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File openbabel.changes of Package openbabel
------------------------------------------------------------------- Tue Jul 18 08:29:25 UTC 2023 - Andreas Schwab <schwab@suse.de> - Skip problematic tests and increase timeout on riscv64 ------------------------------------------------------------------- Fri Aug 26 20:05:18 UTC 2022 - Antoine Belvire <antoine.belvire@opensuse.org> - Don't define %upstream version from %version: %upstream_version is used in Source tag and osc download service does not evaluate %() nor %{lua:} in Source tags for security reasons. - Drop entirely baselibs.conf: 32bit libraries seem unnecessary. ------------------------------------------------------------------- Tue Aug 23 18:56:50 UTC 2022 - Antoine Belvire <antoine.belvire@opensuse.org> - Remove libinchi0 from baselibs.conf: Bundled inchi is not built anymore. ------------------------------------------------------------------- Sun Aug 14 16:02:16 UTC 2022 - Antoine Belvire <antoine.belvire@opensuse.org> - Update to version 3.1.1: * Fixes for packaging. * No features or significant bug fixes were involved. - Changes from version 3.1.0: * This version represents additional API and is backwards-compatible with the 3.0 release. * For a full list of changes, see: https://open-babel.readthedocs.io/en/latest/ReleaseNotes/ob310.html - Changes from version 3.0.0: * This release represents a major update and is strongly recommended for all users. * It also removes deprecated components and breaks the API in a few places. For information on migrating from the previous version, please see: https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#migrating-to-3-0 * A sample of major new features: + Code for handling implicit hydrogens and kekulization has been entirely replaced. As well as being accurate, the new approach is much faster. + Speed of reading and writing SMILES has been improved by more than 50-fold. + Removal of the old 'babel' binary in favor of the newer 'obabel' command-line tool. + New improved fragment-based 3D coordinate generation code. + New API for handling reactions stored as molecules (e.g. Reaction InChI, etc.). + New API for copying part of an OBMol as a substructure. + Support for Maestro file format. * For a full list of changes, see: https://open-babel.readthedocs.io/en/latest/ReleaseNotes/ob300.html - Remove upstreamed patches: * fix_narrowing.patch * fix_yasara.patch - Add patches: * openbabel-3.1.1-test-python3-escape-chars.patch: Fix python test failure (gh#openbabel/openbabel#2217). * openbabel-3.1.1-test-python3-imports.patch: Fix ImportError in python tests (gh#openbabel/openbabel!2378). * openbabel-3.1.1-version-number.patch: Fix version number. * openbabel-3.1.1-gcc-12.patch: Fix build with GCC 12 (gh#openbabel/openbabel!2493). * openbabel-3.1.1-wx-stl-compat.patch: Fix GUI build against wxWidgets compiled with STL (gh#openbabel/openbabel!2527). - Build against system's inchi library instead of the bundled one. - Add maeparser-devel as build dependency: Needed for Maestro support. - Update subpackages: * Compile and package GUI. * Move plugins from CLI package (i.e. main package) to library package: They should be available to other library clients without requiring the CLI tools. * Move data files from CLI package to library package: Some are required by the library, some are required by its plugins, let's move everything to library package for now. - Drop __DATE__ and __TIME__ tweaks for reproducibility: These GCC macros now use SOURCE_DATE_EPOCH. - Enable tests. ------------------------------------------------------------------- Mon Mar 30 11:23:08 UTC 2020 - Martin Pluskal <mpluskal@suse.com> - Modernise spec file - Drop old conditionals - Use ninja as builder - Build only python3 bindings ------------------------------------------------------------------- Wed May 16 06:43:44 UTC 2018 - guillaume.gardet@opensuse.org - Backport https://github.com/openbabel/openbabel/commit/e26491 * fix_narrowing.patch - Backport https://github.com/openbabel/openbabel/commit/8d707b * fix_yasara.patch ------------------------------------------------------------------- Sun May 13 17:29:16 UTC 2018 - wbauer@tmo.at - Don't delete command line tools, include them in the main package as with openbabel < 2.4 - Pass -ULIB_INSTALL_DIR to unset this var, the %cmake macro sets it to %{_libdir} resulting in a duplicate /usr in the module search path which causes the plugins not to be found (boo#997190) ------------------------------------------------------------------- Wed Feb 21 22:01:13 UTC 2018 - wbauer@tmo.at - Provide/Obsolete libopenbabel-devel for compatibility ------------------------------------------------------------------- Sun Feb 18 12:18:20 UTC 2018 - jengelh@inai.de - Fix RPM groups. Update descriptions. ------------------------------------------------------------------- Sat Feb 3 21:54:05 UTC 2018 - wbauer@tmo.at - Force python2 by passing -DPYTHON_EXECUTABLE=%{_bindir}/python2 to cmake to fix build on Tumbleweed ------------------------------------------------------------------- Mon Feb 6 12:34:16 UTC 2017 - mailaender@opensuse.org - build with wxWidgets support - add baselibs.conf - enable python support (for real now) - add libinchi0 and openbabel sub packages - correct the .so version suffix for libopenbabel - Drop openbabel-2.3.1-no-build-date.patch ------------------------------------------------------------------- Sun Nov 20 08:29:20 UTC 2016 - aloisio@gmx.com - Update to version 2.4.1, see https://sourceforge.net/projects/openbabel/files/openbabel/2.4.0 for changelog - Dropped cripple_source.sh - Replaced openbabel-2.2.3-no-build-date.patch with sed regex - Dropped build-checks.diff due to significant source changes - Dropped python-installdir.patch (included upstream) - Dropped openbabel-gcc5.patch (included upstream) ------------------------------------------------------------------- Sun Jun 19 11:22:13 UTC 2016 - schwab@suse.de - openbabel-gcc6.patch: remove obsolete hunk ------------------------------------------------------------------- Fri Jun 17 09:02:52 UTC 2016 - martin.liska@suse.com - Fix errors seen by 02-check-gcc-output script. ------------------------------------------------------------------- Thu Jun 16 14:39:01 UTC 2016 - tchvatal@suse.com - Version update to 2.3.2 and cripple the tarball * various small bugfixes, the git is far away from this but upstream seems not to do releases * Add patch to properly install bindings to right location: + python-installdir.patch ------------------------------------------------------------------- Thu Jun 16 13:00:32 UTC 2016 - mliska@suse.cz - Add patch to build with gcc6 openbabel-gcc6.patch ------------------------------------------------------------------- Fri Jun 19 12:02:45 UTC 2015 - dimstar@opensuse.org - Add openbabel-gcc5.patch: Fix build with gcc5. ------------------------------------------------------------------- Mon Aug 5 18:04:00 UTC 2013 - hrvoje.senjan@gmail.com - enable CMAKE_SKIP_INSTALL_RPATH option so RPATH is ommited from install tree ------------------------------------------------------------------- Tue Nov 20 17:23:54 UTC 2012 - nico.kruber@gmail.com - Fix the SLES build (%make_install is not expanded on SLES) ------------------------------------------------------------------- Thu Apr 5 08:13:07 UTC 2012 - coolo@suse.com - add -32bit libs for avogadro ------------------------------------------------------------------- Fri Mar 23 20:02:36 UTC 2012 - dhall@wustl.edu - Add python bindings ------------------------------------------------------------------- Tue Nov 29 01:55:33 CET 2011 - ro@suse.de - determine arch suffix from _lib macro ------------------------------------------------------------------- Tue Oct 18 00:17:21 UTC 2011 - dhall@wustl.edu - updated to OpenBabel 2.3.1 * Better support for unknown stereochemistry, including a "wobbly" bond in 2D depiction. * Many fixes for rare bugs with stereochemical conversions, including unusual valences. * Significantly improved 2D depiction code, improving performance and cis/trans stereochemical accuracy * Added support for direct 2D depiction to PNG files using the Cairo library, if available. * PNG files from Open Babel contain molecular information and can be read to give the MDL Molfile. * SVG files with 2D depiction can now include a grid of molecules with embedded JavaScript to zoom and scroll. * Molecular formulas now include the total charge (e.g., HCO2-) * Added the EEM partial charge model from Bultinck, et. al. * Fixed problems with FastSearch databases larger than 4GB, now checking for large files. * Improved performance with force field minimization, particularly the UFF and GAFF methods. * Several MMFF94 atom typing bugs fixed. * Updated GAFF parameters from the AmberTools distribution. * Improvements in 3D coordinate generation, particularly more accurate sp3 bond angles * Fixed tests for auto-typing molecules with force fields when running through different isomers. * Improvements in scripting bindings, particularly Python, Ruby, and Java * Pybel now uses the built-in 2D depiction, and no longer needs OASA. * Added initial support for MM3 atom typing with the Tinker package * Significant bug fixes for the PDBQT format. * Reading FASTA files can now generate 3D coordinates for single-stranded DNA in addition to the default double-strand. * Support for reading/writing unit cell information from MOPAC files. * Support for re-numbering SMILES by specifying the first and last atoms with -xf and -xl flags. * Better support for InChI -> InChI key generation by direct conversion, rather than re-perception of the InChI. * Fix for rare stack overflow crash in SMARTS perception. * Improved UNIX man pages. * Many bug fixes and small enhancements * New File Formats * Import and Export: * Gromacs GRO * Import: * ABINIT * XCrySDen XSF * Export: * InChI Key ------------------------------------------------------------------- Sat Jun 18 10:52:25 UTC 2011 - dhall@wustl.edu - use rpm %ifarch ------------------------------------------------------------------- Fri Jun 17 23:55:56 UTC 2011 - dhall@wustl.edu - Updated to OpenBabel 2.3.0 * Completely rewritten stereochemistry perception, including support for tetrahedral, square planar, and higher-order stereochemistry. * Dramatically improved canonicalization algorithm (Note that in general, canonical SMILES have changed since the 2.2.x release.) * 2D depiction, including SVG vector graphics generation using code from MCDL. * New Spectrophore generation, contributed by Silicos NV. * New ChargeMethod API including support for partial charge assignment from Gasteiger, MMFF94, QEq, QTPIE methods and plugin interface for adding more. * Improved 3D coordinate generation. * New conformer generation framework, including support for diverse conformer generation and genetic algorithm lowest-energy searching. * Improved user documentation. * Improved aromaticity / Kekule bond assignment. * Improved unit test suite using the CMake-based CTest program. * Improved support for crystallographic unit cells (e.g., in CIF format). * Improved UFF force field method, including hypervalent 5, 6, 7 and higher coordination numbers. * Support for the GAFF (Generalized Amber Force Field) method. * Support for reading geometry optimizations as multiple conformers from Gaussian, GAMESS-US, and other quantum chemistry packages. * Support for reading molecular orbital energies from quantum chemistry formats. * Several memory leaks fixed. * Fixed many compiler warnings. * Fixed support for MinGW and Cygwin environments. * Fixed bugs with Gaussian 09 output files. * Latest released version of the InChI library (1.0.3) generating standard InChI. * Many more bug fixes and small feature improvements. ------------------------------------------------------------------- Mon Sep 13 00:54:59 UTC 2010 - cristian.rodriguez@opensuse.org - Do not include build dates in binaries. ------------------------------------------------------------------- Sat Sep 11 17:16:44 UTC 2010 - alinm.elena@gmail.com - added pkg-config to remove the error during the build ------------------------------------------------------------------- Sat Sep 11 09:03:40 UTC 2010 - alinm.elena@gmail.com - Updated to OpenBabel 2.2.3 * Improved Java interface * Many fixes to the fingerprint code * Added support of the pH parameter to the GUI * Several bug fixes and small enhancements- ------------------------------------------------------------------- Sat Jul 25 23:48:41 CEST 2009 - beineri@opensuse.org - update to OpenBabel 2.2.2: * Fixed many stereochemistry errors when reading/writing SMILES. * Significantly improved aromaticity and Kekule bond assignment. * Improved 2D -> 3D coordinate generation * Improved coordinate generation using --gen3d command-line operation * Improved performance for coordinate generation. * New --fillUC command-line operation for babel. * Fixes to pH-dependent hydrogen addition. * Added support for reading vibrational data from Molden, Molpro, and NWChem output files. * Updated atomic radii from recent theoretical calculations. * Fixed bug when reading gzip-compressed Mol2 or XML files. * Close files after an error. Fixes a bug with Pybel where files would remain open. * New File Formats Import & Export: - Molpro input and output. -VASP coordinate files (CONTCAR and POSCAR). - update to OpenBabel 2.2.1: * Added support for MACCS fingerprints. * Many fixes and enhancements to the force field code. * Improved 3D coordinate generation, particularly with ring fragments. * Fixed a variety of PDB import errors with atom types. * Added support for reading charges and radii from PQR file formats. * Added support for reading and writing unit cells in PDB formats. * New "output" file format for taking generic ".out", ".log", and ".dat" files and reading with appropriate file type based on contents. * Added improved error handling/reporting when unable to load file formats. * Improved CIF file format support. * Generic "output" format for reading from quantum chemistry files. ------------------------------------------------------------------- Tue Jul 22 14:13:26 CEST 2008 - dmueller@suse.de - cripple tarball to remove binary dll's we don't need (bnc#411171) ------------------------------------------------------------------- Sat Jul 19 12:43:49 CEST 2008 - dmueller@suse.de - various fixes, fix library package name ------------------------------------------------------------------- Wed Jul 9 16:02:10 CEST 2008 - dmueller@suse.de - review last change ------------------------------------------------------------------- Wed Jul 9 15:52:31 CEST 2008 - cniehaus@kde.org - update to OpenBabel 2.2.0: * http://openbabel.org/wiki/Open_Babel_2.2.0 ------------------------------------------------------------------- Sun Oct 21 12:44:24 CEST 2007 - dmueller@suse.de - gcc 4.3 fixes ------------------------------------------------------------------- Tue Oct 9 01:07:21 CEST 2007 - dmueller@suse.de - Initial package (2.1.1)
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