semvec/pypi-packages huggingface dataset:
scatac-fragment-tools 0.1.4
Tools for working with scATAC-seq fragment files.
Requires Python: >=3.8
Keywords: scATAC-seq, scATAC, fragment files

# scATAC Fragment Tools

[![PyPI](https://img.shields.io/pypi/v/scatac-fragment-tools?color=green)](https://pypi.org/project/scatac-fragment-tools/)
[![Docs](https://img.shields.io/badge/Docs-blue)](https://aertslab.github.io/scatac_fragment_tools/)

Tools for working with scATAC-seq fragment files.

## Installation

```bash

pip install scatac-fragment-tools

```

## Usage

Please visit the [documentation](https://aertslab.github.io/scatac_fragment_tools/)
icis-mcp-server 0.1.1
ICIS MCP server, giving you access to the data
Requires Python: >=3.13.2

# ICIS MCP

## What this is

You can get your AI agent of choice to get ICIS data from your subscription

> This does need your username and password!

Supported requests:

- Commodities (names and id's)
- Prices for a given commodity
- Commentary for given commodity (WIP)

## Install

### Package setup

> TODO

Linux/Mac

```bash
curl -LsSf https://astral.sh/uv/install.sh | sh
```

Windows

```powershell
powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"`
```

```powershell
[Environment]::SetEnvironmentVariable("Path", $env:Path + ";$env:USERPROFILE\.local\bin", [EnvironmentVariableTarget]::User)
```

Setup required binaries: 

`uv pip install playwright`

> Restart everything!

### Config setup

Add to your agent of choices MCP server config

- Claude: https://docs.anthropic.com/en/docs/claude-code/mcp#add-mcp-servers-from-json-configuration

- VS Code: https://code.visualstudio.com/docs/copilot/chat/mcp-servers

Add this config to your config

```json
    "icis-mcp": {
        "command": "uvx",
        "args": [
            "icis-mcp-server"
        ],      
        "env": {
            "ICIS_USERNAME": "user-email",
            "ICIS_PASSWORD": "password"
        }
    },
```

## Debug install

Linux/Mac

`curl -LsSf https://astral.sh/uv/install.sh | sh`

Windows

```powershell
powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"`
```

```powershell
[Environment]::SetEnvironmentVariable("Path", $env:Path + ";$env:USERPROFILE\.local\bin", [EnvironmentVariableTarget]::User)
```

Restart everything!


in the command terminal of your choice

```uv python install```
```uv sync```

## Debug time

`uv run ./main.py --mcp_type=HTTP`

> in Postman use the path: http://127.0.0.1:8000/mcp as the MCP server

## Debug in vs-code + agent mode

```json

            "icis-mcp": {
                "command": "uv",
                "args": [
                    "--directory",
                    "C:\\your-path\\icis-mcp-server\\",
                    "run",
                    "C:\\your-path\\icis-mcp-server\\main.py",
                    "--mcp_type=STDIO",
                ],      
                "env": {
                    "ICIS_USERNAME": "user-email",
                    "ICIS_PASSWORD": "password"
                }
            },
```

> You can add the env values to a .env file