diff --git a/README.md b/README.md index 2639220..e25776f 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,9 @@ [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) -Python library for general bioinformatics, comparative genomics and GCP wrappers +A python library for comparative genomics of microbial "islands" + +# Installation Clone the repository and install with pip: >pip install -e . @@ -13,7 +15,7 @@ Project Organization │ ├── README.md <- The top-level README for developers using this project. │ - ├── docs <- A default Sphinx project; see sphinx-doc.org for details + ├── docs <- *TBD* A default Sphinx project; see sphinx-doc.org for details │ │── bin <- Miscellaneous standalone scripts │ @@ -24,28 +26,28 @@ Project Organization ├── pyIsland <- Source code for use in this project. │   ├── __init__.py <- Makes pyIsland a Python module │ │ - │   ├── data <- Reference data │ │ - │   ├── drivers <- Python wrappers around cmd line programs + │   ├── Drivers <- Python wrappers around cmd line programs │   │ │ ├── GCP <- Convenience fxns for working with GCP │ │ │   ├── Parsers <- Common parsers │ │ - │   ├── FastaIO <- Wrappers around BioPython for fasta manipulation + │   ├── FastaUtils <- Wrappers around BioPython for fasta manipulation │ │ │   ├── Islands <- Extracting genomic regions and annotating them │ │ │   ├── tests <- Unit tests with pytest │ │ │   ├── TBD <- TBD - │ - └── tox.ini <- **TBD** tox file with settings for running tox; see tox.readthedocs.io - -------- -## Testing / code formating +# Usage + +TBD + +# Testing / code formating This project comes with `pytest` and `black`. Run pytest using >pytest pyIsland/tests/ --cov=pyIsland