codenib 0.1.0__tar.gz

codenib-0.1.0/CHANGELOG.md

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+<!--
+SPDX-FileCopyrightText: 2025-2026 CodeNib Contributors
+
+SPDX-License-Identifier: Apache-2.0
+-->
+
+# Changelog
+
+All notable user-facing changes are recorded here. CodeNib follows
+[Semantic Versioning](https://semver.org/).
+
+## [Unreleased]
+
+## [0.1.0] - 2026-07-26
+
+### Added
+
+- A unified `codenib` CLI with `index`, `wiki`, `mcp`, and `doctor` commands.
+- A two-command local Wiki path with automatic language detection and reusable
+  repository manifests.
+- Fast, semantic, and full indexing presets with explicit optional
+  dependencies.
+- A deterministic static Wiki that requires no LLM credentials.
+- A source-linked MCP server for retrieval, graph, and static navigation tools.
+- Multi-view incremental maintenance and evaluation infrastructure.
+
+### Changed
+
+- Renamed the maintained package, command, state, and protocol namespace to
+  CodeNib.
+- Reduced the default installation to the BM25 and Wiki runtime; model, graph,
+  dataset, MCP, and agent dependencies now use named extras.
+- Made public package imports lazy so CLI startup does not initialize model or
+  graph runtimes.
+
+### Security
+
+- Prepared secretless PyPI publishing through a dedicated GitHub Actions OIDC
+  workflow.
+
+[Unreleased]: https://github.com/sysevol-ai/CodeNib/compare/v0.1.0...HEAD
+[0.1.0]: https://github.com/sysevol-ai/CodeNib/releases/tag/v0.1.0

codenib-0.1.0/CONTRIBUTING.md

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+<!--
+SPDX-FileCopyrightText: 2025-2026 CodeNib Contributors
+
+SPDX-License-Identifier: Apache-2.0
+-->
+
+# Contributing To CodeNib
+
+CodeNib accepts bug reports, design proposals, documentation fixes, and focused
+code changes. Open an issue before starting a broad architectural change so its
+scope and ownership boundary are explicit.
+
+## Development Setup
+
+```bash
+git clone https://github.com/sysevol-ai/CodeNib.git
+cd CodeNib
+make dev
+pre-commit install
+```
+
+Toolchain-heavy graph work may also need:
+
+```bash
+make bootstrap
+make toolchain-doctor
+```
+
+## Change Workflow
+
+1. Create a focused branch from current `main`.
+2. Add or update tests at the lightest tier that exercises the behavior.
+3. Run the targeted test first, then the matching wider tier.
+4. Run `pre-commit run --all-files`.
+5. Open a PR using the repository template and include exact verification
+   commands.
+
+Use Conventional Commit subjects such as
+`fix(cli): reject missing manifests`. Keep unrelated refactors out of the same
+change. Do not commit generated caches, credentials, model weights, or
+repository-local `.codenib_cache` artifacts.
+
+## Test Tiers
+
+The default unit tier is:
+
+```bash
+pytest -m "not slow and not integration and not integration_serial and not integration_serial_consumer" -x --tb=short
+```
+
+Run heavier tiers only when the changed surface requires them:
+
+```bash
+pytest -m integration --tb=short
+pytest -m integration_serial -v --tb=short
+make lsp-smoke
+make scip-cold-start-smoke
+```
+
+Tests marked slow may require LLM credentials, GPU resources, external
+repositories, or language toolchains. A failing infrastructure prerequisite
+should be reported separately from a code regression.
+
+## Code And Documentation
+
+- Python targets 3.10+ and is formatted with Black at line length 88.
+- Use the language registry and centralized graph types instead of adding
+  isolated dispatch maps or string literals.
+- Persisted graph schema changes require a schema-version bump and C++ decoder
+  parity review.
+- User-facing commands and docs use CodeNib's canonical package and repository
+  names.
+
+See [AGENTS.md](AGENTS.md) for the full repository contract and
+[Contributing a Language](docs/contributing-a-language.md) for backend work.
+
+## License
+
+By submitting a contribution, you agree that it may be distributed under the
+repository's [Apache License 2.0](LICENSE).

codenib-0.1.0/LICENSE

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codenib-0.1.0/MANIFEST.in

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+# SPDX-FileCopyrightText: 2025-2026 CodeNib Contributors
+#
+# SPDX-License-Identifier: Apache-2.0
+
+graft web
+include CHANGELOG.md
+include CONTRIBUTING.md
+prune web/.next
+prune web/node_modules
+prune web/playwright-report
+prune web/test-results
+global-exclude *.py[cod]

codenib-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: codenib
+Version: 0.1.0
+Summary: A multi-view data system for serving repository context to coding agents
+Author-email: Zhongming Yu <zhy025@ucsd.edu>
+License-Expression: Apache-2.0
+Project-URL: Documentation, https://docs.codenib.ai/
+Project-URL: Homepage, https://codenib.ai
+Project-URL: Issues, https://github.com/sysevol-ai/CodeNib/issues
+Project-URL: Repository, https://github.com/sysevol-ai/CodeNib.git
+Keywords: code-search,coding-agents,model-context-protocol,repository-context,static-analysis
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: fastapi>=0.100.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: rank_bm25>=0.2.2
+Requires-Dist: rich>=14.0.0
+Requires-Dist: tree-sitter>=0.25.2
+Requires-Dist: tree-sitter-language-pack<1.9.0,>=1.8.1
+Requires-Dist: uvicorn>=0.20.0
+Provides-Extra: agent
+Requires-Dist: litellm>=1.40.0; extra == "agent"
+Provides-Extra: datasets
+Requires-Dist: datasets>=4.0.0; extra == "datasets"
+Provides-Extra: graph
+Requires-Dist: igraph>=0.11.6; extra == "graph"
+Requires-Dist: protobuf>=3.20.0; extra == "graph"
+Provides-Extra: mcp
+Requires-Dist: mcp<3,>=2.0.0; extra == "mcp"
+Provides-Extra: semantic
+Requires-Dist: einops>=0.8.0; extra == "semantic"
+Requires-Dist: faiss-cpu>=1.7.0; extra == "semantic"
+Requires-Dist: numpy>=1.24.0; extra == "semantic"
+Requires-Dist: openai>=1.0.0; extra == "semantic"
+Requires-Dist: sentence-transformers>=2.2.0; extra == "semantic"
+Provides-Extra: vertex
+Requires-Dist: litellm[google]>=1.93.0; extra == "vertex"
+Provides-Extra: zoekt
+Requires-Dist: requests>=2.25.0; extra == "zoekt"
+Provides-Extra: full
+Requires-Dist: datasets>=4.0.0; extra == "full"
+Requires-Dist: einops>=0.8.0; extra == "full"
+Requires-Dist: faiss-cpu>=1.7.0; extra == "full"
+Requires-Dist: igraph>=0.11.6; extra == "full"
+Requires-Dist: litellm[google]>=1.93.0; extra == "full"
+Requires-Dist: mcp<3,>=2.0.0; extra == "full"
+Requires-Dist: numpy>=1.24.0; extra == "full"
+Requires-Dist: openai>=1.0.0; extra == "full"
+Requires-Dist: protobuf>=3.20.0; extra == "full"
+Requires-Dist: requests>=2.25.0; extra == "full"
+Requires-Dist: sentence-transformers>=2.2.0; extra == "full"
+Provides-Extra: dev
+Requires-Dist: black>=22.3.0; extra == "dev"
+Requires-Dist: build>=1.2.0; extra == "dev"
+Requires-Dist: isort>=5.10.1; extra == "dev"
+Requires-Dist: mypy>=0.950; extra == "dev"
+Requires-Dist: flake8>=4.0.1; extra == "dev"
+Requires-Dist: flake8-bugbear>=24.4.0; extra == "dev"
+Requires-Dist: mkdocs-material>=9.5.0; extra == "dev"
+Provides-Extra: test
+Requires-Dist: datasets>=4.0.0; extra == "test"
+Requires-Dist: einops>=0.8.0; extra == "test"
+Requires-Dist: faiss-cpu>=1.7.0; extra == "test"
+Requires-Dist: filelock>=3.0.0; extra == "test"
+Requires-Dist: igraph>=0.11.6; extra == "test"
+Requires-Dist: litellm>=1.40.0; extra == "test"
+Requires-Dist: matplotlib>=3.4.0; extra == "test"
+Requires-Dist: mcp<3,>=2.0.0; extra == "test"
+Requires-Dist: numpy>=1.24.0; extra == "test"
+Requires-Dist: openai>=1.0.0; extra == "test"
+Requires-Dist: protobuf>=3.20.0; extra == "test"
+Requires-Dist: pytest>=6.0.0; extra == "test"
+Requires-Dist: pytest-cov>=3.0.0; extra == "test"
+Requires-Dist: pytest-timeout>=2.1.0; extra == "test"
+Requires-Dist: pytest-xdist>=3.0.0; extra == "test"
+Requires-Dist: requests>=2.25.0; extra == "test"
+Requires-Dist: sentence-transformers>=2.2.0; extra == "test"
+Requires-Dist: tomli>=1.1.0; python_version < "3.11" and extra == "test"
+Dynamic: license-file
+
+<!--
+SPDX-FileCopyrightText: 2025-2026 CodeNib Contributors
+
+SPDX-License-Identifier: Apache-2.0
+-->
+
+<div align="center">
+  <img src="https://raw.githubusercontent.com/sysevol-ai/CodeNib/main/assets/codenib_logo.svg" alt="CodeNib" width="560">
+  <h1>A Multi-View Data System for Serving Repository Context to Coding Agents</h1>
+  <p>
+    Incremental compilation, explicit per-view manifests, and agent-native context serving.
+  </p>
+  <p>
+    <a href="#quickstart">Quickstart</a>
+    &nbsp;&middot;&nbsp;
+    <a href="https://codenib.ai">Website</a>
+    &nbsp;&middot;&nbsp;
+    <a href="https://discord.gg/ySer6CGn4">Discord</a>
+    &nbsp;&middot;&nbsp;
+    <a href="https://docs.codenib.ai/">Documentation</a>
+    &nbsp;&middot;&nbsp;
+    <a href="https://docs.codenib.ai/mcp/">MCP</a>
+    &nbsp;&middot;&nbsp;
+    <a href="https://docs.codenib.ai/language_capabilities/">Languages</a>
+  </p>
+  <p>
+    <a href="https://github.com/sysevol-ai/CodeNib/actions/workflows/ci.yml"><img src="https://github.com/sysevol-ai/CodeNib/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
+    <a href="https://github.com/sysevol-ai/CodeNib/blob/main/LICENSE"><img src="https://img.shields.io/badge/License-Apache_2.0-blue.svg" alt="License: Apache 2.0"></a>
+    <a href="https://github.com/sysevol-ai/CodeNib/blob/main/pyproject.toml"><img src="https://img.shields.io/badge/Python-3.10%2B-3776AB.svg" alt="Python 3.10+"></a>
+    <img src="https://img.shields.io/badge/Release-Developer_Preview-EA580C.svg" alt="Developer Preview">
+  </p>
+</div>
+
+CodeNib is a multi-view data system for serving repository context to coding
+agents. Its native runtime compiles a checkout into manifest-linked lexical,
+semantic, structural, and static-navigation views, incrementally maintains
+supported transitions, and serves bounded source evidence through MCP,
+LSP-shaped providers, Python, and HTTP APIs.
+
+The Wiki, Ask view, and Dependency Map are inspection clients of that same
+runtime, not the system boundary. The core implementation lives in CodeNib;
+optional model endpoints and language servers are providers rather than a host
+agent or code-Wiki framework.
+
+## System Architecture
+
+| Layer | Responsibility |
+|---|---|
+| Incremental compiler | Chunk source and materialize BM25, dense, graph, and navigation views; reuse or repair supported artifacts and rebuild when an update cannot be admitted |
+| View manifest | Record repository identity, source fingerprint, builder profile, capabilities, status, and artifact location independently for each view |
+| Context serving | Execute lexical, semantic, hybrid, reranked, and structural query plans while preserving repository-relative source locations |
+| Agent runtime | Expose capability-aware MCP and LSP-shaped tools, assemble bounded evidence, and return citations that agents and humans can inspect |
+
+```text
+repository change
+  -> materialize or repair affected views
+  -> publish a capability-bearing manifest
+  -> plan repository queries
+  -> deliver bounded, source-linked context
+```
+
+On a later commit, CodeNib can reuse unchanged vector content and patch
+supported graph transitions at file or symbol granularity. Unsupported,
+inconsistent, or unverified transitions fall back to a fresh build instead of
+publishing a partially updated view.
+
+## Quickstart
+
+Requires Python 3.10+ and Git.
+
+```bash
+pip install codenib
+codenib wiki /path/to/repository
+```
+
+CodeNib detects the repository languages, builds a reusable index under
+`~/.codenib/repositories`, launches the local Wiki, and opens
+[http://localhost:3000](http://localhost:3000). The wheel includes the
+production Wiki frontend, so normal use does not require Node.js or npm and
+the target repository stays untouched. This command exercises the same compiler
+and serving runtime used by agents. Set `CODENIB_HOME` to relocate state.
+
+Check the environment or index without opening the Wiki:
+
+```bash
+codenib doctor --require core --require wiki
+codenib index /path/to/repository
+```
+
+See the
+[Quickstart](https://docs.codenib.ai/quickstart/)
+for ports, advanced indexing, and troubleshooting.
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/sysevol-ai/CodeNib/main/assets/codenib_wiki.png" alt="CodeNib Wiki showing the source-linked reverse proxy guide for Caddy" width="100%">
+</p>
+
+## Serve An Agent
+
+Install the MCP extra, build once, and serve the same repository manifest over
+stdio:
+
+```bash
+pip install "codenib[mcp]"
+codenib index /path/to/repository
+codenib mcp /path/to/repository
+```
+
+The MCP server advertises its full tool set and uses the compiled manifest to
+decide which calls have a fresh backing view. An agent can therefore reuse
+available repository work instead of rebuilding context through unbounded
+`grep` and `read` loops, while unavailable searches fail explicitly. BM25,
+semantic, regex, Zoekt, dependency, and static-navigation results retain source
+locations for follow-up reads and citations. See
+[MCP Server](https://docs.codenib.ai/mcp/)
+for client configuration and tool contracts.
+
+## What CodeNib Provides
+
+| Surface | Purpose |
+|---|---|
+| Incremental compiler | Build independently managed views, reuse unchanged content, repair supported transitions, and conservatively rebuild outside those boundaries |
+| Agent context runtime | Plan capability-aware retrieval and navigation, then assemble bounded source-linked evidence |
+| Retrieval | BM25, dense-vector, regex/trigram, Zoekt, fusion, and reranking paths |
+| Structural context | SCIP/LSP-backed symbol graphs with source locations and typed edges |
+| MCP and LSP-shaped tools | Serve one manifest to coding agents without tying the runtime to one agent framework |
+| Local inspection | Audit the same context through Wiki pages, Ask answers, citations, and the Dependency Map |
+| Evaluation harness | Measure retrieval, navigation, incremental maintenance, and context policies on the same artifacts |
+
+Language support varies by surface. The generated
+[capability matrix](https://docs.codenib.ai/language_capabilities/)
+records chunking, graph, incremental, and C++ decoder support.
+
+## Documentation
+
+- [Quickstart](https://docs.codenib.ai/quickstart/)
+- [MCP Server](https://docs.codenib.ai/mcp/)
+- [Web UI](https://docs.codenib.ai/web_demo/)
+- [Language Capabilities](https://docs.codenib.ai/language_capabilities/)
+- [Concepts and development guides](https://docs.codenib.ai/)
+
+Build the documentation site locally with:
+
+```bash
+pip install "codenib[dev]"
+mkdocs serve
+```
+
+## Development
+
+```bash
+git clone https://github.com/sysevol-ai/CodeNib.git
+cd CodeNib
+make dev
+make test
+```
+
+The test suite is split into unit, integration, serial integration, core,
+graph-consumer, and slow tiers. See
+[CI/CD](https://docs.codenib.ai/ci_cd/) before
+running the credential- or toolchain-dependent tiers.
+
+## Status
+
+CodeNib `0.1.0` is a developer preview. The CLI and manifest format are usable,
+but public interfaces may still change before a stable release. Historical
+research artifacts retain their published dataset identifiers; the maintained
+package, import namespace, commands, and repository use `CodeNib`. See
+[Naming](https://docs.codenib.ai/branding/).
+
+## Citation
+
+If you use CodeNib in your research, please cite our
+[arXiv paper](https://arxiv.org/abs/2607.25431):
+
+```bibtex
+@misc{yu2026codenibmultiviewdataserving,
+      title={CodeNib: A Multi-View Data System for Serving Repository Context to Coding Agents},
+      author={Zhongming Yu and Hengjia Yu and Boqin Yuan and Shuting Zhao and Yizhao Chen and Aryan Dokania and Mihir Jagtap and Jiayu Chang and Yitong Ma and Yash Jayswal and Wentao Ni and Hejia Zhang and Zhaoling Chen and Gangda Deng and Jishen Zhao},
+      year={2026},
+      eprint={2607.25431},
+      archivePrefix={arXiv},
+      primaryClass={cs.SE},
+      url={https://arxiv.org/abs/2607.25431},
+}
+```
+
+## Project
+
+[Website](https://codenib.ai)
+&nbsp;&middot;&nbsp;
+[Changelog](https://github.com/sysevol-ai/CodeNib/blob/main/CHANGELOG.md)
+&nbsp;&middot;&nbsp;
+[Contributing](https://github.com/sysevol-ai/CodeNib/blob/main/CONTRIBUTING.md)
+
+## License
+
+CodeNib is licensed under the
+[Apache License, Version 2.0](https://github.com/sysevol-ai/CodeNib/blob/main/LICENSE).