Merge pull request #1083 from griffithlab/4.1.1_release

Update to version 4.1.1
griffithlab · Mar 13, 2024 · 7c4b383 · 7c4b383
2 parents d6e9acb + 0b5d5d4
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diff --git a/docs/conf.py b/docs/conf.py
@@ -70,7 +70,7 @@
 # The short X.Y version.
 version = '4.1'
 # The full version, including alpha/beta/rc tags.
-release = '4.1.0'
+release = '4.1.1'
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

diff --git a/docs/index.rst b/docs/index.rst
@@ -54,29 +54,30 @@ Contents
 New in Release |release|
 ------------------------
 
-This is a minor feature release. It adds the following features:
-
-- This release adds support for two new prediction algorithms: BigMHC and
-  DeepImmuno (`#1063 <https://github.com/griffithlab/pVACtools/pull/1063>`_).
-  BigMHC includes predictions for elution (BigMHC_EL) and
-  immunogenicity (BigMHC_IM). DeepImmuno is a prediction algorithms for
-  immunogenicty.
-- This release includes several updates to pVACview (`#1012
-  <https://github.com/griffithlab/pVACtools/pull/1012>`_):
-
-  - The tab containing the anchor heatmaps for each well-binding peptide of a
-    variant has been moved to the "Transcript and Peptide Set Data" panel.
-  - The anchor heatmap tab now also contains a table of all the per-length and
-    per-allele anchor weights for each position in a peptide.
-  - The pVACtools version is now displayed at the bottom of the sidebar.
-  - A new panel has been added to show the tiering parameters currently
-    applied.
-  - Where there are multiple transcript sets for a variant, the one containing
-    the best peptide is now selected by default.
-
-- This release adds a new command ``pvactools download_wdls`` (`#1055
-  <https://github.com/griffithlab/pVACtools/pull/1055>`_). This command
-  can be used to download WDL workflow files for pVACseq and pVACfuse.
+This is a bugfix release. It fixes the following problem(s):
+
+- The previous version updated how the all_epitopes.tsv file was parsed when creating
+  the aggregated report and NA values are now parsed as native pandas nan. However,
+  this update was not handled correctly for the Mutation Position column,
+  leading to errors with NA values in that column. This release fixes this error.
+  (`#1079 <https://github.com/griffithlab/pVACtools/pull/1079>`_)
+- The previous version would write the DeepImmuno output file in the same location for
+  multiple prediction calls. This would lead to errors when running in multi-threaded mode.
+  This releases updates the code to write DeepImmuno outputs to unique file locations.
+  (`#1078 <https://github.com/griffithlab/pVACtools/pull/1078>`_)
+- This release updates how the list of combinatorial class II alleles is created in order
+  to return it as a sorted list, creating a consistent order when writing the
+  input.yml log file. (`#1077 <https://github.com/griffithlab/pVACtools/pull/1077>`_)
+- This release updates the GitHub commit for the pVACview demo data in order to pull the
+  latest version of this data, including DeepImmuno and BigMHC prediction data.
+  (`#1073 <https://github.com/griffithlab/pVACtools/pull/1073>`_)
+- This release fixes an issue where the pVACvector visualization images were saved in a
+  low resolution format resulting in blurry images.  (`#1071
+  <https://github.com/griffithlab/pVACtools/pull/1071>`_)
+- This release fixes an issue where the method to determine the matched wildtype result
+  didn't return where appropriate, causing the mutation position to not be set correctly.
+  (`#1082 <https://github.com/griffithlab/pVACtools/pull/1082>`_)
+- This release fixes some typos. (`#1072 <https://github.com/griffithlab/pVACtools/pull/1072>`_)
 
 Past release notes can be found on our :ref:`releases` page.
 

diff --git a/docs/releases/4_1.rst b/docs/releases/4_1.rst
@@ -27,3 +27,31 @@ This is a minor feature release. It adds the following features:
 - This release adds a new command ``pvactools download_wdls`` (`#1055
   <https://github.com/griffithlab/pVACtools/pull/1055>`_). This command
   can be used to download WDL workflow files for pVACseq and pVACfuse.
+
+Version 4.1.1
+-------------
+
+This is a bugfix release. It fixes the following problem(s):
+
+- The previous version updated how the all_epitopes.tsv file was parsed when creating
+  the aggregated report and NA values are now parsed as native pandas nan. However,
+  this update was not handled correctly for the Mutation Position column,
+  leading to errors with NA values in that column. This release fixes this error.
+  (`#1079 <https://github.com/griffithlab/pVACtools/pull/1079>`_)
+- The previous version would write the DeepImmuno output file in the same location for
+  multiple prediction calls. This would lead to errors when running in multi-threaded mode.
+  This releases updates the code to write DeepImmuno outputs to unique file locations.
+  (`#1078 <https://github.com/griffithlab/pVACtools/pull/1078>`_)
+- This release updates how the list of combinatorial class II alleles is created in order
+  to return it as a sorted list, creating a consistent order when writing the
+  input.yml log file. (`#1077 <https://github.com/griffithlab/pVACtools/pull/1077>`_)
+- This release updates the GitHub commit for the pVACview demo data in order to pull the
+  latest version of this data, including DeepImmuno and BigMHC prediction data.
+  (`#1073 <https://github.com/griffithlab/pVACtools/pull/1073>`_)
+- This release fixes an issue where the pVACvector visualization images were saved in a
+  low resolution format resulting in blurry images.  (`#1071
+  <https://github.com/griffithlab/pVACtools/pull/1071>`_)
+- This release fixes an issue where the method to determine the matched wildtype result
+  didn't return where appropriate, causing the mutation position to not be set correctly.
+  (`#1082 <https://github.com/griffithlab/pVACtools/pull/1082>`_)
+- This release fixes some typos. (`#1072 <https://github.com/griffithlab/pVACtools/pull/1072>`_)
diff --git a/pvactools/tools/pvacview/server.R b/pvactools/tools/pvacview/server.R
@@ -19,7 +19,7 @@ options(shiny.port = 3333)
 
 server <- shinyServer(function(input, output, session) {
   ## pVACtools version
-  output$version <- renderText({"pVACtools version 4.1.0"})
+  output$version <- renderText({"pVACtools version 4.1.1"})
 
   ##############################DATA UPLOAD TAB###################################
   ## helper function defined for generating shinyInputs in mainTable (Evaluation dropdown menus)

diff --git a/setup.py b/setup.py
@@ -51,7 +51,7 @@
 
 setup(
     name="pvactools",
-    version="4.1.0",
+    version="4.1.1",
     packages=[
         "pvactools.tools",
         "pvactools.tools.pvacbind",