Upgrade to version 1.5.8

griffithlab · Apr 28, 2020 · 02dfaeb · 02dfaeb
1 parent 12db5ff
commit 02dfaeb
Show file tree

Hide file tree

Showing 4 changed files with 28 additions and 6 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -69,7 +69,7 @@
 # The short X.Y version.
 version = '1.5'
 # The full version, including alpha/beta/rc tags.
-release = '1.5.7'
+release = '1.5.8'
 
 # 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
@@ -52,10 +52,16 @@ New in release |release|
 
 This is a hotfix release. It fixes the following issues:
 
-- The ``pvacbind run`` command would previously allow fasta input files with
-  duplicated headers. However, it would silently skip subsequent entries with
-  duplicated headers even if the fasta sequence was novel. With this release
-  pVACbind will now error out if a duplicate fasta header is encounterd.
+- The ``pvacseq run``, ``pvacfuse run``, and ``pvacbind run`` commands would
+  previously error out when running with both MHC class I and MHC class II
+  algorithms but one or the other would not produce an all_eptiopes.tsv file.
+  This version fixes this bug.
+- MHCflurry version 1.6.0 and higher changed the output file headers. This
+  would cause errors when trying to parse these output files. pVACtools now
+  supports both the old and the new headers.
+- AGFusion updated their output file naming convention in newer versions and
+  is now outputting .exons.csv files instead of .exons.txt files.
+  pVACfuse is now able to process either version.
 
 New in version |version|
 ------------------------

diff --git a/docs/releases/1_5.rst b/docs/releases/1_5.rst
@@ -174,3 +174,19 @@ This is a hotfix release. It fixes the following issues:
   duplicated headers. However, it would silently skip subsequent entries with
   duplicated headers even if the fasta sequence was novel. With this release
   pVACbind will now error out if a duplicate fasta header is encounterd.
+
+1.5.8
+-----
+
+This is a hotfix release. It fixes the following issues:
+
+- The ``pvacseq run``, ``pvacfuse run``, and ``pvacbind run`` commands would
+  previously error out when running with both MHC class I and MHC class II
+  algorithms but one or the other would not produce an all_eptiopes.tsv file.
+  This version fixes this bug.
+- MHCflurry version 1.6.0 and higher changed the output file headers. This
+  would cause errors when trying to parse these output files. pVACtools now
+  supports both the old and the new headers.
+- AGFusion updated their output file naming convention in newer versions and
+  is now outputting .exons.csv files instead of .exons.txt files.
+  pVACfuse is now able to process either version.
diff --git a/setup.py b/setup.py
@@ -61,7 +61,7 @@
 
 setup(
     name="pvactools",
-    version="1.5.7",
+    version="1.5.8",
     packages=[
         "tools",
         "tools.pvacbind",