v1.0.1: peer review response — package restructure, calibration study, docs overhaul

Structural:
- Move all modules under aethermor/ namespace (aethermor.physics, etc.)
- Remove all 20 sys.path.insert hacks
- Split monolithic app.py into aethermor/app/ (6 tab modules)
- Add CLI entry point: aethermor dashboard|validate|version
- Add python -m aethermor support

Documentation:
- Calibration case study: 15 real chips vs model (A100, H100, i9-13900K, etc.)
- Datacenter GPU case study: 8-GPU node air vs liquid vs substrate
- Uncertainty/sensitivity analysis with Monte Carlo propagation
- README: Start Here guide, validation table, error bounds, failure modes,
  CFD comparison, reproducibility section, academic references
- Consistency audit: test counts, import paths, app.py refs across all docs

Version bump to 1.0.1.

Author: Aethermor

.github/workflows/ci.yml

@@ -30,7 +30,7 @@ jobs:
         run: python -m pytest tests/ -q
 
       - name: Run validation suite
-        run: python -m validation.validate_all
+        run: python -m aethermor.validation.validate_all
 
       - name: Run literature validation
         run: python benchmarks/literature_validation.py

CHANGELOG.md

@@ -4,6 +4,37 @@ All notable changes to this project are documented in this file.
 
 ## [Unreleased]
 
+## [1.0.1] - 2026-03-31
+
+### Added — Peer Review Response
+- **Package restructure**: All modules moved under `aethermor/` namespace
+  (`aethermor.physics`, `aethermor.analysis`, `aethermor.validation`,
+  `aethermor.simulation`). Proper installable package with `pip install -e .`.
+- **CLI entry point**: `aethermor dashboard`, `aethermor validate`,
+  `aethermor version` via `[project.scripts]` in pyproject.toml.
+- **Dashboard split**: Monolithic `app.py` (730 lines) replaced with modular
+  `aethermor/app/` package — 6 tab modules + shared utils + main entry point.
+- **Calibration case study**: `docs/calibration_case_study.md` — 15 real
+  production chips (A100, H100, MI300X, i9-13900K, Ryzen 7950X, RTX 4090, etc.)
+  validated against datasheet Tj_max values.
+- **Datacenter GPU case study**: `docs/case_study_datacenter_gpu.md` — 8-GPU
+  node cooling decision matrix (air vs liquid vs substrate).
+- **Uncertainty & sensitivity analysis**: `docs/uncertainty_sensitivity.md` —
+  Monte Carlo uncertainty propagation, OAT sensitivity, transient roadmap.
+- **README enhancements**: "Start Here" evaluation guide, validation summary
+  table, expected accuracy section, "When This Model Breaks" failure modes,
+  CFD comparison table, reproducibility section, academic references.
+
+### Changed
+- All 65+ source files updated from `physics.*` → `aethermor.physics.*` imports.
+- All `sys.path.insert` hacks removed (20 files).
+- All documentation updated for new package paths and consistent test counts.
+- pyproject.toml: `packages.find` now includes only `aethermor*`.
+
+### Removed
+- Monolithic `app.py` — replaced by `aethermor/app/` modular architecture.
+- All `sys.path` manipulation from `tests/conftest.py`.
+
 ## [1.0.0] - 2026-03-25
 
 ### Added — Experimental Measurement Validation
@@ -94,7 +125,7 @@ All notable changes to this project are documented in this file.
   - `thermal_map.py`: Hotspot detection, cooling efficiency maps
 
 ### Added — Interactive Explorer UI
-- `app.py`: Dash-based interactive explorer with 6 tabs:
+- `aethermor/app/`: Modular Dash-based interactive explorer with 6 tabs:
   - Material Ranking, Cooling Analysis, Paradigm Comparison,
     Technology Roadmap, SoC Thermal Map, Custom Material registration
 
@@ -119,7 +150,7 @@ All notable changes to this project are documented in this file.
 
 ### Added — Validation & Testing
 - 254 unit, integration, regression, and performance tests (pytest)
-- 133 physics cross-checks (`python -m validation.validate_all`) against
+- 133 physics cross-checks (`python -m aethermor.validation.validate_all`) against
   CODATA 2018, CRC Handbook, ITRS/IRDS, analytical solutions
 - 43 registry-specific tests covering all three extensible registries
 

CITATION.cff

@@ -17,7 +17,7 @@ abstract: >
   power redistribution), technology roadmap projection (130 nm to 1.4 nm),
   and an interactive explorer dashboard. All models are cross-validated against
   CODATA 2018, the CRC Handbook, and ITRS/IRDS roadmaps (133 physics checks,
-  254 tests).
+  277 tests).
 keywords:
   - thermal analysis
   - chip thermal modeling

CONTRIBUTING.md

@@ -39,15 +39,15 @@ pip install -e ".[all]"    # core + dashboard + dev tools
 Run tests:
 
 ```bash
-python -m pytest tests/ -v              # 254 tests
-python -m validation.validate_all       # 133 physics cross-checks
+python -m pytest tests/ -v              # 277 tests
+python -m aethermor.validation.validate_all       # 133 physics cross-checks
 ```
 
 Run examples:
 
 ```bash
 python examples/custom_material.py      # extensibility walkthrough
-python app.py                           # interactive explorer UI
+aethermor dashboard                     # interactive explorer UI
 ```
 
 ## Pull Request Requirements

HONEST_REVIEW.md

@@ -27,7 +27,7 @@ These are questions hardware researchers currently answer through manual
 COMSOL sweeps, HotSpot configurations, or custom scripts. Aethermor integrates
 them into a single API and interactive dashboard.
 
-**Test suite**: 254 tests passing, 1 skipped (dashboard requires optional `dash`).
+**Test suite**: 277 tests passing, 1 skipped (dashboard requires optional `dash`).
 **Energy conservation**: 0.00 % error in 3D Fourier solver (tolerance: 5 %).
 
 ---
@@ -135,7 +135,7 @@ cross-checks every physics model against published reference data, analytical
 solutions, conservation laws, and internal self-consistency.
 
 ```bash
-python -m validation.validate_all    # 133 checks, ~13 seconds
+python -m aethermor.validation.validate_all    # 133 checks, ~13 seconds
 ```
 
 | Validation Area | Checks | Reference Source |
@@ -162,27 +162,27 @@ and interpretation guide.
 ### 2.3 Code Structure
 
 ```
-physics/          # SI-unit models
+aethermor/physics/          # SI-unit models
   constants.py    # k_B, Planck, Boltzmann, landauer_limit()
   materials.py    # 9 substrates + extensible registry with validation
   energy_models.py  # 4 paradigms + extensible registry with protocol checking
   thermal.py      # FourierThermalTransport (3D solver)
   cooling.py      # CoolingStack + extensible layer registry
   chip_floorplan.py  # ChipFloorplan, FunctionalBlock
 
-analysis/         # Research tools
+aethermor/analysis/         # Research tools
   thermal_optimizer.py  # Inverse design (8 capabilities)
   design_space.py       # Pareto sweeps
   landauer_gap.py       # Gap analysis
   regime_map.py         # Operating regime classification
   thermal_map.py        # Temperature field analysis
   tech_roadmap.py       # Node projection (130nm to 1.4nm)
 
-simulation/       # Legacy Monte Carlo / evolutionary simulation engine
+aethermor/simulation/       # Monte Carlo / evolutionary simulation engine
 examples/         # 7 runnable research scripts
 experiments/      # Reproducibility scripts (ablations, scaling, fault sweeps)
 tests/            # 277 tests (pytest)
-validation/       # 133 physics cross-checks (validate_all.py)
+aethermor/validation/       # 133 physics cross-checks (validate_all.py)
 ```
 
 ### 2.4 Reproducibility