deeprefine-cli 0.1.3__tar.gz

deeprefine_cli-0.1.3/LICENSE

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+MIT License
+
+Copyright (c) 2026 HKUST-KnowComp
+
+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.

deeprefine_cli-0.1.3/MANIFEST.in

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+include README.md
+include LICENSE
+include SKILL.md

deeprefine_cli-0.1.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: deeprefine-cli
+Version: 0.1.3
+Summary: CLI and Cursor skill to refine graphify knowledge graphs with DeepRefine
+Author: HKUST-KnowComp
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/HKUST-KnowComp/DeepRefine
+Project-URL: Documentation, https://github.com/HKUST-KnowComp/DeepRefine
+Project-URL: Repository, https://github.com/HKUST-KnowComp/DeepRefine
+Project-URL: Issues, https://github.com/HKUST-KnowComp/DeepRefine/issues
+Keywords: deeprefine,graphify,knowledge-graph,rag,cursor,agent-skill
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: openai>=1.0
+Dynamic: license-file
+
+# DeepRefine-Skill
+
+Cursor skill and CLI to refine **[graphify](https://github.com/safishamsi/graphify)** knowledge graphs with **[DeepRefine](https://github.com/HKUST-KnowComp/DeepRefine)** (`graphify-out/graph.json` + session query history).
+
+This repository is **standalone**. The DeepRefine model code (`autorefiner`, `atlas_rag`) lives in a separate **DeepRefine** checkout.
+
+---
+
+## Repository layout
+
+```
+DeepRefine-Skill/          ← this repo (pip install -e .)
+├── README.md
+├── SKILL.md
+├── pyproject.toml
+├── deeprefine_skill/
+└── scripts/deeprefine.py
+
+DeepRefine/                ← separate clone (training + Reafiner)
+├── autorefiner/
+├── AutoSchemaKG/
+└── ...
+
+your-kb-project/           ← your data (graphify-out/)
+└── graphify-out/graph.json
+```
+
+Recommended clone layout:
+
+```text
+www/code/
+├── DeepRefine/
+└── DeepRefine-Skill/      # sibling → auto-detected if DEEPREFINE_REPO unset
+```
+
+---
+
+## How graphify and DeepRefine fit together
+
+| Stage | Tool | Input | Output |
+|-------|------|-------|--------|
+| Build | **graphify** | Project files | `graphify-out/graph.json`, report, HTML |
+| Query | **graphify** | Questions | `graphify query "..."` |
+| Refine | **DeepRefine** (this repo) | Graph + **query history** | Updated `graph.json`, logs |
+
+DeepRefine does not build the graph; it edits `graph.json` incrementally so later `graphify query` works better.
+
+---
+
+## Setup
+
+### 1. DeepRefine environment (`atlastune`)
+
+Follow [DeepRefine/README](https://github.com/HKUST-KnowComp/DeepRefine) **Environment** to create `atlastune` and install the main repo:
+
+```bash
+conda activate atlastune
+cd /path/to/DeepRefine
+pip install -e .
+```
+
+### 2. Install this CLI
+
+**From PyPI:**
+
+```bash
+conda activate atlastune
+pip install deeprefine-cli
+```
+
+**From source (development):**
+
+```bash
+pip install -e /path/to/DeepRefine-Skill
+```
+
+Verify:
+
+```bash
+deeprefine --help
+```
+
+> `deeprefine refine` still requires a local [DeepRefine](https://github.com/HKUST-KnowComp/DeepRefine) checkout (`autorefiner`, `atlas_rag`) and running vLLM services — see below.
+
+### 3. Point to DeepRefine (if not cloned as sibling)
+
+Only needed when `DeepRefine` is **not** at `../DeepRefine` relative to this repo and not found by walking up from your cwd:
+
+```bash
+export DEEPREFINE_REPO=/path/to/DeepRefine
+```
+
+Add to `~/.bashrc` if you use a fixed path.
+
+### 4. Start vLLM (before `deeprefine refine`)
+
+From the **DeepRefine** repo:
+
+```bash
+conda activate atlastune
+bash /path/to/DeepRefine/scripts/vllm_serve/qwen3-0.6b-emb.sh
+bash /path/to/DeepRefine/scripts/vllm_serve/qwen3-8b-vllm-reafiner.sh
+```
+
+| Variable | Default |
+|----------|---------|
+| `DEEPREFINE_LLM_URL` | `http://127.0.0.1:8134/v1` |
+| `DEEPREFINE_EMBED_URL` | `http://127.0.0.1:8128/v1` |
+| `DEEPREFINE_MODEL` | `HaoyuHuang2/DeepRefine-v1-8B` |
+| `DEEPREFINE_EMBED_MODEL` | `Qwen/Qwen3-Embedding-0.6B` |
+
+### 5. Install Cursor skill (KB project root)
+
+```bash
+cd /path/to/your-kb-project    # must contain or will contain graphify-out/
+deeprefine cursor install
+```
+
+Same pattern as `graphify cursor install`. Use `--user` for all projects.
+
+---
+
+## Workflow with graphify
+
+**One-time**
+
+```bash
+pip install graphifyy
+graphify cursor install          # in KB project
+pip install -e /path/to/DeepRefine-Skill   # in atlastune
+deeprefine cursor install        # in KB project
+```
+
+**Per session** (KB project root)
+
+1. `/graphify .` or `graphify .` → `graphify-out/graph.json`
+2. `graphify query "..."` or `/graphify query "..."`
+3. `deeprefine history add --query "..."`
+4. `/deeprefine` or `deeprefine refine`
+5. Optional: `graphify query "..."` again to verify
+
+```
+project files ──graphify──► graph.json
+                                 │
+                       graphify query
+                                 │
+                 deeprefine history add
+                                 │
+                 deeprefine refine
+                                 │
+                       graphify query
+```
+
+---
+
+## Command cheat sheet (KB project root)
+
+```bash
+deeprefine history add --query "..."
+deeprefine history list --pending
+deeprefine refine
+deeprefine refine --query "..."
+deeprefine index --rebuild
+```
+
+---
+
+## Where to run commands
+
+| Command | Directory |
+|---------|-----------|
+| `pip install -e .../DeepRefine-Skill` | Any |
+| `pip install -e .../DeepRefine` | DeepRefine repo |
+| `graphify` / `deeprefine cursor install` | **KB project root** |
+| `deeprefine refine` | **KB project root** |
+| vLLM serve scripts | **DeepRefine repo** |
+
+Agent instructions: [SKILL.md](./SKILL.md).
+
+---
+
+## Publish to PyPI (maintainers)
+
+```bash
+cd /path/to/DeepRefine-Skill
+python -m pip install --upgrade build twine
+python -m build
+twine check dist/*
+twine upload dist/*    # needs PyPI token: TWINE_USERNAME=__token__ TWINE_PASSWORD=pypi-...
+```
+
+Test install from TestPyPI first (optional):
+
+```bash
+twine upload --repository testpypi dist/*
+pip install -i https://test.pypi.org/simple/ deeprefine-cli
+```

deeprefine_cli-0.1.3/README.md

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+# DeepRefine-Skill
+
+Cursor skill and CLI to refine **[graphify](https://github.com/safishamsi/graphify)** knowledge graphs with **[DeepRefine](https://github.com/HKUST-KnowComp/DeepRefine)** (`graphify-out/graph.json` + session query history).
+
+This repository is **standalone**. The DeepRefine model code (`autorefiner`, `atlas_rag`) lives in a separate **DeepRefine** checkout.
+
+---
+
+## Repository layout
+
+```
+DeepRefine-Skill/          ← this repo (pip install -e .)
+├── README.md
+├── SKILL.md
+├── pyproject.toml
+├── deeprefine_skill/
+└── scripts/deeprefine.py
+
+DeepRefine/                ← separate clone (training + Reafiner)
+├── autorefiner/
+├── AutoSchemaKG/
+└── ...
+
+your-kb-project/           ← your data (graphify-out/)
+└── graphify-out/graph.json
+```
+
+Recommended clone layout:
+
+```text
+www/code/
+├── DeepRefine/
+└── DeepRefine-Skill/      # sibling → auto-detected if DEEPREFINE_REPO unset
+```
+
+---
+
+## How graphify and DeepRefine fit together
+
+| Stage | Tool | Input | Output |
+|-------|------|-------|--------|
+| Build | **graphify** | Project files | `graphify-out/graph.json`, report, HTML |
+| Query | **graphify** | Questions | `graphify query "..."` |
+| Refine | **DeepRefine** (this repo) | Graph + **query history** | Updated `graph.json`, logs |
+
+DeepRefine does not build the graph; it edits `graph.json` incrementally so later `graphify query` works better.
+
+---
+
+## Setup
+
+### 1. DeepRefine environment (`atlastune`)
+
+Follow [DeepRefine/README](https://github.com/HKUST-KnowComp/DeepRefine) **Environment** to create `atlastune` and install the main repo:
+
+```bash
+conda activate atlastune
+cd /path/to/DeepRefine
+pip install -e .
+```
+
+### 2. Install this CLI
+
+**From PyPI:**
+
+```bash
+conda activate atlastune
+pip install deeprefine-cli
+```
+
+**From source (development):**
+
+```bash
+pip install -e /path/to/DeepRefine-Skill
+```
+
+Verify:
+
+```bash
+deeprefine --help
+```
+
+> `deeprefine refine` still requires a local [DeepRefine](https://github.com/HKUST-KnowComp/DeepRefine) checkout (`autorefiner`, `atlas_rag`) and running vLLM services — see below.
+
+### 3. Point to DeepRefine (if not cloned as sibling)
+
+Only needed when `DeepRefine` is **not** at `../DeepRefine` relative to this repo and not found by walking up from your cwd:
+
+```bash
+export DEEPREFINE_REPO=/path/to/DeepRefine
+```
+
+Add to `~/.bashrc` if you use a fixed path.
+
+### 4. Start vLLM (before `deeprefine refine`)
+
+From the **DeepRefine** repo:
+
+```bash
+conda activate atlastune
+bash /path/to/DeepRefine/scripts/vllm_serve/qwen3-0.6b-emb.sh
+bash /path/to/DeepRefine/scripts/vllm_serve/qwen3-8b-vllm-reafiner.sh
+```
+
+| Variable | Default |
+|----------|---------|
+| `DEEPREFINE_LLM_URL` | `http://127.0.0.1:8134/v1` |
+| `DEEPREFINE_EMBED_URL` | `http://127.0.0.1:8128/v1` |
+| `DEEPREFINE_MODEL` | `HaoyuHuang2/DeepRefine-v1-8B` |
+| `DEEPREFINE_EMBED_MODEL` | `Qwen/Qwen3-Embedding-0.6B` |
+
+### 5. Install Cursor skill (KB project root)
+
+```bash
+cd /path/to/your-kb-project    # must contain or will contain graphify-out/
+deeprefine cursor install
+```
+
+Same pattern as `graphify cursor install`. Use `--user` for all projects.
+
+---
+
+## Workflow with graphify
+
+**One-time**
+
+```bash
+pip install graphifyy
+graphify cursor install          # in KB project
+pip install -e /path/to/DeepRefine-Skill   # in atlastune
+deeprefine cursor install        # in KB project
+```
+
+**Per session** (KB project root)
+
+1. `/graphify .` or `graphify .` → `graphify-out/graph.json`
+2. `graphify query "..."` or `/graphify query "..."`
+3. `deeprefine history add --query "..."`
+4. `/deeprefine` or `deeprefine refine`
+5. Optional: `graphify query "..."` again to verify
+
+```
+project files ──graphify──► graph.json
+                                 │
+                       graphify query
+                                 │
+                 deeprefine history add
+                                 │
+                 deeprefine refine
+                                 │
+                       graphify query
+```
+
+---
+
+## Command cheat sheet (KB project root)
+
+```bash
+deeprefine history add --query "..."
+deeprefine history list --pending
+deeprefine refine
+deeprefine refine --query "..."
+deeprefine index --rebuild
+```
+
+---
+
+## Where to run commands
+
+| Command | Directory |
+|---------|-----------|
+| `pip install -e .../DeepRefine-Skill` | Any |
+| `pip install -e .../DeepRefine` | DeepRefine repo |
+| `graphify` / `deeprefine cursor install` | **KB project root** |
+| `deeprefine refine` | **KB project root** |
+| vLLM serve scripts | **DeepRefine repo** |
+
+Agent instructions: [SKILL.md](./SKILL.md).
+
+---
+
+## Publish to PyPI (maintainers)
+
+```bash
+cd /path/to/DeepRefine-Skill
+python -m pip install --upgrade build twine
+python -m build
+twine check dist/*
+twine upload dist/*    # needs PyPI token: TWINE_USERNAME=__token__ TWINE_PASSWORD=pypi-...
+```
+
+Test install from TestPyPI first (optional):
+
+```bash
+twine upload --repository testpypi dist/*
+pip install -i https://test.pypi.org/simple/ deeprefine-cli
+```

deeprefine_cli-0.1.3/SKILL.md

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+---
+name: deeprefine
+description: >-
+  Refines a graphify knowledge graph (graphify-out/graph.json) using DeepRefine
+  Reafiner based on session query history. Use when the user runs /deeprefine,
+  asks to improve the graphify KB after Q&A, or wants to patch graph.json from
+  failed retrieval queries.
+disable-model-invocation: true
+---
+
+# DeepRefine (graphify)
+
+Refine a **[graphify](https://github.com/safishamsi/graphify)** `graph.json` with the DeepRefine agent loop.
+
+## Setup
+
+**DeepRefine-Skill** (CLI + this file) is separate from the **DeepRefine** model repo.
+
+```bash
+# 1) DeepRefine env (atlastune) + main package
+conda activate atlastune
+cd /path/to/DeepRefine && pip install -e .
+
+# 2) This skill CLI
+pip install -e /path/to/DeepRefine-Skill
+
+# 3) Optional if DeepRefine is not ../DeepRefine
+export DEEPREFINE_REPO=/path/to/DeepRefine
+
+# 4) Cursor skill in KB project root
+cd /path/to/your-kb-project
+deeprefine cursor install
+```
+
+Start vLLM from DeepRefine: embedding `8128`, refine model `8134` (see DeepRefine `scripts/vllm_serve/`).
+
+## `/deeprefine`
+
+From the **KB project root** (with `graphify-out/graph.json`):
+
+```bash
+deeprefine history add --query "..."   # after graph Q&A
+deeprefine refine                      # all pending queries
+```
+
+Do not hand-edit `graph.json` for refinement.
+
+## Paths
+
+- History: `graphify-out/.deeprefine/history.jsonl`
+- Log: `graphify-out/.deeprefine/refinement_results_*.jsonl`
+- Backup: `graphify-out/.deeprefine/graph.json.bak`