04/04: gnu: Add python-omero-py.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit d7673b49c086c898a8e749fd042081dc9d4631b8
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Mar 28 17:56:53 2023 +0200

    gnu: Add python-omero-py.
    
    * gnu/packages/python-xyz.scm (python-omero-py): New variable.
---
 gnu/packages/python-xyz.scm | 78 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 78 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 58c28b68a7..615ee37537 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -2891,6 +2891,84 @@ from @code{lxml}.  It aims to provide a low memory, 
compatible implementation
 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
+           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
+server.")
+    (license license:gpl2)))
+
 (define-public python-openpyxl
   (package
     (name "python-openpyxl")