brainiac-cli 0.16.0__tar.gz

brainiac_cli-0.16.0/LICENSE

@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   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
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   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
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

brainiac_cli-0.16.0/PKG-INFO

@@ -0,0 +1,306 @@
+Metadata-Version: 2.4
+Name: brainiac-cli
+Version: 0.16.0
+Summary: Brainiac — local any-LLM second-brain core engine + brain CLI (Markdown truth, derived SQLite index).
+License-Expression: Apache-2.0
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: onnxruntime>=1.17
+Requires-Dist: tokenizers>=0.15
+Requires-Dist: numpy<3,>=1.24
+Requires-Dist: sqlite-vec>=0.1.6
+Requires-Dist: huggingface-hub>=0.20
+Requires-Dist: cryptography>=41
+Requires-Dist: PyYAML>=6
+Requires-Dist: regex>=2023.0.0
+Requires-Dist: keyring>=24; sys_platform == "win32"
+Requires-Dist: pypdf>=4.0
+Requires-Dist: python-docx>=1.1
+Requires-Dist: python-pptx>=0.6.23
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: Pillow>=10
+Provides-Extra: vec
+Requires-Dist: sqlite-vec>=0.1.6; extra == "vec"
+Provides-Extra: audit
+Requires-Dist: cryptography>=41; extra == "audit"
+Provides-Extra: embed
+Requires-Dist: fastembed>=0.3; extra == "embed"
+Provides-Extra: corporate
+Requires-Dist: onnxruntime>=1.17; extra == "corporate"
+Requires-Dist: tokenizers>=0.15; extra == "corporate"
+Requires-Dist: numpy<3,>=1.24; extra == "corporate"
+Requires-Dist: sqlite-vec>=0.1.6; extra == "corporate"
+Requires-Dist: huggingface-hub>=0.20; extra == "corporate"
+Requires-Dist: cryptography>=41; extra == "corporate"
+Requires-Dist: PyYAML>=6; extra == "corporate"
+Provides-Extra: yaml
+Requires-Dist: PyYAML>=6; extra == "yaml"
+Provides-Extra: ingest
+Requires-Dist: pypdf>=4.0; extra == "ingest"
+Requires-Dist: python-docx>=1.1; extra == "ingest"
+Requires-Dist: python-pptx>=0.6.23; extra == "ingest"
+Requires-Dist: openpyxl>=3.1; extra == "ingest"
+Requires-Dist: Pillow>=10; extra == "ingest"
+Provides-Extra: dev
+Requires-Dist: pytest>=7; extra == "dev"
+Requires-Dist: build>=1; extra == "dev"
+Provides-Extra: eval
+Requires-Dist: ranx>=0.3.20; extra == "eval"
+Requires-Dist: numpy>=1.24; extra == "eval"
+Provides-Extra: quant-tools
+Requires-Dist: onnx>=1.14; extra == "quant-tools"
+Provides-Extra: mcp
+Requires-Dist: mcp>=1.0; extra == "mcp"
+Provides-Extra: index
+Requires-Dist: regex>=2023.0.0; extra == "index"
+Dynamic: license-file
+
+# Brainiac
+
+A local, any-LLM **second brain**: your notes stay plain Markdown + YAML on
+your own disk, and the `brain` CLI gives any LLM harness (Claude Code, Codex,
+Gemini CLI, Claude Desktop / Cowork, ...) fast, sourced search over them — no
+vendor lock-in, no cloud index, no plugin ecosystem to keep alive.
+
+## Why
+
+Retrieval-augmented note-taking usually means picking a proprietary app and
+trusting its plugin/embedding pipeline forever. Brainiac inverts that: the
+substrate is just files (`vault/brain/`, `vault/raw/`), the search index is a
+disposable cache you can rebuild any time, and every read goes through a
+deny-by-default classification filter (the **egress gate** — see
+`docs/glossary.md`) before it reaches a model — so you control what an LLM is
+allowed to see, note by note. See `AGENTS.md` for the full conventions and
+security model.
+
+## Installing Brainiac for the first time
+
+**Installing? → [`docs/install/README.md`](docs/install/README.md) (pick your
+platform: Claude Code, Cowork, Codex, or Gemini CLI).**
+
+The single most common path (Claude Code, on your own machine):
+
+```text
+claude> /plugin marketplace add Autopsias/brainiac
+claude> /plugin install brainiac-manager@brainiac
+claude> /brainiac-install <path-to-your-vault>
+```
+
+**Or the one-command way** (PyPI-first, no clone needed):
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/Autopsias/brainiac/main/install.sh -o /tmp/brainiac-install.sh
+bash /tmp/brainiac-install.sh
+```
+
+`install.sh` tries, in order, `uv tool install`, `pipx install`, then
+`pip install --user` — first success wins, and it tells you which one it
+used. Every channel installs `brainiac-cli[mcp]` so `brain-mcp` (the
+optional Claude Desktop bridge) works out of the box. Plain `pip install
+brainiac-cli[mcp]` works too, without the channel-fallback convenience.
+
+**Windows (PowerShell)?** Same install, no bash/WSL required:
+
+```powershell
+irm https://raw.githubusercontent.com/Autopsias/brainiac/main/install.ps1 -OutFile install.ps1
+.\install.ps1
+```
+
+**Contributing to Brainiac, or no PyPI/network access?** Clone and pass
+`--dev` / `-Dev` — an editable install from the checkout, the pre-PyPI
+behavior:
+
+```bash
+git clone https://github.com/Autopsias/brainiac.git && cd brainiac
+./install.sh --dev          # macOS/Linux
+# or: .\install.ps1 -Dev    # Windows
+```
+
+The `--dev` path also builds a **lexical-only** index for the checkout's
+bundled sample vault (`BRAIN_EMBEDDER=hash` — no model download, no network
+needed) — try `brain search "arctic-embed vs e5" --json` against it right
+away. The default PyPI-first path has no local sample vault to index — run
+this against your own vault instead (see `docs/install/README.md`):
+
+```bash
+BRAIN_VAULT=<workspace>/vault brain init --full --apply   # scaffolds + seeds 3 sample notes AND indexes them
+BRAIN_VAULT=<workspace>/vault brain search "welcome" --json   # first search works right away
+```
+
+Either way, semantic search downloads its embedding model (a few hundred MB)
+lazily on first real use, or run `brain warmup` up front.
+
+Then ask your first question:
+
+```bash
+brain search "welcome" --json          # fresh vault (matches the seeded sample notes)
+brain search "arctic-embed vs e5" --json   # --dev checkout's own bundled vault
+```
+
+Every search hit carries the note's file path and its classification tier,
+and an `egress` block reports how many notes were withheld by the
+classification filter.
+
+Two things worth knowing about where files live:
+
+- **Your notes** live in the vault (`vault/` by default — plain Markdown, the
+  single source of truth).
+- **The search index** lives in your per-user app-data folder
+  (`~/Library/Application Support/profile-a-brain` on macOS,
+  `%LOCALAPPDATA%\profile-a-brain` on Windows, `~/.local/share/...` on
+  Linux). It is a derived cache — deleting it loses nothing; `brain rebuild`
+  recreates it from the vault.
+
+Per-client walkthroughs (Claude Code vs Codex vs Cowork):
+`docs/install/README.md`. Run `brain --help` any time — the CLI is self-describing and is the one
+source of truth for what's shipped.
+
+## Updating an existing install
+
+Already installed? Don't re-run the first-time setup — update in place.
+
+**Check where you stand (read-only).** In your terminal:
+
+```
+brain doctor
+```
+
+prints one health + version table across every surface — engine venv, CLI
+plugins, staged Cowork workspaces, marketplace cache, and the Desktop/Cowork
+store — each ✅/⚠️ with the exact command to fix anything stale. It changes
+nothing and exits non-zero when a required surface is behind. (Available from
+v0.10.0 onward.)
+
+**Bring everything current.** In Claude Code on the host:
+
+```
+/brainiac-update
+```
+
+now **runs** the update instead of printing a checklist: marketplace refresh →
+downgrade-safe CLI-plugin reinstall → engine venv reinstall → every registered
+Cowork workspace re-staged → a final `brain doctor` verify — then a before→after
+version table and one pass/fail. It handles the reconciliation downgrade
+(installed newer than the marketplace) automatically and never touches your
+notes, audit chain, or runtime state. Prefer the terminal? `brain update` is the
+same flow — add `--dry-run` to preview every decision without mutating anything.
+Full detail: **`docs/install/README.md`** (§ Updating).
+
+**Installed under the old names?** Marketplace `profile-a-marketplace` and
+plugins `profile-a-kernel`/`profile-a-extras` were renamed to `brainiac` /
+`brainiac-kernel`/`brainiac-extras` (2026-07-11). `brain doctor` flags a
+stale-name registration under either old name. Recovery (add-new-before-
+remove-old — never the reverse):
+
+```
+claude plugin marketplace add Autopsias/brainiac
+claude plugin install brainiac-manager@brainiac
+```
+
+then run `/brainiac-update` — it detects the old-name registrations and
+finishes the migration automatically (installs the new-name plugins,
+verifies the lifecycle skills resolve, then removes the old marketplace and
+plugins). See `docs/adr/0006-distribution-naming.md`.
+
+## Using it with a new project (second vault, third, ...)
+
+The install is **per machine**; vaults are **per project**. You never
+reinstall — you point the same `brain` at a different vault folder, and each
+vault automatically gets its own index and audit chain (no configuration):
+
+```bash
+export BRAIN_VAULT=~/vaults/my-new-project   # which vault to use
+brain init --full --apply                     # once per vault: scaffold + seed + index
+```
+
+Full detail (per-vault overlay, the scheduled-task gotcha):
+**`docs/install/second-vault.md`**.
+
+## For technical & security teams
+
+A plain summary of what this repo does and doesn't do, for a corporate
+review:
+
+- **All data stays on the local disk.** Notes are plain Markdown; the index
+  is a local SQLite file. There is no server, no telemetry, no cloud sync,
+  and the project holds **no model API keys** — the only egress is whatever
+  LLM client the owner already runs.
+- **Deny-by-default egress gate.** Every read command filters notes by their
+  `classification` tier before printing; a note with a missing or unknown
+  label is treated as most-restrictive and withheld. Scheme:
+  `docs/classification-scheme.md`.
+- **Signed audit chain.** Every committed write is Ed25519-signed and
+  hash-chained; the key lives in the OS secret store, fail-closed (no file
+  fallback). Rotation runbook and stated limitations: `SECURITY.md`.
+- **Trust split.** Untrusted/sandboxed legs (the Cowork Linux VM) get a
+  read-only snapshot and a draft inbox — they can never sign, index, or
+  mutate the canonical store. `AGENTS.md` §6.
+- **Dependencies.** The default install pulls a small, auditable set
+  (onnxruntime, tokenizers, numpy, sqlite-vec, huggingface-hub,
+  cryptography, PyYAML, regex — see `pyproject.toml`, which documents why
+  each exists). The code degrades gracefully without any of them, so a
+  constrained deployment (Intune, air-gapped) can install with
+  `pip install --no-deps .` and re-add only what policy allows; an SBOM
+  generator ships at `tools/generate_sbom.py`. Offline model provisioning:
+  set `$BRAIN_MODEL_CACHE` to a pre-fetched model dir and no download is
+  attempted.
+- **License & provenance.** Apache-2.0. Built clean-room; the AGPL project
+  consulted as a design reference was never forked or vendored — log and
+  audit gate: `docs/clean-room-log.md`, `tools/code_origin_audit.py`.
+- **Vulnerability reporting:** `SECURITY.md`. Deeper notes:
+  `docs/SECURITY_NOTES.md`, `docs/operations/`.
+
+## How the AI assistants are wired
+
+`AGENTS.md` is the canonical instruction file. `CLAUDE.md` imports it
+verbatim (`@AGENTS.md`) so Claude Code reads the same contract; Codex reads
+`AGENTS.md` natively; Gemini CLI is pointed at it via `.gemini/`. All of them
+call the `brain` CLI through their normal shell — **no MCP required**. The
+one exception is the Claude Desktop **Chat tab** (the only surface that
+can't run a command): for that, `pip install -e ".[mcp]"` adds the optional,
+deletable `brain-mcp` bridge. Full matrix: `docs/harness-wiring.md`.
+
+## More
+
+- **`AGENTS.md`** — the conventions/schema every harness reads at startup:
+  note shape, link style, capture rules, the four agent-facing verbs
+  (search/get/recent/draft-capture), and the security posture.
+- **`docs/install/`** — installation, starting at the
+  [platform picker](docs/install/README.md) (Claude Code, Cowork — the Claude
+  Desktop Linux VM sandbox client — Codex, Gemini CLI) and
+  `docs/install/new-owner.md` for the five-minute "what runs where" mental model.
+- **`docs/glossary.md`** — one-line definitions for the jargon used across
+  these docs (PARA, MNPI, egress gate, Cowork, host-broker, overlay, ...).
+- **`SECURITY.md`** — vulnerability reporting, supported versions, audit-key
+  rotation.
+- **`LICENSE`** — Apache-2.0.
+
+## Layout
+
+```
+AGENTS.md            conventions + frontmatter schema
+src/brain/           the brain CLI + engine (index, search, audit, ...)
+docs/                specs (substrate, classification, install, security notes)
+tools/validate.py    conventions validator (stdlib-only; PyYAML optional)
+vault/               the tiny sample vault used in the quickstart above
+  raw/   immutable captured sources
+  brain/ agent-owned atomic notes + index.md + generated backlinks.md
+  .brain/  per-vault runtime (published snapshot, capture inbox) — gitignored
+```
+
+## Validate
+
+```bash
+python3 tools/validate.py vault              # exit 0 = conventions clean
+python3 tools/validate.py vault --backlinks  # regenerate brain/backlinks.md
+python3 tools/validate.py vault --okf        # + optional OKF lint
+```
+
+## Scope note
+
+Substrate readiness is not the same as operational cutover. This repo makes
+the substrate *ready* to replace an existing tool (e.g. Obsidian + Smart
+Connections) and emits the cutover hooks (`docs/corpus-migration.md`,
+`docs/dependency-inventory.md`); actually retiring your old setup is a
+separate, owner-specific step. See `AGENTS.md` §7.