Metadata-Version: 2.4
Name: mcp_pyphotomol
Version: 1.0.1
Summary: Analysis of mass photometry data
Project-URL: Documentation, https://github.com/osvalB/mcp_pyphotomol/tree/main/docs
Project-URL: Homepage, https://github.com/osvalB/mcp_pyphotomol
Project-URL: Source, https://github.com/osvalB/mcp_pyphotomol
Author: Osvaldo Burastero
Maintainer-email: Osvaldo Burastero <oburastero@gmail.com>
License: 
        MIT License
        
        Copyright (c) 2026, Osvaldo Burastero
        
        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,
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        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
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.12
Requires-Dist: click
Requires-Dist: fastmcp
Requires-Dist: h5py>=3.15.1
Requires-Dist: kaleido>=1.2.0
Requires-Dist: mcp[cli]>=1.26.0
Requires-Dist: numpy>=2.4.2
Requires-Dist: pandas>=3.0.1
Requires-Dist: plotly>=6.6.0
Requires-Dist: pyphotomol>=0.1.5
Requires-Dist: scipy>=1.17.1
Provides-Extra: dev
Requires-Dist: pre-commit; extra == 'dev'
Requires-Dist: twine>=4.0.2; extra == 'dev'
Provides-Extra: doc
Requires-Dist: docutils!=0.18.*,!=0.19.*,>=0.8; extra == 'doc'
Requires-Dist: ipykernel; extra == 'doc'
Requires-Dist: ipython; extra == 'doc'
Requires-Dist: nbsphinx>=0.9.7; extra == 'doc'
Requires-Dist: numpydoc>=1.6.0; extra == 'doc'
Requires-Dist: pandas; extra == 'doc'
Requires-Dist: setuptools; extra == 'doc'
Requires-Dist: sphinx-copybutton; extra == 'doc'
Requires-Dist: sphinx-design>=0.5.0; extra == 'doc'
Requires-Dist: sphinx-rtd-theme>=3.1.0; extra == 'doc'
Requires-Dist: sphinx>=8.1; extra == 'doc'
Provides-Extra: test
Requires-Dist: coverage; extra == 'test'
Requires-Dist: pytest; extra == 'test'
Requires-Dist: pytest-asyncio; extra == 'test'
Requires-Dist: pytest-cov; extra == 'test'
Description-Content-Type: text/markdown

# This package is being developed and breaking changes may occur at any moment


# mcp_pyphotomol

<!--
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[![Tests][badge-tests]][tests]
[![Documentation][badge-docs]][documentation]

[badge-tests]: https://img.shields.io/github/actions/workflow/status/osvalB/mcp_pyphotomol/test.yaml?branch=main
[badge-docs]: https://img.shields.io/badge/docs-Sphinx-0a507a

This repository contains an MCP server for the analysis of mass photometry data.
It is based on the Python package [pyphotomol](https://github.com/osvalB/pyphotomol).

## Video demonstration

Watch a demonstration of the MCP server in action: [Video Demo](https://drive.google.com/file/d/1NQNWErh1wtd1XFVcd_Lsf-STHb5QfaaC/view?usp=share_link).

## Getting started

Please refer to the [documentation]

## Installation

You need to have Python 3.12 or newer installed on your system.
If you don't have Python installed, we recommend installing [uv][].

### Run from the command line

```bash
uvx mcp_pyphotomol
```

By default, plots and log files are saved in
`~/user_data_mcp_pyphotomol/<YYYY-MM-DD>/`. To choose a different results
folder, set `RESULTS_DIR` before starting the server. This folder is
where results are stored; each server run writes into a date-stamped subfolder.

```bash
RESULTS_DIR=~/Documents/user_data_mcp_pyphotomol uvx mcp_pyphotomol
```

### Configure an MCP client

Add the server to any MCP-compatible client that supports the `mcpServers`
configuration format:

```json
{
  "mcpServers": {
    "mcp_pyphotomol": {
      "command": "uvx",
      "args": ["mcp_pyphotomol"],
      "env": {
        "RESULTS_DIR": "/absolute/path/to/results-folder"
      }
    }
  }
}
```

After updating the configuration, restart the MCP client so it can launch the
server.

#### Claude Desktop

In Claude Desktop, open **Settings**, go to **Developer**, and click
**Edit Config**. Add `mcp_pyphotomol` to `claude_desktop_config.json`:

```json
{
  "mcpServers": {
    "mcp_pyphotomol": {
      "command": "uvx",
      "args": ["mcp_pyphotomol"],
      "env": {
        "RESULTS_DIR": "/Users/your-name/Documents/user_data_mcp_pyphotomol"
      }
    }
  }
}
```

Claude Desktop stores this file at:

- macOS: `~/Library/Application Support/Claude/claude_desktop_config.json`
- Windows: `%APPDATA%\Claude\claude_desktop_config.json`

Save the file, then fully quit and reopen Claude Desktop.

### Local development

To run the server from a local checkout, use an absolute path to the repository:

```json
{
  "mcpServers": {
    "mcp_pyphotomol": {
      "command": "uvx",
      "args": [
        "--refresh",
        "--from",
        "/absolute/path/to/mcp_pyphotomol",
        "mcp_pyphotomol"
      ]
    }
  }
}
```

If you want to reuse the checkout's existing environment, run it through `uv`:

```json
{
  "mcpServers": {
    "mcp_pyphotomol": {
      "command": "uv",
      "args": ["run", "--directory", "/absolute/path/to/mcp_pyphotomol", "mcp_pyphotomol"]
    }
  }
}
```

### Install with pip

```bash
pip install --user mcp_pyphotomol
```

Then run the server with:

```bash
mcp_pyphotomol
```

If your shell cannot find the command, make sure your user-level Python scripts
directory is on `PATH`.

You can use the same output-folder setting when running the installed command:

```bash
RESULTS_DIR=~/Documents/user_data_mcp_pyphotomol mcp_pyphotomol
```

## Contact

If you found a bug, please use the [issue tracker][].

## Citation

If you use `mcp_pyphotomol`, please cite it as:

Burastero, O. (2026). `mcp_pyphotomol` (Version 1.0) [Computer software].
GitHub. https://github.com/osvalB/mcp_pyphotomol

```bibtex
@software{burastero_2026_mcp_pyphotomol,
  author = {Burastero, Osvaldo},
  title = {mcp_pyphotomol},
  version = {1.0},
  year = {2026},
  url = {https://github.com/osvalB/mcp_pyphotomol}
}
```

[uv]: https://github.com/astral-sh/uv
[issue tracker]: https://github.com/osvalB/mcp_pyphotomol/issues
[tests]: https://github.com/osvalB/mcp_pyphotomol/actions/workflows/test.yaml
[documentation]: https://osvalb.github.io/mcp_pyphotomol
[api documentation]: https://github.com/osvalB/mcp_pyphotomol/blob/main/docs/modules.rst
[pypi]: https://pypi.org/project/mcp_pyphotomol
