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pygtftk: add linux-aarch64 build #47404

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merged 3 commits into from
May 2, 2024
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@martin-g
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The Linux ARM64 build fails with the same reason as:

@mencian mencian added the aarch64 Related to adding linux-aarch64 support label Apr 25, 2024
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
…nd 1.0.0

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
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martin-g commented May 1, 2024

@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 pygtftk-1.6.2-py39h4e691d4_2.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 pygtftk-1.6.2-py39hd999155_2.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>
linux-aarch64 pygtftk-1.6.2-py39h73eeb99_2.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/ef88d15e-8e9d-499f-ac9a-0aeb3a45b121/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
pygtftk 1.6.2--py39h4e691d4_2 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/pygtftk:1.6.2--py39h4e691d4_2.tar.gz | docker load

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martin-g commented May 1, 2024


mgrigorov in 🌐 euler-arm-22 in /tmp/pygtftk via 🅒 test123 took 16s 
❯ tar xvf pygtftk-1.6.2-py39h73eeb99_2.tar.bz2                                                                                                                                                             (test123) 
info/run_exports.json
info/test/run_test.py
info/hash_input.json
info/has_prefix
info/recipe/run_test.sh
info/test/run_test.sh
info/index.json
info/recipe/meta.yaml.template
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/files
info/git
info/paths.json
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lib/python3.9/site-packages/pygtftk/data/mini_real_ens/hg38_ens.genome
lib/python3.9/site-packages/pygtftk/data/mini_real_noov_rnd_tx/hg38.genome
lib/python3.9/site-packages/pygtftk/data/tiny_real/hg38.genome
lib/python3.9/site-packages/pygtftk/data/mini_real/hg38.genome
lib/python3.9/site-packages/pygtftk/data/simple/simple.join_mat_2
lib/python3.9/site-packages/pygtftk/stats/intersect/read_bed/exclude.hpp
lib/python3.9/site-packages/pygtftk/src/libgtftk/README.md
lib/python3.9/site-packages/pygtftk/data/simple/add_attr_to_pos.tab
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lib/python3.9/site-packages/pygtftk/data/ologram_2/multiple_overlap_trivial_ologram_stats.tsv
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lib/python3.9/site-packages/pygtftk/data/ologram_1/H3K4me3_ologram_stats.tsv
lib/python3.9/site-packages/pygtftk/data/ologram_1/H3K36me3_ologram_stats.tsv
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lib/python3.9/site-packages/pygtftk/data/hg38_chr1/H3K36me3_ologram_stats.tsv
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lib/python3.9/site-packages/pygtftk/data/hg38_chr1/hg38_chr1_counts_ENCFF630HEX.tsv
lib/python3.9/site-packages/pygtftk/data/tiny_real/mini_real_counts_ENCFF630HEX.tsv
lib/python3.9/site-packages/pygtftk/data/mini_real/mini_real_counts_ENCFF630HEX.tsv
lib/python3.9/site-packages/pygtftk/lib/libgtftk.cpython-39-aarch64-linux-gnu.so
lib/python3.9/site-packages/pygtftk/stats/intersect/create_shuffles.cpython-39-aarch64-linux-gnu.so
lib/python3.9/site-packages/pygtftk/stats/intersect/read_bed/read_bed_as_list.cpython-39-aarch64-linux-gnu.so
lib/python3.9/site-packages/pygtftk/stats/multiprocessing/multiproc.cpython-39-aarch64-linux-gnu.so
lib/python3.9/site-packages/pygtftk/stats/intersect/overlap/overlap_regions.cpython-39-aarch64-linux-gnu.so
lib/python3.9/site-packages/pygtftk/src/libgtftk/version.h
lib/python3.9/site-packages/pygtftk/src/libgtftk/config.h
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mgrigorov in 🌐 euler-arm-22 in /tmp/pygtftk via 🅒 test123 
❯ file bin/*                                                                                                                                                                                               (test123) 
bin/gtftk: a /opt/conda/conda-bld/pygtftk_1714545167509/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho script, ASCII text executable

mgrigorov in 🌐 euler-arm-22 in /tmp/pygtftk via 🅒 test123 
❯ conda install ./pygtftk-1.6.2-py39h73eeb99_2.tar.bz2                                                                                                                                                     (test123) 

Downloading and Extracting Packages:
                                                                                                                                                                                                                     

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done


mgrigorov in 🌐 euler-arm-22 in /tmp/pygtftk via 🅒 test123 took 29s 
❯ gtftk                                                                                                                                                                                                    (test123) 
Traceback (most recent call last):
  File "/home/mgrigorov/miniconda3/envs/test123/bin/gtftk", line 25, in <module>
    import pygtftk
ModuleNotFoundError: No module named 'pygtftk'

It is weird that it cannot find its own module ...

@martin-g
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martin-g commented May 1, 2024

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label May 1, 2024
@rpetit3
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rpetit3 commented May 1, 2024

@martin-g "It is weird that it cannot find its own module ..."

If you think its ok, please feel free to merge

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martin-g commented May 1, 2024

If you think its ok, please feel free to merge

I don't have permissions to merge PRs

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rpetit3 commented May 1, 2024

Want to be added to the bioconda/all group?

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martin-g commented May 1, 2024

Only if others think that I deserve it! :-)

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rpetit3 commented May 1, 2024

Should have an email, this would at least allow you to merge these already approved PR's

Thank you so much of helping with the ARM rollout!

@martin-g
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martin-g commented May 1, 2024

Thank you, @rpetit3 !
It is my pleasure! And it is a lot of fun!

I will leave this PR open for a while so others can take a look if they have time and interest in it.

@mencian mencian merged commit 3646a56 into bioconda:master May 2, 2024
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@martin-g martin-g deleted the aarch64-pygtftk branch May 3, 2024 06:28
daler pushed a commit that referenced this pull request May 14, 2024
* pygtftk: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* Pin cython to 0.2x

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* Try to fix the Max OSX build by pinning scikit-learn between 0.21.2 and 1.0.0

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

---------

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
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4 participants