(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 git-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 git-fetch)
        (uri (git-reference
              (url "https://github.com/brentp/cyvcf2")
              (commit (string-append "v" version))))
        (sha256
          (base32 "16yhfax509zyip8kkq2b0lflx5bdq5why7d785ayrqyzzq2rxqkk"))
        (modules '((guix build utils)))
        (snippet
         '(begin
            (delete-file-recursively "htslib")))))
    (build-system pyproject-build-system)
    (arguments
     `(#:tests? #f
       #:phases
        (modify-phases %standard-phases
          ; (add-before 'check 'rm-folder
          ;   (lambda _
          ;           (copy-recursively "cyvcf2/tests" "./tests")
          ;           (delete-file-recursively "cyvcf2")
          ;           (mkdir-p "cyvcf2")
          ;           (copy-recursively "tests" "cyvcf2/tests")))
          (add-after 'unpack 'fix-setup
             (lambda* (#:key inputs #:allow-other-keys)
                     (substitute* "setup.py"
                                  ((" or not check_libhts\\(\\)") "")
                                  (("library_dirs=htslib_library_dirs")
                                   (string-append "library_dirs=[\"" (assoc-ref inputs "htslib") "/lib\"]"))
                                  (("\\+ htslib_include_dirs")
                                   (string-append "+ [\"" (assoc-ref inputs "htslib") "/include\"]")))))
          (add-before 'build 'setenv
             (lambda _
                     (setenv "CYTHONIZE" "1")
                     (setenv "CYVCF2_HTSLIB_MODE" "EXTERNAL"))))))
    (inputs (list htslib zlib libdeflate curl openssl python-cython))
    (native-inputs (list python-pytest))
    (propagated-inputs (list python-click
                             python-coloredlogs
                             python-numpy))
    (home-page "https://github.com/brentp/cyvcf2/")
    (synopsis "fast vcf parsing with cython + htslib")
    (description "fast vcf parsing with cython + htslib")
    (license license:expat)))