Merge pull request #148 from mgalardini/1.3.7

Version bump

CHANGELOG.md

@@ -1,4 +1,14 @@
 # CHANGELOG
+v1.3.7 (May 2020)
+- Enhancement: check that provided phenotypes are of numeric type
+- Bugfix: properly report all filtered variants
+- Bugfix: don't crash if regression fails for missing data
+- Bugfix for whole genome regression and lineages
+- Bugfix/docs: properly report that the covariates file should have a header
+- scripts/summarise_annotations.py can work with unadjusted p-values (new option, thanks to Lindsay Clark)
+- scripts/phylogeny_distance.py: no need to reroot twice with updated dendropy
+- CI: transition to GitHub actions
+
 v1.3.6 (May 2020)
 - Bugfix for missing variants in VCF files (now properly handled)
 - Bugfixes for k-mer mapping (lack of annotation, bwa fastmap with many hits

docs/conf.py

@@ -76,9 +76,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.3.6'
+version = '1.3.7'
 # The full version, including alpha/beta/rc tags.
-release = '1.3.6'
+release = '1.3.7'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

pyseer/__init__.py

@@ -2,4 +2,4 @@
 
 '''Python reimplementation of SEER for bacterial GWAS'''
 
-__version__ = '1.3.7-dev'
+__version__ = '1.3.7'

setup.py

@@ -37,7 +37,7 @@ def find_version(*file_paths):
     long_description_content_type='text/markdown',
     url='https://github.com/mgalardini/pyseer',
     author='Marco Galardini and John Lees',
-    author_email='marco@ebi.ac.uk',
+    author_email='galardini.marco@mh-hannover.de',
     license='Apache Software License',
     classifiers=[
         'Development Status :: 4 - Beta',