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

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* 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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@ -5155,84 +5155,98 @@ of @code{xmlfile}.")
(license license:expat))) (license license:expat)))
(define-public python-omero-py (define-public python-omero-py
(package (let ((omero-blitz-version "5.8.2"))
(name "python-omero-py") (package
(version "5.13.1") (name "python-omero-py")
(source (origin (version "5.20.0")
(method git-fetch) (source
(uri (git-reference (origin
(url "https://github.com/ome/omero-py") (method git-fetch)
(commit (string-append "v" version)))) (uri (git-reference
(file-name (git-file-name name version)) (url "https://github.com/ome/omero-py")
(sha256 (commit (string-append "v" version))))
(base32 (file-name (git-file-name name version))
"0n94v5dpmh873hjqd9k9ky85iab4xh37ibmi13rqpclv01ibvvxa")))) (sha256
(build-system pyproject-build-system) (base32 "02zsw1p35n6lkqh410qpgw7c4467dkbg0hxly3gjqrwdh349j47g"))))
(arguments (build-system pyproject-build-system)
(list (arguments
#:test-flags (list
'(list "-m" "not broken" "-rf" "test" "-s" ;; #:tests? #f
;; TestImport tries to download Java things; TestSessions #:test-flags
;; and TestBuildQuery require networking. #~(list
"-k" "not TestImport and not TestSessions and not TestBuildQuery") "-m" "not broken" "-rf" "test" "-s"
#:modules '((guix build pyproject-build-system) ;; XXX: Failing collection because of Numpy compatibility.
(guix build utils) "--ignore=test/unit/tablestest/test_hdfstorage.py"
(ice-9 match) "--ignore=test/unit/tablestest/test_servants.py"
(srfi srfi-1) ;; TestImport tries to download Java things; TestSessions
(srfi srfi-26)) ;; and TestBuildQuery require networking.
#:phases "-k" "not TestImport and not TestSessions and not TestBuildQuery")
#~(modify-phases %standard-phases #:modules '((guix build pyproject-build-system)
(add-after 'unpack 'find-artifacts (guix build utils)
(lambda* (#:key inputs #:allow-other-keys) (ice-9 match)
(let ((zip-file (srfi srfi-1)
(match inputs (srfi srfi-26))
(((labels . files) ...) #:phases
(find (cut string-suffix? "omero-blitz-5.5.5-python.zip" <>) #~(modify-phases %standard-phases
files))))) (add-after 'unpack 'find-artifacts
(setenv "ZIP_FILE" (lambda* (#:key inputs #:allow-other-keys)
(or zip-file (error "failed to find artifact file")))))) (let ((zip-file
;; Some tests need this, such as TestTempFileManager (match inputs
(add-after 'build 'set-HOME (((labels . files) ...)
(lambda _ (setenv "HOME" "/tmp"))) (find (cut string-suffix?
;; The sanity check mistakes omero_model_TypeAnnotationI.py for a (string-append "omero-blitz-"
;; module to load. #$omero-blitz-version
(delete 'sanity-check) "-python.zip")
;; The argument parser is picky and interprets the "-real" part as <>)
;; the first argument. files)))))
(add-after 'wrap 'rename-executable (setenv "ZIP_FILE"
(lambda _ (or zip-file (error "failed to find artifact file"))))))
(with-directory-excursion (string-append #$output "/bin") ;; Some tests need this, such as TestTempFileManager
(rename-file ".omero-real" ".omero") (add-after 'build 'set-HOME
(substitute* "omero" (lambda _ (setenv "HOME" "/tmp")))
(("bin/.omero-real") "bin/.omero")))))))) ;; The sanity check mistakes omero_model_TypeAnnotationI.py for a
(propagated-inputs ;; module to load.
(list python-appdirs (delete 'sanity-check)
python-future ;; The argument parser is picky and interprets the "-real" part as
python-numpy ;; the first argument.
python-pillow (add-after 'wrap 'rename-executable
python-pyyaml (lambda _
python-requests (with-directory-excursion (string-append #$output "/bin")
python-tables (rename-file ".omero-real" ".omero")
python-zeroc-ice-3.6)) (substitute* "omero"
(native-inputs (("bin/.omero-real") "bin/.omero"))))))))
(list python-mox3 (propagated-inputs
python-pytest (list python-appdirs
python-pytest-rerunfailures python-future
python-pytest-xdist python-numpy-2
python-setuptools python-pillow
python-wheel python-pyyaml
unzip python-requests
(origin python-tables
(method url-fetch) python-zeroc-ice-3.6))
(uri "https://artifacts.openmicroscopy.org/artifactory/\ (native-inputs
ome.releases/org/openmicroscopy/omero-blitz/5.5.5/omero-blitz-5.5.5-python.zip") (list python-portalocker
(sha256 python-pytest
(base32 "0wyja1zv19c1r3m31gsp555jzj3cg2v2pl00zlybpw3qd36yffwc"))))) python-pytest-mock
(home-page "https://github.com/ome/omero-py") python-pytest-rerunfailures
(synopsis "Python bindings to the OMERO.blitz server") python-pytest-xdist
(description "This package provides Python bindings to the OMERO.blitz python-setuptools
python-wheel
unzip
(origin
(method url-fetch)
(uri (format #f "\
https://artifacts.openmicroscopy.org/artifactory/ome.releases/org/\
openmicroscopy/omero-blitz/~a/omero-blitz-~a-python.zip"
omero-blitz-version
omero-blitz-version))
(sha256
(base32 "1nb17xmx6n7i5vkcw661iq42yfgc3i0gmhz3x8iwcrhp8pajzm3l")))))
(home-page "https://github.com/ome/omero-py")
(synopsis "Python bindings to the OMERO.blitz server")
(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