diff --git a/README.rst b/README.rst index e0c28cb..bc74f9d 100644 --- a/README.rst +++ b/README.rst @@ -85,6 +85,10 @@ Or with the Arrow client: History ------- +- 4.3.0 + - Biopython requires are now more strict, there is a maximum that bcbio_gff supports + - loading GFF3 now has a new flag, --cds_cleaning, to enable more apollo conformant behaviour for multi-exon transcripts + (https://github.com/galaxy-genome-annotation/python-apollo/issues/60, https://github.com/galaxy-genome-annotation/python-apollo/pull/62) - 4.2.13 - Relax biopython requirements - 4.2.12 diff --git a/apollo/annotations/__init__.py b/apollo/annotations/__init__.py index d7e383b..4ac593e 100644 --- a/apollo/annotations/__init__.py +++ b/apollo/annotations/__init__.py @@ -1333,7 +1333,7 @@ def load_gff3(self, organism, gff3, source=None, batch_size=1, :param cds_cleaning: This changes the behaviour of creating GFF3 features in apollo to match more closely to what it expects. Generally you'll probably want this on if you have transcripts with multiple - exons and CDSs, but we don't want to change existing scripts + exons and CDSs, but we don't want to change existing scripts so we are not defaulting this on. :type timing: bool diff --git a/arrow/__init__.py b/arrow/__init__.py index aa33e3a..5ee6158 100644 --- a/arrow/__init__.py +++ b/arrow/__init__.py @@ -1 +1 @@ -__version__ = '4.2.13' +__version__ = '4.3.0' diff --git a/arrow/commands/annotations/load_gff3.py b/arrow/commands/annotations/load_gff3.py index 48f0dcc..949b68e 100644 --- a/arrow/commands/annotations/load_gff3.py +++ b/arrow/commands/annotations/load_gff3.py @@ -35,7 +35,7 @@ ) @click.option( "--cds_cleaning", - help="This changes the behaviour of creating GFF3 features in apollo to match more closely to what it expects. Generally you'll probably want this on if you have transcripts with multiple exons and CDSs, but we don't want to change existing scripts so we are not defaulting this on." + help="This changes the behaviour of creating GFF3 features in apollo to match more closely to what it expects. Generally you'll probably want this on if you have transcripts with multiple exons and CDSs, but we don't want to change existing scripts so we are not defaulting this on.", is_flag=True ) @click.option( diff --git a/setup.py b/setup.py index e4cc11f..0bea9cc 100644 --- a/setup.py +++ b/setup.py @@ -16,11 +16,11 @@ setup( name="apollo", - version='4.2.13', + version='4.3.0', description="Apollo API library", long_description=readme, author="Helena Rasche;Anthony Bretaudeau;Nathan Dunn", - author_email="hxr@hx42.org", + author_email="hexylena@galaxians.org", url='https://github.com/galaxy-genome-annotation/python-apollo', packages=['apollo', 'arrow'] + subpackages, entry_points='''