Metadata-Version: 2.4
Name: bamread
Version: 0.0.20
Summary: Read bam files quickly into dataframes in Python
Author-email: Endre Bakken Stovner <endbak@pm.me>
License: MIT
Project-URL: Homepage, http://github.com/pyranges/bamread
Keywords: bioinformatics,bam,pysam
Classifier: Programming Language :: Python :: 3
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Other Environment
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Topic :: Scientific/Engineering
Description-Content-Type: text/markdown
Requires-Dist: scipy
Requires-Dist: numpy
Requires-Dist: natsort
Requires-Dist: pysam
Requires-Dist: pandas
Provides-Extra: dev
Requires-Dist: black; extra == "dev"
Requires-Dist: bumpver; extra == "dev"
Requires-Dist: isort; extra == "dev"
Requires-Dist: pip-tools; extra == "dev"
Requires-Dist: pytest; extra == "dev"

# bamread

Read bam files quickly into dataframes in Python

## Development

### Development

See [How to Publish an Open-Source Python Package to PyPI](https://realpython.com/pypi-publish-python-package/)

Install

```bash
pip install -e .  # -e flag means editing affects the installed package
```

Create sdist and wheel (requires [build](https://pypa-build.readthedocs.io/en/stable/))

```bash
python -m build
```

Check whether the package archives look fine:

```bash
twine check dist/*
```

Upload to PyPI test server

```bash
twine upload -r testpypi dist/*
```

Chek that the package can be installed from the test server

```bash
python -m pip install -i https://test.pypi.org/simple bamread
python -c "import bamread; print(bamread.read_bam('Some.bam'))"
```

Upload to pypi

```bash
twine upload -r testpypi dist/*
```

# Run github actions locally

See [act](https://github.com/nektos/act)

```bash
act -l # list available jobs
act -j <job> # run a job
act pull_request # run jobs triggered upon pull_request
```
