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Commit db264304 authored by Martin Larralde's avatar Martin Larralde
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Import all public classes to the main `pyfastani` module

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# 🐍⏩🧬 pyFastANI [![Stars](https://img.shields.io/github/stars/althonos/pyfastani.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/pyfastani/stargazers)
# 🐍⏩🧬 PyFastANI [![Stars](https://img.shields.io/github/stars/althonos/pyfastani.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/pyfastani/stargazers)
*[Cython](https://cython.org/) bindings and Python interface to [FastANI](https://github.com/ParBLiSS/FastANI/), a method for fast whole-genome similarity estimation.*
......@@ -29,9 +29,9 @@ language, that provides bindings to FastANI. It directly interacts with the
FastANI internals, which has the following advantages over CLI wrappers:
- **simpler compilation**: FastANI requires several additional libraries,
which make compilation of the original binary non-trivial. In pyFastANI,
which make compilation of the original binary non-trivial. In PyFastANI,
libraries that were needed for threading or I/O are provided as stubs,
and `Boost::math` headers are vendored so you can build the package without
and `Boost::math` headers are vendored so you can build the package without
hassle. Or even better, just install from one of the provided wheels!
- **single dependency**: If your software or your analysis pipeline is
distributed as a Python package, you can add `pyfastani` as a dependency to
......@@ -47,15 +47,15 @@ but it should already pack enough features to be used in a standard pipeline.*
## 🔧 Installing
pyFastANI can be installed directly from [PyPI](https://pypi.org/project/pyfastani/),
PyFastANI can be installed directly from [PyPI](https://pypi.org/project/pyfastani/),
which hosts some pre-built CPython wheels for x86-64 Unix platforms, as well
as the code required to compile from source with Cython:
```console
$ pip install pyfastani
```
In the event you have to compile the package from source, all the required
libraries are vendored in the source distribution, so you'll only need a
In the event you have to compile the package from source, all the required
libraries are vendored in the source distribution, so you'll only need a
C/C++ compiler.
## 💡 Example
......@@ -125,7 +125,7 @@ for hit in hits:
### ⚠️ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the [GitHub issue
tracker](https://github.com/althonos/pyFastANI/issues) if you need to report
tracker](https://github.com/althonos/pyfastani/issues) if you need to report
or ask something. If you are filing in on a bug, please include as much
information as you can about the issue, and try to recreate the same bug
in a simple, easily reproducible situation.
......@@ -133,7 +133,7 @@ in a simple, easily reproducible situation.
### 🏗️ Contributing
Contributions are more than welcome! See
[`CONTRIBUTING.md`](https://github.com/althonos/pyFastANI/blob/master/CONTRIBUTING.md)
[`CONTRIBUTING.md`](https://github.com/althonos/pyfastani/blob/master/CONTRIBUTING.md)
for more details.
......@@ -146,11 +146,9 @@ and is distributed under the terms of the
[Apache License 2.0](https://choosealicense.com/licenses/apache-2.0/),
unless otherwise specified in vendored sources. See `vendor/FastANI/LICENSE`
for more information.
The `cpu_features` code was written by [Guillaume Chatelet](https://github.com/gchatelet)
and is distributed under the terms of the [Apache License 2.0](https://choosealicense.com/licenses/apache-2.0/).
See `vendor/cpu_features/LICENSE` for more information.
The `Boost::math` headers were written by [Boost Libraries](https://www.boost.org/) contributors
and is distributed under the terms of the [Boost Software License](https://choosealicense.com/licenses/bsl-1.0/).
See `vendor/boost-math/LICENSE` for more information.
......
from . import _fastani
from ._fastani import Sketch, Mapper, Hit, MAX_KMER_SIZE
from ._fastani import (
Sketch,
Mapper,
Hit,
Minimizers,
MinimizerInfo,
MinimizerIndex,
Position,
MAX_KMER_SIZE
)
__author__ = "Martin Larralde <martin.larralde@embl.de>"
__license__ = "MIT"
__version__ = "0.3.0"
__all__ = ["Sketch", "Mapper", "Hit", "MAX_KMER_SIZE"]
__doc__ = _fastani.__doc__
__all__ = [
"Sketch",
"Mapper",
"Hit",
"Minimizers",
"MinimizerInfo",
"MinimizerIndex",
"Position",
"MAX_KMER_SIZE"
]
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