deepcode paper implementation

DeepCode/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug Report
+description: File a bug report
+title: "[Bug]:"
+labels: ["bug", "triage"]
+
+body:
+  - type: checkboxes
+    id: existingcheck
+    attributes:
+      label: Do you need to file an issue?
+      description: Please help us manage our time by avoiding duplicates and common bugs with the steps below.
+      options:
+        - label: I have searched the existing issues and this bug is not already filed.
+        - label: I believe this is a legitimate bug, not just a question or feature request.
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the bug
+      description: A clear and concise description of what the bug is.
+      placeholder: What went wrong?
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps to reproduce
+      description: Steps to reproduce the behavior.
+      placeholder: How can we replicate the issue?
+  - type: textarea
+    id: expected_behavior
+    attributes:
+      label: Expected Behavior
+      description: A clear and concise description of what you expected to happen.
+      placeholder: What should have happened?
+  - type: textarea
+    id: configused
+    attributes:
+      label: DeepCode Config Used
+      description: The DeepCode configuration used for the run.
+      placeholder: The settings content or DeepCode configuration
+      value: |
+        # Paste your config here
+  - type: textarea
+    id: screenshotslogs
+    attributes:
+      label: Logs and screenshots
+      description: If applicable, add screenshots and logs to help explain your problem.
+      placeholder: Add logs and screenshots here
+  - type: textarea
+    id: additional_information
+    attributes:
+      label: Additional Information
+      description: |
+        - DeepCode Version: e.g., v0.1.1
+        - Operating System: e.g., Windows 10, Ubuntu 20.04
+        - Python Version: e.g., 3.8
+        - Related Issues: e.g., #1
+        - Any other relevant information.
+      value: |
+        - DeepCode Version:
+        - Operating System:
+        - Python Version:
+        - Related Issues:

DeepCode/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false

DeepCode/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature Request
+description: File a feature request
+labels: ["enhancement"]
+title: "[Feature Request]:"
+
+body:
+  - type: checkboxes
+    id: existingcheck
+    attributes:
+      label: Do you need to file a feature request?
+      description: Please help us manage our time by avoiding duplicates and common feature request with the steps below.
+      options:
+        - label: I have searched the existing feature request and this feature request is not already filed.
+        - label: I believe this is a legitimate feature request, not just a question or bug.
+  - type: textarea
+    id: feature_request_description
+    attributes:
+      label: Feature Request Description
+      description: A clear and concise description of the feature request you would like.
+      placeholder: What this feature request add more or improve?
+  - type: textarea
+    id: additional_context
+    attributes:
+      label: Additional Context
+      description: Add any other context or screenshots about the feature request here.
+      placeholder: Any additional information

DeepCode/.github/ISSUE_TEMPLATE/question.yml

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+name: Question
+description: Ask a general question
+labels: ["question"]
+title: "[Question]:"
+
+body:
+  - type: checkboxes
+    id: existingcheck
+    attributes:
+      label: Do you need to ask a question?
+      description: Please help us manage our time by avoiding duplicates and common questions with the steps below.
+      options:
+        - label: I have searched the existing question and discussions and this question is not already answered.
+        - label: I believe this is a legitimate question, not just a bug or feature request.
+  - type: textarea
+    id: question
+    attributes:
+      label: Your Question
+      description: A clear and concise description of your question.
+      placeholder: What is your question?
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional Context
+      description: Provide any additional context or details that might help us understand your question better.
+      placeholder: Add any relevant information here

DeepCode/.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

DeepCode/.github/pull_request_template.md

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+<!--
+Thanks for contributing to DeepCode!
+
+Please ensure your pull request is ready for review before submitting.
+
+About this template
+
+This template helps contributors provide a clear and concise description of their changes. Feel free to adjust it as needed.
+-->
+
+## Description
+
+[Briefly describe the changes made in this pull request.]
+
+## Related Issues
+
+[Reference any related issues or tasks addressed by this pull request.]
+
+## Changes Made
+
+[List the specific changes made in this pull request.]
+
+## Checklist
+
+- [ ] Changes tested locally
+- [ ] Code reviewed
+- [ ] Documentation updated (if necessary)
+- [ ] Unit tests added (if applicable)
+
+## Additional Notes
+
+[Add any additional notes or context for the reviewer(s).]

DeepCode/.github/workflows/linting.yaml

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+name: Linting and Formatting
+
+on:
+    push:
+        branches:
+            - main
+    pull_request:
+        branches:
+            - main
+
+jobs:
+    lint-and-format:
+        runs-on: ubuntu-latest
+
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v2
+
+            - name: Set up Python
+              uses: actions/setup-python@v2
+              with:
+                python-version: '3.x'
+
+            - name: Install dependencies
+              run: |
+                python -m pip install --upgrade pip
+                pip install pre-commit
+
+            - name: Run pre-commit
+              run: pre-commit run --all-files --show-diff-on-failure

DeepCode/.github/workflows/pypi-publish.yml

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+name: Upload DeepCode Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      id-token: write
+
+    environment:
+      name: pypi
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

DeepCode/.gitignore

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+# Python-related files
+__pycache__/
+*.py[cod]
+*.egg-info/
+.eggs/
+*.tgz
+*.tar.gz
+*.ini
+
+# Virtual Environment
+.venv/
+env/
+venv/
+*.env*
+.env_example
+
+
+# Build / Distribution
+dist/
+build/
+site/
+
+# Logs / Reports
+*.log
+*.log.*
+*.logfire
+*.coverage/
+log/
+
+# Caches
+.cache/
+.mypy_cache/
+.pytest_cache/
+.ruff_cache/
+.gradio/
+.history/
+temp/
+
+# IDE / Editor Files
+.idea/
+.vscode/
+.vscode/settings.json
+
+# Framework-specific files
+local_neo4jWorkDir/
+neo4jWorkDir/
+
+# Data & Storage
+inputs/
+rag_storage/
+examples/input/
+examples/output/
+deepcode-mcp/agent_folders
+
+# Miscellaneous
+.DS_Store
+TODO.md
+ignore_this.txt
+*.ignore.*
+
+# unit-test files
+test_*
+run_indexer_with_filtering.py
+
+# Cline files
+memory-bank/

DeepCode/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: requirements-txt-fixer
+
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.4
+    hooks:
+      - id: ruff-format
+      - id: ruff
+        args: [--fix, --ignore=E402]
+
+  - repo: https://github.com/mgedmin/check-manifest
+    rev: "0.49"
+    hooks:
+      - id: check-manifest
+        stages: [manual]

DeepCode/LICENSE

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+MIT License
+
+Copyright (c) 2025 ✨Data Intelligence Lab@HKU✨
+
+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.

DeepCode/MANIFEST.in

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+include README.md
+include LICENSE
+include requirements.txt
+include __init__.py
+include *.png
+include *.yaml
+recursive-include config *.yaml
+recursive-include prompts *
+recursive-include schema *
+recursive-include ui *.py
+recursive-include cli *.py
+recursive-include utils *.py
+recursive-include tools *.py
+recursive-include workflows *.py
+global-exclude *.pyc
+global-exclude .git*
+global-exclude .history*
+global-exclude .ruff_cache*
+global-exclude __pycache__*