From 0914f3ca48a538e49bd8b487d30ead7961c06e5d Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 18 Jul 2022 15:22:33 +0200
Subject: [PATCH] Fix badges and text in Sphinx documentation [ci skip]
---
docs/index.rst | 43 ++++++++++++++++++++++++-------------------
docs/install.rst | 28 ++++++++++++++--------------
2 files changed, 38 insertions(+), 33 deletions(-)
diff --git a/docs/index.rst b/docs/index.rst
index 5363d43..de24c40 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -4,15 +4,15 @@ PyFastANI |Stars|
.. |Stars| image:: https://img.shields.io/github/stars/althonos/pyfastani.svg?style=social&maxAge=3600&label=Star
:target: https://github.com/althonos/pyfastani/stargazers
-`Cython <https://cython.org/>`_ *bindings and Python interface to* `trimAl <http://trimal.cgenomics.org/>`_,
-*a tool for automated alignment trimming.*
+`Cython <https://cython.org/>`_ *bindings and Python interface to* `FastANI <ttps://github.com/ParBLiSS/FastANI/>`_,
+*a method for fast whole-genome similarity estimation.*
|Actions| |Coverage| |PyPI| |Bioconda| |AUR| |Wheel| |Versions| |Implementations| |License| |Source| |Mirror| |Issues| |Docs| |Changelog| |Downloads|
.. |Actions| image:: https://img.shields.io/github/workflow/status/althonos/pyfastani/Test/main?logo=github&style=flat-square&maxAge=300
:target: https://github.com/althonos/pyfastani/actions
-.. |Coverage| image:: https://img.shields.io/codecov/c/gh/althonos/pyfastani?style=flat-square&maxAge=600
+.. |Coverage| image:: https://img.shields.io/codecov/c/gh/althonos/pyfastani/branch/main.svg?style=flat-square&maxAge=600
:target: https://codecov.io/gh/althonos/pyfastani/
.. |PyPI| image:: https://img.shields.io/pypi/v/pyfastani.svg?style=flat-square&maxAge=3600
@@ -58,22 +58,27 @@ PyFastANI |Stars|
Overview
--------
-PytrimAl is a Python module that provides bindings to trimAl using
-`Cython <https://cython.org/>`_. It directly interacts with the trimAl
-internals, which has the following advantages:
-
-- **single dependency**: PytrimAl is distributed as a Python package, so you
- can add it as a dependency to your project, and stop worrying about the
- trimAl binary being present on the end-user machine.
-- **no intermediate files**: Everything happens in memory, in a Python object
- you control, so you don't have to invoke the trimAl CLI using a
- sub-process and temporary files. `Alignment` objects can be created
- directly from Python code.
-- **friendly interface**: The different trimming methods are implement as
- Python classes that can be configured independently.
-- **error management**: Errors occuring in trimAl are converted
- transparently into Python exceptions, including an informative
- error message.
+FastANI is a method published in 2018 by Jain *et al.* for high-throughput
+computation of whole-genome `Average Nucleotide Identity (ANI) <https://img.jgi.doe.gov/docs/ANI.pdf>`_.
+It uses `MashMap <https://github.com/marbl/MashMap>`_ to compute orthologous mappings
+without the need for expensive alignments.
+
+``pyfastani`` is a Python module, implemented using the `Cython <https://cython.org/>`_
+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,
+ 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
+ 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
+ your project, and stop worrying about the FastANI binary being present on
+ the end-user machine.
+- **sans I/O**: Everything happens in memory, in Python objects you control,
+ making it easier to pass your sequences to FastANI
+ without needing to write them to a temporary file.
Setup
diff --git a/docs/install.rst b/docs/install.rst
index c7a651d..df5aacb 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -33,20 +33,20 @@ one is available, or from source after compiling the Cython code :
..
.. $ conda install -c bioconda pyfastani
..
-..
-.. Arch User Repository
-.. ^^^^^^^^^^^^^^^^^^^^
-..
-.. A package recipe for Arch Linux can be found in the Arch User Repository
-.. under the name `python-pyfastani <https://aur.archlinux.org/packages/python-pyfastani>`_.
-.. It will always match the latest release from PyPI.
-..
-.. Steps to install on ArchLinux depend on your `AUR helper <https://wiki.archlinux.org/title/AUR_helpers>`_
-.. (``yaourt``, ``aura``, ``yay``, etc.). For ``aura``, you'll need to run:
-..
-.. .. code:: console
-..
-.. $ aura -A python-pyfastani
+
+Arch User Repository
+^^^^^^^^^^^^^^^^^^^^
+
+A package recipe for Arch Linux can be found in the Arch User Repository
+under the name `python-pyfastani <https://aur.archlinux.org/packages/python-pyfastani>`_.
+It will always match the latest release from PyPI.
+
+Steps to install on ArchLinux depend on your `AUR helper <https://wiki.archlinux.org/title/AUR_helpers>`_
+(``yaourt``, ``aura``, ``yay``, etc.). For ``aura``, you'll need to run:
+
+.. code:: console
+
+ $ aura -A python-pyfastani
GitHub + ``pip``
--
GitLab