Update to versin 1.3.5

griffithlab · Apr 4, 2019 · d72c196 · d72c196
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commit d72c196
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Showing 4 changed files with 24 additions and 8 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -69,7 +69,7 @@
 # The short X.Y version.
 version = '1.3'
 # The full version, including alpha/beta/rc tags.
-release = '1.3.4'
+release = '1.3.5'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/index.rst b/docs/index.rst
@@ -47,12 +47,14 @@ New in version |release|
 
 This version is a hotfix release. It fixes the following issues:
 
-- We were previously using nested multi-threading which would cause defunct
-  child jobs and stalled runs. Switching to single-level multi-threading fixes
-  this issue.
-- When running pVACvector from a pVACseq result file the creation of the
-  peptide fasta file might cause an error if the epitope was situated near the
-  beginning of the transcript. This issue has been fixed.
+- While the previous release fixed the issue of stalled processes when running
+  IEDB-based prediction algorithms in multiprocessing mode, we were still experience a similar problem
+  when running with MHCflurry and MHCnuggets. These two prediction algorithms
+  are tensorflow-based which in the way it is currently used in pVACtools is
+  not compatible with being run in multiprocessing mode. As a stop-gap measure
+  this release removes MHCnuggets and MHCflurry from being run in
+  multiprocessing mode. This resolves the problem until we can change our
+  usage of these predictin algorithms to be multiprocessing-compatible.
 
 Past release notes can be found on our :ref:`releases` page.
 

diff --git a/docs/releases/1_3.rst b/docs/releases/1_3.rst
@@ -83,3 +83,17 @@ This version is a hotfix release. It fixes the following issues:
 - When running pVACvector from a pVACseq result file the creation of the
   peptide fasta file might cause an error if the epitope was situated near the
   beginning of the transcript. This issue has been fixed.
+
+1.3.5
+-----
+
+This version is a hotfix release. It fixes the following issues:
+
+- While the previous release fixed the issue of stalled processes when running
+  IEDB-based prediction algorithms in multiprocessing mode, we were still experience a similar problem
+  when running with MHCflurry and MHCnuggets. These two prediction algorithms
+  are tensorflow-based which in the way it is currently used in pVACtools is
+  not compatible with being run in multiprocessing mode. As a stop-gap measure
+  this release removes MHCnuggets and MHCflurry from being run in
+  multiprocessing mode. This resolves the problem until we can change our
+  usage of these predictin algorithms to be multiprocessing-compatible.
diff --git a/setup.py b/setup.py
@@ -56,7 +56,7 @@
 
 setup(
     name="pvactools",
-    version="1.3.4",
+    version="1.3.5",
     packages=[
         "tools",
         "tools.pvacfuse",