packaging python-cyvcf2

[Alexis Simon via Guix-Science <guix-science@gnu.org>]

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Hi, I've spent nearly the day on this and it's driving me crazy.

I am trying to package this cyvcf2 [1]
I am attaching the packaging I've tried.

The build is failing with this error:
running build_ext
# cyvcf2: htslib mode is BUILTIN
# cyvcf2: htslib configure options is None
error: [Errno 2] No such file or directory: './configure'
error: in phase 'build': uncaught exception:
%exception #<&invoke-error program: "python" arguments: ("./setup.py" 
"build") exit-status: 1 term-signal: #f stop-signal: #f>

What is very disturbing is that it builds fine in a debugging 
environment following the documentation [2]

The .configure file is present in the failed build, so there must be 
something going on with the setup.py not managing to change directory to 
htslib in the build_htslib function.

If anyone has any guidelines to debug this further it would be much 
appreciated.

Thanks,
Alexis

[1] https://github.com/brentp/cyvcf2/
[2] https://guix.gnu.org/manual/en/guix.html#Debugging-Build-Failures

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(define-module (cyvcf2)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cmake)
  #:use-module (gnu packages check)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-check)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages tls)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system python)
  #:use-module (guix build-system cargo)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system pyproject))

(define-public python-cyvcf2
  (package
    (name "python-cyvcf2")
    (version "0.30.28")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "cyvcf2" version))
       (sha256
        (base32 "03ycp7php5nzvhgj89k8js8z2xm3i8d1f76jlsfdy472f0apgryx"))))
    (build-system python-build-system)
    (arguments
     `(#:use-setuptools? #f
       #:phases
        (modify-phases %standard-phases
          (add-before 'build 'setenv
             (lambda _
                     (setenv "CYVCF2_HTSLIB_MODE" "BUILTIN")))))) ; unnecessary
    (propagated-inputs (list python-click
                             python-coloredlogs
                             python-numpy))
    (native-inputs (list zlib
                         libdeflate
                         curl
                         openssl
                         autoconf
                         automake
                         ; htslib
                         python-cython))
    (home-page "https://github.com/brentp/cyvcf2/")
    (synopsis "fast vcf parsing with cython + htslib")
    (description "fast vcf parsing with cython + htslib")
    (license license:expat)))