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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
Sharlatan Hellseher
parent
03c4dc54a7
commit
3901b539d2
1 changed files with 91 additions and 77 deletions
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@ -5155,84 +5155,98 @@ of @code{xmlfile}.")
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(license license:expat)))
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(define-public python-omero-py
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(package
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(name "python-omero-py")
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(version "5.13.1")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/ome/omero-py")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0n94v5dpmh873hjqd9k9ky85iab4xh37ibmi13rqpclv01ibvvxa"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:test-flags
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'(list "-m" "not broken" "-rf" "test" "-s"
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;; TestImport tries to download Java things; TestSessions
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;; and TestBuildQuery require networking.
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"-k" "not TestImport and not TestSessions and not TestBuildQuery")
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#:modules '((guix build pyproject-build-system)
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(guix build utils)
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(ice-9 match)
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(srfi srfi-1)
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(srfi srfi-26))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'find-artifacts
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((zip-file
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(match inputs
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(((labels . files) ...)
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(find (cut string-suffix? "omero-blitz-5.5.5-python.zip" <>)
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files)))))
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(setenv "ZIP_FILE"
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(or zip-file (error "failed to find artifact file"))))))
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;; Some tests need this, such as TestTempFileManager
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(add-after 'build 'set-HOME
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(lambda _ (setenv "HOME" "/tmp")))
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;; The sanity check mistakes omero_model_TypeAnnotationI.py for a
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;; module to load.
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(delete 'sanity-check)
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;; The argument parser is picky and interprets the "-real" part as
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;; the first argument.
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(add-after 'wrap 'rename-executable
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(lambda _
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(with-directory-excursion (string-append #$output "/bin")
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(rename-file ".omero-real" ".omero")
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(substitute* "omero"
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(("bin/.omero-real") "bin/.omero"))))))))
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(propagated-inputs
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(list python-appdirs
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python-future
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python-numpy
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python-pillow
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python-pyyaml
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python-requests
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python-tables
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python-zeroc-ice-3.6))
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(native-inputs
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(list python-mox3
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python-pytest
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python-pytest-rerunfailures
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python-pytest-xdist
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python-setuptools
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python-wheel
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unzip
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(origin
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(method url-fetch)
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(uri "https://artifacts.openmicroscopy.org/artifactory/\
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ome.releases/org/openmicroscopy/omero-blitz/5.5.5/omero-blitz-5.5.5-python.zip")
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(sha256
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(base32 "0wyja1zv19c1r3m31gsp555jzj3cg2v2pl00zlybpw3qd36yffwc")))))
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(home-page "https://github.com/ome/omero-py")
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(synopsis "Python bindings to the OMERO.blitz server")
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(description "This package provides Python bindings to the OMERO.blitz
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(let ((omero-blitz-version "5.8.2"))
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(package
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(name "python-omero-py")
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(version "5.20.0")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/ome/omero-py")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "02zsw1p35n6lkqh410qpgw7c4467dkbg0hxly3gjqrwdh349j47g"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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;; #:tests? #f
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#:test-flags
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#~(list
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"-m" "not broken" "-rf" "test" "-s"
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;; XXX: Failing collection because of Numpy compatibility.
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"--ignore=test/unit/tablestest/test_hdfstorage.py"
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"--ignore=test/unit/tablestest/test_servants.py"
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;; TestImport tries to download Java things; TestSessions
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;; and TestBuildQuery require networking.
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"-k" "not TestImport and not TestSessions and not TestBuildQuery")
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#:modules '((guix build pyproject-build-system)
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(guix build utils)
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(ice-9 match)
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(srfi srfi-1)
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(srfi srfi-26))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'find-artifacts
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((zip-file
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(match inputs
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(((labels . files) ...)
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(find (cut string-suffix?
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(string-append "omero-blitz-"
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#$omero-blitz-version
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"-python.zip")
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<>)
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files)))))
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(setenv "ZIP_FILE"
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(or zip-file (error "failed to find artifact file"))))))
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;; Some tests need this, such as TestTempFileManager
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(add-after 'build 'set-HOME
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(lambda _ (setenv "HOME" "/tmp")))
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;; The sanity check mistakes omero_model_TypeAnnotationI.py for a
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;; module to load.
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(delete 'sanity-check)
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;; The argument parser is picky and interprets the "-real" part as
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;; the first argument.
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(add-after 'wrap 'rename-executable
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(lambda _
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(with-directory-excursion (string-append #$output "/bin")
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(rename-file ".omero-real" ".omero")
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(substitute* "omero"
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(("bin/.omero-real") "bin/.omero"))))))))
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(propagated-inputs
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(list python-appdirs
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python-future
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python-numpy-2
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python-pillow
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python-pyyaml
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python-requests
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python-tables
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python-zeroc-ice-3.6))
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(native-inputs
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(list python-portalocker
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python-pytest
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python-pytest-mock
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python-pytest-rerunfailures
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python-pytest-xdist
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python-setuptools
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python-wheel
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unzip
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(origin
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(method url-fetch)
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(uri (format #f "\
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https://artifacts.openmicroscopy.org/artifactory/ome.releases/org/\
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openmicroscopy/omero-blitz/~a/omero-blitz-~a-python.zip"
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omero-blitz-version
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omero-blitz-version))
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(sha256
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(base32 "1nb17xmx6n7i5vkcw661iq42yfgc3i0gmhz3x8iwcrhp8pajzm3l")))))
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(home-page "https://github.com/ome/omero-py")
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(synopsis "Python bindings to the OMERO.blitz server")
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(description "This package provides Python bindings to the OMERO.blitz
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server.")
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(license license:gpl2)))
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(license license:gpl2))))
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(define-public python-openpyxl
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(package
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