‘locus’ (type ‘locus<any>’)

[skr3178]

What happened?

ValueError: Method ‘variant_qc’ requires row key to be two fields ‘locus’ (type ‘locus’) and ‘alleles’ (type ‘array’)
Found:
‘locus’: struct{contig: str, position: int32}
‘alleles’: array

I am aware the standard locus column is a format

whereas the format I have is

Version

version 0.2.112-31ceff2fb5fd

Relevant log output

No response

[danking]

@tpoterba this seems overly restrictive no?

[tpoterba]

Yeah, we could relax this to just require the alleles.

[danking]

Thanks for the report!

[skr3178]

thank you for these changes.
I am facing trouble in installing this branch of the package.

i tried

pip install git+https://github.com/danking/hail.git@relax-variant-qc

git clone https://github.com/danking/hail.git --branch relax-variant-qc --single-branch
cd hail
pip install .

[danking]

I can’t help you without an error message or description of what didn’t work. I recommend waiting for the next release which should come out today.

[skr3178]

pip install -e .
Defaulting to user installation because normal site-packages is not writeable
Obtaining file:///home/skr/hail2/hail
Installing build dependencies ... done
Checking if build backend supports build_editable ... done
Getting requirements to build editable ... error
error: subprocess-exited-with-error

× Getting requirements to build editable did not run successfully.
│ exit code: 1
╰─> [14 lines of output]
error: Multiple top-level packages discovered in a flat-layout: ['tls', 'gear', 'hail', 'auth', 'blog', 'infra', 'batch', 'query', 'docker', 'memory', 'devbin', 'gateway', 'website', 'grafana', 'notebook', 'graphics', 'datasets', 'monitoring', 'web_common', 'prometheus', 'letsencrypt'].

  To avoid accidental inclusion of unwanted files or directories,
  setuptools will not proceed with this build.
  
  If you are trying to create a single distribution with multiple packages
  on purpose, you should not rely on automatic discovery.
  Instead, consider the following options:
  
  1. set up custom discovery (`find` directive with `include` or `exclude`)
  2. use a `src-layout`
  3. explicitly set `py_modules` or `packages` with a list of names
  
  To find more information, look for "package discovery" on setuptools docs.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build editable did not run successfully.
│ exit code: 1
╰─> See above for output.

[danking]

The Hail python package is not a pure-Python package. Installing it from source requires building a JAR file. We have instructions here, but I recommend waiting for the next PyPI release.

[skr3178]

Ok I will for the new release.