Comments (12)
I can replicate this on my M2 when installing cyvcf2 via pip (python 3.10, 3.11, and 3.12).
I have cyvcf2 working via another route. I'll see if I can figure out how I did that, and post here.
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I can get a working cyvcf2 by compiling via pip --no-binary=cyvcf2
. This requires both autoconf
and automake
. Make sure you python -m pip uninstall cyvcf2
first if you have previously installed a non-working version:
mamba install automake autoconf # or could equivalently use conda
python -m pip install cyvcf2 --no-binary=cyvcf2
it might be that you also require htslib for compilation: I didn't try it on a completely clean OS install. Let me know if there are still compilation failures and I can see what else I previously installed to get it to work.
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I pushed a new tag for this with the fix from @graphenn . v0.31.0
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🥳 thanks @graphenn
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Sounds a lot like you were running into a similar problem to pysam-developers/pysam#1231, which we too worked around by ensuring we were compiling on e.g. ARM macOS rather than cross-compiling from a different architecture.
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@graphenn do you have an idea about this?
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I don't have a Mac either. Additionally, the GitHub action can't test with macOS ARM. We need someone with this environment to assist.
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@hyanwong or @tomwhite - would either of you be able to replicate? I think this is going to hit us downstream so it's would be great if we could track down the issue and hopefully fix the wheels.
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Looking at the wheel building, it seems like we're cross-compiling for ARM on a macos-12 host. Would it be simpler to use the newer macos-14 GitHub actions runner and compile natively?
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Or maybe use cibuildwheel directly? I don't know what the history of the wheel building process is here, sorry if we're going over old ground!
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Looking at the wheel building, it seems like we're cross-compiling for ARM on a macos-12 host. Would it be simpler to use the newer macos-14 GitHub actions runner and compile natively?
Yes, the new macos-14 action runner makes it much easier. I create a PR for changing macos ARM to this runner.
#306
NO cp38 wheel for macos arm
@hyanwong Could you test with the building wheel? https://github.com/graphenn/cyvcf2/actions/runs/9229532344
artifact-cp3xx-macosx_arm64
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Confirmed packages are working on macos-14 GitHub Action runner! Thanks very much!
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Related Issues (20)
- Floating point imprecision HOT 8
- Dealing with missing values in INFO column HOT 2
- Processing BED? HOT 2
- Any method available to split vcf files into individual sample vcf files
- Importing 64bit integers in FORMAT? HOT 4
- Add setter for POS HOT 1
- Crash with single GT allele value - UnicodeDecodeError: 'ascii' codec can't decode byte 0x81 in position 1: ordinal not in range(128) HOT 2
- Could you bump a new version to the pip HOT 1
- Provide access to index stats HOT 6
- Suggest not to remove htslib/config.status at setup.py
- No macOS arm64 wheels available for 0.30.26 and 0.30.27 HOT 1
- Adding new variant record
- Multiallelic VCF with annotation in INFO field doesn't query all available infromation HOT 3
- ##INFO fields being dropped HOT 6
- Skip the warnings? HOT 2
- Missing values for multi-allelic variants result in large negative numbers in `.format("AD")`, not all the same HOT 1
- Error importing cyvcf2 with numpy 2.0.0 HOT 10
- record.FILTER vs. record.FILTERS HOT 1
- Return sparse representation for genotype
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