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galaxy-genome-annotation · Jan 31, 2024 · 55287f0 · 55287f0
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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='''