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>
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guix-patches <at> gnu.org:bug#77986; Package guix-patches.
(Tue, 22 Apr 2025 12:03:01 GMT) Full text and rfc822 format available.Nicolas Graves <ngraves <at> ngraves.fr>:guix-patches <at> gnu.org.
(Tue, 22 Apr 2025 12:03:01 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: guix-patches <at> gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 0/2] Update and fix python-omero-py. Date: Tue, 22 Apr 2025 14:02:01 +0200
Nicolas Graves (2): gnu: python-zeroc-ice-3.6: Fix build with Python <at> 3.11. gnu: python-omero-py: Update to 5.20.0. ...-zeroc-ice-3.6.5-python-3.11-support.patch | 33 ++++ gnu/packages/python-xyz.scm | 173 ++++++++++-------- 2 files changed, 128 insertions(+), 78 deletions(-) create mode 100644 gnu/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch -- 2.49.0
guix-patches <at> gnu.org:bug#77986; Package guix-patches.
(Tue, 22 Apr 2025 12:05:01 GMT) Full text and rfc822 format available.Message #8 received at 77986 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77986 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [PATCH 1/2] gnu: python-zeroc-ice-3.6: Fix build with Python <at> 3.11. Date: Tue, 22 Apr 2025 14:04:03 +0200
* gnu/packages/python-xyz.scm (python-zeroc-ice-3.6)
[source]: Add patch.
* gnu/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch:
Add patch.
---
...-zeroc-ice-3.6.5-python-3.11-support.patch | 33 +++++++++++++++++++
gnu/packages/python-xyz.scm | 5 ++-
2 files changed, 37 insertions(+), 1 deletion(-)
create mode 100644 gnu/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch
diff --git a/gnu/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch b/gnu/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch
new file mode 100644
index 00000000000..17cae7297c0
--- /dev/null
+++ b/gnu/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch
@@ -0,0 +1,33 @@
+Only in zeroc-ice-3.6.5: setup.py.orig
+diff --color -ur zeroc-ice-3.6.5.orig/src/Slice.cpp zeroc-ice-3.6.5/src/Slice.cpp
+--- zeroc-ice-3.6.5.orig/src/Slice.cpp 2019-07-31 21:49:38.000000000 +0200
++++ zeroc-ice-3.6.5/src/Slice.cpp 2023-10-12 10:52:07.029069937 +0200
+@@ -17,12 +17,6 @@
+ #include <Slice/Util.h>
+ #include <IceUtil/Options.h>
+
+-//
+-// Python headers needed for PyEval_EvalCode.
+-//
+-#include <compile.h>
+-#include <eval.h>
+-
+ using namespace std;
+ using namespace IcePy;
+ using namespace Slice;
+diff --color -ur zeroc-ice-3.6.5.orig/src/Util.cpp zeroc-ice-3.6.5/src/Util.cpp
+--- zeroc-ice-3.6.5.orig/src/Util.cpp 2019-07-31 21:49:38.000000000 +0200
++++ zeroc-ice-3.6.5/src/Util.cpp 2023-10-12 10:49:15.033366926 +0200
+@@ -214,7 +214,12 @@
+ //
+ // Get name of current function.
+ //
++ // Use PyEval_GetFrame with Pyhthon >= 3.11
++#if PY_VERSION_HEX >= 0x030B0000
++ PyFrameObject *f = PyEval_GetFrame();
++#else
+ PyFrameObject *f = PyThreadState_GET()->frame;
++#endif
+ PyObjectHandle code = PyObject_GetAttrString(reinterpret_cast<PyObject*>(f), STRCAST("f_code"));
+ assert(code.get());
+ PyObjectHandle func = PyObject_GetAttrString(code.get(), STRCAST("co_name"));
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ef66d071677..1fbd1730b01 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -40633,7 +40633,10 @@ (define-public python-zeroc-ice-3.6
(uri (pypi-uri "zeroc-ice" version))
(sha256
(base32
- "0mikjfvq26kh8asnn9v55z41pap4c5ypymqnwwi4xkavc3mzyda2"))))))
+ "0mikjfvq26kh8asnn9v55z41pap4c5ypymqnwwi4xkavc3mzyda2"))
+ (patches
+ (search-patches
+ "python-zeroc-ice-3.6.5-python-3.11-support.patch"))))))
(define-public python-whenever
(package
--
2.49.0
guix-patches <at> gnu.org:bug#77986; Package guix-patches.
(Tue, 22 Apr 2025 12:05:02 GMT) Full text and rfc822 format available.Message #11 received at 77986 <at> debbugs.gnu.org (full text, mbox):
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 77986 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [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
--
2.49.0
Sharlatan Hellseher <sharlatanus <at> gmail.com>:Nicolas Graves <ngraves <at> ngraves.fr>:Message #16 received at 77986-done <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 77986-done <at> debbugs.gnu.org Subject: [PATCH 0/2] Update and fix python-omero-py. Date: Wed, 23 Apr 2025 23:19:05 +0100
[Message part 1 (text/plain, inline)]
Hi, Thanks for resolving it! Pushed to master as: 3901b539d2 * gnu: python-omero-py: Update to 5.20.0. 03c4dc54a7 * gnu: python-zeroc-ice-3.6: Fix build with Python <at> 3.11. -- Oleg
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