Metadata-Version: 2.1
Name: anospp-analysis
Version: 0.1.1
Summary: ANOSPP data analysis
License: MIT
Author: Alex Makunin
Author-email: am60@sanger.ac.uk
Requires-Python: >=3.10,<4.0
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Dist: BioPython
Requires-Dist: cutadapt
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: seaborn
Description-Content-Type: text/markdown

# anospp-analysis
Python package for ANOSPP data analysis

## Installation

TODO

## Documentation

TODO

## Development

### Setup

Installation is hybrid with conda + poetry:
```
git clone git@github.com:malariagen/anospp-analysis.git
cd anospp-analysis
mamba env create -f environment.yml
conda activate anospp_analysis
poetry install
```

Activate development environment:
```
poetry shell
```

### Usage & testing

The code in this repository can be accessed via wrapper scripts:
```
python anospp_analysis/qc.py \
    --haplotypes test_data/haplotypes.tsv \
    --samples test_data/samples.csv \
    --stats test_data/stats.tsv \
    --outdir test_data/qc
```

Besides, individual functions are available as an API 

TODO testing & CI

### Adding Python deps

Introducing python dependencies should be done via poetry:
```
poetry add package_name
``` 
This should update both `pyproject.toml` and `poetry.lock` files

If the package should be used in development environment only, use
```
poetry add package_name --dev
```

### Adding non-Python deps

Introducing non-python dependencies should be done via conda: edit `environment.yml`, 
then re-create the conda environment and poetry deps:
```
mamba env create -f environment.yml
conda activate anospp_analysis
poetry install
```

Changes in conda environment might also introduce changes to the python installation, 
in which case one should update poetry lock file
```
poetry lock
```

