c4reqber 5.6.0__tar.gz

c4reqber-5.6.0/.cgcignore

@@ -0,0 +1,25 @@
+# Auto-generated by CodeGraphContext
+# Default ignore patterns for binary/media files
+# Add your own patterns below
+
+node_modules/
+venv/
+.venv/
+env/
+.env/
+dist/
+build/
+target/
+out/
+.git/
+__pycache__/
+*.png
+*.jpg
+*.jpeg
+*.gif
+*.svg
+*.mp4
+*.mp3
+*.zip
+*.tar
+*.gz

c4reqber-5.6.0/.coveragerc

@@ -0,0 +1,17 @@
+[run]
+source = src
+branch = true
+parallel = true
+concurrency = thread
+
+[report]
+fail_under = 60
+show_missing = true
+skip_covered = false
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    raise AssertionError
+    raise NotImplementedError
+    if __name__ == .__main__.:
+    if TYPE_CHECKING:

c4reqber-5.6.0/.dockerignore

@@ -0,0 +1,60 @@
+# Git
+.git
+.gitignore
+
+# Python
+__pycache__
+*.pyc
+*.pyo
+*.egg-info
+.pytest_cache
+.mypy_cache
+.coverage
+htmlcov
+
+# Virtual environments
+venv/
+.venv/
+env/
+
+# Environment files
+.env
+.env.*
+!.env.example
+
+# IDE
+.vscode
+.idea
+*.swp
+*.swo
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Node (for web-v2 submodule builds)
+web-v2/node_modules
+web-v2/dist
+web-v2/dist-ssr
+
+# Data
+data/
+*.db
+*.sqlite3
+
+# Logs
+*.log
+logs/
+
+# Docker
+docker-compose*.yml
+Dockerfile*
+.dockerignore
+
+# Documentation
+*.md
+!README.md
+
+# CI/CD
+.github
+.pre-commit-config.yaml

c4reqber-5.6.0/.env.example

@@ -0,0 +1,203 @@
+# ── c4reqber — Environment Variables ──
+# Copy this file to .env and fill in your keys.
+# Registration guide: docs/API_KEYS.md (mini: landing/docs/setup/api-keys.html)
+# Required for core functionality: OPENROUTER_API_KEY
+
+# ── LLM Provider Keys ──
+OPENROUTER_API_KEY=sk-or-...
+DEEPSEEK_API_KEY=
+MISTRAL_API_KEY=
+MOONSHOT_API_KEY=sk-...
+XAI_API_KEY=
+PERPLEXITY_API_KEY=
+ANTHROPIC_API_KEY=
+GOOGLE_API_KEY=
+NVIDIA_API_KEY=nvapi-...
+VASTAI_API_KEY=
+
+# ── Local LLM ──
+OLLAMA_URL=http://localhost:11434
+LM_STUDIO_URL=http://localhost:1234/v1
+LM_STUDIO_API_KEY=
+
+# ── Search & Knowledge APIs ──
+BRAVE_API_KEY=
+TAVILY_API_KEY=                   # Free tier: 1000 credits/month at app.tavily.com
+SEMANTIC_SCHOLAR_API_KEY=          # Optional (free without key; key increases limits)
+CROSSREF_MAILTO=
+CROSSREF_API_KEY=                  # Optional (free polite pool without key)
+CINII_APPID=
+PUBMED_API_KEY=
+SCIMATIC_API_KEY=
+UNPAYWALL_EMAIL=
+CORE_API_KEY=
+
+# ── Scientific Data Sources (P6) ──
+NCBI_API_KEY=                      # Optional (increases rate limits 3→10 req/sec)
+NCBI_EMAIL=                        # Required by NCBI when using API key
+MATERIALS_PROJECT_API_KEY=         # Free academic API key
+KAGGLE_USERNAME=                   # Required for dataset download
+KAGGLE_KEY=                        # Required for dataset download
+BIBSONOMY_API_KEY=                 # Free academic bookmarking
+BIBSONOMY_USERNAME=                # Default: "public"
+NOAA_API_KEY=                      # Free token from NOAA CDO
+OPENFDA_API_KEY=                   # Free via api.data.gov/signup
+OPENALEX_API_KEY=                  # Optional (OpenAlex works without key)
+STRING_DB_API_KEY=                 # Optional STRING enrichment key
+GBIF_USER=                         # GBIF account for bulk downloads
+GBIF_PASSWORD=
+DRUGBANK_API_KEY=                  # Paid subscription only — stub when empty
+BASE_API_KEY=                      # Manual approval required
+# GTEX, UNIPROT, EUROPE_PMC — no API key required
+
+# ── Social & Publishing ──
+X_BEARER_TOKEN=
+MASTODON_ACCESS_TOKEN=
+BLUESKY_HANDLE=
+BLUESKY_APP_PASSWORD=
+TELEGRAM_BOT_TOKEN=
+TELEGRAM_CHAT_ID=
+ORCID_CLIENT_ID=
+ORCID_CLIENT_SECRET=
+GITHUB_TOKEN=
+
+# ── Security ──
+# For development, set a dummy secret. NEVER use these in production.
+JWT_SECRET=dev-secret-change-me-in-production-min-32-chars
+C4REQBER_JWT_SECRET=dev-secret-change-me-in-production-min-32-chars
+CSRF_SECRET=dev-csrf-secret-change-me-min-32-chars-long
+HSM_MODE=stub
+HSM_HOST=
+HSM_PORT=
+HSM_SLOT_ID=
+HSM_PASSWORD=
+HSM_KEY_LABEL=
+HSM_USER_PIN=
+
+# ── Database ──
+DATABASE_URL=sqlite:///data/c4reqber.db
+DB_HOST=
+DB_PORT=
+DB_NAME=c4reqber
+DB_USER=
+DB_PASSWORD=
+
+# ── Cache & Storage ──
+CACHE_BACKEND=memory
+REDIS_URL=redis://localhost:6379
+CACHE_TTL=3600
+
+# ── Verification Tools ──
+LEAN4_PATH=
+COQ_PATH=
+DAFNY_PATH=
+Z3_PATH=
+
+# ── API Server ──
+API_HOST=0.0.0.0
+API_PORT=8000
+API_WORKERS=1
+API_KEYS=
+RATE_LIMIT_ENABLED=true
+RATE_LIMIT_REQUESTS=30
+
+# ── Observability ──
+LOG_LEVEL=INFO
+SENTRY_DSN=
+ENABLE_OPENTELEMETRY=false
+
+# ── Feature Flags ──
+LLM_COUNCIL=false
+LLM_COUNCIL_BUDGET=balanced
+RETRY_MAX_ATTEMPTS=3
+SKIP_EXPENSIVE_VERIFICATION=false
+
+# ── Additional LLM Providers ──
+OPENAI_API_KEY=
+OPENAI_BASE_URL=
+GROK_API_KEY=
+LIQUID_API_KEY=
+LIQUID_URL=
+MLX_MODEL=
+YANDEX_API_KEY=
+YANDEX_API_URL=
+YANDEX_FOLDER_ID=
+LAMBDA_API_KEY=
+RUNPOD_API_KEY=
+OPENFANG_API_KEY=
+OPENFANG_API_URL=
+
+# ── Auto-Formalization (P0) ──
+AUTO_FORMALIZATION_ENABLED=true
+AUTO_FORMALIZATION_MIN_CONFIDENCE=0.7
+AUTO_FORMALIZATION_MAX_COST=5.0
+AUTO_FORMALIZATION_HUMAN_GATE=0.9
+
+# ── Database Pool ──
+POOL_SIZE=5
+MAX_OVERFLOW=10
+POOL_TIMEOUT=30
+POOL_RECYCLE=3600
+POOL_PRE_PING=true
+
+# ── Rate Limiting ──
+RATE_LIMIT_BACKEND=memory
+RATE_LIMIT_ENDPOINTS=default
+RATE_LIMIT_RPM=60
+
+# ── Payment Providers ──
+SUPABASE_URL=
+SUPABASE_ANON_KEY=
+
+# ── Social / Integrations (additional) ──
+DISCORD_WEBHOOK_URL=
+SLACK_WEBHOOK_URL=
+REDDIT_CLIENT_ID=
+REDDIT_CLIENT_SECRET=
+REDDIT_USERNAME=
+REDDIT_PASSWORD=
+TWITTER_API_KEY=
+TWITTER_API_SECRET=
+TWITTER_ACCESS_TOKEN=
+TWITTER_ACCESS_SECRET=
+XAI_BASE_URL=
+DEEPSEEK_BASE_URL=
+MISTRAL_BASE_URL=
+MOONSHOT_BASE_URL=
+NVIDIA_API_URL=
+OPENROUTER_BASE_URL=
+
+# ── Archive / Export ──
+ARXIV_SUBMISSION_KEY=
+ZENODO_ACCESS_TOKEN=
+AI_ARCHIVE_API_KEY=
+RSCI_API_KEY=
+SCHOLARA_API_KEY=
+
+# ── Misc ──
+APP_VERSION=
+RELEASE_VERSION=
+ENV=development
+ENVIRONMENT=development
+C4REQBER_MODE=standard
+C4REQBER_KEYRING_TOKEN=
+DEV_MODE=false
+DEV_MODE_BYPASS_TOKEN=
+DEV_USER_ID=
+DEV_USER_NAME=
+AUDIT_LOG_DIR=./audit
+TEMP=
+TMPDIR=/tmp
+WEBHOOK_SECRET=
+SECURE_COOKIES=true
+FEDERATED_PEERS=
+OTLP_ENDPOINT=
+SENTRY_DEV=
+LOG_FORMAT=text
+EIGENT_API_PORT=
+EIGENT_HOME=
+ENABLE_MATLAB=false
+
+# ── Retry Configuration ──
+RETRY_ENABLED=true
+RETRY_BACKOFF_BASE=2.0

c4reqber-5.6.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug Report
+description: Report a bug in TURBO-CDI
+labels: [bug]
+body:
+  - type: textarea
+    attributes:
+      label: Describe the bug
+      description: A clear description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Steps to reproduce
+      placeholder: |
+        1. Go to '...'
+        2. Click on '...'
+        3. See error
+  - type: input
+    attributes:
+      label: TURBO-CDI version
+      placeholder: e.g., v7.0.0
+  - type: input
+    attributes:
+      label: Python version
+      placeholder: e.g., 3.11.0

c4reqber-5.6.0/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,21 @@
+name: Feature Request
+description: Suggest a feature for TURBO-CDI
+labels: [enhancement]
+body:
+  - type: textarea
+    attributes:
+      label: Is your feature request related to a problem?
+      placeholder: I'm always frustrated when...
+  - type: textarea
+    attributes:
+      label: Describe the solution
+      placeholder: A clear description of what you want to happen.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Alternatives considered
+  - type: dropdown
+    attributes:
+      label: Priority for you
+      options: [Nice to have, Important, Critical]

c4reqber-5.6.0/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,18 @@
+## Summary
+<!-- Brief description of changes -->
+
+## Type
+- [ ] Bug fix
+- [ ] New feature
+- [ ] Breaking change
+- [ ] Documentation
+- [ ] Test improvement
+- [ ] Refactor
+
+## Checklist
+- [ ] Tests added/updated
+- [ ] Mypy strict: 0 errors (verify with `make typecheck`)
+- [ ] Ruff: 0 errors (verify with `make lint`)
+- [ ] CHANGELOG.md updated
+- [ ] Breaking changes documented
+- [ ] No .env files committed

c4reqber-5.6.0/.github/dependabot.yml

@@ -0,0 +1,14 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "npm"
+    directory: "/web-v2"
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

c4reqber-5.6.0/.github/workflows/build-desktop.yml

@@ -0,0 +1,69 @@
+name: Build Desktop
+
+on:
+  push:
+    tags: ['v*']
+    paths:
+      - 'web-v2/**'
+      - 'src-tauri/**'
+      - '.github/workflows/build-desktop.yml'
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: macos-latest
+            target: aarch64-apple-darwin
+            artifact: turbo-cdi-macos-arm64
+          - os: macos-13
+            target: x86_64-apple-darwin
+            artifact: turbo-cdi-macos-x64
+          - os: windows-latest
+            target: x86_64-pc-windows-msvc
+            artifact: turbo-cdi-windows-x64
+          - os: ubuntu-latest
+            target: x86_64-unknown-linux-gnu
+            artifact: turbo-cdi-linux-x64
+
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Setup Rust
+        uses: dtolnay/rust-action@stable
+        with:
+          targets: ${{ matrix.target }}
+
+      - name: Install system deps (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libwebkit2gtk-4.1-dev libappindicator3-dev librsvg2-dev patchelf libgtk-3-dev libjavascriptcoregtk-4.1-dev libsoup-3.0-dev
+
+      - name: Install deps
+        working-directory: web-v2
+        run: npm ci
+
+      - name: Build frontend
+        working-directory: web-v2
+        run: npm run build
+
+      - name: Build Tauri
+        uses: tauri-apps/tauri-action@v0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          projectPath: web-v2
+          tagName: ${{ github.ref_name }}
+          releaseName: 'TURBO-CDI ${{ github.ref_name }}'
+          releaseBody: 'See the assets to download this version.'
+          releaseDraft: true
+          prerelease: false

c4reqber-5.6.0/.github/workflows/build.yml

@@ -0,0 +1,95 @@
+name: Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  build-backend:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Cache pip packages
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Verify backend imports
+        run: |
+          PYTHONPATH=src python -c "from src.api.server import app; print('Backend OK')"
+
+      - name: Build backend artifact
+        run: |
+          mkdir -p dist
+          tar czf dist/backend.tar.gz src/ requirements.txt pyproject.toml
+
+      - name: Upload backend artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: backend-artifact
+          path: dist/backend.tar.gz
+
+  build-frontend:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+          cache: "npm"
+          cache-dependency-path: web-v2/package-lock.json
+
+      - name: Install dependencies
+        run: |
+          cd web-v2
+          npm ci --legacy-peer-deps
+
+      - name: Build frontend
+        run: |
+          cd web-v2
+          npm run build
+
+      - name: Upload frontend artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: frontend-artifact
+          path: web-v2/dist/
+
+  verify-artifacts:
+    runs-on: ubuntu-latest
+    needs: [build-backend, build-frontend]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download backend artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: backend-artifact
+          path: dist/
+
+      - name: Download frontend artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: frontend-artifact
+          path: web-v2/dist/
+
+      - name: Verify artifacts exist
+        run: |
+          test -f dist/backend.tar.gz && echo "Backend artifact OK"
+          test -d web-v2/dist && echo "Frontend artifact OK"

c4reqber-5.6.0/.github/workflows/ci.yml

@@ -0,0 +1,100 @@
+name: CI/CD Pipeline
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test-backend:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+    
+    - name: Cache pip packages
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install pytest pytest-asyncio pytest-cov ruff
+    
+    - name: Run Ruff lint
+      run: ruff check src/ --exclude="archive/"
+    
+    - name: Run tests
+      env:
+        DATABASE_URL: sqlite:///tmp/test.db
+        CACHE_BACKEND: memory
+        JWT_SECRET: test-secret-min-32-chars-long
+      run: |
+        PYTHONPATH=. pytest tests/ --cov=src --cov-report=term-missing --cov-config=.coveragerc --cov-fail-under=60 -v --tb=short
+
+  test-frontend:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Node.js
+      uses: actions/setup-node@v4
+      with:
+        node-version: '20'
+        cache: 'npm'
+        cache-dependency-path: web-v2/package-lock.json
+    
+    - name: Install dependencies
+      run: |
+        cd web-v2
+        npm ci --legacy-peer-deps
+    
+    - name: Run ESLint
+      run: |
+        cd web-v2
+        npm run lint
+    
+    - name: Type check
+      run: |
+        cd web-v2
+        npx tsc --noEmit
+    
+    - name: Run tests
+      run: |
+        cd web-v2
+        npm run test
+    
+    - name: Build
+      run: |
+        cd web-v2
+        npm run build
+
+  docker-build:
+    runs-on: ubuntu-latest
+    needs: [test-backend, test-frontend]
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+    
+    - name: Build API Docker image
+      run: |
+        docker build -t turbo-cdi-api:${{ github.sha }} .
+    
+    - name: Build Web Docker image
+      run: |
+        cd web-v2
+        docker build -t turbo-cdi-web:${{ github.sha }} .
+    
+    - name: Test API container
+      run: |
+        docker run --rm -e JWT_SECRET=test-secret-min-32-chars-long -e DATABASE_URL=sqlite:///tmp/test.db -e CACHE_BACKEND=memory turbo-cdi-api:${{ github.sha }} python -c "from src.api.server import app; print('OK')"