gnu: python-omero-py: Update to 5.20.0.

* gnu/packages/python-xyz.scm (python-omero-py): Update to 5.20.0.
  [arguments]<test-flags>: Ignore collection of some tests (which should
  be fixed when updating to numpy@2).
  [native-inputs]: Add python-portalocker. Update omero-blitz to 5.8.2.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
This commit is contained in:
Nicolas Graves 2025-04-22 14:04:04 +02:00 committed by Sharlatan Hellseher
parent 03c4dc54a7
commit 3901b539d2
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@ -5155,23 +5155,29 @@ of @code{xmlfile}.")
(license license:expat))) (license license:expat)))
(define-public python-omero-py (define-public python-omero-py
(let ((omero-blitz-version "5.8.2"))
(package (package
(name "python-omero-py") (name "python-omero-py")
(version "5.13.1") (version "5.20.0")
(source (origin (source
(origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/ome/omero-py") (url "https://github.com/ome/omero-py")
(commit (string-append "v" version)))) (commit (string-append "v" version))))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32 "02zsw1p35n6lkqh410qpgw7c4467dkbg0hxly3gjqrwdh349j47g"))))
"0n94v5dpmh873hjqd9k9ky85iab4xh37ibmi13rqpclv01ibvvxa"))))
(build-system pyproject-build-system) (build-system pyproject-build-system)
(arguments (arguments
(list (list
;; #:tests? #f
#:test-flags #:test-flags
'(list "-m" "not broken" "-rf" "test" "-s" #~(list
"-m" "not broken" "-rf" "test" "-s"
;; XXX: Failing collection because of Numpy compatibility.
"--ignore=test/unit/tablestest/test_hdfstorage.py"
"--ignore=test/unit/tablestest/test_servants.py"
;; TestImport tries to download Java things; TestSessions ;; TestImport tries to download Java things; TestSessions
;; and TestBuildQuery require networking. ;; and TestBuildQuery require networking.
"-k" "not TestImport and not TestSessions and not TestBuildQuery") "-k" "not TestImport and not TestSessions and not TestBuildQuery")
@ -5187,7 +5193,11 @@ of @code{xmlfile}.")
(let ((zip-file (let ((zip-file
(match inputs (match inputs
(((labels . files) ...) (((labels . files) ...)
(find (cut string-suffix? "omero-blitz-5.5.5-python.zip" <>) (find (cut string-suffix?
(string-append "omero-blitz-"
#$omero-blitz-version
"-python.zip")
<>)
files))))) files)))))
(setenv "ZIP_FILE" (setenv "ZIP_FILE"
(or zip-file (error "failed to find artifact file")))))) (or zip-file (error "failed to find artifact file"))))))
@ -5208,15 +5218,16 @@ of @code{xmlfile}.")
(propagated-inputs (propagated-inputs
(list python-appdirs (list python-appdirs
python-future python-future
python-numpy python-numpy-2
python-pillow python-pillow
python-pyyaml python-pyyaml
python-requests python-requests
python-tables python-tables
python-zeroc-ice-3.6)) python-zeroc-ice-3.6))
(native-inputs (native-inputs
(list python-mox3 (list python-portalocker
python-pytest python-pytest
python-pytest-mock
python-pytest-rerunfailures python-pytest-rerunfailures
python-pytest-xdist python-pytest-xdist
python-setuptools python-setuptools
@ -5224,15 +5235,18 @@ of @code{xmlfile}.")
unzip unzip
(origin (origin
(method url-fetch) (method url-fetch)
(uri "https://artifacts.openmicroscopy.org/artifactory/\ (uri (format #f "\
ome.releases/org/openmicroscopy/omero-blitz/5.5.5/omero-blitz-5.5.5-python.zip") https://artifacts.openmicroscopy.org/artifactory/ome.releases/org/\
openmicroscopy/omero-blitz/~a/omero-blitz-~a-python.zip"
omero-blitz-version
omero-blitz-version))
(sha256 (sha256
(base32 "0wyja1zv19c1r3m31gsp555jzj3cg2v2pl00zlybpw3qd36yffwc"))))) (base32 "1nb17xmx6n7i5vkcw661iq42yfgc3i0gmhz3x8iwcrhp8pajzm3l")))))
(home-page "https://github.com/ome/omero-py") (home-page "https://github.com/ome/omero-py")
(synopsis "Python bindings to the OMERO.blitz server") (synopsis "Python bindings to the OMERO.blitz server")
(description "This package provides Python bindings to the OMERO.blitz (description "This package provides Python bindings to the OMERO.blitz
server.") server.")
(license license:gpl2))) (license license:gpl2))))
(define-public python-openpyxl (define-public python-openpyxl
(package (package