Accepting request 1253250 from devel:languages:python:numeric

- changes to .spec file:
  * to make build work on leap 15.6, add sle15_python_module_pythons
    and conditional BuildRequires: gcc12-c++
  * drop skip_python2 and oldpython

OBS-URL: https://build.opensuse.org/request/show/1253250
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-pymol?expand=0&rev=16

no-build-date.patch

@@ -1,23 +0,0 @@
-From: David Hall <dhall@wustl.edu>
-Date: 2013-11-11 12:41:00 -0500
-Subject: do not include build date in package
-References:
-Upstream: never
-
-Patch removes including build date in binary
-
----
- create_shadertext.py |    2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
---- a/create_shadertext.py
-+++ b/create_shadertext.py
-@@ -133,7 +133,7 @@ def create_buildinfo(outputdir, pymoldir
-         print('''
- #define _PyMOL_BUILD_DATE %d
- #define _PYMOL_BUILD_GIT_SHA "%s"
--        ''' % (time.time(), sha), file=out)
-+        ''' % (0, sha), file=out)
- 
- if __name__ == "__main__":
-     create_shadertext(*sys.argv[1:6])

no-o3.patch

@@ -1,11 +0,0 @@
---- a/setup.py
-+++ b/setup.py
-@@ -272,8 +272,6 @@ ext_comp_args = [
-     "-Wno-narrowing",
-     # legacy stuff
-     '-Wno-char-subscripts',
--    # optimizations
--    "-Og" if DEBUG else "-O3",
- ] if not WIN else []
- ext_link_args = []
- ext_objects = []

pymol-open-source-3.0.0.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:45e800a02680cec62dff7a0f92283f4be7978c13a02934a43ac6bb01f67622cf
-size 29510174

pymol-open-source-3.1.0.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:54306d65060bd58ed8b3dab1a8af521aeb4fd417871f15f463ff05ccb4e121fe
+size 29550866

python-pymol.changes

@@ -1,3 +1,58 @@
+-------------------------------------------------------------------
+Fri Mar 14 17:31:28 UTC 2025 - Friedrich Haubensak <hsk17@mail.de>
+
+- changes to .spec file:
+  * to make build work on leap 15.6, add sle15_python_module_pythons
+    and conditional BuildRequires: gcc12-c++
+  * drop skip_python2 and oldpython
+
+-------------------------------------------------------------------
+Wed Mar 12 22:14:37 UTC 2025 - Friedrich Haubensak <hsk17@mail.de>
+
+- update to 3.1.0
+  * File Support
+    - BCIF import support
+    - gzipped-compressed SDF (SDFGZ) import support
+  * Python API
+    - "delete_states" command (removal of one or more states)
+    - "declare_command" extension for improved ergonomics of introducing
+      and customizing PyMOL functionality
+    - "cell_color" setting for altering unit cell colors
+  * Developer & Infrastructure
+    - Migration from distutils to setuptools
+
+-------------------------------------------------------------------
+Tue Nov 12 14:18:22 UTC 2024 - Bernhard Wiedemann <bwiedemann@suse.com>
+
+- Add reproducible.patch to normalize build date (boo#1047218)
+- Remove no-build-date.patch
+
+-------------------------------------------------------------------
+Thu Oct 10 23:20:52 UTC 2024 - mcepl@cepl.eu
+
+- Update to version 3.0.0+git.1725549602.9d3061c:
+  * Symbol renaming in molfile_plugin and internal linkage
+  * New command: delete_states
+  * mark bind() calls with override where needed
+  * Separate CGO to VBO logic out into functions
+  * Remove unused returnData
+  * Use vector for memory alloc
+  * Use struct for total vert counts in CGO.cpp
+  * Remove _PYMOL_IOS (Discontinued; prep for MVK)
+  * Python 3.12 TypeError: convert progress to int for progress bar
+  * Fix ray/draw panel error when modifying units
+- Remove upstream patches:
+  * pymol3-version-compare.patch
+  * no-o3.patch
+  * pymol3-numpy2.patch
+
+-------------------------------------------------------------------
+Tue Oct  1 19:23:57 UTC 2024 - <hsk17@mail.de>
+
+- add patches:
+  * pymol3-numpy2.patch:  add numpy-2 compatability
+  * pymol3-version-compare.patch:  fix tests/helpers/test_utils.py
+
 -------------------------------------------------------------------
 Tue Jun 18 15:42:12 UTC 2024 - <hsk17@mail.de>
 

python-pymol.spec

@@ -16,55 +16,56 @@
 #
 
 
-%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
+%{?sle15_python_module_pythons}
 Name:           python-pymol
-Version:        3.0.0
+Version:        3.1.0
 Release:        0
 Summary:        A Molecular Viewer
 License:        Python-2.0
 Group:          Productivity/Scientific/Chemistry
 URL:            https://pymol.org/
 Source0:        https://github.com/schrodinger/%{modname}/archive/v%{version}/%{modname}-%{version}.tar.gz
-# PATCH-FIX-OPENSUSE no-build-date.patch dhall@wustl.edu -- patch eliminates build date
-Patch0:         no-build-date.patch
-# PATCH-FIX-OPENSUSE no-o3.patch tchvatal@suse.com -- do not add O3 to the code
-Patch1:         no-o3.patch
+Patch0:         https://github.com/schrodinger/pymol-open-source/pull/404.patch#/reproducible.patch
 BuildRequires:  %{python_module devel}
 BuildRequires:  %{python_module numpy-devel}
+BuildRequires:  %{python_module pip}
 BuildRequires:  %{python_module qt5-devel}
 BuildRequires:  %{python_module setuptools}
+BuildRequires:  %{python_module wheel}
 BuildRequires:  fdupes
 BuildRequires:  freetype2-devel
+%if 0%{?sle_version} >= 150500 && 0%{?is_opensuse}
+BuildRequires:  gcc12-c++
+%else
 BuildRequires:  gcc-c++
+%endif
 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
@@ -84,15 +85,18 @@ The file formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile,
 ChemDraw, CCP4 maps, XPLOR maps and Gaussian cube maps.
 
 %prep
-%setup -q -n %{modname}-%{version}
-%autopatch -p1
+%autosetup -p1 -n %{modname}-%{version}
 
 %build
+%if 0%{?sle_version} >= 150500 && 0%{?is_opensuse}
+export CC=gcc-12
+export CXX=g++-12
+%endif
 export CXXFLAGS="%{optflags} -fno-strict-aliasing"
-%python_build %{?with_test:--testing}
+%pyproject_wheel
 
 %install
-%python_install
+%pyproject_install
 %python_clone -a %{buildroot}%{_bindir}/pymol
 %python_expand %fdupes %{buildroot}%{$python_sitearch}
 
@@ -103,13 +107,11 @@ 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
+## 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
+PYTHONPATH=%{buildroot}%{python_sitearch} python%{python_bin_suffix} -m pymol -ckqy testing/testing.py --offline --run all
 %endif
 
 %post
@@ -122,6 +124,12 @@ PYTHONPATH=%{buildroot}%{python_sitearch} python%{python_version} -m pymol -ckqy
 %doc README ChangeLog
 %license LICENSE
 %python_alternative %{_bindir}/pymol
-%{python_sitearch}*
+%{python_sitearch}/chempy
+%{python_sitearch}/pmg_qt
+%{python_sitearch}/pmg_tk
+%{python_sitearch}/pymol
+%{python_sitearch}/pymol-*-info
+%{python_sitearch}/pymol2
+%{python_sitearch}/web
 
 %changelog

reproducible.patch

@@ -0,0 +1,40 @@
+From 1aa8682968dbc5df74e35fab224221a3829260f6 Mon Sep 17 00:00:00 2001
+From: "Bernhard M. Wiedemann" <bwiedemann@suse.de>
+Date: Sun, 20 Oct 2024 20:02:01 +0200
+Subject: [PATCH] Allow to override build date with SOURCE_DATE_EPOCH
+
+to make builds reproducible.
+See https://reproducible-builds.org/ for why this is good
+and https://reproducible-builds.org/specs/source-date-epoch/
+for the definition of this variable.
+---
+ create_shadertext.py | 2 +-
+ setup.py             | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/create_shadertext.py b/create_shadertext.py
+index f6857087e..ea68dc22e 100644
+--- a/create_shadertext.py
++++ b/create_shadertext.py
+@@ -127,7 +127,7 @@ def create_buildinfo(outputdir, pymoldir='.'):
+         print('''
+ #define _PyMOL_BUILD_DATE %d
+ #define _PYMOL_BUILD_GIT_SHA "%s"
+-        ''' % (time.time(), sha), file=out)
++        ''' % (int(os.environ.get('SOURCE_DATE_EPOCH', time.time())), sha), file=out)
+ 
+ if __name__ == "__main__":
+     create_shadertext(*sys.argv[1:6])
+diff --git a/setup.py b/setup.py
+index 507dd32d0..4cec85057 100644
+--- a/setup.py
++++ b/setup.py
+@@ -168,7 +168,7 @@ def create_buildinfo(outputdir, pymoldir="."):
+ #define _PyMOL_BUILD_DATE %d
+ #define _PYMOL_BUILD_GIT_SHA "%s"
+         """
+-            % (time.time(), sha),
++            % (int(os.environ.get('SOURCE_DATE_EPOCH', time.time())), sha),
+             file=out,
+         )
+