feat: Implement SEU Gearbox validation and fix physics config

Author: TasfinMahmud

.github/workflows/ci.yml

@@ -0,0 +1,93 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: tests (py${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install core dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .
+          pip install pytest
+
+      - name: Run unit tests
+        run: pytest test/ -v
+
+  import-independence:
+    name: import-independence (no TensorFlow)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install core dependencies only
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .
+
+      - name: Assert TensorFlow is absent
+        run: |
+          python - <<'PY'
+          import importlib.util, sys
+          if importlib.util.find_spec("tensorflow") is not None:
+              sys.exit("TensorFlow is installed; this job must run without it.")
+          print("confirmed: TensorFlow not installed")
+          PY
+
+      - name: Import dependency-light subpackages
+        run: |
+          python - <<'PY'
+          import importlib
+          for mod in ("cnsd.causal", "cnsd.physics", "cnsd.config", "cnsd.scm"):
+              importlib.import_module(mod)
+              print(f"imported {mod} without TensorFlow")
+          PY
+
+  install:
+    name: editable install
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install package (editable, core extras)
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .
+
+      - name: Import installed package
+        run: python -c "import cnsd; print('cnsd installed and importable')"

.github/workflows/lint.yml

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+name: Lint
+
+# Static checks: Ruff handles both linting and formatting in a single tool.
+# Fast (seconds), no project dependencies needed, runs on every push and PR.
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: lint-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  ruff:
+    name: ruff (lint + format)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install Ruff
+        run: pip install ruff
+
+      # Linting: flags unused imports, undefined names, common bugs.
+      - name: Ruff lint
+        run: ruff check .
+
+      # Formatting: verifies code matches the formatter (does not modify it).
+      # Run `ruff format .` locally to fix before pushing.
+      - name: Ruff format check
+        run: ruff format --check .

100.mat

@@ -0,0 +1,45 @@
+# Changelog
+
+All notable changes to CNSD are documented here. The format is based on
+[Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project
+adheres to semantic versioning once it reaches 1.0.
+
+## [Unreleased]
+
+### Added
+- Pluggable `PhysicsProvider` interface — the diagnosis engine is now
+  domain-agnostic; machine classes plug in as providers.
+- `BearingProvider` (ball-pass-frequency physics) and `SpectralProvider` (the
+  universal zero-knowledge fallback).
+- `GearProvider` and gear-mesh physics (GMF + sidebands) for gearbox diagnosis.
+- Configuration layer: YAML-driven physics and taxonomy, resolved into providers
+  by `cnsd/builder.py`.
+- Real Pearl Rung-3 counterfactuals via DoWhy `gcm`, with a local-sensitivity
+  fallback when DoWhy is unavailable.
+- Universal `Dataset` contract (`Dataset.from_arrays`) so any vibration dataset
+  plugs in without a bespoke loader.
+- Validation scripts for CWRU (`validate_run.py`) and SEU gears
+  (`validate_seu.py`), and a cross-condition robustness script.
+- Test suite covering the physics, symbolic, causal, consensus, and provider
+  layers.
+
+### Changed
+- Symbolic layer rewritten to verify predictions against physics via a provider
+  and a configurable taxonomy (replacing a hardcoded, CWRU-specific lookup).
+- Causal layer scoped honestly to Pearl Rung 2 (effect of operating condition)
+  on a corrected DAG; the counterfactual layer carries Rung 3.
+
+### Notes
+- Pre-1.0 research software. Interfaces may change. Not intended for
+  safety-critical deployment without independent validation.
+
+## History
+
+CNSD began as a five-layer causal-neuro-symbolic diagnosis prototype and was
+rebuilt into a domain-agnostic framework: the physics-verification layer was made
+real (independent characteristic-frequency checks that can override the neural
+prediction), the causal claims were scoped honestly, and the system was
+reorganized into a deployable package.
+
+## Project history
+

CHANGELOG.md

@@ -0,0 +1,59 @@
+# Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and maintainers pledge to make participation in
+CNSD a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment:
+
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility, apologizing to those affected by our mistakes, and
+  learning from the experience
+- Focusing on what is best for the project and the community
+
+Examples of unacceptable behavior:
+
+- The use of sexualized language or imagery, and sexual attention or advances
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Project maintainers are responsible for clarifying and enforcing these standards
+and will take appropriate and fair corrective action in response to any behavior
+they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies within all project spaces and also applies when an
+individual is officially representing the project in public spaces.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the maintainers listed in MAINTAINERS.md. All complaints will be
+reviewed and investigated promptly and fairly. Maintainers are obligated to
+respect the privacy and security of the reporter of any incident.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.
+
+[homepage]: https://www.contributor-covenant.org

CODE_OF_CONDUCT.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Abhimanyu Prasad and Kazi Tasfin Mahmud
+
+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

@@ -0,0 +1,17 @@
+# Maintainers
+
+CNSD is developed and maintained by:
+
+- **Abhimanyu Prasad** ([@abhiprd2000](https://github.com/abhiprd2000)) — lead developer
+- **Kazi Tasfin Mahmud** ([@TasfinMahmud](https://github.com/TasfinMahmud)) — lead developer
+
+Both maintainers review and merge changes. For substantial changes, open a pull
+request and request review from a maintainer.
+
+## Areas
+
+The codebase is organized one concern per package (`cnsd/diagnosis`,
+`cnsd/causal`, `cnsd/counterfactual`, `cnsd/physics`, `cnsd/symbolic`,
+`cnsd/datasets`). Either maintainer can review any area; tag both for changes
+that cross package boundaries or touch the public API (`cnsd/__init__.py`,
+`cnsd/diagnosis/system.py`).

MAINTAINERS.md

@@ -0,0 +1,30 @@
+# Security Policy
+
+CNSD is a research framework for machine fault diagnosis. It is not intended for
+safety-critical deployment without independent validation (see the limitations
+in the README).
+
+## Reporting a vulnerability
+
+If you find a security issue — for example, a way for crafted input data or a
+malicious config/YAML file to cause unsafe behavior — please report it privately
+rather than opening a public issue.
+
+- Use GitHub's **private vulnerability reporting** (the "Report a vulnerability"
+  button under the repository's *Security* tab), or
+- Contact a maintainer directly (see MAINTAINERS.md).
+
+Please include a description, steps to reproduce, and the affected version or
+commit. We will acknowledge reports and address confirmed issues as promptly as 
+we can.
+
+## Supported versions
+
+This is 1.0 research software. Only the latest
+commit on `main` is supported; fixes are not backported.
+
+## Scope
+
+CNSD loads user-supplied data and configuration (including YAML). Treat data and
+config files from untrusted sources with the same caution as any code — a
+configuration file can change which physics and taxonomy the system applies.

SECURITY.md

@@ -20,6 +20,7 @@
 intervention_effect_of_condition` does NOT require TensorFlow. Only the full
 CNSD system (which trains the CNN) needs the perception backend.
 """
+
 __version__ = '1.0.0'
 
 # Lazy top-level names (PEP 562): keeps `from cnsd import CNSD` working without
@@ -37,6 +38,7 @@
 def __getattr__(name):
     if name in _LAZY:
         import importlib
+
         module, attr = _LAZY[name]
         return getattr(importlib.import_module(module), attr)
     raise AttributeError(f"module 'cnsd' has no attribute '{name}'")