From 839a06187a59adbffa579d51a406cd555604f550 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Wed, 11 Sep 2024 14:07:47 -0500 Subject: [PATCH] Update to version 4.1.1 --- docs/conf.py | 2 +- docs/index.rst | 43 ++++++++++--------------------- docs/releases/4_4.rst | 17 ++++++++++++ pvactools/tools/pvacview/server.R | 2 +- setup.py | 2 +- 5 files changed, 33 insertions(+), 33 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index c0c2f280..a66c2d4e 100644 --- a/docs/conf.py +++ b/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 diff --git a/docs/index.rst b/docs/index.rst index 7ea540ba..f6586b60 100644 --- a/docs/index.rst +++ b/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. diff --git a/docs/releases/4_4.rst b/docs/releases/4_4.rst index 1acfaaae..09403062 100644 --- a/docs/releases/4_4.rst +++ b/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 diff --git a/pvactools/tools/pvacview/server.R b/pvactools/tools/pvacview/server.R index d3b4a1e9..1f55629f 100644 --- a/pvactools/tools/pvacview/server.R +++ b/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) diff --git a/setup.py b/setup.py index a71159b8..1d8cd1ef 100644 --- a/setup.py +++ b/setup.py @@ -51,7 +51,7 @@ setup( name="pvactools", - version="4.4.0", + version="4.4.1", packages=[ "pvactools.tools", "pvactools.tools.pvacbind",