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update PASTA to 1.9.2 and SEPP to 4.5.4, i.e. unpin HMMER and lift py <=3.9 #47895

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merged 34 commits into from
Aug 14, 2024

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@sjanssen2 sjanssen2 commented May 15, 2024

This PR shall enable to changes:

  1. We want to lift the version pinning of the HMMER dependency. Newer version do introduce slight changes to the output, but @Sann5, @smirarab and my analysis conclude that user should not really be affected by them. To highlight potential differences between upstream SEPP stand-alone (using old bundled binaries) and bioconda versions (using latest HMMER packages), SEPP now reports the used version. Therefore, upstream SEPP got a version bump.
  2. In preparation for a new QIIME2 release, which will migrate to py3.10, we needed to introduce slight code changes in upstream SEPP. These changes are now included in the release 4.5.4, which this PR is going to use.
  3. As SEPP depends on PASTA and to avoid dependency conflicts, PASTA also had to be updated to version 1.9.2

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sjanssen2 and others added 25 commits December 8, 2020 17:54
lifting the hmmer pinning and relaxing py to <= 3.10
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regarding the HMMER pin lifting, see also our discussion in #48294

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ready for review @Sann5

@sjanssen2 sjanssen2 added the please review & merge set to ask for merge label Aug 14, 2024
@sjanssen2 sjanssen2 requested a review from aliciaaevans August 14, 2024 07:51
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@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 pasta-1.9.2-py310h2eb23f3_0.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 pasta-1.9.2-py311hfad2c56_0.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 pasta-1.9.2-py38h703aefd_0.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 pasta-1.9.2-py39h9194a71_0.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 sepp-4.5.4-py310h9ee0642_0.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
osx-64 pasta-1.9.2-py310h8cda308_0.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-64 pasta-1.9.2-py311h29d3010_0.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-64 pasta-1.9.2-py38h647dd61_0.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-64 pasta-1.9.2-py39hc3b6a10_0.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>
osx-64 sepp-4.5.4-py310h527b516_0.tar.bz2 OSXArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
pasta 1.9.2--py310h2eb23f3_0 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/pasta:1.9.2--py310h2eb23f3_0.tar.gz | docker load
pasta 1.9.2--py311hfad2c56_0 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/pasta:1.9.2--py311hfad2c56_0.tar.gz | docker load
pasta 1.9.2--py38h703aefd_0 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/pasta:1.9.2--py38h703aefd_0.tar.gz | docker load
pasta 1.9.2--py39h9194a71_0 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/pasta:1.9.2--py39h9194a71_0.tar.gz | docker load
sepp 4.5.4--py310h9ee0642_0 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/sepp:4.5.4--py310h9ee0642_0.tar.gz | docker load

@sjanssen2 sjanssen2 changed the title SEPP: upgrade to py3.10 update PASTA to 1.9.2 and SEPP to 4.5.4, i.e. unpin HMMER and lift py <=3.9 Aug 14, 2024
@sjanssen2 sjanssen2 requested a review from aliciaaevans August 14, 2024 21:02
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Thanks for the background information on this one.

@aliciaaevans aliciaaevans merged commit a336de2 into master Aug 14, 2024
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@aliciaaevans aliciaaevans deleted the sepp_py3.10 branch August 14, 2024 21:47
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