GNU bug report logs - #58261
[PATCH 00/11] Add rdkit.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Liliana Marie Prikler <liliana.prikler <at> gmail.com>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#58261: closed ([PATCH 00/11] Add rdkit.)
Date: Sat, 15 Oct 2022 14:38:02 +0000

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Your message dated Sat, 15 Oct 2022 16:37:27 +0200
with message-id <d7500c15de3f502785c9825e938ab8cc4d3f8861.camel <at> gmail.com>
and subject line Re: [PATCH v3 00/15] Add rdkit v3.
has caused the debbugs.gnu.org bug report #58261,
regarding [PATCH 00/11] Add rdkit.
to be marked as done.

(If you believe you have received this mail in error, please contact
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From: David Elsing <david.elsing <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: David Elsing <david.elsing <at> posteo.net>
Subject: [PATCH 00/11] Add rdkit.
Date: Sun,  2 Oct 2022 22:55:26 +0000

Hello!

This patch series adds rdkit and its new dependencies.

Most optional components are enabled, except for the additional wrappers,
the "StructChecker" and the "compressed MolSuppliers".
All bundled software in External/ is unbundled and the included pickled data
(only used for a few tests) is removed.

freesasa is built as a shared library and the flex and bison files are generated.

For yaehmop-tightbind, I removed the transpiled Fortran->C files and built the
Fortran parts with GFortran instead.

gemmi included a patched version of sajson where numbers are kept as the
original strings, so I made a package variant and added a check for
sajson::TYPE_INTEGER in gemmi.
sajson also requires another small patch
(gnu/packages/patches/sajson-parse_flags-linking.patch) which I took from the
unmerged upstream pull request
https://github.com/chadaustin/sajson/pull/54/files, is that ok?

The packages were reproducible after two rounds (when setting the environment
variables as in python-build-system for rdkit), but I only built them on
x86_64 as emulation would take quite long.

David Elsing (11):
  gnu: Add fast-float.
  gnu: Add pocketfft.
  gnu: Add sajson.
  gnu: Add tinydir.
  gnu: Add optionparser.
  gnu: Add gemmi.
  gnu: Add freesasa.
  gnu: Add maeparser.
  gnu: Add coordgenlibs.
  gnu: Add yaehmop-tightbind.
  gnu: Add rdkit.

 gnu/packages/chemistry.scm                    | 531 ++++++++++++++++++
 gnu/packages/cpp.scm                          | 201 +++++++
 .../patches/gemmi-fix-sajson-types.patch      |  11 +
 .../rdkit-cmake-external-dependencies.patch   | 102 ++++
 .../sajson-for-gemmi-numbers-as-strings.patch | 195 +++++++
 .../patches/sajson-parse_flags-linking.patch  |  45 ++
 6 files changed, 1085 insertions(+)
 create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch
 create mode 100644 gnu/packages/patches/rdkit-cmake-external-dependencies.patch
 create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
 create mode 100644 gnu/packages/patches/sajson-parse_flags-linking.patch

-- 
2.37.0

[Message part 3 (message/rfc822, inline)]

From: Liliana Marie Prikler <liliana.prikler <at> gmail.com>
To: David Elsing <david.elsing <at> posteo.net>, 58261-done <at> debbugs.gnu.org
Subject: Re: [PATCH v3 00/15] Add rdkit v3.
Date: Sat, 15 Oct 2022 16:37:27 +0200

Am Donnerstag, dem 13.10.2022 um 21:04 +0000 schrieb David Elsing:
> Thanks again for your comments! Here is the next version. :)
> Now all packages were reproducible again after two rounds.
I've made some adjustments – some cosmetic, some otherwise – and pushed
this series.

Cheers

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