diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e2f025c13b2..0d5535263d1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5155,84 +5155,98 @@ of @code{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