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Update b2bTools to v3.0.7 #48749

Merged
merged 26 commits into from
Jul 5, 2024
Merged

Update b2bTools to v3.0.7 #48749

merged 26 commits into from
Jul 5, 2024

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agdiaz
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@agdiaz agdiaz commented Jun 26, 2024

Update b2bTools package to v3.0.7 published on 24th April 2024 on PyPi.


What's new?

  • The package b2btools v3.0.7, developed by the Bio2Byte group (VUB, Brussels), includes metadata in the output results, a better CLI, and some minor fixes to solve bugs.
  • We have added the missing LICENSE file and identifiers (DOI and biotools reference)
  • We have fixed the dependencies to support multiple Python versions:
    • Python v3.7
    • Python v3.8
    • Python v3.9
    • Python v3.10
    • Python v3.11: TBD soon in a new version due to issues related to dependency pomegranate<1.0
    • Python v3.12: TBD soon in a new version due to issues related to dependency pomegranate<1.0

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recipes/b2btools/meta.yaml Outdated Show resolved Hide resolved
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agdiaz commented Jun 28, 2024

@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
noarch b2btools-3.0.7-py310hdfd78af_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>

Docker image(s) built:

Package Tag CI Install with docker
b2btools 3.0.7--py310hdfd78af_0 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/b2btools:3.0.7--py310hdfd78af_0.tar.gz | docker load
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agdiaz commented Jul 5, 2024

@BiocondaBot please fetch artifacts

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No artifacts found on the most recent builds. Either the builds failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped.

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agdiaz commented Jul 5, 2024

@BiocondaBot please fetch artifacts

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No artifacts found on the most recent builds. Either the builds failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped.


build:
number: 0
script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv"
noarch: python
skip: true # [py >= 311]
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I think this is the reason why nothing has been built.

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Thanks for your help @martin-g, really appreciated. We are trying to finish this recipe as soon as possible.

Unfortunately there is a dependency (pomegranate) that doesn't support neither Py311 nor Py312 for the version we need to install >=0.14.8, <0.14.10. That limits our support to both Py311 and Py312 :/ The only way we found to install it using conda was requesting the dependency from pip, but that is not a possibility in bioconda recipes, isn't it ? Otherwise we could try to build that dependency from the sources, but I couldn't figure out how to make it. Would it be possible to do it in the build script ? Basically we would need to do:

pip install "cython~=0.29.14" "scipy>=0.17.0"
git clone -b v0.14.9 --single-branch https://github.com/jmschrei/pomegranate.git
cd pomegranate
python setup.py install
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agdiaz commented Jul 5, 2024

@BiocondaBot please fetch artifacts

@agdiaz agdiaz marked this pull request as ready for review July 5, 2024 12:27
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agdiaz commented Jul 5, 2024

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Jul 5, 2024
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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 b2btools-3.0.7-py310hdbdd923_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 b2btools-3.0.7-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
b2btools 3.0.7--py310hdbdd923_0 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/b2btools:3.0.7--py310hdbdd923_0.tar.gz | docker load
@bgruening bgruening merged commit 9e72876 into bioconda:master Jul 5, 2024
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