Metadata-Version: 2.1
Name: pybedlite
Version: 0.1.0
Summary: Python classes for interfacing with bed intervals
Home-page: https://github.com/fulcrumgenomics/pybedlite
License: MIT
Keywords: bioinformatics
Author: Nils Homer
Author-email: nils@fulcrumgenomics.com
Requires-Python: >=3.8.0,<4.0.0
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Documentation
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Provides-Extra: docs
Requires-Dist: attrs (>=23.0.0,<24.0.0)
Requires-Dist: sphinx (>=7.0.0,<8.0.0) ; extra == "docs"
Project-URL: Repository, https://github.com/fulcrumgenomics/pybedlite
Description-Content-Type: text/markdown


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---

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---

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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
```

