diff --git a/docs/conf.py b/docs/conf.py index 02ca5ead..c674af67 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -70,7 +70,7 @@ # The short X.Y version. version = '4.0' # The full version, including alpha/beta/rc tags. -release = '4.0.7' +release = '4.0.8' # The language for content autogenerated by Sphinx. Refer to documentation diff --git a/docs/index.rst b/docs/index.rst index 1925c64c..17466395 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -56,32 +56,10 @@ New in Release |release| This is a bugfix release. It fixes the following problem(s): -- The multithreading capabilities in pVACtools are not available for Mac OSX. - Attempting to use the -t parameter would result in the forked processes - crashing but the run would still complete successfully leading to results - with incomplete data. This release will result in an error when multithreading is - used under Mac OSX. -- We've observed issues with IEDB's API sometimes returning incorrect or - incomplete data. This results in downstream errors. This release updates the prediction - calling to log such occurrences and to retry the API when they are observed. -- MHCflurry sometimes returns no binding affinity percentile data. This - resulted in errors when parsing such prediction data. This release fixes our - parsing logic to handle this case. -- TSL parsing of the input VCF in pVACseq used to be limited to human data - only. This release adds support for TSL parsing in mouse data. -- When running with the --noncanonical flag, the exons.csv file will contain - exon postions for all possible transcript combinations. However, the transcripts - weren't being taken into account when parsing this file to determine the fusion - positions. This release fixes this issue by looking up the positions for the - specific transcripts of the record currently being parsed. -- When using BLASTp for the reference proteome match step, we applied the word-size - parameter in order to only return perfect matches. However, for short sequences, - word-size must be less than half the query length, or reliable hits can be missed. - This release updates how the word-size parameter is calculated in order to - meet this criteria. -- This release addresses in error in pVACview that would occur in the - Transcripts in Set window when there are - no peptides passing the aggregate inclusion binding threshold. +- pVACbind was not parsing the individual El prediction algorithm scores correctly + resulting in them being missing from the all epitopes file. +- This release fixes some display issues in pVACview. It also implements a + Docker file and bash script for deploying pVACview to GCP. New in Version |version| ------------------------ diff --git a/docs/releases/4_0.rst b/docs/releases/4_0.rst index 4a1e6126..43e071ed 100644 --- a/docs/releases/4_0.rst +++ b/docs/releases/4_0.rst @@ -173,3 +173,13 @@ This is a bugfix release. It fixes the following problem(s): - This release addresses in error in pVACview that would occur in the Transcripts in Set window when there are no peptides passing the aggregate inclusion binding threshold. + +Version 4.0.8 +------------- + +This is a bugfix release. It fixes the following problem(s): + +- pVACbind was not parsing the individual El prediction algorithm scores correctly + resulting in them being missing from the all epitopes file. +- This release fixes some display issues in pVACview. It also implements a + Docker file and bash script for deploying pVACview to GCP. diff --git a/setup.py b/setup.py index a21525d3..77f8d3f8 100644 --- a/setup.py +++ b/setup.py @@ -51,7 +51,7 @@ setup( name="pvactools", - version="4.0.7", + version="4.0.8", packages=[ "pvactools.tools", "pvactools.tools.pvacbind",