semvec/pypi-packages huggingface dataset:
wormcat3 0.1.11
WormCat is a tool for annotating and visualizing gene set enrichment data from C. elegans microarray, RNA seq or RNAi screen data.
License: MIT
Requires Python: >=3.13
Keywords: wormcat, gene enrichment, C. elegans

# Analysis of genome-scale data with WormCat identifies novel enriched gene categories in studies from metabolic, tissue-specific, and lifespan-drug data

#### Authors: Amy Holdorf, Daniel Higgins, Anne Hart, Peter Boag, Gregory Pazour, Marian Walhout,and Amy Walker

[GENETICS February 1, 2020 vol. 214 no. 2 279-294;](https://academic.oup.com/genetics/article/214/2/279/5930455)


## Abstract
The emergence of large sets of gene regulation data has revealed the need for improved tools to 1) identify enriched functional gene categories and 2) visualize enrichment patterns across comparative datasets.  Gene ontogeny enrichment (GO) has several limitations for C. elegans analysis. First, around 30% of C. elegans genes are not represented in commonly used search engines. Second, it is difficult to compare multiple GO analyses. To allow visualization and categorization of C. elegans gene sets, we have developed a web-based tool, WormCat.  This tool uses a near complete annotation of C. elegans genes to determine category enrichment and define potential co-regulated or co-functioning gene sets. Then WormCat provides a scaled heat map for visualization along with enrichment statistics and annotation of each input gene. We have developed an annotation strategy based on a nested category approach where each gene is annotated at three levels.  Enrichment scores are generated at each level, allowing both broad (Cat1) and more detailed analysis (Cat2, Cat3).  Using WormCat on published RNA seq datasets from metabolic, tissue-specific or after treatment with lifespan-increasing drugs, we show that WormCat finds major categories appearing in GO searches and also identifies additional enriched categories that are informative for interpreting phenotypes or predicting biological function.  Thus, WormCat is a powerful tool that will allow a sophisticated analysis of gene enrichment in different types of C. elegans datasets.

## Overview Wormcat
Wormcat is also available as an online tool at [www.wormcat.com](http://www.wormcat.com); the online version greatly simplifies the use of Wormcat and is maintained by the [Walker Lab at UMASS Medical School](https://amywalkerlab.com/).

###### The diagram below shows the flow of the Wormcat process:
<img src="http://wormcat.com/static/images/WormCat-Flow.png" alt="Flow" width="700"/>

###### The diagrams below shows sample output from a Wormcat.com run:
<img src="http://wormcat.com/static/images/results_screen.png" alt="Results" width="700"/>


##### Starburst view of categorical data
<img src="http://wormcat.com/static/images/sunburst.png" alt="starburst" width="400"/>
alsa-midi 1.0.4
Python interface for ALSA MIDI sequencer
License: MIT
Keywords: ALSA MIDI sequencer

python-alsa-midi – Python interface to ALSA MIDI Sequencer
==========================================================

This project provides Python interface to ALSA sequencer API.

Features
--------

* Pythonic API to most of the ALSA sequencer functionality

* Access to ALSA sequencer features not available when using other ('portable')
  Python MIDI libraries:

  * Precise timestamping of messages sent and received
  * Port connection management, including connection between ports on different
    clients
  * Access to non-MIDI events, like announcements about new clients, ports and
    connections

* Python 3.9 – 3.14 compatibility

* Both synchronous (blocking) and asynchronous (asyncio) I/O

* Only Python code, no need to compile a binary module. Requires `cffi`_, though.

* `MIDO`_ backend provided

Installation
------------

This package requires ALSA library to be installed (``libasound.so.2`` –
'libasound2' package on Debian-like systems). On a typical Linux system it is
probably already installed for some other audio or MIDI software.

python-alsa-midi package may be installed with pip::

  python3 -m pip install alsa-midi

This should normally install a binary wheel compiled on a compatible system or
pure-python wheel working without compilation.

If no compatible wheel is found build from source package will be triggered,
which will also require ALSA library development files (libasound2-dev).

To force installing from source (and compiling the binary extension) use::

  python3 -m pip install --no-binary=alsa-midi alsa-midi

To force installing from source without compiling the extension::

  PY_ALSA_MIDI_NO_COMPILE=1 python3 -m pip install --no-binary=alsa-midi alsa-midi

Alternatively one can just add the source directory (as checked out from
https://github.com/Jajcus/python-alsa-midi.git) to `$PYTHONPATH` and use the
packages directly, with no compilation.

Usage
-----

Detailed documentation is available at https://python-alsa-midi.readthedocs.io/

Simple example::

  import time
  from alsa_midi import SequencerClient, READ_PORT, NoteOnEvent, NoteOffEvent

  client = SequencerClient("my client")
  port = client.create_port("output", caps=READ_PORT)
  dest_port = client.list_ports(output=True)[0]
  port.connect_to(dest_port)
  event1 = NoteOnEvent(note=60, velocity=64, channel=0)
  client.event_output(event1)
  client.drain_output()
  time.sleep(1)
  event2 = NoteOffEvent(note=60, channel=0)
  client.event_output(event2)
  client.drain_output()

Using with MIDO
---------------

python-alsa-midi can be used as a `MIDO`_ back-end too::

  export MIDO_BACKEND=alsa_midi.MIDO_BACKEND
  mido/examples/midifiles/play_midi_file.py file.mid


.. _cffi: http://cffi.readthedocs.org/
.. _MIDO: https://mido.readthedocs.io/
mcp-obsidian-vault 0.5.0
Claude Desktop MCP server for Obsidian vaults
License: MIT
Requires Python: <4,>=3.10
Keywords: obsidian, mcp, claude, ai, notes

# Obsidian MCP

**Give Claude Desktop access to your Obsidian vault. No plugins required.**

Install the extension, and Claude can read your notes, search them, and create new ones.

## Installation

### Option 1: mcpb bundle (recommended)
Download `obsidian-mcp.mcpb` from [releases](https://github.com/ldraney/obsidian-mcp/releases) and open it with Claude Desktop.

### Option 2: uvx
```bash
uvx mcp-obsidian-vault
```

### Option 3: Manual config
Add to `~/Library/Application Support/Claude/claude_desktop_config.json`:
```json
{
  "mcpServers": {
    "obsidian": {
      "command": "uvx",
      "args": ["mcp-obsidian-vault"]
    }
  }
}
```

## Tools

| Tool | Description |
|------|-------------|
| `list_vaults` | List all Obsidian vaults on your machine |
| `list_notes` | List all notes in a vault |
| `read_note` | Read note contents with parsed YAML frontmatter |
| `write_note` | Create or update a note |
| `search_notes` | Full-text search across notes |
| `open_in_obsidian` | Open a note directly in Obsidian app |

## How It Works

No plugins required — we use Obsidian's native interfaces:

| What | How |
|------|-----|
| Find vaults | Read `obsidian.json` (Obsidian stores vault paths here) |
| Read/write notes | Direct filesystem access (your vault is just markdown files) |
| Frontmatter | YAML parsing with structured JSON output |
| Search | Full-text search |
| Open in app | Native `obsidian://` URI scheme |

## Status

| Feature | Status |
|---------|--------|
| Vault discovery | ✅ |
| Read/write notes | ✅ |
| Search | ✅ |
| Frontmatter parsing | ✅ |
| Open in Obsidian | ✅ |
| PyPI release | ✅ |
| mcpb bundle | ✅ |

## Security

This MCP is designed with minimal access:

- **No network calls** — Nothing leaves your machine
- **No files outside vaults** — Only accesses your Obsidian notes
- **No credentials** — Never touches passwords or tokens
- **Open source** — Audit the code yourself

See [SECURITY.md](SECURITY.md) for full details, or visit the [Security page](https://ldraney.github.io/obsidian-mcp/security.html) on our website.

## Documentation

| Document | What's Inside |
|----------|---------------|
| [CLAUDE.md](CLAUDE.md) | Development approach, current status |
| [SECURITY.md](SECURITY.md) | Security model and what we access |
| [docs/](docs/) | Architecture diagrams, roadmap |

## Contributing

Check the [issues](https://github.com/ldraney/obsidian-mcp/issues) if you want to help.

## License

MIT
SackosArt 0.0.23
SackosArt Software
License: MIT
Requires Python: >=3.12

This Python package contains tools that I am developing/using for manipulating images for my art hobby. In it you will find mathematical tools, filters, etc., that may be of use to you if you are a digital artist for any reason.

As of now there are no plans to create a GUI, but perhaps I will in the futrue, or perhaps someone else will end up creating one using my package ;)

This Package's libraries are free to use for any purpose.

NOTE: Although it is not necessary to write my own methods for handling certain tasks like coordinate system conversions, unit conversions, etc., I do so for the purpose of provding an example (i.e. the real math) of how to actually do it, and to keep my brain refreshed on the topics.

Be your own light to guide yourself out of the darkness! Maybe use the light for a mathematical projection onto the (x,y)-plane :P   AND   then engrave it >:)

Cheers!