diff --git a/CHANGELOG.md b/CHANGELOG.md index c3d080b..c2e8889 100644 --- 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 index 12d2cd3..90834a0 100644 --- 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 index 0f83f2c..5318c28 100644 --- 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 index f4c69e4..02a3d89 100644 --- 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',