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A TODO in the "for phylogenetics" is now done: remove comment#239

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benjeffery merged 1 commit intotskit-dev:mainfrom
hyanwong:phylo-issue-solved
Aug 3, 2023
Merged

A TODO in the "for phylogenetics" is now done: remove comment#239
benjeffery merged 1 commit intotskit-dev:mainfrom
hyanwong:phylo-issue-solved

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@hyanwong
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@hyanwong
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Seems to be failing because of a scikit-allel installation issue:

Collecting scikit-allel==1.3.5
[624](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:625)
  Downloading scikit-allel-1.3.5.tar.gz (9.7 MB)
[625](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:626)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.7/9.7 MB 19.4 MB/s eta 0:00:00
[626](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:627)
  Installing build dependencies: started
[627](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:628)
  Installing build dependencies: finished with status 'done'
[628](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:629)
  Getting requirements to build wheel: started
[629](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:630)
  Getting requirements to build wheel: finished with status 'error'
[630](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:631)
  error: subprocess-exited-with-error
[631](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:632)
  
[632](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:633)
  × Getting requirements to build wheel did not run successfully.
[633](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:634)
  │ exit code: 1
[634](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:635)
  ╰─> [36 lines of output]
[635](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:636)
      [scikit-allel] setup extensions with cython
[636](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:637)
      Compiling allel/opt/model.pyx because it changed.
[637](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:638)
      Compiling allel/opt/stats.pyx because it changed.
[638](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:639)
      Compiling allel/opt/io_vcf_read.pyx because it changed.
[639](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:640)
      [1/3] Cythonizing allel/opt/io_vcf_read.pyx
[640](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:641)
      [2/3] Cythonizing allel/opt/model.pyx
[641](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:642)
      [3/3] Cythonizing allel/opt/stats.pyx
[642](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:643)
      Traceback (most recent call last):
[643](https://github.com/tskit-dev/tutorials/actions/runs/5322396285/jobs/9638785813?pr=239#step:5:644)

@benjeffery
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Looks like cggh/scikit-allel#397

@hyanwong hyanwong force-pushed the phylo-issue-solved branch from e15e76a to 819954e Compare August 1, 2023 20:22
@benjeffery benjeffery merged commit eaf2050 into tskit-dev:main Aug 3, 2023
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2 participants