------:|:--------:|:--------:|:---------:|
+| ADCD (ours, seed=42) | 9/9 (100%) | 9/9 (100%) | 8/9 (88.9%) | 8/9 (88.9%) |
+| PySR fair | 4/9 (44.4%) | 5/9 (55.6%) | 1/9 (11.1%) | 5/9 (55.6%) |
+
+ADCD outperforms PySR fair by **77.8 percentage points** at 5% noise (88.9% vs 11.1%). A legacy fast profile (wall-clock matched) is retained in `pysr_baseline_results.json` for historical comparison only.
+
+## Project Structure
+
+```
+PhysicsPaper/
+├── src/adcd/                       # Installable package
+│   ├── __init__.py                 # Public API (adcd.fit, adcd.discover_correction)
+│   ├── anomaly_scenarios.py        # 9 standard + 3 blind benchmark scenarios
+│   ├── arc_scorer.py               # Asymptotic consistency gate (ARC)
+│   ├── coarse_evaluator.py         # Coarse numerical pre-filter
+│   ├── correction_orchestrator.py  # Main multi-iteration discovery loop
+│   ├── dimensional_checker.py      # Dimensional homogeneity + transcendental guardrail
+│   ├── jax_optimizer.py            # JAX L-BFGS-B optimizer (parameter-scaled)
+│   ├── llm_proposer.py             # Mock + Gemini + OpenAI-compatible proposers
+│   ├── metrics.py                  # NMSE, BIC, structural classification
+│   ├── pipeline.py                 # Stage 1 filter cascade
+│   ├── real_data_loader.py         # Real-world data loading (JPL, NIST, CODATA)
+│   ├── real_scenarios.py           # Real-world validation scenarios
+│   ├── residual_analyzer.py        # Statistical residual feature extraction
+│   └── result.py                   # CorrectionResult: summary, LaTeX, plot
+├── tests/                          # 58 unit + integration tests
+├── paper/                          # LaTeX source (main.tex) + figures
+├── run_correction_discovery.py     # Standard 9-scenario benchmark runner
+├── run_real_data_benchmark.py      # Real-world physical constants benchmark
+├── run_reproducibility.py          # Multi-seed reproducibility study (5 seeds)
+├── run_ablation.py                 # Gate ablation study
+├── run_pysr_baseline.py            # PySR comparison baseline
+├── run_mlp_baseline.py             # MLP comparison baseline
+├── run_misspecification_benchmark.py  # Baseline misspecification fail-safe test
+├── generate_figures.py             # Paper figure generator
+├── .github/workflows/              # CI (test + lint + LaTeX) and PyPI publish
+├── pyproject.toml                  # PEP 517/518 build configuration
+└── README.md                       # This file
+```
+
+## Running Tests
+
+```bash
+pip install -e ".[dev]"
+pytest --cov=adcd
+```
+
+All 77 tests pass on Python 3.10 and 3.11 (Ubuntu and Windows).
+
+## Submission & Release
+
+Paper submission guide (GitHub Release → Zenodo → arXiv): [docs/SUBMISSION_CHECKLIST_v2.1.2.md](docs/SUBMISSION_CHECKLIST_v2.1.2.md)
+
+Current release tag: **v2.1.2** | Package version: **2.1.2**
+
+## Reproducing Paper Results
+
+Verify claims before citing numbers:
+
+```bash
+python scripts/verify_paper_claims.py   # expect [ALL OK]
+```
+
+One-command reproduction (Windows):
+
+```powershell
+.\reproduce_all.ps1
+```
+
+Or step-by-step:
+
+```bash
+python run_correction_discovery.py --proposer mock   # Main benchmark + gate telemetry
+python run_real_data_benchmark.py                    # Real-world (5 scenarios)
+python run_pysr_baseline.py --profile fair           # Fair PySR comparison
+python run_ablation.py                               # Gate ablation study
+python run_oracle_ablation.py                        # Oracle ground-truth injection test
+python run_correction_scaling.py                     # Correction magnitude sweep
+python scripts/generate_experiment_report.py         # Sync experiment_results.md
+python scripts/generate_efficiency_table.py          # ADCD vs PySR efficiency table
+python scripts/validate_results.py                   # Consistency checks
+python generate_figures.py                           # All paper figures
+```
+
+> **Proposer regimes:** Mock Proposer = template-assisted recovery; Hybrid/Gemini = zero-shot discovery. Report both separately (see paper Section 4).
+
+```bash
+# LLM benchmark (requires GEMINI_API_KEY) — writes results/llm_benchmark.json
+python run_llm_benchmark.py --proposer hybrid
+```
+
+## Citing This Work
+
+If you use ADCD in your research, please cite:
+
+```bibtex
+@software{erdita2026adcd,
+  author    = {Erdita, Muhammad Afif},
+  title     = {{Anomaly-Driven Correction Discovery (ADCD): Physics-Constrained
+                Symbolic Regression for Evolutionary Scientific Discovery}},
+  year      = {2026},
+  publisher = {Zenodo},
+  version   = {2.1.2},
+  doi       = {10.5281/zenodo.20534940},
+  url       = {https://doi.org/10.5281/zenodo.20534940}
+}
+```
+
+## AI Disclosure
+
+This project was developed with assistance from Google DeepMind's Antigravity AI assistant. AI was used as a pair-programming and writing tool. All scientific content, experimental design decisions, and intellectual contributions are the author's own.
+
+## License
+
+[MIT](LICENSE)

adcd-2.1.2/README.md

@@ -0,0 +1,256 @@
+# ADCD — Anomaly-Driven Correction Discovery
+
+[![DOI](https://zenodo.org/badge/20534940.svg)](https://doi.org/10.5281/zenodo.20534940)
+[![CI](https://github.com/apiprdt/PhysicsPaper/actions/workflows/ci.yml/badge.svg)](https://github.com/apiprdt/PhysicsPaper/actions/workflows/ci.yml)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+**Physics-Constrained Symbolic Regression for Evolutionary Scientific Discovery**
+
+ADCD is a symbolic regression framework that discovers *physical correction terms* rather than learning equations from scratch. Given a known classical law and anomalous observations, ADCD recovers the dimensionless correction Δ that reconciles theory with experiment — mirroring how physics actually evolves.
+
+> **82.8% (±7.7%) mean structural recovery** across 5 random seeds, with peak **94.4%** at the reference seed.  
+> **4/4 real-world structural class matches** (Mercury, Lamb Shift, Muon g-2, Blackbody).  
+> **77 automated unit tests** passing on Python 3.10 and 3.11.
+
+---
+
+## Key Features
+
+- **Correction-first paradigm** — starts from a known classical law, not a blank slate; designed for anomaly-driven theory refinement where the baseline is structurally correct
+- **Physics-gated search cascade** — AST complexity, dimensional homogeneity + transcendental guardrails, and asymptotic consistency (ARC) gates screen unphysical candidates *before* optimization
+- **JAX-traced L-BFGS-B optimizer** — parameter-scaled differentiable fitting with multi-restart log-uniform initialization
+- **BIC reranking** — selects the most parsimonious correction over purely numerical fits
+- **Residual feature intelligence** — statistical priors (monotonicity, curvature, oscillation, decay rate, symmetry) bias the template sampler toward the correct mathematical family
+- **Coarse empirical evaluation** — data-driven pre-filter ranks gate survivors before full JAX optimization
+- **Noise-robust** — 93.3% mean at 0% noise, 91.1% at 1%, 71.1% at 5%, 68.9% at 10%
+
+## Quick Start
+
+### Installation
+
+```bash
+pip install adcd
+```
+
+Or install from source:
+
+```bash
+git clone https://github.com/apiprdt/PhysicsPaper.git
+cd PhysicsPaper
+pip install -e ".[dev]"
+```
+
+### Usage
+
+Running ADCD is extremely simple using the high-level scientific API:
+
+```python
+import adcd
+
+# 1. Load a pre-defined benchmark scenario
+scenarios = adcd.get_all_scenarios()
+scenario = scenarios[0]  # Relativistic Kinetic Energy
+
+# 2. Run discovery in a single line!
+result = adcd.discover_correction(scenario, max_iterations=5, proposer="mock")
+
+print(f"Discovered correction: {result.best_expr}")
+print(f"Residual NMSE: {result.best_nmse_residual:.2e}")
+print(f"Parameters: {result.best_theta}")
+
+# 3. Export LaTeX or plot residuals
+print(result.export_latex())
+result.plot_residuals()
+```
+
+For custom experimental data, use `adcd.fit(...)`:
+
+```python
+import numpy as np
+import adcd
+
+x = np.linspace(1.0, 5.0, 100)
+X = {"x": x}
+y_classical = 2.0 * x
+y_observed  = 2.0 * x + 0.5 * x**2   # hidden x² correction
+
+result = adcd.fit(
+    X=X,
+    y_obs=y_observed,
+    y_classical=y_classical,
+    limit_variable="x",
+    limit_direction="0",
+    correction_mode="additive"
+)
+
+result.summary()
+```
+
+## Benchmark Results
+
+### Standard Benchmark (seed=42, Mock Proposer)
+
+Results from `run_correction_discovery.py --proposer mock` (reference seed=42, 4 iterations per scenario).
+
+| Scenario | Tier | 0% Noise | 1% Noise | 5% Noise | 10% Noise |
+|----------|------|:--------:|:--------:|:--------:|:---------:|
+| Relativistic KE | Textbook | ✓ | ✓ | ✓ | ✓ |
+| Yukawa Gravity | Textbook | ✓ | ✓ | ✓ | ✓ |
+| Anharmonic Spring | Textbook | ✓ | ✓ | ✓ | ✓ |
+| Screened Coulomb | Cross-Domain | ✓ | ✓ | ✗ | ✗ |
+| Net Radiation | Cross-Domain | ✓ | ✓ | ✓ | ✓ |
+| Nonlinear Drag | Cross-Domain | ✓ | ✓ | ✓ | ✓ |
+| Mystery-A (tanh²) | Synthetic | ✓ | ✓ | ✓ | ✓ |
+| Mystery-B (sinc) | Synthetic | ✓ | ✓ | ✓ | ✓ |
+| Mystery-C (log-quotient) | Synthetic | ✓ | ✓ | ✓ | ✓ |
+| **Overall** | | **100%** | **100%** | **88.9%** | **88.9%** |
+
+> **Note**: Screened Coulomb fails at ≥5% noise because exponential decay ($e^{-r/\lambda}$) and rational saturation ($r/(r+\lambda)$) are numerically indistinguishable at the tested SNR with limited dynamic range — an information-theoretic limit, not a framework deficiency.
+
+### Multi-Seed Reproducibility
+
+All results are reported across 5 independent random seeds (0, 7, 21, 42, 99):
+
+| Seed | Class Match Rate |
+|:----:|:----------------:|
+| 0 | 86.1% (31/36) |
+| 7 | 75.0% (27/36) |
+| 21 | 77.8% (28/36) |
+| 42 | 94.4% (34/36) |
+| 99 | 80.6% (29/36) |
+| **Mean** | **82.8% ± 7.7%** |
+
+Performance variation reflects stochastic template sampling in the MockProposer. Physics gates ensure that **when** the correct functional family is sampled, it consistently survives filtering and is selected by BIC reranking.
+
+### Real-World Physical Constants Benchmark
+
+Synthetic-real hybrid data using experimentally validated constants from JPL DE440, NIST, and CODATA:
+
+| Physical Scenario | Discovered Correction | Converged | Class Match | NMSE |
+|---|---|:---:|:---:|:---:|
+| Mercury Perihelion (GR) | `θ₀·vc²` | — | ✓ polynomial | 1.11e-05 |
+| Hydrogen Lamb Shift (QED) | `θ₀(n/θ₁)^(-θ₂)` | ✓ | ✓ power_law | 1.82e-18 |
+| Muon g-2 (Schwinger) | `θ₀(α/π)^θ₁` | ✓ | ✓ polynomial | 7.94e-07 |
+| Blackbody (Planck) | `-1 + e^(-f/θ₁)` | — | ✓ exponential | 2.59e-02 |
+
+All 4 scenarios achieve correct structural class identification. 2 scenarios (Lamb Shift, Muon g-2) achieve full convergence with NMSE < 10⁻⁶. Mercury and Blackbody achieve correct structural identification but quantitative convergence is limited by parametrization sensitivity and dynamic range, respectively.
+
+### PySR Comparison (fair profile: 100 iterations, maxsize 30, 60s timeout)
+
+| Method | 0% Noise | 1% Noise | 5% Noise | 10% Noise |
+|--------|:--------:|:--------:|:--------:|:---------:|
+| ADCD (ours, seed=42) | 9/9 (100%) | 9/9 (100%) | 8/9 (88.9%) | 8/9 (88.9%) |
+| PySR fair | 4/9 (44.4%) | 5/9 (55.6%) | 1/9 (11.1%) | 5/9 (55.6%) |
+
+ADCD outperforms PySR fair by **77.8 percentage points** at 5% noise (88.9% vs 11.1%). A legacy fast profile (wall-clock matched) is retained in `pysr_baseline_results.json` for historical comparison only.
+
+## Project Structure
+
+```
+PhysicsPaper/
+├── src/adcd/                       # Installable package
+│   ├── __init__.py                 # Public API (adcd.fit, adcd.discover_correction)
+│   ├── anomaly_scenarios.py        # 9 standard + 3 blind benchmark scenarios
+│   ├── arc_scorer.py               # Asymptotic consistency gate (ARC)
+│   ├── coarse_evaluator.py         # Coarse numerical pre-filter
+│   ├── correction_orchestrator.py  # Main multi-iteration discovery loop
+│   ├── dimensional_checker.py      # Dimensional homogeneity + transcendental guardrail
+│   ├── jax_optimizer.py            # JAX L-BFGS-B optimizer (parameter-scaled)
+│   ├── llm_proposer.py             # Mock + Gemini + OpenAI-compatible proposers
+│   ├── metrics.py                  # NMSE, BIC, structural classification
+│   ├── pipeline.py                 # Stage 1 filter cascade
+│   ├── real_data_loader.py         # Real-world data loading (JPL, NIST, CODATA)
+│   ├── real_scenarios.py           # Real-world validation scenarios
+│   ├── residual_analyzer.py        # Statistical residual feature extraction
+│   └── result.py                   # CorrectionResult: summary, LaTeX, plot
+├── tests/                          # 58 unit + integration tests
+├── paper/                          # LaTeX source (main.tex) + figures
+├── run_correction_discovery.py     # Standard 9-scenario benchmark runner
+├── run_real_data_benchmark.py      # Real-world physical constants benchmark
+├── run_reproducibility.py          # Multi-seed reproducibility study (5 seeds)
+├── run_ablation.py                 # Gate ablation study
+├── run_pysr_baseline.py            # PySR comparison baseline
+├── run_mlp_baseline.py             # MLP comparison baseline
+├── run_misspecification_benchmark.py  # Baseline misspecification fail-safe test
+├── generate_figures.py             # Paper figure generator
+├── .github/workflows/              # CI (test + lint + LaTeX) and PyPI publish
+├── pyproject.toml                  # PEP 517/518 build configuration
+└── README.md                       # This file
+```
+
+## Running Tests
+
+```bash
+pip install -e ".[dev]"
+pytest --cov=adcd
+```
+
+All 77 tests pass on Python 3.10 and 3.11 (Ubuntu and Windows).
+
+## Submission & Release
+
+Paper submission guide (GitHub Release → Zenodo → arXiv): [docs/SUBMISSION_CHECKLIST_v2.1.2.md](docs/SUBMISSION_CHECKLIST_v2.1.2.md)
+
+Current release tag: **v2.1.2** | Package version: **2.1.2**
+
+## Reproducing Paper Results
+
+Verify claims before citing numbers:
+
+```bash
+python scripts/verify_paper_claims.py   # expect [ALL OK]
+```
+
+One-command reproduction (Windows):
+
+```powershell
+.\reproduce_all.ps1
+```
+
+Or step-by-step:
+
+```bash
+python run_correction_discovery.py --proposer mock   # Main benchmark + gate telemetry
+python run_real_data_benchmark.py                    # Real-world (5 scenarios)
+python run_pysr_baseline.py --profile fair           # Fair PySR comparison
+python run_ablation.py                               # Gate ablation study
+python run_oracle_ablation.py                        # Oracle ground-truth injection test
+python run_correction_scaling.py                     # Correction magnitude sweep
+python scripts/generate_experiment_report.py         # Sync experiment_results.md
+python scripts/generate_efficiency_table.py          # ADCD vs PySR efficiency table
+python scripts/validate_results.py                   # Consistency checks
+python generate_figures.py                           # All paper figures
+```
+
+> **Proposer regimes:** Mock Proposer = template-assisted recovery; Hybrid/Gemini = zero-shot discovery. Report both separately (see paper Section 4).
+
+```bash
+# LLM benchmark (requires GEMINI_API_KEY) — writes results/llm_benchmark.json
+python run_llm_benchmark.py --proposer hybrid
+```
+
+## Citing This Work
+
+If you use ADCD in your research, please cite:
+
+```bibtex
+@software{erdita2026adcd,
+  author    = {Erdita, Muhammad Afif},
+  title     = {{Anomaly-Driven Correction Discovery (ADCD): Physics-Constrained
+                Symbolic Regression for Evolutionary Scientific Discovery}},
+  year      = {2026},
+  publisher = {Zenodo},
+  version   = {2.1.2},
+  doi       = {10.5281/zenodo.20534940},
+  url       = {https://doi.org/10.5281/zenodo.20534940}
+}
+```
+
+## AI Disclosure
+
+This project was developed with assistance from Google DeepMind's Antigravity AI assistant. AI was used as a pair-programming and writing tool. All scientific content, experimental design decisions, and intellectual contributions are the author's own.
+
+## License
+
+[MIT](LICENSE)

adcd-2.1.2/pyproject.toml

@@ -0,0 +1,85 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "adcd"
+version = "2.1.2"
+description = "Anomaly-Driven Correction Discovery: Physics-Constrained Symbolic Regression for Evolutionary Scientific Discovery"
+readme = "README.md"
+license = { text = "MIT" }
+authors = [
+    { name = "Muhammad Afif Erdita", email = "maeapip10@gmail.com" }
+]
+keywords = ["symbolic regression", "physics", "machine learning", "scientific discovery", "JAX"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+]
+requires-python = ">=3.10"
+dependencies = [
+    "numpy>=1.24",
+    "scipy>=1.11",
+    "sympy>=1.12",
+    "jax>=0.4.20",
+    "jaxlib>=0.4.20",
+    "matplotlib>=3.7",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.4",
+    "pytest-cov>=4.1",
+    "flake8>=6.1",
+    "black>=23.0",
+]
+llm = [
+    "google-generativeai>=0.3",
+]
+all = ["adcd[dev,llm]"]
+
+[project.urls]
+Homepage = "https://zenodo.org/records/20534940"
+Repository = "https://github.com/apiprdt/PhysicsPaper"
+"Bug Tracker" = "https://github.com/apiprdt/PhysicsPaper/issues"
+DOI = "https://doi.org/10.5281/zenodo.20534940"
+
+[project.scripts]
+adcd-discover = "adcd.correction_orchestrator:main_cli"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-dir]
+"" = "src"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = "--tb=short -q"
+filterwarnings = [
+    # matplotlib emits DeprecationWarning when plt.show() is called on a
+    # non-interactive (Agg) backend. This is a third-party warning not under
+    # our control; we already guard plt.show() with plt.isinteractive().
+    "ignore:FigureCanvasAgg is non-interactive:DeprecationWarning",
+]
+
+[tool.coverage.run]
+source = ["adcd"]
+omit = ["tests/*", "scratch/*"]
+
+[tool.black]
+line-length = 100
+target-version = ["py310", "py311"]
+
+[tool.flake8]
+max-line-length = 100
+exclude = [".git", "__pycache__", "scratch", "*.egg-info"]

adcd-2.1.2/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+