Upgrade to version 4.0.2

docs/conf.py

@@ -70,7 +70,7 @@
 # The short X.Y version.
 version = '4.0'
 # The full version, including alpha/beta/rc tags.
-release = '4.0.1'
+release = '4.0.2'
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

docs/index.rst

@@ -56,11 +56,23 @@ New in Release |release|
 
 This is a bugfix release. It fixes the following problem(s):
 
-- It fixes errors for a few edge cases when determining the mutation
-  position(s).
-- Update the HCC1395 demo date for pVACview to include elution data.
-- Correctly set NA columns in pVACview export dataframe.
-- Handle Arriba files with empty peptide_sequence fields.
+- 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.
 
 New in Version |version|
 ------------------------

docs/releases/4_0.rst

@@ -75,3 +75,26 @@ This is a bugfix release. It fixes the following problem(s):
 - Update the HCC1395 demo date for pVACview to include elution data.
 - Correctly set NA columns in pVACview export dataframe.
 - Handle Arriba files with empty peptide_sequence fields.
+
+New in Version 4.0.2
+--------------------
+
+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.

setup.py

@@ -51,7 +51,7 @@
 
 setup(
     name="pvactools",
-    version="4.0.1",
+    version="4.0.2",
     packages=[
         "pvactools.tools",
         "pvactools.tools.pvacbind",