Commit de9edc7e authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.16

parent 500335b7

CHANGES.rst

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Changes

=======



v1.16 (2018-02-21)

------------------



* Fix :issue:`291`: When processing paired-end reads with multiple cores, there

  could be errors about incomplete FASTQs although the files are intact.

* Fix :issue:`280`: Quality trimming statistics incorrectly show the same

  values for R1 and R2.



v1.15 (2017-11-23)

------------------
@@ -15,10 +23,9 @@ v1.15 (2017-11-23) 
* The plan is to make multi-core the default (automatically using as many cores as

  are available) in future releases, so please test it and `report an

  issue <https://github.com/marcelm/cutadapt/issues/>`_ if you find problems!

* `Issue #256 <https://github.com/marcelm/cutadapt/issues/256>`_: ``--discard-untrimmed`` did not

* Issue :issue:`256`: ``--discard-untrimmed`` did not

  have an effect on non-anchored linked adapters.

* `Issue #118 <https://github.com/marcelm/cutadapt/issues/118>`_:

  Added support for demultiplexing of paired-end data.

* Issue :issue:`118`: Added support for demultiplexing of paired-end data.





v1.14 (2017-06-16)

LICENSE

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Copyright (c) 2010-2017 Marcel Martin <marcel.martin@scilifelab.se>

Copyright (c) 2010-2018 Marcel Martin <marcel.martin@scilifelab.se>



Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

PKG-INFO

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Metadata-Version: 1.1

Name: cutadapt

Version: 1.15

Version: 1.16

Summary: trim adapters from high-throughput sequencing reads

Home-page: https://cutadapt.readthedocs.io/

Author: Marcel Martin

doc/conf.py

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@@ -30,6 +30,7 @@ sys.path.insert(0, os.path.abspath(os.path.join(os.pardir, 'src'))) 
# ones.

extensions = [

	'sphinx.ext.autodoc',

	'sphinx_issues',

]



# Add any paths that contain templates here, relative to this directory.
@@ -46,7 +47,7 @@ master_doc = 'index' 


# General information about the project.

project = u'cutadapt'

copyright = u'2010-2017, Marcel Martin'

copyright = u'2010-2018, Marcel Martin'



# The version info for the project you're documenting, acts as replacement for

# |version| and |release|, also used in various other places throughout the
@@ -66,6 +67,8 @@ if version.endswith('.dirty') and os.environ.get('READTHEDOCS') == 'True': 
# The full version, including alpha/beta/rc tags.

release = version



issues_uri = 'https://github.com/marcelm/cutadapt/issues/{issue}'



suppress_warnings = ['image.nonlocal_uri']



# The language for content autogenerated by Sphinx. Refer to documentation

doc/develop.rst

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@@ -17,7 +17,7 @@ using a virtualenv. This sequence of commands should work:: 
	git clone https://github.com/marcelm/cutadapt.git  # or clone your own fork

	cd cutadapt

	virtualenv -p python3 venv  # or omit the "-p python3" for Python 2

	venv/bin/pip3 install Cython nose tox  # pip3 becomes just pip for Python 2

	venv/bin/pip3 install Cython pytest nose tox  # pip3 becomes just pip for Python 2

	venv/bin/pip3 install -e .



Then you can run Cutadapt like this (or activate the virtualenv and omit the
@@ -27,7 +27,7 @@ Then you can run Cutadapt like this (or activate the virtualenv and omit the 


The tests can then be run like this::



	venv/bin/nosetests

	venv/bin/pytest



Or with tox (but then you will need to have binaries for all tested Python

versions installed)::
@@ -38,13 +38,14 @@ versions installed):: 
Development installation (without virtualenv)

---------------------------------------------



Alternatively, if you do not want to use virtualenv, you can do the following

from within the cloned repository::

Alternatively, if you do not want to use virtualenv, running the following may

work from within the cloned repository::



	python3 setup.py build_ext -i  # omit the "3" for Python 2

	nosetests

	pytest



This requires Cython and nose to be installed.

This requires Cython and pytest to be installed. Avoid this method and use a

virtualenv instead if you can.





Code style