incite-app 0.1.0__tar.gz

incite_app-0.1.0/.env.example

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+# Semantic Scholar API Key (optional, for metadata enrichment)
+# Get yours at: https://www.semanticscholar.org/product/api
+SEMANTIC_SCHOLAR_API_KEY=
+
+# Anthropic API Key (optional, for LLM-powered enrichment)
+# Get yours at: https://console.anthropic.com
+ANTHROPIC_API_KEY=
+
+# Voyage AI API Key (optional, only needed for voyage embedder)
+# Get yours at: https://www.voyageai.com
+VOYAGE_API_KEY=
+
+# Email for OpenAlex/Unpaywall polite pool (optional, for metadata lookup)
+# Required for higher rate limits when fetching paper metadata
+OPENALEX_EMAIL=

incite_app-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install ruff
+        run: pip install ruff
+      - name: Lint with ruff
+        run: ruff check src/incite
+      - name: Format check with ruff
+        run: ruff format --check src/incite
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: pip install -e ".[dev,pdf]"
+      - name: Run tests
+        run: pytest

incite_app-0.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  id-token: write
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    environment: pypi
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build dependencies
+        run: pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

incite_app-0.1.0/.gitignore

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+# OAuth / credentials
+client_secret*.json
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Virtual environments
+venv/
+ENV/
+env/
+.venv/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# Testing
+.tox/
+.coverage
+.coverage.*
+htmlcov/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+
+# Data (large files)
+data/raw/
+data/finetuning/
+data/finetuning_v2/
+data/processed/*.faiss
+data/processed/*.db
+data/processed/index/
+data/processed/chunks.jsonl
+data/processed/sentence_chunks.jsonl
+data/processed/chunk_index_*/
+data/processed/sentence-index-*/
+data/processed/aggregation_test_results.json
+data/processed/paragraph_baseline_report.json
+data/processed/test_set_old.jsonl
+data/processed/openalex_to_arxiv.json
+data/processed/openalex_to_arxiv_all.json
+*.npy
+*.pkl
+
+# Models (large files)
+models/
+*.bin
+*.pt
+*.onnx
+
+# Logs
+*.log
+logs/
+
+# Secrets
+.env
+*.key
+secrets.yaml
+
+# Tailwind standalone CLI binary
+cloud/tailwindcss
+
+# Node.js
+node_modules/
+package-lock.json
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Claude/Swarm runtime state
+.claude-flow/
+.swarm/
+conversation.txt
+
+# Google Apps Script
+.clasp.json
+
+# Jupyter
+.ipynb_checkpoints/

incite_app-0.1.0/CONTRIBUTING.md

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+# Contributing to inCite
+
+## 1. Welcome
+
+Thank you for your interest in contributing to inCite, a local-first citation recommendation system. We appreciate contributions of all kinds: bug fixes, new features, documentation improvements, and issue reports.
+
+inCite is licensed under the Apache 2.0 License. By contributing, you agree that your contributions will be licensed under the same terms.
+
+## 2. Development Setup
+
+```bash
+git clone https://github.com/galenphall/incite.git
+cd incite
+pip install -e ".[dev]"
+pytest
+```
+
+This installs inCite in editable mode with all development dependencies and runs the test suite to verify everything works.
+
+## 3. Code Style
+
+- Follow PEP 8 conventions.
+- Use ruff for linting and formatting: `ruff check src/incite && ruff format src/incite`
+- Use type annotations on all public function signatures.
+- Line length: 100 characters.
+- Keep files under 800 lines. Extract utilities when a file grows beyond that.
+- Keep functions under 50 lines. Avoid deep nesting (more than 4 levels).
+- Prefer immutable data structures where practical (`@dataclass(frozen=True)`, `NamedTuple`).
+- No hardcoded values -- use constants or configuration.
+
+## 4. Testing
+
+- Run the full test suite: `pytest`
+- Mark slow tests (embedding, FAISS, API calls) with `@pytest.mark.slow`.
+- When fixing a bug, write a test that reproduces it first, then fix the code.
+- Mock external APIs (Semantic Scholar, OpenAlex, Voyage AI) in tests.
+- Use small fixture data, not full corpus files.
+- For ML/evaluation changes, also run: `incite evaluate --method hybrid`
+
+## 5. How to Add a New Embedder
+
+1. Create a new class extending `BaseEmbedder` (defined in `src/incite/embeddings/base.py`) in a file under `src/incite/embeddings/`.
+2. Implement the required interface:
+   - `embed(texts: list[str]) -> np.ndarray` -- batch embedding
+   - `embed_query(query: str) -> np.ndarray` -- single query embedding
+   - `dimension` property -- returns the embedding dimensionality
+3. Register the embedder in the `EMBEDDERS` dict in `src/incite/retrieval/factory.py`.
+4. Add tests for the new embedder.
+5. Benchmark against existing embedders: `incite evaluate --method hybrid`
+
+## 6. Architecture Overview
+
+The codebase is organized by feature/domain:
+
+| Path | Purpose |
+|------|---------|
+| `src/incite/models.py` | Data models: `Paper`, `Chunk`, `CitationContext`, `RetrievalResult`, `TrainingExample` |
+| `src/incite/interfaces.py` | ABCs and Protocols: `Retriever`, `VectorStore`, `CorpusSource`, `BaseEmbedder` |
+| `src/incite/embeddings/` | Embedder implementations and FAISS vector stores |
+| `src/incite/retrieval/` | Neural, BM25, and hybrid retrievers, plus the factory for creating them |
+| `src/incite/corpus/` | Data ingestion: Zotero reader, PDF extraction, chunking, enrichment |
+| `src/incite/evaluation/` | Metrics (MRR, R@k, C-index), experiment logging, significance tests |
+| `src/incite/cli/` | CLI subcommands (Click-based) |
+| `src/incite/finetuning/` | Training data generation and model training pipeline |
+| `editor-plugins/` | Editor integrations (Obsidian, VS Code, Google Docs, Chrome) |
+| `cloud/` | Cloud service: multi-user web tier and GROBID processing |
+
+## 7. Canonical Embedding Text Format
+
+All code that formats text for embedding **must** use these functions defined in `src/incite/models.py`:
+
+| Function | Purpose |
+|----------|---------|
+| `format_paper_embedding_text()` | Paper-level embedding text |
+| `format_passage_embedding_text()` | Passage-level embedding text |
+| `format_paper_metadata_prefix()` | Chunk context prefix |
+| `format_author_string()` | Consistent author formatting |
+
+Never use raw string concatenation to build embedding text. Never use `[SEP]` as a separator -- always use period-space (`. `) via the canonical functions. Inconsistent formatting causes train/eval distribution shift and degrades retrieval quality.
+
+## 8. Pull Request Process
+
+1. Fork the repository and create a feature branch from `main`.
+2. Write tests for new features and bug fixes.
+3. Ensure `pytest` passes and `ruff check src/incite` reports no issues.
+4. Keep PRs focused: one feature or fix per PR.
+5. Write a clear PR description explaining **why** the change is needed, not just what changed.
+6. If your change affects retrieval quality, include evaluation results (`incite evaluate --method hybrid`).
+
+## 9. Reporting Issues
+
+Use [GitHub Issues](https://github.com/galenphall/incite/issues) to report bugs or request features.
+
+For bug reports, please include:
+
+- What you expected to happen.
+- What actually happened (include error messages or tracebacks).
+- Steps to reproduce the issue.
+- Your Python version and OS.
+
+For performance issues, also include:
+
+- Which embedder you are using (e.g., `minilm-ft`, `granite-ft`).
+- Your corpus size (number of papers).
+- Whether you are using hybrid or neural-only retrieval.
+
+## 10. Code of Conduct
+
+We are committed to providing a welcoming and respectful environment for everyone. Contributors are expected to:
+
+- Be respectful and constructive in all interactions.
+- Accept constructive criticism gracefully.
+- Focus on what is best for the project and its users.
+- Show empathy toward other contributors.
+
+Harassment, trolling, and deliberately exclusionary behavior will not be tolerated. Maintainers reserve the right to remove, edit, or reject contributions that do not align with these standards.

incite_app-0.1.0/LICENSE

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+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
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