Version bump

mgalardini · Jun 14, 2019 · c5bd77a · c5bd77a
1 parent a52c6dd
commit c5bd77a
Show file tree

Hide file tree

Showing 4 changed files with 16 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,17 @@
 # CHANGELOG
+v1.3.0 (June 2019)
+- Handle missing variants as missing (with new `--max-missing` option to control maximum allowed)
+- Unit testing for enet functionality
+- Added option to perform midpoint rooting on tree used by `phylogeny_distance.py`
+- Updated docs with a new section about the use of unitigs
+- Various bugfixes
+   - Checks on phenotypes file
+   - Improved BWA command and results handling
+   - New optimizer for `fit_null`
+   - Avoid deprecation warnings from pandas
+   - Report to user if multiple chromosome/contigs are found while mapping
+   - Use the correct samples order when using lineages and covariates
+
 v1.2.0 (November 2018)
 - Added elastic net functionality
 - Avoid exiting with error in python 3.7+

diff --git a/pyseer/__init__.py b/pyseer/__init__.py
@@ -2,4 +2,4 @@
 
 '''Python reimplementation of SEER for bacterial GWAS'''
 
-__version__ = '1.2.0'
+__version__ = '1.3.0'
diff --git a/requirements.txt b/requirements.txt
@@ -10,6 +10,6 @@ pytz==2018.5
 scikit-learn==0.20.0
 scipy==1.1.0
 six==1.11.0
-statsmodels==0.9.0
+statsmodels==0.8.0
 tqdm==4.20.0
 pybedtools==0.8.0
diff --git a/setup.py b/setup.py
@@ -66,7 +66,7 @@ def find_version(*file_paths):
     install_requires=['numpy',
                       'scipy',
                       'pandas',
-                      'statsmodels',
+                      'statsmodels<=0.8.0',
                       'scikit-learn',
                       'pysam',
                       'DendroPy',