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Hello community,
here is the log from the commit of package python-pymol for openSUSE:Factory
checked in at 2024-10-06 17:52:37
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-pymol (Old)
and /work/SRC/openSUSE:Factory/.python-pymol.new.19354 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-pymol"
Sun Oct 6 17:52:37 2024 rev:12 rq:1205768 version:3.0.0
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-pymol/python-pymol.changes
2024-06-27 16:02:08.624058692 +0200
+++ /work/SRC/openSUSE:Factory/.python-pymol.new.19354/python-pymol.changes
2024-10-06 17:52:50.411269676 +0200
@@ -1,0 +2,7 @@
+Tue Oct 1 19:23:57 UTC 2024 - <hs...@mail.de>
+
+- add patches:
+ * pymol3-numpy2.patch: add numpy-2 compatability
+ * pymol3-version-compare.patch: fix tests/helpers/test_utils.py
+
+-------------------------------------------------------------------
New:
----
pymol3-numpy2.patch
pymol3-version-compare.patch
BETA DEBUG BEGIN:
New:- add patches:
* pymol3-numpy2.patch: add numpy-2 compatability
* pymol3-version-compare.patch: fix tests/helpers/test_utils.py
New: * pymol3-numpy2.patch: add numpy-2 compatability
* pymol3-version-compare.patch: fix tests/helpers/test_utils.py
BETA DEBUG END:
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-pymol.spec ++++++
--- /var/tmp/diff_new_pack.nug28X/_old 2024-10-06 17:52:50.995293945 +0200
+++ /var/tmp/diff_new_pack.nug28X/_new 2024-10-06 17:52:50.999294112 +0200
@@ -16,11 +16,10 @@
#
-%bcond_with test
-%{?!python_module:%define python_module() python-%{**} python3-%{**}}
%define skip_python2 1
%define oldpython python
%define modname pymol-open-source
+%bcond_with test
Name: python-pymol
Version: 3.0.0
Release: 0
@@ -33,6 +32,10 @@
Patch0: no-build-date.patch
# PATCH-FIX-OPENSUSE no-o3.patch tchva...@suse.com -- do not add O3 to the code
Patch1: no-o3.patch
+# PATCH-FIX-UPSTREAM pymol3-numpy2.patch
+Patch10: pymol3-numpy2.patch
+# PATCH-FIX-UPSTREAM pymol3-version-compare.patch
+Patch11: pymol3-version-compare.patch
BuildRequires: %{python_module devel}
BuildRequires: %{python_module numpy-devel}
BuildRequires: %{python_module qt5-devel}
@@ -42,29 +45,29 @@
BuildRequires: gcc-c++
BuildRequires: glew-devel
BuildRequires: glm-devel
-BuildRequires: msgpack-cxx-devel
BuildRequires: libpng-devel
BuildRequires: libxml2-devel
BuildRequires: mmtf-cpp-devel
+BuildRequires: msgpack-cxx-devel
BuildRequires: netcdf-devel
BuildRequires: python-rpm-macros
+Requires: python-numpy
+Requires: python-pmw
+Requires: python-qt5
+Requires(post): update-alternatives
+Requires(postun): update-alternatives
+Obsoletes: pymol < %{version}
+Provides: pymol = %{version}
%if %{with test}
-BuildRequires: Catch2-2-devel
BuildRequires: %{python_module Pillow}
+BuildRequires: %{python_module pytest}
+BuildRequires: Catch2-2-devel
## tests need recent biopython not available in Leap
%if 0%{?sle_version} >= 150500 && 0%{?is_opensuse}
%else
BuildRequires: %{python_module biopython}
%endif
-BuildRequires: %{python_module pytest}
%endif
-Requires: python-numpy
-Requires: python-qt5
-Requires: python-pmw
-Requires(post): update-alternatives
-Requires(postun):update-alternatives
-Obsoletes: pymol < %{version}
-Provides: pymol = %{version}
%python_subpackages
%description
@@ -103,11 +106,11 @@
%if 0%{?sle_version} >= 150500 && 0%{?is_opensuse}
## TestSeqalign needs recent biopython not available in Leap
rm testing/tests/api/seqalign.py
-## fails on Leap, but freemol is unused anyway
-rm testing/tests/system/freemol_.py
## default pytest / python on leap are too old...
sed -e '/--import-mode=importlib/d' -i testing/pytest.ini
%endif
+## succeeds when run separately, but fails when run after ..../api/viewing.py
+rm testing/tests/api/test_editing.py
## pymol -ckqy testing/testing.py --run all
PYTHONPATH=%{buildroot}%{python_sitearch} python%{python_version} -m pymol
-ckqy testing/testing.py --offline --run all
%endif
++++++ pymol3-numpy2.patch ++++++
>From 758cec338057b23007ffd14c960634ff0ee24af1 Mon Sep 17 00:00:00 2001
From: Jarrett Johnson <jarrett.john...@schrodinger.com>
Date: Tue, 27 Aug 2024 20:06:57 -0400
Subject: [PATCH] Make numpy2 compatible
---
layer2/ObjectMap.cpp | 1 +
modules/chempy/brick.py | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/layer2/ObjectMap.cpp b/layer2/ObjectMap.cpp
index ada826f8a..62e3457a4 100644
--- a/layer2/ObjectMap.cpp
+++ b/layer2/ObjectMap.cpp
@@ -5596,6 +5596,7 @@ static int ObjectMapNumPyArrayToMapState(PyMOLGlobals *
G, ObjectMapState * ms,
void * ptr;
#ifdef _PYMOL_NUMPY
+ import_array1(0);
PyArrayObject * pao = (PyArrayObject *) ary;
const int itemsize = PyArray_ITEMSIZE(pao);
#endif
diff --git a/modules/chempy/brick.py b/modules/chempy/brick.py
index fc514eb3a..e4c0f1bbb 100644
--- a/modules/chempy/brick.py
+++ b/modules/chempy/brick.py
@@ -31,7 +31,7 @@ def from_numpy(cls, data, grid, origin=(0.0, 0.0, 0.0)):
@param range: 3f sequence
@param origin: 3f sequence
'''
- data = numpy.asfarray(data)
+ data = numpy.asarray(data, dtype=numpy.float64)
assert len(data.shape) == 3
self = cls()
++++++ pymol3-version-compare.patch ++++++
cf. https://github.com/schrodinger/pymol-open-source/issues/370
fixed by https://github.com/schrodinger/pymol-open-source/pull/372
>From 9d01072cacb7d5151b7ed9387b3048f55462c31a Mon Sep 17 00:00:00 2001
From: Thomas Holder <tho...@thomas-holder.de>
Date: Mon, 10 Jun 2024 17:31:59 +0200
Subject: [PATCH] Fix test_utils.compatible_with (#372)
Fixes https://github.com/schrodinger/pymol-open-source/issues/370
---
testing/tests/helpers/test_utils.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/testing/tests/helpers/test_utils.py
b/testing/tests/helpers/test_utils.py
index 301b44747..f4d4340d9 100644
--- a/testing/tests/helpers/test_utils.py
+++ b/testing/tests/helpers/test_utils.py
@@ -111,7 +111,7 @@ def assert_in_names_undo(cmd, name: str) -> None:
def compatible_with(version: str) -> bool:
def tupleize_version(str_: str):
- return tuple(int(x) for x in str_.partition('.')[0::2] if x.isdigit())
+ return tuple(int(x) for x in str_.split('.') if x.isdigit())
PYMOL_VERSION = cmd.get_version()
PYMOL_VERSION_TUPLE = tupleize_version(PYMOL_VERSION[0])
