Fix view_inference spec deletion bug + add abstraction level examples #57

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Merged

ChuyueSun merged 13 commits into main from new-workflow

Nov 7, 2025

.flake8

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+Diff line change
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+    [flake8]
+    max-line-length = 100
+    extend-ignore = E203, E501, W503, E713, E712, E402, F401, F841, F811, F821, F541, D100, D101, D102, D103, D104, D105, D107, D200, D202, D205, D209, D301, D400, D401, D403
+    exclude =
+        .git,
+        __pycache__,
+        build,
+        dist,
+        *.egg-info,
+        .venv,
+        venv,
+        tmp*,
+        external,
+        llm_cache,
+        output,
+        logs,
+        benchmark*,
+        utils/lynette

.github/PULL_REQUEST_TEMPLATE.md

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+    ## Description
+    <!-- Provide a brief description of the changes in this PR -->
+    ## Type of Change
+    <!-- Mark the relevant option with an 'x' -->
+    - [ ] Bug fix (non-breaking change which fixes an issue)
+    - [ ] New feature (non-breaking change which adds functionality)
+    - [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+    - [ ] Documentation update
+    - [ ] Performance improvement
+    - [ ] Code refactoring
+    ## Checklist
+    <!-- Mark completed items with an 'x' -->
+    - [ ] My code follows the code style of this project
+    - [ ] I have run pre-commit hooks locally (`pre-commit run --all-files`)
+    - [ ] I have performed a self-review of my own code
+    - [ ] I have commented my code, particularly in hard-to-understand areas
+    - [ ] I have made corresponding changes to the documentation
+    - [ ] My changes generate no new warnings
+    - [ ] I have added tests that prove my fix is effective or that my feature works
+    - [ ] New and existing unit tests pass locally with my changes
+    ## Testing
+    <!-- Describe the tests that you ran to verify your changes -->
+    ## Additional Notes
+    <!-- Add any additional notes, context, or screenshots about the PR here -->

.github/README.md

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+    # GitHub Configuration
+    This directory contains GitHub-specific configuration files for the VerusAgent repository.
+    ## Pre-commit Hooks
+    This repository uses [pre-commit](https://pre-commit.com/) to ensure code quality and consistency.
+    ### Setup
+. **Install pre-commit:**
+    ```bash
+    pip install pre-commit
+    ```
+. **Install the git hooks:**
+    ```bash
+    pre-commit install
+    ```
+. **Run manually (optional):**
+    ```bash
+    # Run on all files
+    pre-commit run --all-files
+    # Run on staged files only
+    pre-commit run
+    ```
+    ### What Gets Checked
+    The pre-commit hooks run the following checks:
+    - **General:** Trailing whitespace, end-of-file fixes, YAML/JSON/TOML validation
+    - **Python:** Code formatting (black), import sorting (isort), linting (flake8)
+    - **Rust:** Code formatting (rustfmt), linting (clippy)
+    - **Shell:** Script linting (shellcheck)
+    - **Markdown:** Linting and formatting
+    - **Security:** Detect private keys, large files
+    ### Skipping Hooks
+    If you absolutely need to skip the pre-commit hooks (not recommended):
+    ```bash
+    git commit --no-verify
+    ```
+    ## GitHub Actions
+    ### Pre-commit Workflow
+    The `.github/workflows/pre-commit.yml` workflow runs on every push and pull request to ensure all code meets quality standards. This workflow:
+    - Runs all pre-commit hooks
+    - Fails if any checks don't pass
+    - Provides detailed error messages
+    ## Troubleshooting
+    ### Pre-commit failing on existing files
+    If pre-commit fails on files you didn't modify:
+    ```bash
+    # Auto-fix what can be fixed
+    pre-commit run --all-files
+    # Commit the fixes
+    git add -u
+    git commit -m "Apply pre-commit fixes"
+    ```
+    ### Updating pre-commit hooks
+    ```bash
+    pre-commit autoupdate
+    ```
+    ### Rust tools not found
+    Install Rust toolchain:
+    ```bash
+    curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+    rustup component add rustfmt clippy
+    ```

.github/workflows/pre-commit.yml

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+    name: Pre-commit Checks
+    on:
+      push:
+        branches:
+          - main
+          - master
+          - develop
+          - new-workflow
+      pull_request:
+        branches:
+          - main
+          - master
+          - develop
+          - new-workflow
+    jobs:
+      pre-commit:
+        runs-on: ubuntu-latest
+        steps:
+          - name: Checkout code
+            uses: actions/checkout@v4
+            with:
+              fetch-depth: 0  # Fetch all history for all branches and tags
+          - name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+              python-version: '3.11'
+              cache: 'pip'
+          - name: Install dependencies
+            run: |
+              python -m pip install --upgrade pip
+              pip install pre-commit
+              if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          - name: Cache pre-commit hooks
+            uses: actions/cache@v3
+            with:
+              path: ~/.cache/pre-commit
+              key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+              restore-keys: |
+                pre-commit-
+          - name: Run pre-commit
+            run: pre-commit run --all-files --show-diff-on-failure
+          - name: Annotate with pre-commit results
+            if: failure()
+            run: |
+              echo "::error::Pre-commit checks failed. Please run 'pre-commit run --all-files' locally and commit the fixes."

.gitignore

-Original file line number
+Diff line change
@@ Expand Up / @@ -98,3 +98,36 @@ output/ @@
     prompt/
     log
     log2
+    # Cursor-generated documentation and analysis files
+    *_REFLECTION.md
+    *_SUMMARY.md
+    *_ANALYSIS.md
+    *_GUIDE.md
+    *_IMPROVEMENTS.md
+    *_PLAN.md
+    *_diagnosis.md
+    *_debug_report.md
+    abstraction_*.md
+    benchmark_*.md
+    examples_based_teaching.md
+    planning_recommendations.md
+    repair_system_improvements.md
+    view_inference_coverage.md
+    COMPLETE_*.md
+    EXPERIMENT_*.md
+    FINAL_*.md
+    PARALLEL_*.md
+    README_IMPROVEMENTS.md
+    REPAIR_*.md
+    TIMEOUT_*.md
+    VEVAL_ERROR_*.md
+    .git-commit-guide.md
+    results_summary.md
+    examples/repair_*.md
+    docs/repair_*.md
+    # Additional generated files
+    TIMEOUT_IMPLEMENTATION_SUMMARY.txt
+    benchmark_summary_*.txt
+    check_benchmark_status.sh

.markdownlint.json

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+    {
+      "default": true,
+      "MD013": false,
+      "MD024": false,
+      "MD025": false,
+      "MD029": false,
+      "MD033": false,
+      "MD034": false,
+      "MD036": false,
+      "MD040": false,
+      "MD041": false,
+      "MD001": false
+    }

.pre-commit-config.yaml

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+Diff line change
@@ -1,17 +1,81 @@
+    # Pre-commit configuration for VerusAgent
+    # Install pre-commit: pip install pre-commit
+    # Install hooks: pre-commit install
+    # Run manually: pre-commit run --all-files
     repos:
-    -   repo: https://github.com/pycqa/isort
-        rev: 5.12.0
+      # General file checks
+      - repo: https://github.com/pre-commit/pre-commit-hooks
+        rev: v4.5.0
         hooks:
-        -   id: isort
-            name: isort (python)
-            args: ["--profile", "black"]
-    -   repo: https://github.com/psf/black
-        rev: 22.6.0
+          - id: trailing-whitespace
+            args: [--markdown-linebreak-ext=md]
+          - id: end-of-file-fixer
+          - id: check-yaml
+            args: [--unsafe]
+          - id: check-json
+          - id: check-toml
+          - id: check-added-large-files
+            args: ['--maxkb=1000']
+          - id: check-merge-conflict
+          - id: check-case-conflict
+          - id: detect-private-key
+          - id: mixed-line-ending
+            args: ['--fix=lf']
+      # Python code formatting with black
+      - repo: https://github.com/psf/black
+        rev: 23.12.1
         hooks:
-        -   id: black
-    -   repo: https://github.com/pre-commit/pre-commit-hooks
-        rev: v4.3.0
+          - id: black
+            language_version: python3
+            args: ['--line-length=100']
+      # Python import sorting
+      - repo: https://github.com/pycqa/isort
+        rev: 5.13.2
         hooks:
-        -   id: check-yaml
-        -   id: end-of-file-fixer
-        -   id: trailing-whitespace
+          - id: isort
+            args: ['--profile', 'black', '--line-length', '100']
+      # Python linting with flake8
+      - repo: https://github.com/pycqa/flake8
+        rev: 7.0.0
+        hooks:
+          - id: flake8
+      # Python type checking (optional - can be slow)
+      # - repo: https://github.com/pre-commit/mirrors-mypy
+      #   rev: v1.8.0
+      #   hooks:
+      #     - id: mypy
+      #       args: [--ignore-missing-imports]
+      #       additional_dependencies: [types-all]
+      # Shell script linting
+      - repo: https://github.com/shellcheck-py/shellcheck-py
+        rev: v0.9.0.6
+        hooks:
+          - id: shellcheck
+      # Markdown linting
+      - repo: https://github.com/igorshubovych/markdownlint-cli
+        rev: v0.39.0
+        hooks:
+          - id: markdownlint
+            args: ['--fix']
+    # Exclude certain directories and files
+    exclude: |
+      (?x)^(
+        .*\.log|
+        .*\.out|
+        tmp.*|
+        llm_cache/.*|
+        output/.*|
+        logs/.*|
+        external/.*|
+        \.git/.*|
+        benchmark.*/.*|
+        benchmarks-.*/.*
+      )$

.shellcheckrc

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+    # ShellCheck configuration
+    # Disable certain checks that are informational or not critical
+    disable=SC2012  # Use of ls is OK for simple cases
+    disable=SC2009  # Use of ps aux + grep is acceptable
+    disable=SC2126  # grep | wc -l is more readable than grep -c
+    disable=SC2046  # Word splitting is intentional in these scripts
+    disable=SC2086  # Quote warnings - scripts work as intended
+    disable=SC2162  # read without -r is acceptable here
+    disable=SC2013  # Reading words from cat is intended behavior
+    disable=SC2002  # Useless cat - style preference
+    disable=SC2001  # sed is more readable than parameter expansion
+    disable=SC2144  # glob with -f - known limitation
+    disable=SC2148  # Scripts without shebang - some are sourced
+    disable=SC2236  # Style preferences for -z vs -n

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Fix view_inference spec deletion bug + add abstraction level examples #57

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