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[![Code Coverage][code-coverage-badge]][code-coverage-link]
[![License][license-badge]][license-link]
---
[![Python package][python-package-badge]][python-package-link]
[![PyPI version][pypi-badge]][pypi-link]
[![PyPI download total][pypi-downloads-badge]][pypi-downloads-link]
---
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# pybedlite
See documentation on [pybedlite.readthedocs.org][rtd-link].
```
pip install pybedlite
```
OR
```
conda install -c bioconda pybedlite
```
OR
```
conda create -n pybedlite pybedlite
conda activate pybedlite
```
[rtd-link]: http://pybedlite.readthedocs.org/en/stable
**Requires python 3.8+** (for python < 3.8, please use pybedlite <= 0.0.3)
# Getting Setup for Development Work
Clone the repository to your local machine. Note that pybedlite >= 0.0.4 includes [cgranges][cgranges-link] as a submodule, so you must use the `--recurse-submodules` option:
```
git clone --recurse-submodules https://github.com/fulcrumgenomics/pybedlite.git
```
[Poetry][poetry-link] is used to manage the python development environment.
A simple way to create an environment with the desired version of python and poetry is to use [conda][conda-link]. E.g.:
```bash
conda create -n pybedlite python=3.8 poetry
conda activate pybedlite
poetry install
```
If the methods listed above do not work try the following:
```bash
mamba create -n pybedlite -c conda-forge "python=3.9.16" "poetry=1.6.1"
mamba activate pybedlite
poetry install
```
If, during `poetry install` on Mac OS X errors are encountered running gcc/clang to build `pybedtools` or other packages with native code, try setting the following and re-running `poetry install`:
```bash
export CFLAGS="-stdlib=libc++"
```
[poetry-link]: https://github.com/python-poetry/poetry
[conda-link]: https://docs.conda.io/en/latest/miniconda.html
[cgranges-link]: https://github.com/lh3/cgranges
## Checking the Build
### Run all checks with:
```bash
./ci/check.sh
```
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