From 94f6c3b7507a17c41703282d85d1270a8ab0eca5 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Thu, 22 Dec 2022 11:20:15 -0600 Subject: [PATCH] Upgrade to version 3.1.1 --- docs/conf.py | 2 +- docs/index.rst | 81 +++++++------------------------------------ docs/releases.rst | 1 + docs/releases/3_1.rst | 12 +++++++ setup.py | 2 +- 5 files changed, 27 insertions(+), 71 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index e59e6bfec..b8ca386a8 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -69,7 +69,7 @@ # The short X.Y version. version = '3.1' # The full version, including alpha/beta/rc tags. -release = '3.1.0' +release = '3.1.1' # The language for content autogenerated by Sphinx. Refer to documentation diff --git a/docs/index.rst b/docs/index.rst index e8bde6a9b..0fdf0869c 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -54,6 +54,18 @@ Contents New in Release |release| ------------------------ +This is a bugfix release. It fixes the following problem(s): + +- The ``--exclude-NAs`` flag was not being passed along correctly to the main + pipeline and didn't have any effect on downstream filtering. +- The aggregate report creation step had some inefficiencies which caused its + runtime to be much longer than necessary. +- An unneeded import statement for the PyVCF package had the potential to + cause errors while running the pVACseq pipeline. + +New in Version |version| +------------------------ + This release adds the following new features: - When running the pipelines with the ``--netmhc-stab`` flag enabled, the @@ -72,75 +84,6 @@ This release also fixes the following problem(s): - For very large result sets the filtering steps would stall or be killed because the steps would run out of memory. This release fixes this issue. - This release adds better handling of timeout errors while running - NetMHCstabpan and/or NetChop. - -New in Version |version| ------------------------- - -This version adds the following features, outlined below. Please note that -pVACtools 3.0 is not backwards-compatible and certain changes will break old -workflows. - -Breaking Changes -________________ - -- The pVACapi and pVACviz tools have been removed. They have been replaced by - the :ref:`pvacview` tool. -- The package namespace has been updated. The files will now be installed - underneath a ``pvactools`` directory in your python package installation - path. -- The aggregated report format has been updated. The headers have been updated for - clarity. An additional column ``Allele Expr`` has been added, representing - RNA expression * RNA VAF. For more information see :ref:`aggregated`. -- pVACfuse no longer supports inputs from Integrate NEO. Only AGFusion inputs - will be supported going forward. -- The format of the pVACfuse all_epitopes and filtered reports has been updated to - remove columns that aren't applicable for the tool. Please see the documentation - for the pVACfuse :ref:`pvacfuse_all_ep_and_filtered` for more information. - -New Features -____________ - -- This release adds a new tool, :ref:`pvacview`. pVACview is an R Shiny application that - allows for that visualization of the pVACseq aggregated report file to review, explore, - and prioritize the different neoantigen candidates predicted by pVACseq. -- The 3.0 release adds several improvements to the reference proteome - similarity step: - - - Users can now run the reference proteome similarity step with a standalone - Protein BLAST installation. To use a standalone BLASTp installation, provide the - installation path using the ``--blastp-path`` parameter. The supported - Protein BLAST databases are ``refseq_select_prot`` and ``refseq_protein``. - Please reference the :ref:`blast` documentation for further instructions. - - When running the reference proteome similarity step using the NCBI Protein BLAST API, - users can now pick between the ``refseq_select_prot`` and ``refseq_protein`` - databases. - - Parallelization has been added to the reference proteome similarity step. - When running this step as part of the pVACseq, pVACfuse, or pVACbind - pipelines, the existing ``--t`` parameter will also be used to set the number of - parallel threads in this step. - -- This release adds standalone commands to run stability predictions, cleavage - site predictions, and the reference proteome similarity step on the output - of the :ref:`pVACseq`, :ref:`pVACfuse`, and :ref:`pVACbind` pipelines. - -Minor Updates -_____________ - -- Previously, when running NetChop for cleavage site predictions, predictions - were made for each epitope individually. However, these predictions will - differ if additional flanking amino acids are provided and will be stable - with 9 or more flanking amino acids. We updated this step to make predictions - with 9 flanking amino acids around each epitope to generate stable - predictions. -- This release adds a ``--species`` option to the ``valid_alleles`` commands - to filter alleles on a species of interest. -- This release adds a ``--pass-only`` flag to the ``pvacseq - generate_protein_fasta`` commands to only process VCF entries that do not - have a FILTER set. -- This release adds a new parameter ``--tumor-purity``. This parameter indicates - the fraction of tumor cells in the tumor sample and is used during aggregate - report creation for a simple estimation whether variants are subclonal or clonal based on VAF. Past release notes can be found on our :ref:`releases` page. diff --git a/docs/releases.rst b/docs/releases.rst index f5cc0059f..966896e77 100644 --- a/docs/releases.rst +++ b/docs/releases.rst @@ -14,3 +14,4 @@ Release Notes releases/1_5 releases/2_0 releases/3_0 + releases/3_1 diff --git a/docs/releases/3_1.rst b/docs/releases/3_1.rst index d2d45e34f..1432d7106 100644 --- a/docs/releases/3_1.rst +++ b/docs/releases/3_1.rst @@ -22,4 +22,16 @@ This release also fixes the following problem(s): - For very large result sets the filtering steps would stall or be killed because the steps would run out of memory. This release fixes this issue. - This release adds better handling of timeout errors while running + +Version 3.1.1 +------------- + +This is a bugfix release. It fixes the following problem(s): + +- The ``--exclude-NAs`` flag was not being passed along correctly to the main + pipeline and didn't have any effect on downstream filtering. +- The aggregate report creation step had some inefficiencies which caused its + runtime to be much longer than necessary. NetMHCstabpan and/or NetChop. +- An unneeded import statement for the PyVCF package had the potential to + cause errors while running the pVACseq pipeline. diff --git a/setup.py b/setup.py index 082347a71..f75daa890 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ setup( name="pvactools", - version="3.1.0", + version="3.1.1", packages=[ "pvactools.tools", "pvactools.tools.pvacbind",