~ruther/guix-local

08b18b4422b797ece6b8bb50fc3a425fcd039bbe — Sharlatan Hellseher 2 months ago 8225669 
gnu: gdc-client: Update to 2.3, fix build.

* gnu/packages/bioinformatics.scm (gdc-client): Update to 2.3.
[arguments] <phases>: Rework 'relax-requirements for the refresh
criteria; add 'fix-pytest-config.
[inputs]: Remove python-cryptography, python-ndg-httpsclient,
python-pyasn1, and python-pyopenssl; add python-importlib-metadata.
[native-inputs]: Remove python-wheel; add python-flask, python-httmock,
python-moto, python-pytest, and python-requests-mock.

Change-Id: Ia51c934fcac473f0b88e1d69077c66fbf62e0ebc
patch browse .tar.gz 
1 files changed, 32 insertions(+), 22 deletions(-)

M gnu/packages/bioinformatics.scm

M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +32 -22
@@ 14426,36 14426,46 @@ quality control are provided.")
(define-public gdc-client
  (package
    (name "gdc-client")
    (version "1.6.0")
    (version "2.3")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/NCI-GDC/gdc-client.git")
             (commit version)))
              (url "https://github.com/NCI-GDC/gdc-client.git")
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0cagawlzjwj3wam10lv64xgbfx4zcnzxi5sjpsdhq7rn4z24mzc2"))))
        (base32 "1yzd8j3p7w9x00qj6mx8kvlv253063pdnf7ixpkqmmwzbjhv072s"))))
    (build-system pyproject-build-system)
    (arguments
     `(#:phases (modify-phases %standard-phases
                  (add-after 'unpack 'relax-requirements
                    (lambda _
                      (substitute* "requirements.txt"
                        (("==")
                         ">=")))))))
    (inputs (list python-cryptography
                  python-intervaltree
                  python-jsonschema
                  python-lxml
                  python-ndg-httpsclient
                  python-progressbar2
                  python-pyasn1
                  python-pyopenssl
                  python-pyyaml
                  python-requests
                  python-termcolor))
    (native-inputs (list python-setuptools python-wheel))
     (list
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'relax-requirements
            (lambda _
              (substitute* "setup.cfg"
                (("intervaltree~=3.0.2") "intervaltree")
                (("termcolor~=1.1.0") "termcolor"))))
          (add-after 'unpack 'fix-pytest-config
            (lambda _
              (substitute* "pyproject.toml"
                ((" --cov=gdc_client --cov-report term") "")))))))
    (native-inputs
     (list python-flask
           python-httmock
           python-moto
           python-pytest
           python-requests-mock
           python-setuptools))
    (inputs
     (list python-importlib-metadata
           python-intervaltree
           python-jsonschema
           python-lxml
           python-progressbar2
           python-pyyaml
           python-requests
           python-termcolor))
    (home-page "https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool")
    (synopsis "GDC data transfer tool")
    (description