Subject: [PATCH 00/11] Add rdkit.
From: David Elsing <[email-masked]>
To: [email-masked]
Cc: David Elsing <[email-masked]>
Date: Sun, 2 Oct 2022 22:55:26 +0000
List-Id: <debbugs-submit.debbugs.gnu.org>

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