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Update Kalamari

Open lskatz opened this issue 1 month ago • 7 comments

  • Added more informative messages into .messages.txt to explain how to build Kalamari databases
  • It was using curl to pull individual files from the source repo. Now it copies them correctly in build.sh.

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Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes. This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe. If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation). Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x) {{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions {{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions {{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning {{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

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lskatz avatar May 10 '24 14:05 lskatz

@bioconda-bot please fetch artifacts

lskatz avatar May 10 '24 15:05 lskatz

Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
noarch kalamari-5.5.0-pl5321hdfd78af_1.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
kalamari 5.5.0--pl5321hdfd78af_1 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/kalamari:5.5.0--pl5321hdfd78af_1.tar.gz | docker load

BiocondaBot avatar May 10 '24 15:05 BiocondaBot

@bioconda-bot please fetch artifacts

lskatz avatar May 10 '24 16:05 lskatz

Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
noarch kalamari-5.5.0-pl5321hdfd78af_1.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
kalamari 5.5.0--pl5321hdfd78af_1 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/kalamari:5.5.0--pl5321hdfd78af_1.tar.gz | docker load

BiocondaBot avatar May 10 '24 16:05 BiocondaBot

I'm not clear on this OSX error ##[error]No hosted parallelism has been purchased or granted. To request a free parallelism grant, please fill out the following form https://aka.ms/azpipelines-parallelism-request

lskatz avatar May 10 '24 18:05 lskatz

I'm not clear on this OSX error ##[error]No hosted parallelism has been purchased or granted. To request a free parallelism grant, please fill out the following form https://aka.ms/azpipelines-parallelism-request

This isn't specific to this PR. It seems to be some issue with the pipeline on Azure.

aliciaaevans avatar May 10 '24 19:05 aliciaaevans

👀 at #41025

lskatz avatar May 14 '24 01:05 lskatz