guix_mirror_bot pushed a commit to branch next-master
in repository guix.
commit a8f38ce9148e159dacac2372f878f91ea093af5d
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Thu Dec 4 21:23:32 2025 +0000
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
---
gnu/packages/bioinformatics.scm | 54 ++++++++++++++++++++++++-----------------
1 file changed, 32 insertions(+), 22 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1af7e21245..c08339bfd3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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
