Metadata-Version: 2.1
Name: mito-utils
Version: 0.0.2
Summary: Utilities for MT-based single cell Lineage Tracing (scLT).
Home-page: https://github.com/andrecossa5/MiTo
Author: Your Name
Author-email: your.email@example.com
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE

# MiTo
This is the first release of `MiTo`: a python package for robust inference of mitochondrial clones and phylogenies.
See also [nf-MiTo](https://github.com/andrecossa5/nf-MiTo), the companion Nextflow pipeline.

## Documentation
A preliminary documentation of key functionalitites and APIs is available at [MiTo Docs](https://andrecossa5.readthedocs.io/en/latest/index.html).

## Installation
1. Install [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) (or conda)
2. Reproduce the environment with all needed dependencies at once, with:

```bash
mamba env create -f ./envs/environment.yml -n MiTo
```

3. Activate the environment, and manually install cassiopeia-lineage (no dependencies: it is all already present in the environment):

```bash
mamba activate MiTo
pip install --no-deps git+https://github.com/YosefLab/Cassiopeia.git@e7606afd10035a75f718ffb988666264e721700e
```

4. Install `MiTo`:

```bash
pip install mito-utils
```

5. Verify successfull installation:

```python
import mito as mt
```

## Releases
See [CHANGELOG.md](CHANGELOG.md) for a history of notable changes.
