Update to version 4.1.1

Author: susannasiebert

docs/conf.py

@@ -70,7 +70,7 @@
 # The short X.Y version.
 version = '4.4'
 # The full version, including alpha/beta/rc tags.
-release = '4.4.0'
+release = '4.4.1'
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

docs/index.rst

@@ -56,36 +56,19 @@ Contents
 New in Release |release|
 ------------------------
 
-This is a minor feature release. It adds the following features:
-
-- Various updates to the pVACview main interface:
-
-  - Users can no select a row to investigate by clicking on the row
-  - Users are now able to select an evaluation for a candidate by clicking on
-    one of three buttons on the right of the candidate's row.
-
-- Various updates to the pVACview NeoFox interface:
-
-  - By default, only a subset of NeoFox columns will be shown in order to
-    reduce the width of the table. Additional columns can be enabled by
-    selecting them in the "Column visibility" dropdown.
-  - We have added heatmap cell backgrounds to IC50 binding affinity and rank
-    columns.
-  - We have added horizontal barplot background to VAF and expression columns.
-  - Users are now able to select an evaluation for each candidate.
-  - Users are now able to leave a comment on selected candidates.
-  - The NeoFox table, including the selected evaluations and comments, can now
-    be exported in TSV and excel format.
-
-by @susannasiebert and @evelyn-schmidt in https://github.com/griffithlab/pVACtools/pull/1137
-
-This release also fixes the following bug(s):
-
-- A previous change would no longer allow standalone alpha/beta chain DP and DQ alleles. This change
-  would filter out such alleles before trying to combine them into valid
-  alpha-beta-chain pairs. This update once again enables automatic combination
-  of DP and DQ alleles in to alpha and beta chain pairs.
-  by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1139
+This is a bugfix release. It fixes the following problem(s):
+
+- Previously, pVACview would add an additional header line to Excel spreadsheets
+  when exporting a TSV. This has been fixed so that the first line in the spreadsheet
+  is the actual header line.
+  by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1143
+- One of the pVACview figures used to describe various anchor scenarios has been updated
+  so that the ordering of the scenarios is consistent with other figures and descriptions
+  throughout. Screenshots and documentation has been updated appropriately.
+  by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1144
+- The class II pVACview demo data was out-of-date and not reflecting recent updates to the
+  HLA alpha-beta chain handling. This file has now been updated.
+  by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1145
 
 Past release notes can be found on our :ref:`releases` page.
 

docs/releases/4_4.rst

@@ -34,3 +34,20 @@ This release also fixes the following bug(s):
   alpha-beta-chain pairs. This update once again enables automatic combination
   of DP and DQ alleles in to alpha and beta chain pairs.
   by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1139
+
+Version 4.4.1
+-------------
+
+This is a bugfix release. It fixes the following problem(s):
+
+- Previously, pVACview would add an additional header line to Excel spreadsheets
+  when exporting a TSV. This has been fixed so that the first line in the spreadsheet
+  is the actual header line.
+  by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1143
+- One of the pVACview figures used to describe various anchor scenarios has been updated
+  so that the ordering of the scenarios is consistent with other figures and descriptions
+  throughout. Screenshots and documentation has been updated appropriately.
+  by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1144
+- The class II pVACview demo data was out-of-date and not reflecting recent updates to the
+  HLA alpha-beta chain handling. This file has now been updated.
+  by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1145

pvactools/tools/pvacview/server.R

@@ -24,7 +24,7 @@ options(shiny.port = 3333)
 server <- shinyServer(function(input, output, session) {
   ## pVACtools version
 
-  output$version <- renderText({"pVACtools version 4.4.0"})
+  output$version <- renderText({"pVACtools version 4.4.1"})
 
   ##############################DATA UPLOAD TAB###################################
   ## helper function defined for generating shinyInputs in mainTable (Evaluation dropdown menus)

setup.py

@@ -51,7 +51,7 @@
 
 setup(
     name="pvactools",
-    version="4.4.0",
+    version="4.4.1",
     packages=[
         "pvactools.tools",
         "pvactools.tools.pvacbind",