mcp-environment-setup

MCP environment setup

Diagnoses and resolves ataraxis-communication-interface MCP server connectivity and environment configuration issues.

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Scope

Covers:

• Verifying the ataraxis-communication-interface MCP server is reachable and functional
• Diagnosing why the axci command is unavailable
• Checking Python version compatibility
• Validating ataraxis-communication-interface package installation and dependencies
• Environment-specific guidance for conda, pip, and uv workflows

Does not cover:

• MCP tool usage for microcontroller hardware interaction (see /microcontroller-setup)
• MCP tool usage for extraction configuration management (see /extraction-configuration)
• MCP tool usage for log data processing (see /log-processing, /log-processing-results)
• ataraxis-communication-interface package development or contribution workflows

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Architecture

ataraxis-communication-interface provides a single MCP server accessed through the axci CLI entry point defined in pyproject.toml:

[project.scripts]
axci = "ataraxis_communication_interface.cli:axci_cli"

Server	CLI command	Purpose
ataraxis-communication-interface	axci mcp	Microcontroller discovery, manifest management, log processing tools

The server accepts a --transport option (defaults to stdio). The communication plugin's plugin.json configures the Claude assistant to launch the server automatically:

{
  "mcpServers": {
    "ataraxis-communication-interface": {
      "command": "axci",
      "args": ["mcp"]
    }
  }
}

The axci command must be on PATH when the Claude assistant starts. This means the Python environment where ataraxis-communication-interface is installed must be active before launching the assistant.

Dual-distribution model

The ataraxis communication plugin's Claude integration is split across two distribution channels:

Component	Distributed via	What it provides
Skills (/microcontroller-setup, etc.)	ataraxis communication plugin	Skill files that guide agents through workflows
MCP server registrations	ataraxis communication plugin	Plugin entries that tell the Claude assistant how to start the server
MCP server code (axci mcp)	ataraxis-communication-interface pip package	The actual CLI command and server implementation

Installing the plugin alone registers the MCP server and makes skills available, but the server will fail to start because the axci CLI command is not present. The pip package must also be installed in the active Python environment for the MCP server to function.

This is the most common cause of MCP failures after initial setup: the plugin is installed but the pip package is not, or the pip package is installed in a different Python environment than the one active when the Claude assistant launches.

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Diagnostic workflow

You MUST follow these steps in order when MCP tools are unavailable or the server fails to start.

Step 1: Check MCP server status

Use the /mcp slash command or inspect available tools to determine whether the ataraxis-communication-interface MCP server is connected. If connected, the issue is not environmental — investigate tool-specific errors instead.

Step 2: Verify command availability

which axci

If the command is not found, proceed to step 3. If found, skip to step 4.

Step 3: Identify the environment type and resolve

Run these commands to determine the user's environment setup:

echo "CONDA_PREFIX: ${CONDA_PREFIX:-not set}"
echo "VIRTUAL_ENV: ${VIRTUAL_ENV:-not set}"
python --version
pip list 2>/dev/null | grep ataraxis-communication-interface

Based on the output, guide the user through the appropriate resolution:

Conda environment (CONDA_PREFIX is set but ataraxis-communication-interface is missing):

The user has an active conda environment but ataraxis-communication-interface is not installed in it. Instruct the user to install ataraxis-communication-interface into the active environment:

pip install ataraxis-communication-interface

Or if using uv within conda:

uv pip install ataraxis-communication-interface

Conda environment not activated (CONDA_PREFIX is not set, but conda is available):

The user needs to activate their environment before launching the Claude assistant. Instruct the user to exit the assistant and run:

mamba activate <environment-name>
claude

You MUST explain that the Claude assistant inherits the shell environment at launch time. Activating a conda environment after the assistant has started does not make the axci command available to MCP server subprocesses.

Virtual environment (VIRTUAL_ENV is set but ataraxis-communication-interface is missing):

pip install ataraxis-communication-interface

No environment active (both CONDA_PREFIX and VIRTUAL_ENV are unset):

The user is running in the system Python. If ataraxis-communication-interface is installed globally, which axci would have succeeded. Instruct the user to either activate their environment or install ataraxis-communication-interface into an accessible location.

Step 4: Verify Python version compatibility

python --version

ataraxis-communication-interface requires Python >=3.12,<3.15. If the Python version does not match, inform the user that their environment has an incompatible Python version, and they need to create or activate an environment with a compatible version.

Step 5: Verify package integrity

axci --help

If the command fails with an import error, a dependency is missing or broken. Run:

pip check ataraxis-communication-interface 2>&1 | head -20

Report any missing or incompatible dependencies to the user.

Step 6: Restart the MCP server

After the user resolves the environment issue, they must restart the Claude assistant for the MCP server to pick up the changes. The ataraxis communication plugin will automatically configure the server on the next session.

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Common issues and resolutions

Symptom	Cause	Resolution
axci: command not found	Environment not activated	Activate conda/venv, then restart the Claude assistant
axci: command not found	ataraxis-communication-interface not installed	pip install ataraxis-communication-interface in the active environment
Import error on axci mcp	Missing or incompatible dependency	pip install --force-reinstall ataraxis-communication-interface
Python version mismatch	Wrong environment activated	Activate environment with Python >=3.12,<3.15
MCP server starts but tools are missing	Outdated ataraxis-communication-interface version	pip install --upgrade ataraxis-communication-interface
MCP server connected but tools fail	Not an environment issue	Check tool-specific error messages
Skills available but MCP tools missing	Plugin installed without pip package	pip install ataraxis-communication-interface in the active environment

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Related skills

Skill	Relationship
/microcontroller-setup	Requires the MCP server for hardware discovery and manifest management
/microcontroller-interface	Requires the MCP server for API verification
/extraction-configuration	Requires the MCP server for config read/write/validate tools
/log-processing	Requires the MCP server for batch log processing tools
/log-processing-results	Requires the MCP server for output verification and event query tools
/log-input-format	References MCP server tools for archive discovery and assembly
/pipeline	Orchestrates all phases that depend on MCP server connectivity

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Proactive behavior

You SHOULD proactively invoke this skill when:

• A session begins and MCP tools from the ataraxis-communication-interface server are expected but unavailable
• Any ataraxis-communication-interface MCP tool call fails with a connection or server error
• The user mentions issues with MCP server connectivity or environment setup

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Verification checklist

MCP Environment Setup:
- [ ] Checked MCP server connection status (ataraxis-communication-interface)
- [ ] Verified 'axci' command is on PATH (which axci)
- [ ] Confirmed Python version matches >=3.12,<3.15
- [ ] Identified environment type (conda, venv, system)
- [ ] Provided environment-specific resolution steps
- [ ] Informed user that the Claude assistant must be restarted after environment changes