Merge pull request #214 from mgalardini/1.3.10

Version bump
mgalardini · Jul 11, 2022 · a97322c · a97322c
2 parents 90f06df + 1573c4a
commit a97322c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,14 @@
 # CHANGELOG
+v1.3.10 (July 2022)
+- Docs: more clarity on effect sizes for LMM
+- Bugfix (similarity): make sure the script actually uses all variants
+- Bugfix (QQ-plot): avoid axis inversion with newer versions of statsmodels (thanks to Julian Libiseller-Egger)
+- Bugfix: use kwargs when invoking functions from scikit-learn
+- Bugfix (annotate hits): avoid crashes when full path to reference genomes contains non-ASCII chars
+- Bugfix: WG models should not be ran with the `--output-patterns` function
+- Bugfix: avoid a crash when saving a WG model with covariates
+- Bugfix: add the "lineage" header when running a whole genome model
+
 v1.3.9 (June 2021)
 - Bugfix: avoid a crash when providing lineages in whole genome mode
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -76,9 +76,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.3.9'
+version = '1.3.10'
 # The full version, including alpha/beta/rc tags.
-release = '1.3.9'
+release = '1.3.10'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/options.rst b/docs/options.rst
@@ -19,10 +19,10 @@ Usage::
                  [--min-af MIN_AF] [--max-af MAX_AF] [--max-missing MAX_MISSING]
                  [--filter-pvalue FILTER_PVALUE] [--lrt-pvalue LRT_PVALUE]
                  [--cor-filter COR_FILTER] [--covariates COVARIATES]
-                 [--use-covariates [USE_COVARIATES [USE_COVARIATES ...]]]
-                 [--print-samples] [--print-filtered]
-                 [--output-patterns OUTPUT_PATTERNS] [--uncompressed] [--cpu CPU]
-                 [--block_size BLOCK_SIZE] [--version]
+                 [--use-covariates [USE_COVARIATES ...]] [--print-samples]
+                 [--print-filtered] [--output-patterns OUTPUT_PATTERNS]
+                 [--uncompressed] [--cpu CPU] [--block_size BLOCK_SIZE]
+                 [--version]
 
    SEER (doi: 10.1038/ncomms12797), reimplemented in python
 
@@ -108,18 +108,18 @@ Usage::
      --covariates COVARIATES
                            User-defined covariates file (tab-delimited, with
                            header, first column contains sample names)
-     --use-covariates [USE_COVARIATES [USE_COVARIATES ...]]
+     --use-covariates [USE_COVARIATES ...]
                            Covariates to use. Format is "2 3q 4" (q for
                            quantitative) [Default: load covariates but don't use
                            them]
 
    Other:
      --print-samples       Print sample lists [Default: hide samples]
-     --print-filtered      Print filtered variants (i.e. fitting errors)
-                           [Default: hide them]
+     --print-filtered      Print filtered variants (i.e. fitting errors) (does
+                           not apply if --wg is used) [Default: hide them]
      --output-patterns OUTPUT_PATTERNS
                            File to print patterns to, useful for finding pvalue
-                           threshold
+                           threshold (not used with --wg)
      --uncompressed        Uncompressed kmers file [Default: gzipped]
      --cpu CPU             Processes [Default: 1]
      --block_size BLOCK_SIZE

diff --git a/pyseer/__init__.py b/pyseer/__init__.py
@@ -2,4 +2,4 @@
 
 '''Python reimplementation of SEER for bacterial GWAS'''
 
-__version__ = '1.3.10-dev'
+__version__ = '1.3.10'