openbabel-3.2.0-bp161.1.1

- Drop test fixtures with incompatible licenses (boo#1269820):
  * remove test/fuzz/FuzzedDataProvider.h and
    test/files/fuzz_regress/methane-pointgroup.g09 -- test-only
    data carrying Apache-2.0-WITH-LLVM-exception and proprietary
    Gaussian-09 output; never compiled in or shipped, removed to
    keep the source tree free of incompatible-licensed material
  * add openbabel-3.2.0-drop-incompatible-fuzz-harnesses.patch to
    unwire the fuzz harnesses that include the removed header so
    the test suite keeps building (CVE coverage retained via the
    fuzz_obconversion_{sdf,smiles} harnesses)

- Reference the tracking bugs for the security issues already fixed in
  the 3.2.0 update:
  * CVE-2022-* OSS-Fuzz/TALOS batch (boo#1217676)
  * CVE-2026-2704 (boo#1258501), CVE-2026-2705 (boo#1258507),
    CVE-2026-3408 (boo#1259041)

- Update to version 3.2.0:
  * Add an L-BFGS optimizer, used by default for gen3d and
    conformer searches
  * New macrocycle ring builder (Dale codes) for better initial
    3D geometry of large rings
  * Add KET (Ketcher JSON) and ChemicalJSON (.cjson) format
    support
  * Drop Python 2 support; Python 3.13 supported
  * Faster, vectorized distance-geometry implementation
  * Full CMake 4 compatibility and modernized build
  * Backwards compatible with 3.0 and 3.1
  * Fix many crash and memory-safety bugs found via OSS-Fuzz
    and TALOS, including the following security issues:
    CVE-2022-37331 (boo#1217676), CVE-2022-41793, CVE-2022-42885,
    CVE-2022-43467, CVE-2022-43607, CVE-2022-44451,
    CVE-2022-46280, CVE-2022-46289, CVE-2022-46290,
    CVE-2022-46291, CVE-2022-46292, CVE-2022-46294,
    CVE-2022-46295, CVE-2025-10994, CVE-2025-10995,
    CVE-2025-10996, CVE-2025-10997, CVE-2025-10998,
    CVE-2025-10999, CVE-2025-11000,
    CVE-2026-2704 (boo#1258501), CVE-2026-2705 (boo#1258507) and
    CVE-2026-3408 (boo#1259041)
- Shared library soname bumped to libopenbabel8 (SOVERSION 8)
- Drop patches now fixed upstream:
  * openbabel-3.1.1-test-python3-escape-chars.patch
  * openbabel-3.1.1-test-python3-imports.patch
  * openbabel-3.1.1-version-number.patch
  * openbabel-3.1.1-gcc-12.patch
  * openbabel-3.1.1-std-binary-function.patch
  * openbabel-3.1.1-std-bind1st.patch
  * openbabel-3.1.1-std-bind2nd.patch
  * openbabel-cmake-4.patch
  * openbabel-cmake-4-exports.patch

- Until upstream provides fixed code, disable test_align_{4,5},
  known to fail w/ gcc-15; see gh#openbabel/openbabel/issues/2766
  and ..../2799

- Add openbabel-cmake-4.patch and openbabel-cmake-4-exports.patch
  to fix cmake-4 failures

- Add patches from upstream to fix compiler deprecation warnings
  * openbabel-3.1.1-std-binary-function.patch,
  * openbabel-3.1.1-std-bind1st.patch,
  * openbabel-3.1.1-std-bind2nd.patch

- Add openbabel-CVE-2026-2704.patch: bounds-check the
  transform3d DescribeAsString() matrix scan to fix an
  out-of-bounds read on crafted CIF input (CVE-2026-2704,
  boo#1258501)
- Modernize spec file

- Add BuildRequires on python3-setuptools, needed for Python 3.12+.

- Skip problematic tests and increase timeout on riscv64

- 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.

- Remove libinchi0 from baselibs.conf: Bundled inchi is not built
  anymore.

- 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.

- Modernise spec file
- Drop old conditionals
- Use ninja as builder
- Build only python3 bindings

- Backport https://github.com/openbabel/openbabel/commit/e26491
  * fix_narrowing.patch
- Backport https://github.com/openbabel/openbabel/commit/8d707b
  * fix_yasara.patch

- 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)

- Provide/Obsolete libopenbabel-devel for compatibility

- Fix RPM groups. Update descriptions.

- Force python2 by passing -DPYTHON_EXECUTABLE=%{_bindir}/python2
  to cmake to fix build on Tumbleweed

- 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

- 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)

- openbabel-gcc6.patch: remove obsolete hunk

- Fix errors seen by 02-check-gcc-output script.

- 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

- Add patch to build with gcc6 openbabel-gcc6.patch

- Add openbabel-gcc5.patch: Fix build with gcc5.

- enable CMAKE_SKIP_INSTALL_RPATH option so RPATH is ommited from
  install tree

- Fix the SLES build (%make_install is not expanded on SLES)

- add -32bit libs for avogadro

- Add python bindings

- determine arch suffix from _lib macro

- 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

- use rpm %ifarch

- 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.

- Do not include build dates in binaries.