Package: guix-patches;
Reported by: Nicolas Graves <ngraves <at> ngraves.fr>
Date: Tue, 22 Apr 2025 12:03:01 UTC
Severity: normal
Tags: patch
Done: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77986 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [bug#77986] [PATCH 2/2] gnu: python-omero-py: Update to 5.20.0. Date: Tue, 22 Apr 2025 14:04:04 +0200
* 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 <at> 2).
[native-inputs]: Add python-portalocker. Update omero-blitz to 5.8.2.
---
gnu/packages/python-xyz.scm | 168 +++++++++++++++++++-----------------
1 file changed, 91 insertions(+), 77 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1fbd1730b01..e60d21207e4 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5155,84 +5155,98 @@ (define-public python-et-xmlfile
(license license:expat)))
(define-public python-omero-py
- (package
- (name "python-omero-py")
- (version "5.13.1")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/ome/omero-py")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0n94v5dpmh873hjqd9k9ky85iab4xh37ibmi13rqpclv01ibvvxa"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- '(list "-m" "not broken" "-rf" "test" "-s"
- ;; TestImport tries to download Java things; TestSessions
- ;; and TestBuildQuery require networking.
- "-k" "not TestImport and not TestSessions and not TestBuildQuery")
- #:modules '((guix build pyproject-build-system)
- (guix build utils)
- (ice-9 match)
- (srfi srfi-1)
- (srfi srfi-26))
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'find-artifacts
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((zip-file
- (match inputs
- (((labels . files) ...)
- (find (cut string-suffix? "omero-blitz-5.5.5-python.zip" <>)
- files)))))
- (setenv "ZIP_FILE"
- (or zip-file (error "failed to find artifact file"))))))
- ;; Some tests need this, such as TestTempFileManager
- (add-after 'build 'set-HOME
- (lambda _ (setenv "HOME" "/tmp")))
- ;; The sanity check mistakes omero_model_TypeAnnotationI.py for a
- ;; module to load.
- (delete 'sanity-check)
- ;; The argument parser is picky and interprets the "-real" part as
- ;; the first argument.
- (add-after 'wrap 'rename-executable
- (lambda _
- (with-directory-excursion (string-append #$output "/bin")
- (rename-file ".omero-real" ".omero")
- (substitute* "omero"
- (("bin/.omero-real") "bin/.omero"))))))))
- (propagated-inputs
- (list python-appdirs
- python-future
- python-numpy
- python-pillow
- python-pyyaml
- python-requests
- python-tables
- python-zeroc-ice-3.6))
- (native-inputs
- (list python-mox3
- python-pytest
- python-pytest-rerunfailures
- python-pytest-xdist
- python-setuptools
- python-wheel
- unzip
- (origin
- (method url-fetch)
- (uri "https://artifacts.openmicroscopy.org/artifactory/\
-ome.releases/org/openmicroscopy/omero-blitz/5.5.5/omero-blitz-5.5.5-python.zip")
- (sha256
- (base32 "0wyja1zv19c1r3m31gsp555jzj3cg2v2pl00zlybpw3qd36yffwc")))))
- (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
+ (let ((omero-blitz-version "5.8.2"))
+ (package
+ (name "python-omero-py")
+ (version "5.20.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ome/omero-py")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "02zsw1p35n6lkqh410qpgw7c4467dkbg0hxly3gjqrwdh349j47g"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ ;; #:tests? #f
+ #:test-flags
+ #~(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
+ ;; and TestBuildQuery require networking.
+ "-k" "not TestImport and not TestSessions and not TestBuildQuery")
+ #:modules '((guix build pyproject-build-system)
+ (guix build utils)
+ (ice-9 match)
+ (srfi srfi-1)
+ (srfi srfi-26))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'find-artifacts
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((zip-file
+ (match inputs
+ (((labels . files) ...)
+ (find (cut string-suffix?
+ (string-append "omero-blitz-"
+ #$omero-blitz-version
+ "-python.zip")
+ <>)
+ files)))))
+ (setenv "ZIP_FILE"
+ (or zip-file (error "failed to find artifact file"))))))
+ ;; Some tests need this, such as TestTempFileManager
+ (add-after 'build 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp")))
+ ;; The sanity check mistakes omero_model_TypeAnnotationI.py for a
+ ;; module to load.
+ (delete 'sanity-check)
+ ;; The argument parser is picky and interprets the "-real" part as
+ ;; the first argument.
+ (add-after 'wrap 'rename-executable
+ (lambda _
+ (with-directory-excursion (string-append #$output "/bin")
+ (rename-file ".omero-real" ".omero")
+ (substitute* "omero"
+ (("bin/.omero-real") "bin/.omero"))))))))
+ (propagated-inputs
+ (list python-appdirs
+ python-future
+ python-numpy-2
+ python-pillow
+ python-pyyaml
+ python-requests
+ python-tables
+ python-zeroc-ice-3.6))
+ (native-inputs
+ (list python-portalocker
+ python-pytest
+ python-pytest-mock
+ python-pytest-rerunfailures
+ python-pytest-xdist
+ 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.")
- (license license:gpl2)))
+ (license license:gpl2))))
(define-public python-openpyxl
(package
--
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