[bug#68790] [PATCH 0/9] Update rdkit and its dependencies

[David Elsing]

This patch series updates rdkit and some of its dependencies.

I incorporated the patch from [1], which was addressed upstream, but is
not in a new release yet.

It seems like RDKit is only tested on 64 bit systems upstream and
several tests fail on i686 (including one due to a known bug in
Boost.Python [2]), therefore I set supported-systems to
%64bit-supported-systems.

Avalon Toolkit moved to a new repository [3], which was forked for RDKit
[4]. As the changes in the fork are small and only fixes, I put them in
a patch and use [3] as upstream.

[1] https://issues.guix.gnu.org/64559
[2] https://github.com/boostorg/python/issues/312
[3] https://github.com/rohdebe1/ava-formake
[4] https://github.com/rdkit/ava-formake

David Elsing (9):
  gnu: tinydir: Update to 1.2.6.
  gnu: fast-float: Update to 6.0.0.
  gnu: gemmi: Update to 0.6.4.
  gnu: maeparser: Update to 1.3.1.
  gnu: coordgenlibs: Update to 3.0.2.
  gnu: yaehmop: Update to 2023.03.1.
  gnu: avalon-toolkit: Update to 2.0.5a.
  gnu: freesasa: Fix memerr tests.
  gnu: rdkit: Update to 2023.09.4.

 gnu/local.mk                                  |   2 +
 gnu/packages/c.scm                            |   6 +-
 gnu/packages/chemistry.scm                    | 175 +++++++--------
 gnu/packages/cpp.scm                          |  10 +-
 .../patches/avalon-toolkit-rdkit-fixes.patch  | 110 +++++++++
 ...rdkit-unbundle-external-dependencies.patch | 208 ++++++++++--------
 .../patches/tinydir-fix-cbehave-test.patch    |  16 +-
 7 files changed, 330 insertions(+), 197 deletions(-)
 create mode 100644 gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch

-- 
2.41.0