cognis-engine 0.3.0__tar.gz

cognis_engine-0.3.0/.gitignore

@@ -0,0 +1,129 @@
+# Deprecated duplicate of assets/logo.png (use scripts/prepare-branding.py)
+/logo.png
+
+# cognis runtime state
+.cognis/
+
+# Editor-local MCP wiring (generated by cognis-vscode; paths are machine-specific)
+.cursor/mcp.json
+.vscode/mcp.json
+
+# Generated eval / benchmark output (regenerated by scripts/run_eval.py and the
+# nightly CI workflows). Methodology lives in docs/eval/; the committed CI gate
+# thresholds live in eval-baselines/ (intentionally tracked, NOT ignored).
+eval-reports/
+benchmark-reports/
+.benchmarks/
+audit.log
+audit.log.*
+
+# Python build artifacts
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+*.egg
+*.egg-info/
+.eggs/
+build/
+dist/
+wheels/
+sdist/
+pip-wheel-metadata/
+*.pyd
+*.pyi.bak
+
+# Packaging caches
+.uv/
+.pdm-python
+.pdm-build/
+__pypackages__/
+
+# Tooling caches
+.mypy_cache/
+.dmypy.json
+.pyre/
+.pytype/
+.ruff_cache/
+.pytest_cache/
+.tox/
+.nox/
+.cache/
+.coverage
+.coverage.*
+coverage.xml
+htmlcov/
+.hypothesis/
+
+# Virtual environments
+.venv/
+.venv-*/
+.venv-bootstrap/
+venv/
+.envrc
+.direnv/
+env/
+ENV/
+.python-version
+
+# IDE / editor
+.idea/
+.vscode/
+*.swp
+*.swo
+.DS_Store
+Thumbs.db
+
+# VS Code extension build/package artifacts
+apps/cognis-vscode/.vscode/
+apps/cognis-vscode/out/
+apps/cognis-vscode/.vscode-test/
+apps/cognis-vscode/.vscode-test-web/
+apps/cognis-vscode/*.vsix
+
+# Tree-sitter build outputs
+*.dylib
+*.dll
+build-tree-sitter/
+tree_sitter_languages_build/
+
+# Local secrets — never commit
+.env
+.env.*
+!.env.example
+*.pem
+*.key
+*.p12
+*.pfx
+secrets/
+
+# Local scratch helpers / dumps
+scratch_*
+
+# Logs & local databases / indexes
+*.log
+*.pid
+*.sqlite
+*.sqlite-journal
+*.sqlite-wal
+*.sqlite-shm
+*.db
+*.db-journal
+*.db-wal
+*.db-shm
+*.duckdb
+*.duckdb-journal
+*.idx
+*.index
+
+.kiro/
+.cursor/
+
+# OS / misc
+*.bak
+*.tmp
+*.temp
+*.orig
+*.rej
+Desktop.ini
+node_modules/

cognis_engine-0.3.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project are documented here. Format follows
+[Keep a Changelog](https://keepachangelog.com/en/1.1.0/) and this project
+adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.3.0] — 2026-06-05
+
+### Added
+
+- **One-click backend install/uninstall.** The VS Code / Cursor panel now
+  installs the Cognis Python backend for you — it creates a private environment
+  it manages (no terminal, no `pip`, no choosing a Python) and offers to set up
+  the workspace right after. The **Danger zone → Remove everything** action
+  reverses it, deleting that managed environment cleanly. If you bring your own
+  Python via `cognis.pythonPath`, install/uninstall operate on the `cognis`
+  package there and never touch your environment. New `cognis.installBackend`
+  command and `cognis.backendPackageSpec` setting.
+- **Lifecycle removal commands.** `cognis.removeFromWorkspace` stops indexing,
+  disconnects this repo's MCP entry, and deletes the local `.cognis/`.
+  `cognis.prepareUninstall` additionally strips every `cognis-*` server from the
+  shared MCP config and uninstalls the managed backend, so nothing is orphaned
+  after the extension is removed.
+- **Onboarding stepper.** The panel shows a fixed 4-step path
+  (Backend → Components → Index synced → AI connected) so a first-time user
+  always sees where they are and the single next action. A dedicated "Install
+  the Cognis backend" state guides fresh machines instead of failing setup with
+  a raw import error.
+
+### Changed
+
+- **`.cognis/` is added to `.gitignore` automatically** after setup when the
+  workspace is a git repo and the entry is missing (idempotent), with a
+  non-blocking notice — instead of a prompt with a "Don't ask again" choice.
+- **Plainer, behavior-based wording.** Removed the term "interpreter" from
+  user-facing copy; renamed **Repair Setup → Troubleshoot & Repair** and
+  **Clear Index & Re-index → Rebuild Index** (command IDs unchanged). The status
+  bar now uses a short, stable vocabulary (Indexing / Ready / Action needed /
+  Not set up).
+- The VS Code / Cursor panel's **Prerequisites checklist now collapses** once
+  every required component is installed, showing a one-line "Ready" summary
+  instead of the full list. It auto-expands when a required component is missing
+  so the install action stays obvious, and can be expanded manually any time to
+  re-check or install optional extras.
+
+### Fixed
+
+- **Live indexing from the extension now makes the workspace searchable in
+  seconds instead of appearing to fail.** The `cognis-indexd` cold rebuild
+  (spawned by the extension's "Set Up for AI" / live indexing) embedded *every*
+  symbol before writing any of them, so on a real repository the index DB stayed
+  empty — and the health panel reported `index: fail` ("0 files … excluded by
+  .gitignore") — for the entire multi-minute embed. The daemon now cold-indexes
+  in two phases: lexical + structural data first (fast, commits immediately so
+  search works and health flips to `ok`), then backfills semantic embeddings in
+  the background. Manual `cognis-cli index` was unaffected because operators
+  waited for it (or used `--skip-embeddings`); the failure only surfaced through
+  the daemon path.
+- `cognis-cli health` and the `index --clear` diagnosis no longer blame
+  `.gitignore` / `repo.ignore` when the real cause is an unfinished index run.
+  When indexable source exists but the DB is empty, they now point to running
+  `index --full` instead of asserting the source was excluded.
+
+## [0.2.1] — 2026-06-02
+
+### Added
+
+- **Prerequisite checklist in the VS Code / Cursor panel.** Before setup, the
+  panel now lists each installable backend component (parsers, local embeddings,
+  vector search, MCP server, tokenizers) with an installed/missing marker and a
+  per-item **Install** button (plus **Install all**). Backed by a new
+  `cognis-cli doctor --json` command. **Set Up for AI** is blocked until the
+  required components are installed, so a fresh user is never left with a
+  half-provisioned workspace.
+- **`.gitignore` reminder.** After setup, in a git repository, the extension
+  offers to add `.cognis/` to `.gitignore` (with a "Don't ask again" option) so
+  the local index database, caches, and audit log are never committed.
+
+### Changed
+
+- **The extension no longer auto-creates `.cognis/` on activation.** Opening a
+  folder leaves the repository untouched; `.cognis/` is created only when the
+  user explicitly runs **Set Up for AI**. Activation still auto-manages
+  workspaces that are already configured.
+
+## [0.2.0] — 2026-06-02
+
+### Fixed
+
+- **`semantic_search` (and the semantic stage of `retrieve_context_capsule`)
+  no longer hang / time out on first use over MCP stdio.** The embedder
+  (`sentence-transformers`/`torch`) was being loaded for the first time on a
+  spawned worker thread inside the server; first-time torch initialization off
+  the main thread hangs, so the tool blocked until the MCP deadline fired and
+  returned a `TIMEOUT`. `cognis-mcpd` now warms the shared semantic layer
+  **synchronously on the main thread** before serving, so every tool call
+  reuses the cached singleton. Disable with
+  `COGNIS_MCP_WARM_SEMANTIC_ON_STARTUP=0` (re-exposes the off-main-thread
+  first-load hang for semantic tools).
+- `cognis-mcpd` warms the UCKG `Database` (and the optional `sqlite-vec`/`numpy`
+  import) on the main thread before serving, avoiding an import-lock deadlock
+  when the first tool call would otherwise trigger that import on a FastMCP
+  worker thread (observed on Python 3.14 / Windows).
+- `cognis-indexd` releases its SQLite connections on shutdown (dedicated
+  single-thread writer executor) and writes its status file atomically with a
+  retry, fixing a Windows `os.replace` sharing-violation crash when an IDE polls
+  the status file concurrently.
+
+### Added
+
+- Cross-app **end-to-end test suite** (`tests/e2e/`, marker `e2e`) that drives
+  the real `cognis-cli`, `cognis-indexd`, and `cognis-mcpd` over process
+  boundaries (CLI JSON, the live status file, and MCP stdio), plus committed
+  JSON **contract snapshots** verified against the VS Code extension's
+  TypeScript interfaces (`apps/cognis-vscode/src/test/contractParity.test.ts`).
+  Includes a regression test that indexes with embeddings and asserts
+  `semantic_search` returns over stdio instead of hanging. See
+  `docs/e2e-testing.md`.
+
+## [0.1.17] — 2026-05-31
+
+### Added
+
+- **CSAR — Code Spreading-Activation Retrieval**, the new primary retrieval
+  engine. Seeds a relevance distribution from cheap lexical + semantic matches
+  and diffuses it across the Unified Code Knowledge Graph via Personalized
+  PageRank (random walk with restart), recovering on-path symbols that
+  independent embedding/lexical ranking misses. Includes exact, power-iteration,
+  and Andersen–Chung–Lang forward-push solvers. The forward-push solver has a
+  provable work bound `1/(alpha*eps)` independent of repository size. Math and
+  proofs in `docs/csar.md`; verified by `tests/unit/test_csar.py` and
+  `tests/pbt/test_csar_pbt.py` (CP-CSAR-1..5).
+- MCP tool `diffuse_context` — flagship CSAR retrieval; returns a unified ranked
+  shortlist (with `on_path` flags) in one round trip, replacing separate
+  `discover_symbols` + `dependency_trace` calls. Tunable via `COGNIS_MCP_CSAR_*`.
+- `retrieve_context_capsule` structural stage is now CSAR-powered: lexical +
+  semantic hits seed a graph diffusion whose on-path symbols feed the bug /
+  root-cause sections, replacing the previous single-hop BFS.
+- **Clear & Re-index**: a managed reset that deletes the stored index (UCKG
+  database, WAL/SHM sidecars, capsule cache) and rebuilds from scratch while
+  preserving `config.yaml` and MCP wiring. Available as the VS Code / Cursor
+  command `Cognis: Clear Index & Re-index` (and a button in the panel's Index
+  Status section, with a confirmation prompt) and as the CLI flag
+  `cognis-cli index --clear`.
+- MCP tool `discover_symbols` — hybrid lexical + semantic discovery with
+  reciprocal-rank fusion in one call.
+- MCP tool `resolve_symbols` — batch hydrate up to 50 symbol ids without repeated
+  `symbol_lookup` round trips.
+- Enriched `semantic_search` payloads (file location, signature, docstring) plus
+  optional `kind` / path filters; batch SQL hydration replaces per-hit lookups.
+- Short-lived in-process result cache for search tools (`COGNIS_MCP_CACHE_TTL_S`,
+  default 60s).
+- MCP tool `symbol_search` for top-k symbol discovery with optional `kind` and
+  `file_path` filters.
+- `dependency_trace` hit payloads enriched with symbol metadata (qualified name,
+  kind, file path, line range when available).
+- Process-wide embedder reuse for semantic MCP tools to reduce repeated model
+  load latency.
+
+### Changed
+
+- Default MCP tool allowlist and `McpToolName` now include `diffuse_context` as
+  the first (flagship) tool.
+- Documentation and tests steer agents toward `diffuse_context` for
+  flow-oriented retrieval, `discover_symbols` for quick discovery,
+  `resolve_symbols` for batch hydration, `symbol_lookup` for exact resolution,
+  and `retrieve_context_capsule` for low-round-trip task context.
+- `cognis-cli init` now additively migrates stale `.cognis/config.yaml`
+  defaults, writes config revision metadata, and keeps runtime loading aligned
+  with newer ignore/tool defaults without clobbering user overrides.
+- Generated MCP config now always includes `COGNIS_REPO_ROOT`; on Windows it
+  also applies safer semantic timeout defaults unless the operator overrides the
+  corresponding `COGNIS_MCP_*` env vars.
+- Windows MCP defaults raised to soft/hard/discover timeouts of 30/60/30 seconds
+  and `COGNIS_MCP_WARM_SEMANTIC_ON_STARTUP=1` to reduce first-query timeouts.
+- VS Code / Cursor extension writes MCP config to workspace `.cursor/mcp.json` or
+  `.vscode/mcp.json` by default (`cognis.mcpConfigScope`), with global config as
+  an opt-in fallback.
+- MCP servers are registered as `cognis-<repo-slug>` (for example
+  `cognis-cognis`, `cognis-edittruyentranh`) and merged additively into global
+  MCP config so multiple indexed repositories can stay connected at once.
+- Generated MCP config defaults to minimal env (`COGNIS_DB_PATH` plus Windows
+  timeout defaults); repo root and audit log are inferred by `cognis-mcpd`.
+- Successful semantic retrieval is now checked against the hard timeout only, so
+  cold-start model loads no longer fail with a follow-up soft-timeout after the
+  semantic stage already completed.
+
+[Unreleased]: https://github.com/buimanhtoan-it/cognis/compare/v0.3.0...HEAD
+[0.3.0]: https://github.com/buimanhtoan-it/cognis/compare/v0.2.1...v0.3.0
+[0.2.1]: https://github.com/buimanhtoan-it/cognis/compare/v0.2.0...v0.2.1
+[0.2.0]: https://github.com/buimanhtoan-it/cognis/compare/v0.1.17...v0.2.0
+[0.1.17]: https://github.com/buimanhtoan-it/cognis/compare/v0.1.0...v0.1.17
+
+---
+
+## [0.1.0] — Phase 1 MVP
+
+### Added
+
+**Phase 0 — Foundations**
+
+- Repo scaffold per design "Build and Release" layout (`apps/`, `packages/`, `tests/`).
+- `pyproject.toml` pinning Python ≥ 3.11 and Phase 0/1 dev dependencies (ruff,
+  mypy, pytest, pytest-asyncio, pytest-benchmark, hypothesis).
+- `Makefile` and `tasks.py` recipes for `lint`, `typecheck`, `test`, `bench`, `eval`.
+- GitHub Actions workflows: lint+unit on push, integration on PR, nightly eval.
+- `pre-commit` config: ruff format + lint + mypy.
+- Apache-2.0 `LICENSE`, README skeleton, `.gitignore` covering `.cognis/` and build artifacts.
+- `packages/core/cognis/config.py`: Pydantic-validated config loader for `.cognis/config.yaml`.
+- `cognis-cli` (Click) with commands: `init`, `index`, `eval`, `health`, `up`, `down`,
+  `mcp-conformance`, `profile`.
+- SQLite schema bootstrap in WAL mode with FTS5 and sqlite-vec virtual tables.
+- Migration runner with `meta.index_version` tracking.
+- Eval harness skeleton (`packages/eval/runner.py`) with Recall@k, MRR metrics.
+- Test fixture repos: `mini-ts-app`, `mini-py-svc`, `mini-go-svc` with planted bugs.
+
+**Phase 1 — MVP Cognition**
+
+- Tree-sitter parsers for TypeScript, Python, and Go.
+- File watcher with 200ms debounce and `.gitignore` awareness (`watchdog`).
+- Edge resolver: LSP-first with heuristic fallback, confidence-scored edges.
+- Enricher: `db_table`, `http_route`, `env_var`, `external_call` detection.
+- Secret redactor: Shannon entropy + pattern matching for AWS/GCP/Azure/GitHub/OpenAI/JWT/PEM.
+- Embedder with local `bge-small-en-v1.5` (384d) backend; optional Voyage API.
+- Writer with single-writer thread, per-file transactions, cascade deletion.
+- Retrieval layers: Lexical (FTS5), Semantic (sqlite-vec KNN), Structural (recursive CTE).
+- Cognitive Context Planner: rule-based classify + layer_plan + allocate_budget, < 30ms.
+- Capsule composer v1 with Pydantic schema, tiktoken budget, untrusted content wrapping.
+- MCP server (`cognis-mcpd`) with 4 tools: `symbol_lookup`, `semantic_search`,
+  `dependency_trace`, `retrieve_context_capsule`.
+- Hard limits enforcement: depth ≤ 8, k ≤ 50, max_tokens ≤ 32000, 10s hard timeout.
+- Audit log (append-only JSONL, args hash only).
+
+**Phase 1 — Conformance, Eval, Performance, Release (Tasks 16–18)**
+
+- `cognis-cli mcp-conformance`: built-in conformance check for all 4 tools; optional
+  upstream harness integration when `mcp_conformance` package is installed.
+- Integration tests (`tests/integration/test_mcp_integration.py`) for all 4 tools,
+  planted auth-timeout bug detection, and incremental write API verification.
+- Cross-platform CI: integration tests run on ubuntu-latest, macos-latest, windows-latest.
+- Golden query set expanded to 110 queries (20 each for bugfix/feature/refactor/explain/review,
+  10 for migrate) across all 3 fixture repos.
+- `scripts/run_eval.py`: standalone eval runner script.
+- `docs/eval/phase1-baseline.md`: methodology, baseline placeholder, tuning approach,
+  Phase 1 gate criteria.
+- `docs/eval/swe-bench-methodology.md`: SWE-bench Lite mini-run methodology.
+- `tests/benchmark/test_latency.py`: `@pytest.mark.benchmark` tests for all 4 hot-path
+  latency budgets.
+- `apps/cognis-mcpd/cognis_mcpd/metrics.py`: in-memory Counter/Histogram/Gauge with stdlib only.
+- `docs/install.md`, `docs/quickstart.md`, `docs/mcp-client-config.md`: user-facing docs.
+- `docs/performance.md`: performance guide, known gaps, profiling instructions.
+- `docs/observability.md`: metrics, logging, audit log, Phase 2 Prometheus migration plan.
+- `docs/release.md`: release procedure, Docker, cibuildwheel notes.
+- `docs/release-notes-v0.1.17.md`: release notes for the v0.1.x line.
+- `Dockerfile`: multi-stage build with bge-small-en-v1.5 pre-cached, non-root user.
+
+### Fixed
+
+- `mcp-conformance` CLI command: upgraded from stub to functional implementation.
+
+### Notes on Phase 2+
+
+- Behavioral (runtime) layer: no-op at MVP; OTel adapter planned for Phase 3.
+- Temporal (git history) layer: Phase 2.
+- Reranker (bge-reranker-v2-m3): Phase 2.
+- SSE transport: Phase 2.
+- Prometheus `/metrics` HTTP endpoint: Phase 2.
+
+[0.1.0]: https://github.com/buimanhtoan-it/cognis/releases/tag/v0.1.0

cognis_engine-0.3.0/LICENSE

@@ -0,0 +1,201 @@
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+
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+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
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+
+   Copyright 2026 cognis maintainers
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
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+   See the License for the specific language governing permissions and
+   limitations under the License.

cognis_engine-0.3.0/Makefile

@@ -0,0 +1,79 @@
+# cognis developer Makefile
+#
+# Mirrors `tasks.py` (Invoke). Both expose the same recipes so contributors can
+# pick whichever fits their shell. The CI pipeline uses these targets verbatim.
+
+PYTHON      ?= python
+PIP         ?= $(PYTHON) -m pip
+PYTEST      ?= $(PYTHON) -m pytest
+RUFF        ?= $(PYTHON) -m ruff
+MYPY        ?= $(PYTHON) -m mypy
+COGNIS_CLI  ?= $(PYTHON) -m cognis.cli.main
+
+# Strict-typing scope per Task 1 — start with packages/core, expand later.
+MYPY_STRICT_PATHS ?= packages/core
+PYTEST_ARGS ?=
+
+.DEFAULT_GOAL := help
+
+.PHONY: help
+help:
+	@echo "cognis dev recipes:"
+	@echo "  make lint        # ruff format --check + ruff check"
+	@echo "  make format      # ruff format (writes changes)"
+	@echo "  make typecheck   # mypy (strict on $(MYPY_STRICT_PATHS))"
+	@echo "  make test        # pytest unit + property tests"
+	@echo "  make e2e         # full cross-app end-to-end flow (CLI+indexd+mcpd)"
+	@echo "  make bench       # pytest --benchmark-only"
+	@echo "  make eval        # cognis-cli eval (golden-set runner)"
+	@echo "  make clean       # remove build / cache artifacts"
+	@echo "  make install-dev # editable install + dev deps + extension compile"
+	@echo "  make install-extension # npm install + compile apps/cognis-vscode"
+
+.PHONY: install-extension
+install-extension:
+	$(PYTHON) scripts/setup_extension.py
+
+.PHONY: install-dev
+install-dev:
+	$(PIP) install -e ".[indexer,embed-local,vector,tokenizers,mcp]"
+	$(PIP) install --group dev || $(PIP) install ruff mypy pytest pytest-asyncio pytest-benchmark hypothesis pre-commit invoke
+	pre-commit install || true
+	-$(PYTHON) scripts/prepare-branding.py
+	$(PYTHON) scripts/setup_extension.py
+
+.PHONY: lint
+lint:
+	$(RUFF) format --check .
+	$(RUFF) check .
+
+.PHONY: format
+format:
+	$(RUFF) format .
+	$(RUFF) check --fix .
+
+.PHONY: typecheck
+typecheck:
+	$(MYPY) $(MYPY_STRICT_PATHS)
+
+.PHONY: test
+test:
+	$(PYTEST) -m "not benchmark and not eval and not e2e" $(PYTEST_ARGS)
+
+.PHONY: e2e
+e2e:
+	$(PYTEST) -m e2e $(PYTEST_ARGS)
+
+.PHONY: bench
+bench:
+	$(PYTEST) -m benchmark --benchmark-only $(PYTEST_ARGS)
+
+.PHONY: eval
+eval:
+	$(COGNIS_CLI) eval $(EVAL_ARGS)
+
+.PHONY: clean
+clean:
+	$(PYTHON) -c "import shutil, os; [shutil.rmtree(p, ignore_errors=True) for p in ['build','dist','.pytest_cache','.mypy_cache','.ruff_cache','.hypothesis','.benchmarks','htmlcov']]"
+	$(PYTHON) -c "import pathlib; [p.unlink() for p in pathlib.Path('.').rglob('*.py[co]')]"
+	$(PYTHON) -c "import pathlib, shutil; [shutil.rmtree(p, ignore_errors=True) for p in pathlib.Path('.').rglob('__pycache__')]"