semvec/pypi-packages huggingface dataset:
pytreefind 0.1.1
A CLI tool to list Python backend files, ignoring caches, envs, and system files
License: MIT
Keywords: cli, tree, python, backend, file-structure

# pytreefind

A minimalist CLI tool that lists Python files in a clean tree structure.

## Quick Start

```bash
# Basic usage (current directory, 3 levels deep)
pytreefind

# Custom directory and depth
pytreefind -L 2 /path/to/project
```

## Features

<details>
<summary>What it does</summary>

- Shows only Python (`.py`) files
- Automatically excludes:
  - `__pycache__`
  - Virtual environments (`env`, `venv`)
  - Version control (`.git`)
  - Node modules (`node_modules`)
  - Test artifacts (`.pytest_cache`)
  - Package metadata (`*.egg-info`)
- Customizable depth level
</details>

<details>
<summary>Requirements</summary>

- Python 3.7+
- `tree` command installed on your system
  - Ubuntu/Debian: `apt install tree`
  - macOS: `brew install tree`
  - Windows: `choco install tree`
</details>

## Installation

```bash
pip install pytreefind
```

<details>
<summary>Development Installation</summary>

```bash
git clone git@github.com:preston-56/pytreefind.git
cd pytreefind
pip install -e .
```
</details>

<details>
<summary>For Maintainers</summary>

```bash
python3 -m build
twine upload dist/*
```
</details>

## License

MIT License - Preston Osoro
pytwobit 0.3.1
A fast reader for local or remote UCSC twobit sequence files.
License: MIT

# pyTwobit

Package for fetching sequence from twobit files from local paths or URLs. 

## Installing

```
pip install pyTwobit
```

## Usage

To fetch sequence for a genomic region create a TwoBit object with either a local file path or url.  Sequence
is fetched with the `fetch` function which takes chromosome name, start, and end coordinates.
The UCSC coordinate convention is used (0 start, half-open).


Local file

```python

from pytwobit import TwoBit

twobit = TwoBit('test.2bit')
seq = twobit.fetch("chr1", 50, 57)  # -> "CTATCTA"


```

Remote file

```python

from pytwobit import TwoBit

twobit = TwoBit("https://igv.org/genomes/data/hg38/hg38.2bit")
seq = twobit.fetch("chr1", 120565294, 120565335)  # -> "TATGAACTTTTGTTCGTTGGTgctcagtcctagaccctttt"

```
terra-mcp 0.1.3
Terra Dashboard MCP - A MCP server for managing your Terra Dashboard.
License: MIT
Requires Python: >=3.12

# Terra MCP Server
MCP Server for V5 API

## Development

1. Install project dependencies using `uv`
```sh
uv sync
```

2. Run dev server
```
mcp dev server.py
```

## Deployment

1. In your Claude Desktop `claude_desktop_config.json` add this
```json
{
  "mcpServers": {
    "Terra MCP Server": {
      "command": "uv",
      "args": [
        "--directory",
        "/ABSOLUTE/PATH/TO/terra-mcp",
        "run",
        "server.py"
      ],
      "env": {
        "TERRA_API_KEY": "your_api_key_here",
        "TERRA_DEV_ID": "your-dev-id-here",
      }
    }
  }
}
```

3. Open Claude Desktop