mbox series

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

Message ID 20240128225919.795-2-david.elsing@posteo.net
Headers show
Series Update rdkit and its dependencies | expand

Message

David Elsing Jan. 28, 2024, 10:59 p.m. UTC 
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

Comments

Christopher Baines Feb. 13, 2024, 12:18 p.m. UTC | #1 
David Elsing <david.elsing@posteo.net> writes:

> 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.

Thanks for the patches David, they look good to me so I've pushed them
all to master as e5bfc462dd695a570fe88c4c6d6efee808fd1a56.

Chris