tcm-cli 0.1.0__tar.gz

tcm_cli-0.1.0/.github/workflows/python-package.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

tcm_cli-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 TCM-CLI 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.

tcm_cli-0.1.0/PKG-INFO

@@ -0,0 +1,342 @@
+Metadata-Version: 2.4
+Name: tcm-cli
+Version: 0.1.0
+Summary: An autonomous agent for Traditional Chinese Medicine research and discovery
+Project-URL: Homepage, https://github.com/tigerneil/tcm-cli
+Project-URL: Repository, https://github.com/tigerneil/tcm-cli
+Project-URL: Documentation, https://github.com/tigerneil/tcm-cli#readme
+Project-URL: Bug Tracker, https://github.com/tigerneil/tcm-cli/issues
+Author: TCM-CLI Contributors
+License: MIT License
+        
+        Copyright (c) 2026 TCM-CLI 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.
+License-File: LICENSE
+Keywords: ai-agent,bioinformatics,cli,herbs,llm,network-pharmacology,pharmacology,research,tcm,traditional-chinese-medicine
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Requires-Dist: anthropic>=0.40
+Requires-Dist: httpx>=0.27
+Requires-Dist: markdown>=3.5
+Requires-Dist: numpy>=1.24
+Requires-Dist: openai>=1.0
+Requires-Dist: pandas>=2.0
+Requires-Dist: prompt-toolkit>=3.0
+Requires-Dist: python-dotenv>=1.0
+Requires-Dist: rich>=13.0
+Requires-Dist: typer>=0.12
+Provides-Extra: all
+Requires-Dist: rdkit>=2023.03; extra == 'all'
+Requires-Dist: scikit-learn>=1.3; extra == 'all'
+Requires-Dist: scipy>=1.10; extra == 'all'
+Requires-Dist: seaborn>=0.13; extra == 'all'
+Requires-Dist: torch>=2.0; extra == 'all'
+Requires-Dist: transformers>=4.40; extra == 'all'
+Provides-Extra: analysis
+Requires-Dist: scikit-learn>=1.3; extra == 'analysis'
+Requires-Dist: scipy>=1.10; extra == 'analysis'
+Requires-Dist: seaborn>=0.13; extra == 'analysis'
+Provides-Extra: chemistry
+Requires-Dist: rdkit>=2023.03; extra == 'chemistry'
+Provides-Extra: dev
+Requires-Dist: pytest-asyncio>=0.23; extra == 'dev'
+Requires-Dist: pytest-cov>=5.0; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.5; extra == 'dev'
+Provides-Extra: ml
+Requires-Dist: torch>=2.0; extra == 'ml'
+Requires-Dist: transformers>=4.40; extra == 'ml'
+Description-Content-Type: text/markdown
+
+# tcm-cli
+
+An autonomous agent for Traditional Chinese Medicine research and discovery.
+
+Ask questions in natural language. tcm-cli plans the analysis, selects the right tools, executes them, validates results, and returns data-backed conclusions.
+
+## Why tcm?
+
+- **30+ TCM research tools** — Herb lookup, formula analysis, syndrome differentiation, network pharmacology, safety checks, literature search, and more.
+- **Multi-model reasoning** — Powered by leading LLMs (OpenAI GPT-4o, o3, and more). Automatically plans multi-step research workflows, calls tools, and synthesizes findings.
+- **Bilingual** — Supports both Chinese (中文) and English terminology throughout.
+- **10+ database APIs** — PubMed, TCMSP, UniProt, STRING, KEGG, ClinicalTrials.gov, Open Targets — no setup required.
+- **Research UX** — Interactive terminal with slash commands, session export, and clipboard support.
+- **Open source** — MIT licensed.
+
+## Requirements
+
+- Python 3.10+
+- An LLM API key (OpenAI or compatible)
+
+## Installation
+
+### Quick install (script)
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/tigerneil/tcm-cli/main/install.sh | bash
+```
+
+The script detects `pipx`, `uv`, or falls back to `pip --user`, then runs `tcm setup`.
+
+### With pipx (recommended)
+
+```bash
+pipx install tcm-cli
+```
+
+### With pip
+
+```bash
+# Core install
+pip install tcm-cli
+
+# With chemistry support (RDKit)
+pip install "tcm-cli[chemistry]"
+
+# With ML support (PyTorch + Transformers)
+pip install "tcm-cli[ml]"
+
+# With analysis stack (scikit-learn, seaborn, scipy)
+pip install "tcm-cli[analysis]"
+
+# Everything
+pip install "tcm-cli[all]"
+```
+
+### Authentication
+
+```bash
+# Interactive setup wizard (recommended)
+tcm setup
+
+# Or export directly
+export OPENAI_API_KEY="sk-..."
+
+# Non-interactive (CI/scripting)
+tcm setup --api-key YOUR_API_KEY
+```
+
+API keys are stored at `~/.tcm/config.json`. Check key status with:
+
+```bash
+tcm keys
+```
+
+## Getting Started
+
+### Basic usage
+
+```bash
+# Start interactive session
+tcm
+
+# Single query
+tcm "What herbs are used for Spleen Qi deficiency?"
+
+# Use a specific model
+tcm --model gpt-4o "Analyze 四君子汤"
+
+# Validate setup
+tcm doctor
+```
+
+### Interactive commands
+
+Inside `tcm` interactive mode:
+
+- `/help` — command reference + examples
+- `/tools` — list all tools with status
+- `/model` — switch LLM model/provider
+- `/usage` — token and cost tracking
+- `/copy` — copy last answer to clipboard
+- `/export` — export session transcript
+- `/clear` — clear screen
+- `/exit` — exit
+
+### Quick examples
+
+**Herb lookup**
+
+```
+$ tcm "Tell me about 黄芪 (Astragalus) — properties, compounds, and clinical evidence"
+```
+
+**Formula analysis**
+
+```
+$ tcm "Analyze the composition of 四君子汤 using the 君臣佐使 framework"
+```
+
+**Syndrome differentiation**
+
+```
+$ tcm "Patient has fatigue, loose stools, poor appetite, pale tongue. What TCM syndrome?"
+```
+
+**Network pharmacology**
+
+```
+$ tcm "Build a network pharmacology analysis for 补中益气汤 against diabetes targets"
+```
+
+**Safety check**
+
+```
+$ tcm "Check interactions between 人参, 藜芦, and Warfarin"
+```
+
+## Key Features
+
+### 30+ Domain Tools
+
+| Category | Examples |
+| --- | --- |
+| **Herbs** | Lookup, property classification, meridian search, compound listing |
+| **Formulas** | Classical formula search, 君臣佐使 analysis, modifications |
+| **Syndromes** | Pattern differentiation, symptom-to-syndrome mapping, treatment plans |
+| **Compounds** | Active compound search, ADMET prediction, target identification |
+| **Pharmacology** | Network pharmacology, pathway enrichment, herb-target networks |
+| **Interactions** | 十八反/十九畏 checks, herb-drug interactions, formula safety |
+| **Literature** | PubMed search, systematic review finder, CNKI integration |
+| **Meridians** | Channel lookup, Five Element associations, meridian-herb mapping |
+| **Safety** | Toxicity profiling, pregnancy safety, dosage validation |
+| **Modern** | Clinical trial search, ICD-10 mapping, evidence summaries |
+| **Data APIs** | TCMSP, UniProt, STRING, KEGG, ClinicalTrials.gov, Open Targets |
+| **Code** | Python sandbox for custom analysis (experimental) |
+
+List all tools and their status:
+
+```bash
+tcm tool list
+```
+
+### Supported Models
+
+| Provider | Model | Context | Notes |
+| --- | --- | --- | --- |
+| OpenAI | `gpt-4o` | 128k | Default — best balance |
+| OpenAI | `gpt-4o-mini` | 128k | Fast and affordable |
+| OpenAI | `o3-mini` | 200k | Reasoning model |
+| OpenAI | `gpt-4.1` | 1M | Latest flagship with 1M context |
+| OpenAI | `gpt-4.1-mini` | 1M | Balanced speed and intelligence |
+| OpenAI | `gpt-4.1-nano` | 1M | Fastest, most cost-effective |
+
+Switch models:
+
+```bash
+tcm model list              # Show all models with pricing
+tcm model set gpt-4o        # Switch to GPT-4o
+tcm model show              # Show current model
+```
+
+### Local Datasets
+
+Without local data, tcm works via database APIs and built-in knowledge. To boost accuracy and offline support, install local datasets:
+
+```bash
+tcm data pull herbs      # Install bundled herb monograph data (instant)
+tcm data pull formulas   # Install bundled classical formula data (instant)
+tcm data pull tcmsp      # TCMSP — herbs, compounds, targets (~50 MB)
+tcm data pull tcmid      # TCMID — herb-compound-disease (~30 MB)
+tcm data pull batman     # BATMAN-TCM bioinformatics data (~100 MB)
+tcm data pull symmap     # SymMap symptom-mapping database (~20 MB)
+tcm data status          # Show all dataset statuses
+```
+
+**Install modes:**
+- `herbs` and `formulas` install instantly from bundled package data.
+- Datasets with a direct download URL are fetched automatically with a progress bar and extracted.
+- Datasets that require registration (tcmsp, tcmid, batman, symmap) print step-by-step instructions. After downloading manually, register the file:
+
+```bash
+tcm data import tcmsp ~/Downloads/tcmsp.zip
+tcm data import tcmsp ~/Downloads/tcmsp-extracted/   # or a directory
+```
+
+Use `--force` to re-download or reinstall any dataset:
+
+```bash
+tcm data pull herbs --force
+```
+
+## Configuration
+
+```bash
+tcm config show             # Show all settings
+tcm config set key value    # Set a value
+tcm config get key          # Get a single value
+tcm config validate         # Check for issues
+```
+
+Config is stored at `~/.tcm/config.json`.
+
+### Common config keys
+
+```bash
+tcm config set llm.provider openai          # openai or compatible
+tcm config set llm.model gpt-4o
+tcm config set ui.language zh               # en (default) or zh
+```
+
+### Agent profiles
+
+```bash
+tcm config set agent.profile research    # Default — balanced, allows hypotheses
+tcm config set agent.profile clinical    # Strict evidence only, no hypotheses
+tcm config set agent.profile education   # Relaxed, creative responses
+```
+
+## Troubleshooting
+
+| Symptom | Fix |
+| --- | --- |
+| `tcm` fails at startup | `tcm doctor` |
+| Authentication error | `tcm setup` or `tcm keys` |
+| Missing API key | `export OPENAI_API_KEY=...` or `tcm config set llm.openai_api_key ...` |
+| Missing dependency | `pip install "tcm-cli[all]"` |
+| Tool module failed | `tcm tool list` — check for load errors |
+
+## Contributing
+
+```bash
+git clone https://github.com/tigerneil/tcm-cli.git
+cd tcm-cli
+pip install -e ".[dev]"
+tcm setup
+pytest tests/
+```
+
+## License
+
+MIT

tcm_cli-0.1.0/README.md

@@ -0,0 +1,261 @@
+# tcm-cli
+
+An autonomous agent for Traditional Chinese Medicine research and discovery.
+
+Ask questions in natural language. tcm-cli plans the analysis, selects the right tools, executes them, validates results, and returns data-backed conclusions.
+
+## Why tcm?
+
+- **30+ TCM research tools** — Herb lookup, formula analysis, syndrome differentiation, network pharmacology, safety checks, literature search, and more.
+- **Multi-model reasoning** — Powered by leading LLMs (OpenAI GPT-4o, o3, and more). Automatically plans multi-step research workflows, calls tools, and synthesizes findings.
+- **Bilingual** — Supports both Chinese (中文) and English terminology throughout.
+- **10+ database APIs** — PubMed, TCMSP, UniProt, STRING, KEGG, ClinicalTrials.gov, Open Targets — no setup required.
+- **Research UX** — Interactive terminal with slash commands, session export, and clipboard support.
+- **Open source** — MIT licensed.
+
+## Requirements
+
+- Python 3.10+
+- An LLM API key (OpenAI or compatible)
+
+## Installation
+
+### Quick install (script)
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/tigerneil/tcm-cli/main/install.sh | bash
+```
+
+The script detects `pipx`, `uv`, or falls back to `pip --user`, then runs `tcm setup`.
+
+### With pipx (recommended)
+
+```bash
+pipx install tcm-cli
+```
+
+### With pip
+
+```bash
+# Core install
+pip install tcm-cli
+
+# With chemistry support (RDKit)
+pip install "tcm-cli[chemistry]"
+
+# With ML support (PyTorch + Transformers)
+pip install "tcm-cli[ml]"
+
+# With analysis stack (scikit-learn, seaborn, scipy)
+pip install "tcm-cli[analysis]"
+
+# Everything
+pip install "tcm-cli[all]"
+```
+
+### Authentication
+
+```bash
+# Interactive setup wizard (recommended)
+tcm setup
+
+# Or export directly
+export OPENAI_API_KEY="sk-..."
+
+# Non-interactive (CI/scripting)
+tcm setup --api-key YOUR_API_KEY
+```
+
+API keys are stored at `~/.tcm/config.json`. Check key status with:
+
+```bash
+tcm keys
+```
+
+## Getting Started
+
+### Basic usage
+
+```bash
+# Start interactive session
+tcm
+
+# Single query
+tcm "What herbs are used for Spleen Qi deficiency?"
+
+# Use a specific model
+tcm --model gpt-4o "Analyze 四君子汤"
+
+# Validate setup
+tcm doctor
+```
+
+### Interactive commands
+
+Inside `tcm` interactive mode:
+
+- `/help` — command reference + examples
+- `/tools` — list all tools with status
+- `/model` — switch LLM model/provider
+- `/usage` — token and cost tracking
+- `/copy` — copy last answer to clipboard
+- `/export` — export session transcript
+- `/clear` — clear screen
+- `/exit` — exit
+
+### Quick examples
+
+**Herb lookup**
+
+```
+$ tcm "Tell me about 黄芪 (Astragalus) — properties, compounds, and clinical evidence"
+```
+
+**Formula analysis**
+
+```
+$ tcm "Analyze the composition of 四君子汤 using the 君臣佐使 framework"
+```
+
+**Syndrome differentiation**
+
+```
+$ tcm "Patient has fatigue, loose stools, poor appetite, pale tongue. What TCM syndrome?"
+```
+
+**Network pharmacology**
+
+```
+$ tcm "Build a network pharmacology analysis for 补中益气汤 against diabetes targets"
+```
+
+**Safety check**
+
+```
+$ tcm "Check interactions between 人参, 藜芦, and Warfarin"
+```
+
+## Key Features
+
+### 30+ Domain Tools
+
+| Category | Examples |
+| --- | --- |
+| **Herbs** | Lookup, property classification, meridian search, compound listing |
+| **Formulas** | Classical formula search, 君臣佐使 analysis, modifications |
+| **Syndromes** | Pattern differentiation, symptom-to-syndrome mapping, treatment plans |
+| **Compounds** | Active compound search, ADMET prediction, target identification |
+| **Pharmacology** | Network pharmacology, pathway enrichment, herb-target networks |
+| **Interactions** | 十八反/十九畏 checks, herb-drug interactions, formula safety |
+| **Literature** | PubMed search, systematic review finder, CNKI integration |
+| **Meridians** | Channel lookup, Five Element associations, meridian-herb mapping |
+| **Safety** | Toxicity profiling, pregnancy safety, dosage validation |
+| **Modern** | Clinical trial search, ICD-10 mapping, evidence summaries |
+| **Data APIs** | TCMSP, UniProt, STRING, KEGG, ClinicalTrials.gov, Open Targets |
+| **Code** | Python sandbox for custom analysis (experimental) |
+
+List all tools and their status:
+
+```bash
+tcm tool list
+```
+
+### Supported Models
+
+| Provider | Model | Context | Notes |
+| --- | --- | --- | --- |
+| OpenAI | `gpt-4o` | 128k | Default — best balance |
+| OpenAI | `gpt-4o-mini` | 128k | Fast and affordable |
+| OpenAI | `o3-mini` | 200k | Reasoning model |
+| OpenAI | `gpt-4.1` | 1M | Latest flagship with 1M context |
+| OpenAI | `gpt-4.1-mini` | 1M | Balanced speed and intelligence |
+| OpenAI | `gpt-4.1-nano` | 1M | Fastest, most cost-effective |
+
+Switch models:
+
+```bash
+tcm model list              # Show all models with pricing
+tcm model set gpt-4o        # Switch to GPT-4o
+tcm model show              # Show current model
+```
+
+### Local Datasets
+
+Without local data, tcm works via database APIs and built-in knowledge. To boost accuracy and offline support, install local datasets:
+
+```bash
+tcm data pull herbs      # Install bundled herb monograph data (instant)
+tcm data pull formulas   # Install bundled classical formula data (instant)
+tcm data pull tcmsp      # TCMSP — herbs, compounds, targets (~50 MB)
+tcm data pull tcmid      # TCMID — herb-compound-disease (~30 MB)
+tcm data pull batman     # BATMAN-TCM bioinformatics data (~100 MB)
+tcm data pull symmap     # SymMap symptom-mapping database (~20 MB)
+tcm data status          # Show all dataset statuses
+```
+
+**Install modes:**
+- `herbs` and `formulas` install instantly from bundled package data.
+- Datasets with a direct download URL are fetched automatically with a progress bar and extracted.
+- Datasets that require registration (tcmsp, tcmid, batman, symmap) print step-by-step instructions. After downloading manually, register the file:
+
+```bash
+tcm data import tcmsp ~/Downloads/tcmsp.zip
+tcm data import tcmsp ~/Downloads/tcmsp-extracted/   # or a directory
+```
+
+Use `--force` to re-download or reinstall any dataset:
+
+```bash
+tcm data pull herbs --force
+```
+
+## Configuration
+
+```bash
+tcm config show             # Show all settings
+tcm config set key value    # Set a value
+tcm config get key          # Get a single value
+tcm config validate         # Check for issues
+```
+
+Config is stored at `~/.tcm/config.json`.
+
+### Common config keys
+
+```bash
+tcm config set llm.provider openai          # openai or compatible
+tcm config set llm.model gpt-4o
+tcm config set ui.language zh               # en (default) or zh
+```
+
+### Agent profiles
+
+```bash
+tcm config set agent.profile research    # Default — balanced, allows hypotheses
+tcm config set agent.profile clinical    # Strict evidence only, no hypotheses
+tcm config set agent.profile education   # Relaxed, creative responses
+```
+
+## Troubleshooting
+
+| Symptom | Fix |
+| --- | --- |
+| `tcm` fails at startup | `tcm doctor` |
+| Authentication error | `tcm setup` or `tcm keys` |
+| Missing API key | `export OPENAI_API_KEY=...` or `tcm config set llm.openai_api_key ...` |
+| Missing dependency | `pip install "tcm-cli[all]"` |
+| Tool module failed | `tcm tool list` — check for load errors |
+
+## Contributing
+
+```bash
+git clone https://github.com/tigerneil/tcm-cli.git
+cd tcm-cli
+pip install -e ".[dev]"
+tcm setup
+pytest tests/
+```
+
+## License
+
+MIT

tcm_cli-0.1.0/docs/assets/favicon.svg

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