codenib 0.2.2__tar.gz → 0.2.3__tar.gz

{codenib-0.2.2 → codenib-0.2.3}/CHANGELOG.md

@@ -11,6 +11,64 @@ All notable user-facing changes are recorded here. CodeNib follows
 
 ## [Unreleased]
 
+## [0.2.3] - 2026-09-03
+
+### Added
+
+- A Wiki-only `codenib.storage` facade exposing the domain-local `WikiStore`
+  harness and SQLite WAL implementation, with versioned schema initialization,
+  bounded canonical JSON, integrity checks, atomic publication, and
+  cross-process generation guards.
+
+### Changed
+
+- AgentWiki, the web service, cache audit, prewarming, and Wiki benchmarking
+  now use `wiki_cache/wiki.sqlite3`. Eligible source-compatible JSON entries
+  remain available through read-through compatibility and are not rewritten or
+  deleted.
+- The supported product database boundary is now
+  `codenib.storage.WikiStore`, with `SQLiteWikiStore` as its supported adapter.
+  `RepoManifest`, BM25, FAISS, igraph, and portable context payloads remain file
+  artifacts. Existing compiler caches use `artifact pack`; portable artifacts
+  continue through `artifact verify` and `mcp --artifact`.
+- The v0.2.3 release intentionally narrows the former storage API and CLI.
+  Users who still need data from a v0.2.2 SQLite catalog must run `artifact
+  materialize` with a pinned v0.2.2 environment before upgrading; the resulting
+  portable artifact remains supported.
+
+### Removed
+
+- The optional Web `index_storage` configuration and its catalog-backed local
+  runtime, retained BM25 activation, reconciliation, durable index-job
+  orchestration, `/api/index-jobs` write/read routes, and index-status job or
+  update-capability fields. Index status remains available as a read-only
+  `RepoManifest` projection.
+- The unreleased catalog-selected `codenib mcp` cold-start mode. Portable
+  artifacts remain served through `codenib mcp --artifact [--repo]`.
+- The unreleased `storage audit` command and `index --publish-retained` path.
+  Those two batches removed 1,407 production lines and 1,742 dedicated test
+  lines, including the audit execution path, eight index-only options, and
+  three compiler exports; ordinary indexing remained unchanged in that batch.
+- The post-v0.2.2 retained-storage benchmark gate, its manual Make target, and
+  noncanonical readiness receipt. The report-only experiment had no product or
+  CI workflow caller and could never report `promotion_eligible=true`; removing
+  it deleted a 4,913-line harness, 3,468 test lines, 367 evidence lines, 148
+  documentation lines, eight Make variables, and one manual target.
+- The unreleased `codenib jobs` execution stack and catalog schema v5 through
+  v8. This removed eight production modules (9,615 lines), twelve dedicated
+  test modules (22,170 lines), 73 lazy exports, two interruptible CAS methods,
+  one command with two execution paths, and four schema migrations; changes
+  inside retained files bring the batch total to 21,214 production and 29,352
+  test lines removed.
+- The generic retained-storage surface formerly published by v0.2.2 through
+  `codenib.storage`: its schema-v4 SQLite catalog and local CAS, `artifact
+  import-cache`, `artifact materialize`, and the retained compiler bridge. The
+  name `codenib.storage` now resolves only to the Wiki database facade. Normal
+  index, Wiki, portable-artifact, publish, and MCP paths are unchanged.
+- The catalog-backed clangd FactBatch publication/reuse experiment and its
+  profiling target. Provider-neutral FactBatch models, resolvers, native buffer
+  transport, and the promoted clangd query index remain independent of storage.
+
 ## [0.2.2] - 2026-08-21
 
 ### Added
@@ -193,7 +251,8 @@ All notable user-facing changes are recorded here. CodeNib follows
 - Prepared secretless PyPI publishing through a dedicated GitHub Actions OIDC
   workflow.
 
-[Unreleased]: https://github.com/sysevol-ai/CodeNib/compare/v0.2.2...HEAD
+[Unreleased]: https://github.com/sysevol-ai/CodeNib/compare/v0.2.3...HEAD
+[0.2.3]: https://github.com/sysevol-ai/CodeNib/compare/v0.2.2...v0.2.3
 [0.2.2]: https://github.com/sysevol-ai/CodeNib/compare/v0.2.1...v0.2.2
 [0.2.1]: https://github.com/sysevol-ai/CodeNib/compare/v0.2.0...v0.2.1
 [0.2.0]: https://github.com/sysevol-ai/CodeNib/compare/v0.1.0...v0.2.0

{codenib-0.2.2 → codenib-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: codenib
-Version: 0.2.2
+Version: 0.2.3
 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
@@ -133,6 +133,8 @@ SPDX-License-Identifier: Apache-2.0
     &nbsp;&middot;&nbsp;
     <a href="https://docs.codenib.ai/">Documentation</a>
     &nbsp;&middot;&nbsp;
+    <a href="https://docs.codenib.ai/news/">News</a>
+    &nbsp;&middot;&nbsp;
     <a href="https://docs.codenib.ai/codegraph/">CodeGraph</a>
     &nbsp;&middot;&nbsp;
     <a href="https://docs.codenib.ai/mcp/">MCP</a>
@@ -148,12 +150,11 @@ SPDX-License-Identifier: Apache-2.0
     <a href="https://docs.codenib.ai/codegraph/#one-command-setup"><img src="https://img.shields.io/badge/Codex-000?logo=openai&amp;logoColor=fff" alt="Codex supported"></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-0.2.2-2563EB.svg" alt="CodeNib 0.2.2">
   </p>
 </div>
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.2"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/your/repo
 ```
 
@@ -163,42 +164,6 @@ symbol graph, and registers the resulting MCP server with installed Codex and
 Claude Code clients. It is local, open source, requires no model or cloud, and
 does not write configuration or indexes into the target repository.
 
-## News
-
-- **2026-08-21 — CodeNib 0.2.2 repository source authority.** Authenticated
-  indexing now admits absolute symlinks only when they resolve inside the same
-  pinned checkout, and exact root-relative exclusions persist across indexing,
-  CodeGraph, MCP, Wiki, and Web runtimes.
-  [Release notes](https://docs.codenib.ai/releases/0.2.2/)
-- **2026-08-13 — CodeNib 0.2.1 CodeGraph onboarding.** One command prepares a
-  repository graph and connects it to Codex and Claude Code, with idempotent
-  status, safe uninstall, and installed-wheel MCP graph verification.
-  [CodeGraph guide](https://docs.codenib.ai/codegraph/)
-- **2026-08-08 — RepoNavigator Jump adapter.** The published single-tool
-  [RepoNavigator](https://arxiv.org/abs/2512.20957v6) contract now resolves
-  symbol definitions through a persisted SCIP occurrence or injected LSP
-  signal, with graph-only resolution disclosed as a degraded fallback.
-  [Support boundary](https://docs.codenib.ai/agent_integrations/#reponavigator)
-- **2026-08-05 — CodeNib 0.2.0.** Build a static Wiki and reusable context
-  artifact once, then serve it through Pages or the official MCP package.
-  Hybrid retrieval and managed SCIP/LSP providers ship in the same CLI.
-  [Release notes](https://docs.codenib.ai/releases/0.2.0/)
-- **2026-08-05 — SweRank recipe.** Run
-  [SweRank](https://github.com/SalesforceAIResearch/SweRank) retrieval and
-  reranking over a local checkout. [Example](examples/swerank_retrieve_rerank.py)
-- **2026-08-04 — Native repository explorer.** CodeNib's planner now targets
-  the [SWE-Explore](https://github.com/Qiushao-E/SWE-Explore-Bench)
-  source-region protocol.
-  [Validation](docs/evaluation/swe_explore.md)
-- **2026-08-03 — Native LocAgent policy.**
-  [LocAgent](https://github.com/gersteinlab/LocAgent) runs directly on CodeNib
-  views without LocAgent, LiteLLM, or LlamaIndex dependencies.
-  [Support matrix](https://docs.codenib.ai/agent_integrations/)
-- **2026-08-02 — OrcaLoca SearchAgent.**
-  [OrcaLoca](https://github.com/fishmingyu/OrcaLoca)'s six-tool search loop
-  now reuses CodeNib's symbol graph.
-  [Support matrix](https://docs.codenib.ai/agent_integrations/)
-
 ## System Architecture
 
 | Layer | Responsibility |
@@ -227,7 +192,7 @@ Requires Python 3.10+ and Git. For an agent-ready CodeGraph with no model or API
 key, install the graph and MCP extras and run one command:
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.2"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/repository
 ```
 
@@ -259,22 +224,19 @@ exactly matches the authenticated checkout and contains no tracked path that
 the default policy excludes. It does not currently support a non-empty custom
 exclusion set. A command that explicitly requests the `zoekt` view, including
 `--preset full`, fails closed when either condition is unmet; use the
-CodeGraph, `fast`, or semantic paths instead.
-In 0.2.2 the authenticated MCP `search_zoekt` runtime requires Linux `/proc`
-so the child process can inherit the exact retained shard generation; other
-platforms fail closed instead of reopening a mutable shard path.
+CodeGraph, `fast`, or semantic paths instead. Authenticated MCP serving for
+Zoekt currently requires Linux `/proc`; see the
+[source-surface boundaries](https://docs.codenib.ai/codegraph/#select-the-repository-source-surface).
 
 For a browser Wiki with hybrid BM25+dense retrieval, install the semantic extra:
 
 ```bash
-python -m pip install "codenib[semantic]==0.2.2"
+python -m pip install "codenib[semantic]"
 codenib wiki /path/to/repository
 ```
 
 Both paths keep reusable state under `~/.codenib/repositories` and leave the
-target checkout unchanged. Set `CODENIB_HOME` to relocate state. The
-[0.2.2 release notes](https://docs.codenib.ai/releases/0.2.2/) record the
-upgrade boundary and installed-product evidence.
+target checkout unchanged. Set `CODENIB_HOME` to relocate state.
 
 Preview the CodeGraph operations without installing, indexing, or configuring
 an agent:
@@ -288,7 +250,7 @@ only their package-level providers; operating-system and project prerequisites
 remain explicit:
 
 ```bash
-python -m pip install "codenib[graph]==0.2.2"
+python -m pip install "codenib[graph]"
 codenib toolchain install /path/to/repository --scope graph
 codenib doctor /path/to/repository --require graph
 ```
@@ -330,7 +292,7 @@ The recommended path configures installed Codex and Claude Code clients through
 their native CLIs:
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.2"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/repository
 ```
 
@@ -409,7 +371,7 @@ running the credential- or toolchain-dependent tiers.
 
 ## Status
 
-CodeNib `0.2.2` is a beta release. The CLI and manifest format are usable, but
+CodeNib is currently in beta. 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
@@ -436,6 +398,8 @@ If you use CodeNib in your research, please cite our
 
 [Website](https://codenib.ai)
 &nbsp;&middot;&nbsp;
+[Releases](https://github.com/sysevol-ai/CodeNib/releases)
+&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)

{codenib-0.2.2 → codenib-0.2.3}/README.md

@@ -24,6 +24,8 @@ SPDX-License-Identifier: Apache-2.0
      · 
     <a href="https://docs.codenib.ai/">Documentation</a>
     &nbsp;&middot;&nbsp;
+    <a href="https://docs.codenib.ai/news/">News</a>
+    &nbsp;&middot;&nbsp;
     <a href="https://docs.codenib.ai/codegraph/">CodeGraph</a>
     &nbsp;&middot;&nbsp;
     <a href="https://docs.codenib.ai/mcp/">MCP</a>
@@ -39,12 +41,11 @@ SPDX-License-Identifier: Apache-2.0
     <a href="https://docs.codenib.ai/codegraph/#one-command-setup"><img src="https://img.shields.io/badge/Codex-000?logo=openai&amp;logoColor=fff" alt="Codex supported"></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-0.2.2-2563EB.svg" alt="CodeNib 0.2.2">
   </p>
 </div>
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.2"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/your/repo
 ```
 
@@ -54,42 +55,6 @@ symbol graph, and registers the resulting MCP server with installed Codex and
 Claude Code clients. It is local, open source, requires no model or cloud, and
 does not write configuration or indexes into the target repository.
 
-## News
-
-- **2026-08-21 — CodeNib 0.2.2 repository source authority.** Authenticated
-  indexing now admits absolute symlinks only when they resolve inside the same
-  pinned checkout, and exact root-relative exclusions persist across indexing,
-  CodeGraph, MCP, Wiki, and Web runtimes.
-  [Release notes](https://docs.codenib.ai/releases/0.2.2/)
-- **2026-08-13 — CodeNib 0.2.1 CodeGraph onboarding.** One command prepares a
-  repository graph and connects it to Codex and Claude Code, with idempotent
-  status, safe uninstall, and installed-wheel MCP graph verification.
-  [CodeGraph guide](https://docs.codenib.ai/codegraph/)
-- **2026-08-08 — RepoNavigator Jump adapter.** The published single-tool
-  [RepoNavigator](https://arxiv.org/abs/2512.20957v6) contract now resolves
-  symbol definitions through a persisted SCIP occurrence or injected LSP
-  signal, with graph-only resolution disclosed as a degraded fallback.
-  [Support boundary](https://docs.codenib.ai/agent_integrations/#reponavigator)
-- **2026-08-05 — CodeNib 0.2.0.** Build a static Wiki and reusable context
-  artifact once, then serve it through Pages or the official MCP package.
-  Hybrid retrieval and managed SCIP/LSP providers ship in the same CLI.
-  [Release notes](https://docs.codenib.ai/releases/0.2.0/)
-- **2026-08-05 — SweRank recipe.** Run
-  [SweRank](https://github.com/SalesforceAIResearch/SweRank) retrieval and
-  reranking over a local checkout. [Example](examples/swerank_retrieve_rerank.py)
-- **2026-08-04 — Native repository explorer.** CodeNib's planner now targets
-  the [SWE-Explore](https://github.com/Qiushao-E/SWE-Explore-Bench)
-  source-region protocol.
-  [Validation](docs/evaluation/swe_explore.md)
-- **2026-08-03 — Native LocAgent policy.**
-  [LocAgent](https://github.com/gersteinlab/LocAgent) runs directly on CodeNib
-  views without LocAgent, LiteLLM, or LlamaIndex dependencies.
-  [Support matrix](https://docs.codenib.ai/agent_integrations/)
-- **2026-08-02 — OrcaLoca SearchAgent.**
-  [OrcaLoca](https://github.com/fishmingyu/OrcaLoca)'s six-tool search loop
-  now reuses CodeNib's symbol graph.
-  [Support matrix](https://docs.codenib.ai/agent_integrations/)
-
 ## System Architecture
 
 | Layer | Responsibility |
@@ -118,7 +83,7 @@ Requires Python 3.10+ and Git. For an agent-ready CodeGraph with no model or API
 key, install the graph and MCP extras and run one command:
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.2"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/repository
 ```
 
@@ -150,22 +115,19 @@ exactly matches the authenticated checkout and contains no tracked path that
 the default policy excludes. It does not currently support a non-empty custom
 exclusion set. A command that explicitly requests the `zoekt` view, including
 `--preset full`, fails closed when either condition is unmet; use the
-CodeGraph, `fast`, or semantic paths instead.
-In 0.2.2 the authenticated MCP `search_zoekt` runtime requires Linux `/proc`
-so the child process can inherit the exact retained shard generation; other
-platforms fail closed instead of reopening a mutable shard path.
+CodeGraph, `fast`, or semantic paths instead. Authenticated MCP serving for
+Zoekt currently requires Linux `/proc`; see the
+[source-surface boundaries](https://docs.codenib.ai/codegraph/#select-the-repository-source-surface).
 
 For a browser Wiki with hybrid BM25+dense retrieval, install the semantic extra:
 
 ```bash
-python -m pip install "codenib[semantic]==0.2.2"
+python -m pip install "codenib[semantic]"
 codenib wiki /path/to/repository
 ```
 
 Both paths keep reusable state under `~/.codenib/repositories` and leave the
-target checkout unchanged. Set `CODENIB_HOME` to relocate state. The
-[0.2.2 release notes](https://docs.codenib.ai/releases/0.2.2/) record the
-upgrade boundary and installed-product evidence.
+target checkout unchanged. Set `CODENIB_HOME` to relocate state.
 
 Preview the CodeGraph operations without installing, indexing, or configuring
 an agent:
@@ -179,7 +141,7 @@ only their package-level providers; operating-system and project prerequisites
 remain explicit:
 
 ```bash
-python -m pip install "codenib[graph]==0.2.2"
+python -m pip install "codenib[graph]"
 codenib toolchain install /path/to/repository --scope graph
 codenib doctor /path/to/repository --require graph
 ```
@@ -221,7 +183,7 @@ The recommended path configures installed Codex and Claude Code clients through
 their native CLIs:
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.2"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/repository
 ```
 
@@ -300,7 +262,7 @@ running the credential- or toolchain-dependent tiers.
 
 ## Status
 
-CodeNib `0.2.2` is a beta release. The CLI and manifest format are usable, but
+CodeNib is currently in beta. 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
@@ -327,6 +289,8 @@ If you use CodeNib in your research, please cite our
 
 [Website](https://codenib.ai)
 &nbsp;&middot;&nbsp;
+[Releases](https://github.com/sysevol-ai/CodeNib/releases)
+&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)