coala-client 0.1.0__tar.gz

coala_client-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 coala-info
+
+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.

coala_client-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: coala-client
+Version: 0.1.0
+Summary: A simple command line interface for LLM with MCP server and OpenAI-compatible API support
+License: MIT
+License-File: LICENSE
+Author: coala-info
+Requires-Python: >=3.10
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+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: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering
+Requires-Dist: anyio (>=4.0.0)
+Requires-Dist: click (>=8.1.0)
+Requires-Dist: httpx (>=0.27.0)
+Requires-Dist: mcp (>=1.0.0)
+Requires-Dist: openai (>=1.68.0)
+Requires-Dist: pydantic (>=2.0.0)
+Requires-Dist: pydantic-settings (>=2.0.0)
+Requires-Dist: rich (>=13.0.0)
+Project-URL: Documentation, https://github.com/coala-info/coala_client#readme
+Project-URL: Homepage, https://github.com/coala-info/coala_client
+Project-URL: Repository, https://github.com/coala-info/coala_client
+Description-Content-Type: text/markdown
+
+# Coala Client
+
+A simple command line interface for LLM with MCP (Model Context Protocol) server support and OpenAI-compatible API support.
+
+## Features
+
+- **OpenAI-compatible API support**: Works with OpenAI, Google Gemini, Ollama, and any OpenAI-compatible API
+- **MCP Server integration**: Connect to multiple MCP servers for extended tool capabilities
+- **Interactive chat**: Rich terminal UI with streaming responses
+- **Tool calling**: Automatic tool execution with MCP servers
+
+## Installation
+
+```bash
+pip install coala-client
+```
+
+## Quick Start
+
+### 1. Initialize Configuration
+
+```bash
+coala init
+```
+
+This creates a default MCP servers configuration file at `~/.config/coala/mcps/mcp_servers.json`.
+
+### 2. Set API Key
+
+```bash
+# For OpenAI
+export OPENAI_API_KEY=your-openai-api-key
+
+# For Gemini
+export GEMINI_API_KEY=your-gemini-api-key
+
+# Ollama doesn't require an API key (runs locally)
+```
+
+### 3. Start Chatting
+
+```bash
+# Interactive chat with default provider (OpenAI)
+coala
+
+# Use a specific provider
+coala -p gemini
+coala -p ollama
+
+# Use a specific model
+coala -p openai -m gpt-4-turbo
+
+# Single prompt
+coala ask "What is the capital of France?"
+
+# Disable MCP servers
+coala --no-mcp
+```
+
+## Configuration
+
+### Environment Variables
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `PROVIDER` | Default LLM provider | `openai` |
+| `OPENAI_API_KEY` | OpenAI API key | - |
+| `OPENAI_BASE_URL` | OpenAI base URL | `https://api.openai.com/v1` |
+| `OPENAI_MODEL` | OpenAI model | `gpt-4o` |
+| `GEMINI_API_KEY` | Gemini API key | - |
+| `GEMINI_BASE_URL` | Gemini base URL | `https://generativelanguage.googleapis.com/v1beta/openai` |
+| `GEMINI_MODEL` | Gemini model | `gemini-2.5-flash-lite` |
+| `OLLAMA_BASE_URL` | Ollama base URL | `http://localhost:11434/v1` |
+| `OLLAMA_MODEL` | Ollama model | `qwen3` |
+| `SYSTEM_PROMPT` | System prompt | `You are a helpful assistant.` |
+| `MAX_TOKENS` | Max tokens in response | `4096` |
+| `TEMPERATURE` | Temperature | `0.7` |
+| `MCP_CONFIG_FILE` | MCP config file path | `~/.config/coala/mcps/mcp_servers.json` |
+
+### MCP Servers Configuration
+
+Edit `~/.config/coala/mcps/mcp_servers.json`:
+
+```json
+{
+  "mcpServers": {
+    "filesystem": {
+      "command": "npx",
+      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/allowed/dir"],
+      "env": {}
+    },
+    "github": {
+      "command": "npx",
+      "args": ["-y", "@modelcontextprotocol/server-github"],
+      "env": {
+        "GITHUB_PERSONAL_ACCESS_TOKEN": "your-token"
+      }
+    }
+  }
+}
+```
+
+### Environment Variables for MCP Servers
+
+You can set environment variables that will be available to all MCP servers by editing `~/.config/coala/env`:
+
+```bash
+# Environment variables for MCP servers
+# Format: KEY=value
+
+# Set default provider (openai, gemini, ollama, custom)
+PROVIDER=gemini
+
+# API keys and model settings
+GEMINI_API_KEY=your-gemini-api-key
+GEMINI_MODEL=gemini-2.5-flash-lite
+```
+
+**Note:** The `PROVIDER` variable in the env file will set the default LLM provider. These variables will be merged with server-specific `env` settings in `mcp_servers.json`. Server-specific environment variables take precedence over the base environment variables.
+
+## CLI Commands
+
+### Interactive Chat
+
+```bash
+coala [OPTIONS]
+coala chat [OPTIONS]
+```
+
+Options:
+- `-p, --provider`: LLM provider (openai/gemini/ollama/custom)
+- `-m, --model`: Model name override
+- `--no-mcp`: Disable MCP servers
+- `--sandbox`: Enable `run_command` tool so the LLM can run basic Linux shell commands (timeout 30s)
+
+### Single Prompt
+
+```bash
+coala ask "Your prompt here"
+coala -c "Your prompt here"
+```
+
+### Chat Commands
+
+During interactive chat:
+- `/help` - Show help
+- `/exit` / `/quit` - Exit chat
+- `/clear` - Clear conversation history
+- `/tools` - List available MCP tools
+- `/servers` - List connected MCP servers
+- `/skill` - List installed skills (from ~/.config/coala/skills/)
+- `/skill <name>` - Load a skill into the chat (adds its instructions to context)
+- `/model` - Show current model info
+- `/switch <provider>` - Switch provider
+
+### Configuration
+
+```bash
+coala init    # Create default config files
+coala config  # Show current configuration
+```
+
+### CWL toolset as MCP server
+
+```bash
+# Import one or more CWL files into a named toolset (copied to ~/.config/coala/mcps/<toolset>/)
+coala mcp-import <TOOLSET> file1.cwl [file2.cwl ...]
+
+# Import a zip of CWL files (extracted to ~/.config/coala/mcps/<toolset>/)
+coala mcp-import <TOOLSET> tools.zip
+
+# SOURCES can also be http(s) URLs to a .cwl file or a .zip
+coala mcp-import <TOOLSET> https://example.com/tools.zip
+coala mcp-import <TOOLSET> https://example.com/tool.cwl
+```
+
+This creates `run_mcp.py` in `~/.config/coala/mcps/<toolset>/`, adds the server to `~/.config/coala/mcps/mcp_servers.json`, and prints the MCP entry. The generated script uses `coala.mcp_api` (stdio transport). Ensure the `coala` package is installed in the environment that runs the MCP server.
+
+**List servers and tools:**
+
+```bash
+# List configured MCP server names
+coala mcp-list
+
+# Show tool schemas (name, description, inputSchema) for a server
+coala mcp-list <SERVER_NAME>
+```
+
+**Call an MCP tool directly:**
+
+```bash
+coala mcp-call <SERVER>.<TOOL> --args '<JSON>'
+# Example:
+coala mcp-call gene-variant.ncbi_datasets_gene --args '{"data": [{"gene": "TP53", "taxon": "human"}]}'
+```
+
+### Skills
+
+```bash
+# Import skills from a GitHub folder (e.g. vercel-labs/agent-skills/skills)
+coala skill https://github.com/vercel-labs/agent-skills/tree/main/skills
+
+# Import from a zip URL or local zip/directory
+coala skill http://localhost:3000/files/bedtools/bedtools-skills.zip
+coala skill ./my-skills.zip
+```
+
+All skills are copied to `~/.config/coala/skills/`. Each source gets its own subfolder (e.g. `skills/bedtools/` for a zip from `.../bedtools/bedtools-skills.zip`, `skills/agent-skills/` for the GitHub repo).
+
+## Examples
+
+### Using with Ollama
+
+```bash
+# Start Ollama server
+ollama serve
+
+# Pull a model
+ollama pull llama3.2
+
+# Chat with Ollama
+coala -p ollama -m llama3.2
+```
+
+### Using with Gemini
+
+```bash
+export GEMINI_API_KEY=your-api-key
+coala -p gemini
+```
+
+### Using Custom OpenAI-compatible API
+
+```bash
+export CUSTOM_API_KEY=your-api-key
+export CUSTOM_BASE_URL=https://your-api.com/v1
+export CUSTOM_MODEL=your-model
+coala -p custom
+```
+
+## Development
+
+```bash
+# Install with dev dependencies
+uv pip install -e ".[dev]"
+
+# Run tests
+pytest
+```
+
+## Publishing to PyPI
+
+The repo includes a GitHub Action (`.github/workflows/release.yml`) that builds with Poetry and publishes to PyPI when a release is published.
+
+1. **Create a GitHub environment** named `pypi` (optional but recommended).
+2. **Configure PyPI** using one of:
+   - **Trusted Publishing (recommended)**: In PyPI → Your projects → coala-client → Publishing, add a new trusted publisher: GitHub, this repo, workflow `publish-pypi.yml`, environment `pypi`. No secrets needed.
+   - **API token**: Generate a token at pypi.org, add it as repository (or `pypi` environment) secret `PYPI_API_TOKEN`.
+3. **Publish**: Create a new release (tag e.g. `v0.1.0`). The workflow runs on release and uploads the built package. You can also run it manually (Actions → Build and publish to PyPI → Run workflow).
+
+## License
+
+MIT
+

coala_client-0.1.0/README.md

@@ -0,0 +1,263 @@
+# Coala Client
+
+A simple command line interface for LLM with MCP (Model Context Protocol) server support and OpenAI-compatible API support.
+
+## Features
+
+- **OpenAI-compatible API support**: Works with OpenAI, Google Gemini, Ollama, and any OpenAI-compatible API
+- **MCP Server integration**: Connect to multiple MCP servers for extended tool capabilities
+- **Interactive chat**: Rich terminal UI with streaming responses
+- **Tool calling**: Automatic tool execution with MCP servers
+
+## Installation
+
+```bash
+pip install coala-client
+```
+
+## Quick Start
+
+### 1. Initialize Configuration
+
+```bash
+coala init
+```
+
+This creates a default MCP servers configuration file at `~/.config/coala/mcps/mcp_servers.json`.
+
+### 2. Set API Key
+
+```bash
+# For OpenAI
+export OPENAI_API_KEY=your-openai-api-key
+
+# For Gemini
+export GEMINI_API_KEY=your-gemini-api-key
+
+# Ollama doesn't require an API key (runs locally)
+```
+
+### 3. Start Chatting
+
+```bash
+# Interactive chat with default provider (OpenAI)
+coala
+
+# Use a specific provider
+coala -p gemini
+coala -p ollama
+
+# Use a specific model
+coala -p openai -m gpt-4-turbo
+
+# Single prompt
+coala ask "What is the capital of France?"
+
+# Disable MCP servers
+coala --no-mcp
+```
+
+## Configuration
+
+### Environment Variables
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `PROVIDER` | Default LLM provider | `openai` |
+| `OPENAI_API_KEY` | OpenAI API key | - |
+| `OPENAI_BASE_URL` | OpenAI base URL | `https://api.openai.com/v1` |
+| `OPENAI_MODEL` | OpenAI model | `gpt-4o` |
+| `GEMINI_API_KEY` | Gemini API key | - |
+| `GEMINI_BASE_URL` | Gemini base URL | `https://generativelanguage.googleapis.com/v1beta/openai` |
+| `GEMINI_MODEL` | Gemini model | `gemini-2.5-flash-lite` |
+| `OLLAMA_BASE_URL` | Ollama base URL | `http://localhost:11434/v1` |
+| `OLLAMA_MODEL` | Ollama model | `qwen3` |
+| `SYSTEM_PROMPT` | System prompt | `You are a helpful assistant.` |
+| `MAX_TOKENS` | Max tokens in response | `4096` |
+| `TEMPERATURE` | Temperature | `0.7` |
+| `MCP_CONFIG_FILE` | MCP config file path | `~/.config/coala/mcps/mcp_servers.json` |
+
+### MCP Servers Configuration
+
+Edit `~/.config/coala/mcps/mcp_servers.json`:
+
+```json
+{
+  "mcpServers": {
+    "filesystem": {
+      "command": "npx",
+      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/allowed/dir"],
+      "env": {}
+    },
+    "github": {
+      "command": "npx",
+      "args": ["-y", "@modelcontextprotocol/server-github"],
+      "env": {
+        "GITHUB_PERSONAL_ACCESS_TOKEN": "your-token"
+      }
+    }
+  }
+}
+```
+
+### Environment Variables for MCP Servers
+
+You can set environment variables that will be available to all MCP servers by editing `~/.config/coala/env`:
+
+```bash
+# Environment variables for MCP servers
+# Format: KEY=value
+
+# Set default provider (openai, gemini, ollama, custom)
+PROVIDER=gemini
+
+# API keys and model settings
+GEMINI_API_KEY=your-gemini-api-key
+GEMINI_MODEL=gemini-2.5-flash-lite
+```
+
+**Note:** The `PROVIDER` variable in the env file will set the default LLM provider. These variables will be merged with server-specific `env` settings in `mcp_servers.json`. Server-specific environment variables take precedence over the base environment variables.
+
+## CLI Commands
+
+### Interactive Chat
+
+```bash
+coala [OPTIONS]
+coala chat [OPTIONS]
+```
+
+Options:
+- `-p, --provider`: LLM provider (openai/gemini/ollama/custom)
+- `-m, --model`: Model name override
+- `--no-mcp`: Disable MCP servers
+- `--sandbox`: Enable `run_command` tool so the LLM can run basic Linux shell commands (timeout 30s)
+
+### Single Prompt
+
+```bash
+coala ask "Your prompt here"
+coala -c "Your prompt here"
+```
+
+### Chat Commands
+
+During interactive chat:
+- `/help` - Show help
+- `/exit` / `/quit` - Exit chat
+- `/clear` - Clear conversation history
+- `/tools` - List available MCP tools
+- `/servers` - List connected MCP servers
+- `/skill` - List installed skills (from ~/.config/coala/skills/)
+- `/skill <name>` - Load a skill into the chat (adds its instructions to context)
+- `/model` - Show current model info
+- `/switch <provider>` - Switch provider
+
+### Configuration
+
+```bash
+coala init    # Create default config files
+coala config  # Show current configuration
+```
+
+### CWL toolset as MCP server
+
+```bash
+# Import one or more CWL files into a named toolset (copied to ~/.config/coala/mcps/<toolset>/)
+coala mcp-import <TOOLSET> file1.cwl [file2.cwl ...]
+
+# Import a zip of CWL files (extracted to ~/.config/coala/mcps/<toolset>/)
+coala mcp-import <TOOLSET> tools.zip
+
+# SOURCES can also be http(s) URLs to a .cwl file or a .zip
+coala mcp-import <TOOLSET> https://example.com/tools.zip
+coala mcp-import <TOOLSET> https://example.com/tool.cwl
+```
+
+This creates `run_mcp.py` in `~/.config/coala/mcps/<toolset>/`, adds the server to `~/.config/coala/mcps/mcp_servers.json`, and prints the MCP entry. The generated script uses `coala.mcp_api` (stdio transport). Ensure the `coala` package is installed in the environment that runs the MCP server.
+
+**List servers and tools:**
+
+```bash
+# List configured MCP server names
+coala mcp-list
+
+# Show tool schemas (name, description, inputSchema) for a server
+coala mcp-list <SERVER_NAME>
+```
+
+**Call an MCP tool directly:**
+
+```bash
+coala mcp-call <SERVER>.<TOOL> --args '<JSON>'
+# Example:
+coala mcp-call gene-variant.ncbi_datasets_gene --args '{"data": [{"gene": "TP53", "taxon": "human"}]}'
+```
+
+### Skills
+
+```bash
+# Import skills from a GitHub folder (e.g. vercel-labs/agent-skills/skills)
+coala skill https://github.com/vercel-labs/agent-skills/tree/main/skills
+
+# Import from a zip URL or local zip/directory
+coala skill http://localhost:3000/files/bedtools/bedtools-skills.zip
+coala skill ./my-skills.zip
+```
+
+All skills are copied to `~/.config/coala/skills/`. Each source gets its own subfolder (e.g. `skills/bedtools/` for a zip from `.../bedtools/bedtools-skills.zip`, `skills/agent-skills/` for the GitHub repo).
+
+## Examples
+
+### Using with Ollama
+
+```bash
+# Start Ollama server
+ollama serve
+
+# Pull a model
+ollama pull llama3.2
+
+# Chat with Ollama
+coala -p ollama -m llama3.2
+```
+
+### Using with Gemini
+
+```bash
+export GEMINI_API_KEY=your-api-key
+coala -p gemini
+```
+
+### Using Custom OpenAI-compatible API
+
+```bash
+export CUSTOM_API_KEY=your-api-key
+export CUSTOM_BASE_URL=https://your-api.com/v1
+export CUSTOM_MODEL=your-model
+coala -p custom
+```
+
+## Development
+
+```bash
+# Install with dev dependencies
+uv pip install -e ".[dev]"
+
+# Run tests
+pytest
+```
+
+## Publishing to PyPI
+
+The repo includes a GitHub Action (`.github/workflows/release.yml`) that builds with Poetry and publishes to PyPI when a release is published.
+
+1. **Create a GitHub environment** named `pypi` (optional but recommended).
+2. **Configure PyPI** using one of:
+   - **Trusted Publishing (recommended)**: In PyPI → Your projects → coala-client → Publishing, add a new trusted publisher: GitHub, this repo, workflow `publish-pypi.yml`, environment `pypi`. No secrets needed.
+   - **API token**: Generate a token at pypi.org, add it as repository (or `pypi` environment) secret `PYPI_API_TOKEN`.
+3. **Publish**: Create a new release (tag e.g. `v0.1.0`). The workflow runs on release and uploads the built package. You can also run it manually (Actions → Build and publish to PyPI → Run workflow).
+
+## License
+
+MIT

coala_client-0.1.0/pyproject.toml

@@ -0,0 +1,44 @@
+[tool.poetry]
+name = "coala-client"
+version = "0.1.0"
+description = "A simple command line interface for LLM with MCP server and OpenAI-compatible API support"
+authors = ["coala-info"]
+license = "MIT"
+readme = "README.md"
+packages = [{ include = "coala_client", from = "src" }]
+homepage = "https://github.com/coala-info/coala_client"
+repository = "https://github.com/coala-info/coala_client"
+documentation = "https://github.com/coala-info/coala_client#readme"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering",
+]
+
+[tool.poetry.dependencies]
+python = ">=3.10"
+openai = ">=1.68.0"
+mcp = ">=1.0.0"
+click = ">=8.1.0"
+rich = ">=13.0.0"
+pydantic = ">=2.0.0"
+pydantic-settings = ">=2.0.0"
+httpx = ">=0.27.0"
+anyio = ">=4.0.0"
+
+[tool.poetry.group.dev.dependencies]
+pytest = ">=8.0.0"
+pytest-asyncio = ">=0.24.0"
+
+[tool.poetry.scripts]
+coala = "coala_client.main:cli"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

coala_client-0.1.0/src/coala_client/__init__.py

@@ -0,0 +1,3 @@
+"""Coala Client - A simple CLI for LLM with MCP server support."""
+
+__version__ = "0.1.0"