Upgrade to version 1.5.12

docs/conf.py

@@ -69,7 +69,7 @@
 # The short X.Y version.
 version = '1.5'
 # The full version, including alpha/beta/rc tags.
-release = '1.5.11'
+release = '1.5.12'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -52,14 +52,14 @@ New in release |release|
 
 This is a hotfix release. It fixes the following issues:
 
-- The standalone ``pvacbind top_score_filter`` command woul throw an error
-  because it wasn't set up correctly. This has now been fixed.
-- The standalone ``pvacfuse generate_protein_fasta`` would fail when run with
-  the ``--input-tsv`` option because it wasn't able to associate TSV entries
-  with the fasta entries correctly. Using this option will now correctly limit
-  the output to only entries from the input TSV file.
-- In certain situation the trimming of problematic peptides in pVACvector
-  would not work correctly. This issue has now been addressed.
+- Vaxrank was pinned to an older version because newer versions made
+  backwards-incompatible changes to some code that pVACseq was using. However
+  this was causing installation issues since this older version of the vaxrank
+  pacakge has an indirect dependency on an old version of pysam. We
+  updated the usage of this module so that we could use the latest version of
+  vaxrank and, thus, newer versions of pysam.
+- This version adds error handling for when a normal sample name is provided
+  to pVACseq but the input VCF is a single-sample VCF.
 
 New in version |version|
 ------------------------

docs/releases/1_5.rst

@@ -230,3 +230,17 @@ This is a hotfix release. It fixes the following issues:
   the output to only entries from the input TSV file.
 - In certain situation the trimming of problematic peptides in pVACvector
   would not work correctly. This issue has now been addressed.
+
+1.5.12
+------
+
+This is a hotfix release. It fixes the following issues:
+
+- Vaxrank was pinned to an older version because newer versions made
+  backwards-incompatible changes to some code that pVACseq was using. However
+  this was causing installation issues since this older version of the vaxrank
+  pacakge has an indirect dependency on an old version of pysam. We
+  updated the usage of this module so that we could use the latest version of
+  vaxrank and, thus, newer versions of pysam.
+- This version adds error handling for when a normal sample name is provided
+  to pVACseq but the input VCF is a single-sample VCF.

setup.py

@@ -61,7 +61,7 @@
 
 setup(
     name="pvactools",
-    version="1.5.11",
+    version="1.5.12",
     packages=[
         "tools",
         "tools.pvacbind",
@@ -108,7 +108,7 @@
         'swagger-spec-validator==2.1.0',
         'jsonschema==2.6.0',
         'mock',
-        'vaxrank',
+        'vaxrank>=1.1.0',
     ],
     package_data={
         'tools.pvacseq': pvacseq_data_files,