semvec/pypi-packages huggingface dataset:
FoxDotLink 0.1.0
Sync mechanism for Ableton Link.
Requires Python: <3.15,>=3.11

# FoxDotLink - Sync mechanism for [Ableton Link](https://www.ableton.com)

## Instalation

``` shell
pip install FoxDotLink
# or
pip install git+https://codeberg.org/FoxDotExtensions/FoxDotLink
```

## Usage

Just import the library and this will connect Ableton Link and change
the bpm to be updated by Ableton Link

``` python
import FoxDotLink

Clock.bpm = var([80,120], 4)
```
lsstdesc-dataregistry 1.5.1
Creation and user API for DESC data registry.
Requires Python: >=3.9
Keywords: desc, python, registry

[![python](https://img.shields.io/badge/Python-3.9-3776AB.svg?style=flat&logo=python&logoColor=white)](https://www.python.org)

<img src="docs/source/_static/DREGS_logo_v2.png" width="300"/>

**The ``dataregistry`` is currently undergoing beta testing, if you would like to participate please get in touch!**

### What is the data registry?

The data registry is a facility to store and share datasets from DESC related projects and pipelines.

The data, once registered, are transferred and stored at a central location at NERSC, which can then be later accessed and queried using the ``dataregistry`` Python package, or the CLI. 

### Documentation

The full documentation for the data registry can be found [here](http://lsstdesc.org/dataregistry).

### Contact

For any further information, please get in touch!

- Admin: Joanne Bogart ([@JoanneBogart](https://www.github.com/JoanneBogart))
- Admin: Stuart McAlpine ([@stuartmcalpine](https://www.github.com/stuartmcalpine))
piqtree 0.8.0
Python bindings for IQTree
Requires Python: >=3.12

# piqtree

[![PyPI Version](https://img.shields.io/pypi/v/piqtree)](https://pypi.org/project/piqtree/)
[![Python Version](https://img.shields.io/pypi/pyversions/piqtree)](https://pypi.org/project/piqtree/)
[![License](https://img.shields.io/github/license/iqtree/piqtree)](https://github.com/iqtree/piqtree/blob/main/LICENSE)

[![CI](https://github.com/iqtree/piqtree/workflows/CI/badge.svg)](https://github.com/iqtree/piqtree/actions/workflows/ci.yml)
[![Coverage Status](https://coveralls.io/repos/github/iqtree/piqtree/badge.svg?branch=main)](https://coveralls.io/github/iqtree/piqtree?branch=main)
[![Documentation Status](https://readthedocs.org/projects/piqtree/badge/?version=latest)](https://piqtree.readthedocs.io/en/latest/?badge=latest)
[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)

`piqtree` (pronounced 'pie-cue-tree') is a library which allows you to use IQ-TREE directly from Python! The interface with Python is through [cogent3](https://cogent3.org) objects.
For usage, please refer to the [documentation](https://piqtree.readthedocs.io/) or the examples below.

If you encounter any problems or have any feature requests feel free to raise an [issue](https://github.com/iqtree/piqtree/issues)!

## Contributing

If you would like to help out by contributing to the piqtree project, please check out our [contributor guide](https://piqtree.readthedocs.io/en/latest/developers/)!

## Examples

### Phylogenetic Reconstruction

```python
from piqtree import build_tree
from cogent3 import load_aligned_seqs # Included with piqtree!

# Load Sequences
aln = load_aligned_seqs("tests/data/example.fasta", moltype="dna")
aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Mouse"])

# Reconstruct a phylogenetic tree with IQ-TREE!
tree = build_tree(aln, "JC", rand_seed=1) # Optionally specify a random seed.

print("Tree topology:", tree) # A cogent3 tree object
print("Log-likelihood:", tree.params["lnL"])
# In a Jupyter notebook, try tree.get_figure() to see a dendrogram
```

> **Note**
> See the [cogent3 docs](https://cogent3.org) for examples on what you can do with cogent3 trees.

### Fit Branch Lengths to Tree Topology

```python
from piqtree import fit_tree
from cogent3 import load_aligned_seqs, make_tree

# Load Sequences
aln = load_aligned_seqs("tests/data/example.fasta", moltype="dna")
aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Mouse"])

# Construct tree topology
tree = make_tree("(Human, Chimpanzee, (Rhesus, Mouse));")

# Fit branch lengths with IQ-TREE!
tree = fit_tree(aln, tree, "JC")

print("Tree with branch lengths:", tree)
print("Log-likelihood:", tree.params["lnL"])
```

## More

For more examples ranging from using ModelFinder and AliSim, to making rapid neighbour-joining trees, or randomly generated trees be sure to check out the [documentation](https://piqtree.readthedocs.io/)!