aura-research 0.1.0__tar.gz

aura_research-0.1.0/LICENSE

@@ -0,0 +1,190 @@
+                                 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 the 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 the 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 any 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
+
+   Copyright 2024-2026 Auralith Inc.
+
+   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.

aura_research-0.1.0/PKG-INFO

@@ -0,0 +1,298 @@
+Metadata-Version: 2.4
+Name: aura-research
+Version: 0.1.0
+Summary: LLM-powered research knowledge base — compile raw documents into a living wiki
+Author-email: Rta Labs <info@rtalabs.org>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/Rtalabs-ai/aura-research
+Project-URL: Repository, https://github.com/Rtalabs-ai/aura-research.git
+Project-URL: Issues, https://github.com/Rtalabs-ai/aura-research/issues
+Keywords: ai,research,knowledge-base,wiki,rag,llm,aura,agent-memory
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: auralith-aura>=0.2.3
+Requires-Dist: pyyaml>=6.0
+Provides-Extra: openai
+Requires-Dist: openai>=1.0.0; extra == "openai"
+Provides-Extra: anthropic
+Requires-Dist: anthropic>=0.20.0; extra == "anthropic"
+Provides-Extra: gemini
+Requires-Dist: google-generativeai>=0.5.0; extra == "gemini"
+Provides-Extra: search
+Requires-Dist: duckduckgo-search>=5.0.0; extra == "search"
+Provides-Extra: watch
+Requires-Dist: watchdog>=3.0.0; extra == "watch"
+Provides-Extra: all
+Requires-Dist: aura-research[anthropic,gemini,openai,search,watch]; extra == "all"
+Dynamic: license-file
+
+<p align="center">
+  <img src="https://github.com/Rtalabs-ai/aura-core/raw/main/logo.png" alt="Rta Labs Logo" width="120" />
+</p>
+
+<h1 align="center">Aura Research</h1>
+
+<p align="center">
+  <strong>Turn raw research into a living wiki your LLM agents can read, query, and enhance.</strong>
+</p>
+
+<p align="center">
+  <a href="https://github.com/Rtalabs-ai/aura-research/blob/main/LICENSE"><img src="https://img.shields.io/badge/license-Apache%202.0-blue.svg" alt="License" /></a>
+  <a href="https://github.com/Rtalabs-ai/aura-core"><img src="https://img.shields.io/badge/powered%20by-Aura%20Core-purple" alt="Powered by Aura Core" /></a>
+</p>
+
+---
+
+**Aura Research** is an LLM-powered research knowledge base that compiles raw documents into a structured markdown wiki. Drop your papers, articles, data, and notes into a folder — the LLM reads everything, builds a navigable wiki with summaries and concept articles, and then answers your research questions using that compiled knowledge.
+
+Built on [Aura Core](https://github.com/Rtalabs-ai/aura-core) for document compilation (60+ formats) and the three-tier Memory OS for persistent agent memory across sessions.
+
+## Quick Start
+
+```bash
+# Install
+pip install 'aura-research[openai]'
+
+# Set your API key
+export OPENAI_API_KEY=sk-...
+
+# Initialize a project
+research init my-project
+cd my-project
+
+# Drop your documents in raw/
+cp ~/papers/*.pdf raw/
+
+# Ingest and compile
+research ingest raw/
+research compile
+
+# Ask questions
+research query "what are the key findings across all papers?"
+
+# Search the wiki
+research search "attention mechanism"
+
+# Check wiki health
+research lint
+```
+
+### Agent-Native Mode (no API key)
+
+If you're already using an AI coding agent (Claude Code, Codex, Gemini CLI, Cursor, etc.), **you don't need an API key**. The agent IS the LLM:
+
+```bash
+# In your AI agent's terminal:
+research init my-project
+# Copy documents to raw/
+research ingest raw/
+
+# The agent reads the docs and writes wiki articles directly
+# (it's an LLM — it doesn't need to call another one)
+
+research build          # compile wiki/ → wiki.aura
+research search "topic" # search the wiki
+research memory show    # see what the agent remembers
+```
+
+The API mode (`research compile`, `research query`) exists for headless/batch use when no agent is at the keyboard.
+
+## How It Works
+
+```
+Raw Documents  ──→  Aura Core (.aura)  ──→  LLM Compiler  ──→  Markdown Wiki
+  papers/              compiled &              generates          wiki/
+  articles/            indexed                 summaries,         ├── _index.md
+  data/                (60+ formats)           concepts,          ├── concepts/
+  code/                                        backlinks          ├── sources/
+                                                                  └── queries/
+                              ↕
+                        Memory OS
+                   /pad  /episodic  /fact
+                   (persistent agent memory)
+```
+
+1. **Ingest** — Compile your raw documents into a searchable `.aura` archive using Aura Core
+2. **Compile** — LLM reads all sources and generates a structured wiki: per-source summaries, cross-cutting concept articles, master index, and executive summary
+3. **Query** — Ask questions against the wiki. The LLM uses wiki context + Memory OS facts + optional web search to give you thorough, cited answers
+4. **Remember** — Memory OS automatically stores key findings (`/fact`), session logs (`/episodic`), and working notes (`/pad`) — so the agent never starts cold
+
+## Commands
+
+| Command | Description |
+|---|---|
+| `research init [dir]` | Initialize a new project |
+| `research ingest <dir>` | Ingest raw documents into `.aura` archive |
+| `research ingest <dir> --watch` | Watch directory and auto-re-ingest on changes |
+| `research compile` | Compile wiki using LLM API (needs API key) |
+| `research compile --full` | Full recompile (ignore cache) |
+| `research build` | Build `wiki.aura` from `wiki/` markdown (no LLM needed) |
+| `research query "..."` | Ask a research question (needs API key) |
+| `research query "..." --save` | Ask and save the answer to `wiki/queries/` |
+| `research query "..." --no-web` | Ask without web search |
+| `research search "..."` | Keyword search across wiki articles |
+| `research lint` | Run wiki health checks |
+| `research lint --ai` | Health checks + AI-powered analysis |
+| `research status` | Show knowledge base statistics |
+| `research memory show` | Full overview of all 3 memory tiers |
+| `research memory show --tier fact` | Overview filtered to one tier |
+| `research memory usage` | Show Memory OS storage |
+| `research memory query "..."` | Search agent memory |
+| `research memory write <tier> "..."` | Manually write to memory (pad/episodic/fact) |
+| `research memory list` | List memory shards |
+| `research memory prune --before DATE` | Prune old memory entries |
+
+## LLM Providers
+
+Supports **OpenAI**, **Anthropic**, and **Google Gemini**. Install the one you prefer:
+
+```bash
+pip install 'aura-research[openai]'      # GPT-4o (default)
+pip install 'aura-research[anthropic]'    # Claude 3.5 Sonnet
+pip install 'aura-research[gemini]'       # Gemini 2.0 Flash
+pip install 'aura-research[all]'          # Everything
+```
+
+Configure via environment variables or `research.yaml`:
+
+```yaml
+llm:
+  provider: openai          # openai, anthropic, or gemini
+  model: gpt-4o             # override default model
+  temperature: 0.3
+
+memory:
+  enabled: true
+  auto_write: true           # agent writes to memory automatically
+
+web_search:
+  enabled: true
+  max_results: 5
+
+watch:
+  enabled: false
+  interval: 5               # seconds between checks
+```
+
+## Memory OS
+
+Aura's three-tier **Memory OS v2.1** gives the agent persistent memory across sessions — so it never starts cold:
+
+| Tier | What's Stored | Persistence |
+|---|---|---|
+| `/pad` | Working notes, draft observations | Transient — scratch space |
+| `/episodic` | Session logs, what was compiled/queried | Auto-archived |
+| `/fact` | Key findings, verified observations | Persistent — survives indefinitely |
+
+### How It Operates
+
+Memory OS works **both autonomously and manually**:
+
+- **Autonomous**: During `research compile`, the LLM auto-extracts key facts and writes them to `/fact`. After every compile/query session, an episodic log → `/episodic`. Controlled by `auto_write: true` in config.
+- **Manual**: Write directly with `research memory write <tier> "content"` whenever you (or the agent) want to persist something.
+
+### v2.1 Features
+
+| Feature | What It Does |
+|---|---|
+| **Entry deduplication** | Prevents writing the same fact twice (SimHash fuzzy matching) |
+| **Temporal decay** | Recent memories score higher in queries — older context naturally fades |
+| **Bloom filters** | Skip irrelevant shards during search — fast even with thousands of entries |
+| **Append-only** | Old entries are never overwritten — new ones are added alongside them |
+| **Tiered priority** | Facts > episodic > pad when returning query results |
+
+### Examples
+
+```bash
+# Write a verified fact
+research memory write fact "The model achieves 94.2% accuracy on the test set"
+
+# Log what you did this session
+research memory write episodic "Analyzed training curves, found overfitting at epoch 12"
+
+# Jot a working note
+research memory write pad "TODO: re-run experiment with lower learning rate"
+
+# Search memory by keyword
+research memory query "accuracy"
+
+# Full overview — see everything across all 3 tiers
+research memory show
+
+# Filter to just facts
+research memory show --tier fact
+
+# Storage usage
+research memory usage
+```
+
+## Web Search
+
+During `research query`, the agent can search the web to supplement wiki answers with current information. This is enabled by default and uses DuckDuckGo (no API key required).
+
+```bash
+pip install 'aura-research[search]'
+
+# Query with web search (default)
+research query "latest advances in attention mechanisms"
+
+# Query without web search
+research query "what does our data show" --no-web
+```
+
+## Watch Mode
+
+Auto-detect new files and re-ingest:
+
+```bash
+pip install 'aura-research[watch]'
+
+# Watch for changes (uses watchdog if installed, falls back to polling)
+research ingest ./papers --watch
+```
+
+## Wiki Output
+
+The compiled wiki lives in two places:
+
+**`wiki.aura`** — The primary artifact. An `.aura` archive containing all wiki articles, optimized for agent RAG retrieval. Token-efficient — agents read only what's relevant.
+
+**`wiki/`** — Markdown export for human browsing. Open in **Obsidian**, **VS Code**, **GitHub**, or any markdown viewer:
+
+```
+.research/
+├── knowledge.aura      ← Raw ingested documents
+└── wiki.aura           ← Compiled wiki (agent reads from here)
+
+wiki/
+├── _index.md           ← Master index with links to all articles
+├── _summary.md         ← Executive summary of the knowledge base
+├── concepts/           ← Cross-cutting concept articles
+│   ├── attention.md
+│   ├── tokenization.md
+│   └── ...
+├── sources/            ← Per-source summary articles
+│   ├── vaswani2017.md
+│   ├── devlin2019.md
+│   └── ...
+└── queries/            ← Saved Q&A responses
+    └── ...
+```
+
+After editing wiki articles (or having the agent write them), run `research build` to recompile `wiki.aura`.
+
+## License
+
+Apache License 2.0 — see [LICENSE](LICENSE).
+
+## Links
+
+- **Aura Core**: [github.com/Rtalabs-ai/aura-core](https://github.com/Rtalabs-ai/aura-core) — the universal context compiler
+- **Rta Labs**: [rtalabs.org](https://rtalabs.org)