From 12fa00ed09fb0c3bf5acc18ed4185800d3a52d9b Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Wed, 9 Aug 2023 16:28:32 +0200 Subject: [PATCH] Upgrade to version 4.0.3 --- docs/conf.py | 2 +- docs/index.rst | 19 ++----------------- docs/releases/4_0.rst | 8 ++++++++ setup.py | 2 +- 4 files changed, 12 insertions(+), 19 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index b456f130..5656c04d 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 = '4.0.2' +release = '4.0.3' # The language for content autogenerated by Sphinx. Refer to documentation diff --git a/docs/index.rst b/docs/index.rst index 072544ce..55c0eb49 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -56,23 +56,8 @@ New in Release |release| This is a bugfix release. It fixes the following problem(s): -- Arriba annotated fusion sequences may contain characters that aren't - supported. This update skips such sequences. -- The ``--aggregate-report-evaluation`` parameter in the standalone ``pvacseq - generate_protein_fasta`` command was previously set up with - nargs in order to allow specifying multiple values. However, this - conflicts with required positional parameters. The parameter definiton was - updated so that multiple values are now specified as a comma-separated list. -- pVACfuse would previously fail in an odd way when none of the fusions in the - input were processable. This update now exits pVACfuse more gracefully in - this case. -- The reference proteome similarity step would previously fail when an epitope's - full peptide sequence wasn't found in the input fasta. It now skips such - epitopes and marks the Reference Match column as ``Not Run``. -- There was a mismatch in how proximal variants were incorporated into the - n-mer fasta files vs the "master" fasta file which had the potential of - epitopes not being present in the "master" fasta file. This update brings - both file creation steps in sync. +- The fixes in issue in the reference proteome similarity step in pVACseq + where running with non-human data would cause an error. New in Version |version| ------------------------ diff --git a/docs/releases/4_0.rst b/docs/releases/4_0.rst index c24ac67a..f2426c7e 100644 --- a/docs/releases/4_0.rst +++ b/docs/releases/4_0.rst @@ -98,3 +98,11 @@ This is a bugfix release. It fixes the following problem(s): n-mer fasta files vs the "master" fasta file which had the potential of epitopes not being present in the "master" fasta file. This update brings both file creation steps in sync. + +New in Version 4.0.3 +-------------------- + +This is a bugfix release. It fixes the following problem(s): + +- The fixes in issue in the reference proteome similarity step in pVACseq + where running with non-human data would cause an error. diff --git a/setup.py b/setup.py index 2a2efa86..7e0eff6f 100644 --- a/setup.py +++ b/setup.py @@ -51,7 +51,7 @@ setup( name="pvactools", - version="4.0.2", + version="4.0.3", packages=[ "pvactools.tools", "pvactools.tools.pvacbind",