From efc101fa732262979f38edbadfb3c1060b6e6c2a Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Wed, 19 Jun 2024 08:22:11 -0500
Subject: [PATCH] Upgrade to version 4.2.1

---
 docs/conf.py          |  2 +-
 docs/index.rst        | 22 +++++++++-------------
 docs/releases/4_2.rst | 14 ++++++++++++++
 setup.py              |  2 +-
 4 files changed, 25 insertions(+), 15 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index 99b26f46..f8b603f3 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -70,7 +70,7 @@
 # The short X.Y version.
 version = '4.2'
 # The full version, including alpha/beta/rc tags.
-release = '4.2.0'
+release = '4.2.1'
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation
diff --git a/docs/index.rst b/docs/index.rst
index 6d5dad59..cd83133a 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -51,22 +51,18 @@ Contents
    contact
    mailing_list
 
-New in Version |version|
+New in Release |release|
 ------------------------
 
-This is a minor feature release. It adds the following features:
+This is a bugfix release. It fixes the following problem(s):
 
-- We added two new modules to pVACview: a :ref:`neofox_module` to visualize
-  NeoFox neoantigen annotations and a :ref:`custom_module` to visualize
-  neoantigen data in a TSV file, for example output files from VaxRank,
-  NeoPredPipe, or antigen.garnish.
-- We added a :ref:`vignette <pvacseq_vignette>` to our documentation to provide
-  an extended tutorial on how evaluate neoantigen candidates using pVACview.
-
-This release also fixes the following bug(s):
-
-- When running pVACfuse with Arriba input data, the 3' transcript was not
-  being parsed correctly. This release fixes this issue.
+- When running the reference protome similarity step with a reference protome
+  peptide fasta file and a species other than human or mouse, the run would be aborted
+  with an error that the refseq_protein_prot BLASTp database was incompatible with
+  the species. This error should not be emitted in this circumstance since
+  BLASTp is not run when using a reference proteome peptide fasta file. This
+  release fixes this error and allows users to run the reference proteome
+  similarity step on non-human and non-mouse data with a reference proteome peptide fasta.
 
 Past release notes can be found on our :ref:`releases` page.
 
diff --git a/docs/releases/4_2.rst b/docs/releases/4_2.rst
index de193ebd..2e561b15 100644
--- a/docs/releases/4_2.rst
+++ b/docs/releases/4_2.rst
@@ -17,3 +17,17 @@ This release also fixes the following bug(s):
 
 - When running pVACfuse with Arriba input data, the 3' transcript was not
   being parsed correctly. This release fixes this issue.
+
+Version 4.2.1
+-------------
+
+This is a bugfix release. It fixes the following problem(s):
+
+- When running the reference protome similarity step with a reference protome
+  peptide fasta file and a species other than human or mouse, the run would be aborted
+  with an error that the refseq_protein_prot BLASTp database was incompatible with
+  the species. This error should not be emitted in this circumstance since
+  BLASTp is not run when using a reference proteome peptide fasta file. This
+  release fixes this error and allows users to run the reference proteome
+  similarity step on non-human and non-mouse data with a reference proteome peptide fasta.
+
diff --git a/setup.py b/setup.py
index 1056d28a..bb3dd9e0 100644
--- a/setup.py
+++ b/setup.py
@@ -51,7 +51,7 @@
 
 setup(
     name="pvactools",
-    version="4.2.0",
+    version="4.2.1",
     packages=[
         "pvactools.tools",
         "pvactools.tools.pvacbind",