Update to version 2.0.4

docs/conf.py

@@ -69,7 +69,7 @@
 # The short X.Y version.
 version = '2.0'
 # The full version, including alpha/beta/rc tags.
-release = '2.0.3'
+release = '2.0.4'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -54,18 +54,22 @@ New in release |release|
 
 This is a bugfix release. It fixes the following problem(s):
 
-- A bug in the reference proteome similarity step would cause this step to
-  fail if the full wildtype peptide sequence of the frameshift was longer
-  than its full mutant peptide sequence. This release fixes this issue.
-- A bug in the top score filter would cause this step to fail if it
-  encountered transcripts that do not start with ``ENS``. Support for
-  transcripts that start with ``NM_`` has been added in this release and a
-  more descriptive error message will now be raised if an unsupported
-  transcript name is encountered.
-- This release adds some minor improvements to the reference proteome
-  similarity step. A wait of 10 seconds was added after calling the BLAST API
-  to comply with their usage guidelines. Word size and gapcost parameters were
-  also added to these calls to improve result specificity.
+- Failed calls to the NetChop and NetMHCstab API were not being caught
+  correctly because failures would still result in a 200 return code. This
+  would ultimately result in empty filtered report files. This
+  release adds more error checking around the returned content
+  from these APIs and will fail if the content is not formatted as expected.
+- This release adds handling of some more VCF edge cases that were previously
+  unsupported. Variant transcripts that are annotated with * in the wildtype
+  protein sequence or that have a stop_retained_variant consequence are now
+  skipped. In addition, some variants may encode their postion as ``-/1234``,
+  which was previsouly not supported but has now been added.
+- When running pVACseq, pVACbind, or pVACfuse with the
+  ``--run-reference-proteome-similarity`` option enable this step would create
+  a reference matches file but the pipeline previously failed to copy this
+  file into the output directory. This release fixes that issue.
+- keras is now pinned to version 2.4.3 since newer versions might not be compatible
+  with the pinned tensorflow version.
 
 New in version |version|
 ------------------------

docs/releases/2_0.rst

@@ -121,3 +121,25 @@ This is a bugfix release. It fixes the following problem(s):
   similarity step. A wait of 10 seconds was added after calling the BLAST API
   to comply with their usage guidelines. Word size and gapcost parameters were
   also added to these calls to improve result specificity.
+
+Version 2.0.4
+-------------
+
+This is a bugfix release. It fixes the following problem(s):
+
+- Failed calls to the NetChop and NetMHCstab API were not being caught
+  correctly because failures would still result in a 200 return code. This
+  would ultimately result in empty filtered report files. This
+  release adds more error checking around the returned content
+  from these APIs and will fail if the content is not formatted as expected.
+- This release adds handling of some more VCF edge cases that were previously
+  unsupported. Variant transcripts that are annotated with * in the wildtype
+  protein sequence or that have a stop_retained_variant consequence are now
+  skipped. In addition, some variants may encode their postion as ``-/1234``,
+  which was previsouly not supported but has now been added.
+- When running pVACseq, pVACbind, or pVACfuse with the
+  ``--run-reference-proteome-similarity`` option enable this step would create
+  a reference matches file but the pipeline previously failed to copy this
+  file into the output directory. This release fixes that issue.
+- keras is now pinned to version 2.4.3 since newer versions might not be compatible
+  with the pinned tensorflow version.

setup.py

@@ -61,7 +61,7 @@
 
 setup(
     name="pvactools",
-    version="2.0.3",
+    version="2.0.4",
     packages=[
         "tools",
         "tools.pvacbind",