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Hello community,
here is the log from the commit of package python-pymol for openSUSE:Factory
checked in at 2024-06-27 16:01:26
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-pymol (Old)
and /work/SRC/openSUSE:Factory/.python-pymol.new.18349 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-pymol"
Thu Jun 27 16:01:26 2024 rev:11 rq:1183332 version:3.0.0
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-pymol/python-pymol.changes
2023-08-18 19:29:53.219480297 +0200
+++ /work/SRC/openSUSE:Factory/.python-pymol.new.18349/python-pymol.changes
2024-06-27 16:02:08.624058692 +0200
@@ -1,0 +2,34 @@
+Tue Jun 18 15:42:12 UTC 2024 - <hs...@mail.de>
+
+- update to 3.0.0
+ * Panels
+ - Nucleic Acid Builder supported
+ - Scenes Panel (Basic version)
+ - Improved APBS electrostatics plugin integrated
+ * Distance/Bonding detection
+ - Halogen-bond detection and display
+ * Python API
+ - "fnab" command (sequence to nucleic acid chain)
+ - Improved CGO builder API
+ - get_sasa_relative() "subsele" argument added
+ - new clip modes/API
+ - iterate() adds "explicit_valence" and "explicit_degree"
+ - "cell_centered" setting added
+ - by grid-cell background gradient "bg_gradient=2"
+ - look_at() added
+ - experimental "curve_new" / "move_on_curve"
+ * Developer
+ - C++17 required
+ - pymol-testing integrated
+ - pytest introduced
+ - Github Actions CI
+ * And many other fixes and small additions provided by
+ developers and the community...
+- spec file:
+ * re-add test related stuff as upstream introduced a pytest
+ based testing
+ * drop TestExporting.testglTF - requires an executable from
+ Schrodinger
+ * on Leap, drop / tweak some tests to fit old package versions
+
+-------------------------------------------------------------------
Old:
----
pymol-open-source-2.5.0.tar.gz
New:
----
pymol-open-source-3.0.0.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-pymol.spec ++++++
--- /var/tmp/diff_new_pack.TFM5Uw/_old 2024-06-27 16:02:09.344085126 +0200
+++ /var/tmp/diff_new_pack.TFM5Uw/_new 2024-06-27 16:02:09.344085126 +0200
@@ -1,7 +1,7 @@
#
# spec file for package python-pymol
#
-# Copyright (c) 2021 SUSE LLC
+# Copyright (c) 2024 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -16,17 +16,18 @@
#
+%bcond_with test
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
%define skip_python2 1
%define oldpython python
%define modname pymol-open-source
Name: python-pymol
-Version: 2.5.0
+Version: 3.0.0
Release: 0
Summary: A Molecular Viewer
License: Python-2.0
Group: Productivity/Scientific/Chemistry
-URL: https://pymol.org/2/
+URL: https://pymol.org/
Source0:
https://github.com/schrodinger/%{modname}/archive/v%{version}/%{modname}-%{version}.tar.gz
# PATCH-FIX-OPENSUSE no-build-date.patch dh...@wustl.edu -- patch eliminates
build date
Patch0: no-build-date.patch
@@ -34,7 +35,6 @@
Patch1: no-o3.patch
BuildRequires: %{python_module devel}
BuildRequires: %{python_module numpy-devel}
-BuildRequires: %{python_module pytest}
BuildRequires: %{python_module qt5-devel}
BuildRequires: %{python_module setuptools}
BuildRequires: fdupes
@@ -48,6 +48,16 @@
BuildRequires: mmtf-cpp-devel
BuildRequires: netcdf-devel
BuildRequires: python-rpm-macros
+%if %{with test}
+BuildRequires: Catch2-2-devel
+BuildRequires: %{python_module Pillow}
+## 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
@@ -76,23 +86,38 @@
%prep
%setup -q -n %{modname}-%{version}
%autopatch -p1
+
%build
export CXXFLAGS="%{optflags} -fno-strict-aliasing"
-%python_build
+%python_build %{?with_test:--testing}
%install
%python_install
%python_clone -a %{buildroot}%{_bindir}/pymol
%python_expand %fdupes %{buildroot}%{$python_sitearch}
+%check
+%if %{with test}
+## TestExporting.testglTF requires a special executable from Schrodinger
+sed -e '/def testglTF(self):/,+7d' -i testing/tests/api/exporting.py
+%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
+## pymol -ckqy testing/testing.py --run all
+PYTHONPATH=%{buildroot}%{python_sitearch} python%{python_version} -m pymol
-ckqy testing/testing.py --offline --run all
+%endif
+
%post
%python_install_alternative pymol
%postun
%python_uninstall_alternative pymol
-%check
-
%files %{python_files}
%doc README ChangeLog
%license LICENSE
++++++ pymol-open-source-2.5.0.tar.gz -> pymol-open-source-3.0.0.tar.gz ++++++
/work/SRC/openSUSE:Factory/python-pymol/pymol-open-source-2.5.0.tar.gz
/work/SRC/openSUSE:Factory/.python-pymol.new.18349/pymol-open-source-3.0.0.tar.gz
differ: char 12, line 1
