diff --git a/docs/conf.py b/docs/conf.py index dcb468125..bc2d8d6d0 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -69,7 +69,7 @@ # The short X.Y version. version = '1.3' # The full version, including alpha/beta/rc tags. -release = '1.3.6' +release = '1.3.7' # 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 index f346f0f4a..e6eddb894 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -47,36 +47,10 @@ New in version |release| This version is a hotfix release. It fixes the following issues: -- Tensorflow is incompatible with multiprocessing when the parent process - imports tensorflow or a tensorflow-dependent module. For this reason - MHCflurry and MHCnuggets were removed from parallelization. In this - release we moved to calling MHCflurry and MHCnuggets on the command line, - which allowed us to remove our direct imports of these modules and allows us - to parallelize the calls to these two prediction algorithms. All prediction - algorithms supported by pVACtools can now be used in multiprocessing mode. -- Some users were reporting ``Illegal instruction (core dumped)`` errors - because their hardware was incompatible with the version of tensorflow we - were using. Pinning the tensorflow version to 1.5.0 with this release should - solve this problem. -- When running in multiprocessing mode while using the IEDB API, users would - experience a higher probability of failed requests to the API. The IEDB API - would throw a 403 error when rejecting requests due to too - many simultaneous requests. pVACtools would previously not retry on this type of - error. This release now adds retries on this error code. We also improved - the random wait time calculation between requests so that the likelihood of - multiple retries hitting at the same time has now been reduced. -- When encountering a truncated input VCF, the VCF parser used by pVACtools - would throw an error that was not indicative of the real error source. - pVACseq now catches these errors and emmits a more descriptive error message - when encountering a truncated VCF. -- One option when annotating a VCF with VEP is the ``-total-length`` flag. When - using this flag, the total length would be written to the - ``Protein_position`` field. pVACseq previously did not support a VCF with a - ``Protein_position`` field in this format. This release adds support for it. -- When creating the combined MHC class I and MHC class II all_epitopes file, - we were previously not correctly determining all necessary headers which - would lead to incorrect output of the individual prediction algorithm score - columns. This release fixes this issue. +- The previous version accidentially removed the + ``--additional-input-file-list`` option. It has been restored in this + version. Please note that it is slated for permanent removal in the next + feature release (1.4.0). Past release notes can be found on our :ref:`releases` page. diff --git a/docs/releases/1_3.rst b/docs/releases/1_3.rst index fbf52fe39..1f6271691 100644 --- a/docs/releases/1_3.rst +++ b/docs/releases/1_3.rst @@ -133,3 +133,13 @@ This version is a hotfix release. It fixes the following issues: we were previously not correctly determining all necessary headers which would lead to incorrect output of the individual prediction algorithm score columns. This release fixes this issue. + +1.3.7 +----- + +This version is a hotfix release. It fixes the following issues: + +- The previous version accidentially removed the + ``--additional-input-file-list`` option. It has been restored in this + version. Please note that it is slated for permanent removal in the next + feature release (1.4.0). diff --git a/setup.py b/setup.py index 7532d5733..2eeb4a38d 100644 --- a/setup.py +++ b/setup.py @@ -56,7 +56,7 @@ setup( name="pvactools", - version="1.3.6", + version="1.3.7", packages=[ "tools", "tools.pvacfuse",