weaverx 0.1.1__tar.gz

weaverx-0.1.1/.gitignore

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+__pycache__/
+*.py[cod]
+*.egg-info/
+.dist/
+.mypy_cache/
+.pytest_cache/
+.ruff_cache/
+.coverage
+.venv/
+venv/
+dist/
+build/
+site/
+triage-output.json

weaverx-0.1.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [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]
+
+## [0.1.1] - 2026-05-23
+
+### Added
+
+- PyPI publishing via GitHub Release workflow (trusted publishing)
+- GitHub Pages documentation site at [fratresmedai.github.io/WeaveRx](https://fratresmedai.github.io/WeaveRx/)
+- Governance files: CODE_OF_CONDUCT, SECURITY, SUPPORT, ETHICS
+- Issue and pull request templates
+- MkDocs documentation scaffold
+- Pre-commit hooks, Dependabot, pip-audit in CI
+- pytest coverage gate in CI
+- CLI human-review disclaimer on triage output
+- Configuration reference in docs
+- GitHub Action dry-run screenshot in README
+
+### Changed
+
+- README restructured for scanability (features, quickstart, demo first)
+- Repository description and GitHub topics updated
+- Badges row moved below title for first-impression polish
+
+## [0.1.0] - 2026-05-23
+
+### Added
+
+- Medical AI issue triage CLI with eight domain categories
+- LiteLLM multi-provider support (Grok, Anthropic, OpenAI-compatible)
+- Local safeguard heuristics (entropy, repetition, patterns, relevance)
+- Auditable `sources` and top-level `status` in JSON output
+- GitHub Action for dry-run triage on issues
+- Mock mode for offline demos and CI
+- Human-in-the-loop defaults (`--dry-run`, `--confirm` for writes)
+
+[Unreleased]: https://github.com/FratresMedAI/WeaveRx/compare/v0.1.1...HEAD
+[0.1.1]: https://github.com/FratresMedAI/WeaveRx/releases/tag/v0.1.1
+[0.1.0]: https://github.com/FratresMedAI/WeaveRx/releases/tag/v0.1.0

weaverx-0.1.1/CONTRIBUTING.md

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+# Contributing to WeaveRx
+
+Thank you for helping improve WeaveRx for the medical AI open-source community.
+
+## Community standards
+
+- Read and follow our [Code of Conduct](CODE_OF_CONDUCT.md).
+- Review [ETHICS.md](ETHICS.md) for responsible-use constraints in this domain.
+- Report security issues privately via [SECURITY.md](SECURITY.md) — never in public issues.
+
+## Development setup
+
+```bash
+git clone https://github.com/FratresMedAI/WeaveRx.git
+cd WeaveRx
+pip install -e ".[dev]"
+pre-commit install   # optional but recommended
+```
+
+Run the quality checks before opening a pull request:
+
+```bash
+pre-commit run --all-files   # or: ruff check .
+mypy src/weaverx
+pytest --cov=weaverx
+```
+
+Most tests run offline with `--mock` data. Optional live tests are marked `@pytest.mark.network`.
+
+## Pull request expectations
+
+Use the [pull request template](.github/PULL_REQUEST_TEMPLATE.md). In summary:
+
+- Keep changes focused and explain the **why** in the PR description.
+- Match existing code style (type hints, ruff/mypy clean).
+- Add or update tests for behavior changes.
+- Do not weaken safety defaults (dry-run, confirmation gates, advisory safeguards).
+
+## Safety constraints
+
+WeaveRx is **human-in-the-loop** tooling:
+
+- Never auto-post triage comments without explicit `--post-comment` and `--confirm`.
+- Safeguard checks are advisory — they warn, they do not block.
+- Do not add features that encourage sharing PHI or patient identifiers in GitHub issues.
+
+## Reporting issues
+
+Use the GitHub issue templates:
+
+- [Bug report](.github/ISSUE_TEMPLATE/bug_report.yml)
+- [Feature request](.github/ISSUE_TEMPLATE/feature_request.yml)
+- [WeaveRx feedback](.github/ISSUE_TEMPLATE/triage_feedback.yml)
+
+Include WeaveRx version (`weaverx --version`), the command you ran (redact tokens), and expected vs actual behavior.
+
+See [SUPPORT.md](SUPPORT.md) for response expectations.
+
+## Releases
+
+Maintainers: see [docs/releasing.md](docs/releasing.md) for tagging and GitHub Release workflow.

weaverx-0.1.1/LICENSE

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+MIT License
+
+Copyright (c) 2026 WeaveRx Contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

weaverx-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: weaverx
+Version: 0.1.1
+Summary: AI-powered GitHub issue and PR triage for the medical AI community
+Project-URL: Homepage, https://github.com/FratresMedAI/WeaveRx
+Project-URL: Repository, https://github.com/FratresMedAI/WeaveRx
+Project-URL: Issues, https://github.com/FratresMedAI/WeaveRx/issues
+Project-URL: Changelog, https://github.com/FratresMedAI/WeaveRx/blob/master/CHANGELOG.md
+Author: WeaveRx Contributors
+License-Expression: MIT
+License-File: LICENSE
+Keywords: developer-productivity,github-bot,github-triage,llm-tools,medical-ai,monai,nnunet,safety,triage
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Software Development :: Quality Assurance
+Requires-Python: >=3.11
+Requires-Dist: httpx>=0.27.0
+Requires-Dist: litellm>=1.40.0
+Requires-Dist: pydantic>=2.7.0
+Requires-Dist: rich>=13.7.0
+Requires-Dist: typer>=0.12.0
+Provides-Extra: dev
+Requires-Dist: mypy>=1.10.0; extra == 'dev'
+Requires-Dist: pytest-cov>=5.0.0; extra == 'dev'
+Requires-Dist: pytest-httpx>=0.30.0; extra == 'dev'
+Requires-Dist: pytest>=8.2.0; extra == 'dev'
+Requires-Dist: ruff>=0.4.0; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5.0; extra == 'docs'
+Requires-Dist: mkdocs>=1.6.0; extra == 'docs'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <img src="docs/weaverx-hero.png" alt="WeaveRx — medical AI GitHub issue triage" width="900" />
+</p>
+
+# WeaveRx
+
+**Medical AI GitHub issue triage with auditable drafts, local safeguards, and human-in-the-loop defaults.**
+
+WeaveRx helps maintainers triage issues faster — reproducibility blockers, dataset access, subgroup performance, privacy/DICOM, and clinical validation requests — with **sources** (issue excerpts that grounded the decision) and **safeguard scores** (local heuristics, no extra LLM calls).
+
+Built for medical AI maintainers and research groups who need practical tooling — not a gatekeeper bot.
+
+<p align="center">
+  <a href="https://github.com/FratresMedAI/WeaveRx/actions/workflows/ci.yml"><img src="https://github.com/FratresMedAI/WeaveRx/actions/workflows/ci.yml/badge.svg" alt="CI" /></a>
+  <a href="https://pypi.org/project/weaverx/"><img src="https://img.shields.io/pypi/v/weaverx?label=PyPI" alt="PyPI" /></a>
+  <a href="https://github.com/FratresMedAI/WeaveRx/releases"><img src="https://img.shields.io/github/v/release/FratresMedAI/WeaveRx?label=release" alt="Release" /></a>
+  <img src="https://img.shields.io/badge/python-3.11%20|%203.12-blue" alt="Python" />
+  <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="MIT License" /></a>
+  <a href="https://github.com/FratresMedAI/WeaveRx/stargazers"><img src="https://img.shields.io/github/stars/FratresMedAI/WeaveRx?style=social" alt="GitHub stars" /></a>
+  <a href="https://fratresmedai.github.io/WeaveRx/"><img src="https://img.shields.io/badge/docs-GitHub%20Pages-blue" alt="Docs" /></a>
+</p>
+
+**Contents:** [Features](#features) · [Quickstart](#quickstart) · [See it in action](#see-it-in-action) · [Installation](#installation) · [Safety](#safety-and-responsible-use) · [Reference](#reference) · [Docs](https://fratresmedai.github.io/WeaveRx/)
+
+---
+
+## Features
+
+- **Domain-tuned** — eight medical AI categories (reproducibility, DICOM/privacy, clinical validation, subgroup performance, and more)
+- **Safety by default** — dry-run unless you explicitly post; `--confirm` required for GitHub writes; local safeguard heuristics on every draft
+- **Auditable** — `sources` cite issue excerpts; `safeguard` scores are computed locally with no LLM on that path
+- **Your LLM stack** — Grok, Anthropic, or OpenAI-compatible endpoints via [LiteLLM](https://github.com/BerriAI/litellm); mock mode for offline CI and demos
+
+Full docs: [`docs/index.md`](docs/index.md) · Configuration: [`docs/configuration.md`](docs/configuration.md)
+
+---
+
+## Quickstart
+
+Requires Python 3.11+. Environment variables: [`docs/configuration.md`](docs/configuration.md).
+
+### 1. Mock (zero API keys)
+
+```bash
+weaverx triage --repo Project-MONAI/MONAI --issue 42 --mock
+```
+
+### 2. Dry-run (real GitHub, offline LLM)
+
+```bash
+weaverx triage --repo Project-MONAI/MONAI --issue 1234 --mock-llm --dry-run
+```
+
+### 3. Real LLM (Grok example)
+
+```bash
+export XAI_API_KEY=xai-...
+weaverx triage --repo Project-MONAI/MONAI --issue 1234 --dry-run --json
+```
+
+More providers: [LLM providers](#llm-providers) · [`examples/llm_provider_examples.md`](examples/llm_provider_examples.md)
+
+### 4. JSON for automation
+
+```bash
+weaverx triage --repo Project-MONAI/MONAI --issue 42 --mock --json
+```
+
+---
+
+## See it in action
+
+**Command (no API keys):** `weaverx triage --repo Project-MONAI/MONAI --issue 42 --mock`
+
+### Clean triage
+
+<p align="center">
+  <img src="docs/screenshots/triage-clean.png"
+       alt="WeaveRx CLI: category, status, sources, clean safeguard, draft panel"
+       width="820" />
+</p>
+
+Typical output: reproducibility category, `ready_for_review` status, source excerpts,
+`CLEAN` safeguard (0.0/10), and a postable draft in the green panel.
+
+<details>
+<summary>Text capture (accessibility / no images)</summary>
+
+See [`examples/captures/triage-clean.txt`](examples/captures/triage-clean.txt).
+
+</details>
+
+### Safeguard warning
+
+Safeguard checks are **advisory** — they flag drafts for review; they never auto-block posting.
+
+<p align="center">
+  <img src="docs/screenshots/safeguard-warning.png"
+       alt="WeaveRx CLI: HIGH RISK safeguard flags and red draft panel border"
+       width="820" />
+</p>
+
+When heuristics fire (e.g. credential-like patterns, heavy repetition), the table shows
+**Safeguard flags**, status escalates to `HIGH RISK` / `REVIEW RECOMMENDED`, and the draft
+panel border turns yellow or red.
+
+<details>
+<summary>Text capture + JSON</summary>
+
+- Text: [`examples/captures/safeguard-warning.txt`](examples/captures/safeguard-warning.txt)
+- JSON: [`examples/sample_safeguard_warning.json`](examples/sample_safeguard_warning.json)
+
+</details>
+
+**Try it:** `weaverx triage --repo Project-MONAI/MONAI --issue 42 --mock -v`
+
+<details>
+<summary>Example JSON output</summary>
+
+```json
+{
+  "repo": "Project-MONAI/MONAI",
+  "status": "ready_for_review",
+  "issue": { "number": 42, "title": "Unable to reproduce nnU-Net training results on BraTS subset" },
+  "analysis": { "category": "reproducibility-environment", "priority": "high" },
+  "sources": [{ "type": "issue_body", "snippet": "...", "reason": "..." }],
+  "draft_response": "Hi @researcher-dev — thank you for documenting this carefully...",
+  "safeguard": { "score": 0.0, "status": "clean", "triggered": [] },
+  "llm": { "provider": "mock", "model": "mock" },
+  "dry_run": true
+}
+```
+
+Full JSON: [`examples/sample_triage_output.json`](examples/sample_triage_output.json)
+
+</details>
+
+---
+
+## Installation
+
+```bash
+pip install weaverx
+```
+
+Or install from GitHub:
+
+```bash
+pip install git+https://github.com/FratresMedAI/WeaveRx.git@v0.1.1
+```
+
+Contributors / local dev:
+
+```bash
+git clone https://github.com/FratresMedAI/WeaveRx.git
+cd WeaveRx
+pip install -e ".[dev]"
+```
+
+Documentation: [fratresmedai.github.io/WeaveRx](https://fratresmedai.github.io/WeaveRx/)
+
+---
+
+## Safety and responsible use
+
+WeaveRx is **human-in-the-loop** by design. Drafts require maintainer review before posting.
+
+1. **Never paste patient data in GitHub issues.** Privacy flags are heuristic, not guaranteed.
+2. **Default is read-only.** Writes need `--post-comment`/`--apply-labels` **and** `--confirm`.
+3. **Use `--dry-run`** on repos you don't maintain.
+4. **Use `--mock`** in CI and local demos without tokens.
+5. **Review safeguard warnings** before posting flagged drafts.
+
+**Not for clinical use** — maintainer support tooling only, not medical advice or a clinical decision system. Does not replace IRB, legal, or compliance review.
+
+Read more: [`ETHICS.md`](ETHICS.md) · [`SECURITY.md`](SECURITY.md) · [`SUPPORT.md`](SUPPORT.md)
+
+---
+
+## GitHub Action
+
+Dry-run triage when issues are opened:
+
+```yaml
+- uses: FratresMedAI/WeaveRx@v0.1.1
+  with:
+    repo: ${{ github.repository }}
+    issue_number: ${{ github.event.issue.number }}
+    dry_run: "true"
+    llm_provider: "grok"
+  env:
+    XAI_API_KEY: ${{ secrets.XAI_API_KEY }}
+```
+
+<p align="center">
+  <img src="docs/screenshots/github-action-dry-run.png"
+       alt="GitHub Actions log showing WeaveRx dry-run triage output"
+       width="820" />
+</p>
+
+See [`action.yml`](action.yml) and [`.github/workflows/triage-on-issue.yml`](.github/workflows/triage-on-issue.yml).
+
+---
+
+## Reference
+
+<details>
+<summary><strong>LLM providers</strong></summary>
+
+| Provider | CLI | API key env | Default model |
+|---|---|---|---|
+| Grok | `--llm-provider grok` | `XAI_API_KEY` | `xai/grok-2-latest` |
+| Anthropic | `--llm-provider anthropic` | `ANTHROPIC_API_KEY` | `anthropic/claude-3-5-sonnet-20241022` |
+| OpenAI-compatible | `--llm-provider openai` | `OPENAI_API_KEY` | `openai/gpt-4o` |
+
+Override: `WEAVERX_LLM_MODEL`, `WEAVERX_LLM_PROVIDER`. Details: [`docs/reference/llm-providers.md`](docs/reference/llm-providers.md)
+
+</details>
+
+<details>
+<summary><strong>Medical AI categories</strong></summary>
+
+| Category | What we look for |
+|---|---|
+| **Dataset Access & Licensing** | Download links, usage terms, attribution |
+| **Model Performance (Pathology/Subgroup)** | Accuracy on specific diseases or patient groups |
+| **Reproducibility & Environment** | MONAI/nnU-Net versions, CUDA/PyTorch, can't reproduce results |
+| **Clinical Validation Request** | External validation, reader studies, deployment |
+| **Privacy/Compliance/DICOM** | PHI, de-identification, HIPAA/GDPR, DICOM metadata |
+| **Bug** | Crashes, incorrect outputs |
+| **Feature/Integration Request** | New capabilities, framework hooks |
+| **Documentation** | Missing or unclear tutorials and API docs |
+
+Full table: [`docs/reference/categories.md`](docs/reference/categories.md)
+
+</details>
+
+<details>
+<summary><strong>Draft safeguards</strong></summary>
+
+Local-only checks after every draft — **advisory**, never auto-block posting. See [Safeguard warning](#safeguard-warning) above.
+
+| Score | Status | Meaning |
+|---|---|---|
+| 0.0 – 2.9 | `clean` | No meaningful red flags |
+| 3.0 – 6.9 | `review_recommended` | Skim draft before posting |
+| 7.0 – 10.0 | `high_risk` | Multiple or severe heuristics fired |
+
+Full reference: [`docs/reference/safeguards.md`](docs/reference/safeguards.md)
+
+</details>
+
+<details>
+<summary><strong>CLI reference</strong></summary>
+
+```
+weaverx triage --repo owner/repo [--issue N | --recent N] [options]
+```
+
+Key flags: `--mock`, `--dry-run`, `--json`, `--llm-provider`, `--confirm`, `--post-comment`, `--safeguards`
+
+Full reference: [`docs/reference/cli.md`](docs/reference/cli.md)
+
+</details>
+
+---
+
+## Related projects
+
+- [MONAI](https://github.com/Project-MONAI/MONAI) — open-source medical AI framework
+- [nnU-Net](https://github.com/MIC-DKFZ/nnUNet) — self-configuring segmentation
+- [LiteLLM](https://github.com/BerriAI/litellm) — unified LLM API (used by WeaveRx)
+- [Safire](https://github.com/FratresMedAI/Safire) — related audit tooling from the same org
+
+---
+
+## Citing WeaveRx
+
+If you use WeaveRx in research or evaluations, cite via [`CITATION.cff`](CITATION.cff) (GitHub can generate a BibTeX entry from that file).
+
+---
+
+## Roadmap (near-term)
+
+1. **Embedding-based duplicate detection** — optional `weaverx[embeddings]` extra
+2. **PR triage mode** — `--pr` for pull request review drafts
+3. **Expanded provider presets** — more medical-AI-tuned prompt templates
+
+See [CHANGELOG.md](CHANGELOG.md) for release history.
+
+---
+
+## Development and contributing
+
+```bash
+pip install -e ".[dev]"
+pre-commit install
+ruff check .
+mypy src/weaverx
+pytest --cov=weaverx
+```
+
+[`CONTRIBUTING.md`](CONTRIBUTING.md) · [`CODE_OF_CONDUCT.md`](CODE_OF_CONDUCT.md) · [docs/releasing.md](docs/releasing.md)
+
+---
+
+## License
+
+MIT — see [`LICENSE`](LICENSE).