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* [bug#58261] [PATCH 00/11] Add rdkit.
@ 2022-10-02 22:55 David Elsing
  2022-10-03  0:19 ` [bug#58261] [PATCH 01/11] gnu: Add fast-float David Elsing
                   ` (24 more replies)
  0 siblings, 25 replies; 87+ messages in thread
From: David Elsing @ 2022-10-02 22:55 UTC (permalink / raw)
  To: 58261; +Cc: David Elsing

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





^ permalink raw reply	[flat|nested] 87+ messages in thread

end of thread, other threads:[~2022-10-17  9:56 UTC | newest]

Thread overview: 87+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2022-10-02 22:55 [bug#58261] [PATCH 00/11] Add rdkit David Elsing
2022-10-03  0:19 ` [bug#58261] [PATCH 01/11] gnu: Add fast-float David Elsing
2022-10-04  6:57   ` Liliana Marie Prikler via Guix-patches via
2022-10-07 15:08     ` David Elsing
2022-10-03  0:19 ` [bug#58261] [PATCH 02/11] gnu: Add pocketfft David Elsing
2022-10-04  7:09   ` Liliana Marie Prikler
2022-10-07 15:10     ` David Elsing
2022-10-03  0:19 ` [bug#58261] [PATCH 03/11] gnu: Add sajson David Elsing
2022-10-04  7:22   ` Liliana Marie Prikler
2022-10-07 15:10     ` David Elsing
2022-10-03  0:19 ` [bug#58261] [PATCH 04/11] gnu: Add tinydir David Elsing
2022-10-04  7:27   ` Liliana Marie Prikler
2022-10-07 15:11     ` David Elsing
2022-10-07 15:13       ` Liliana Marie Prikler
2022-10-03  0:19 ` [bug#58261] [PATCH 05/11] gnu: Add optionparser David Elsing
2022-10-04  7:42   ` Liliana Marie Prikler
2022-10-07 15:11     ` David Elsing
2022-10-03  0:19 ` [bug#58261] [PATCH 06/11] gnu: Add gemmi David Elsing
2022-10-04  7:49   ` Liliana Marie Prikler
2022-10-07 15:11     ` David Elsing
2022-10-07 15:17       ` Liliana Marie Prikler
2022-10-03  0:19 ` [bug#58261] [PATCH 07/11] gnu: Add freesasa David Elsing
2022-10-04  8:02   ` Liliana Marie Prikler
2022-10-07 15:12     ` David Elsing
2022-10-07 15:19       ` Liliana Marie Prikler
2022-10-03  0:19 ` [bug#58261] [PATCH 08/11] gnu: Add maeparser David Elsing
2022-10-03  0:19 ` [bug#58261] [PATCH 09/11] gnu: Add coordgenlibs David Elsing
2022-10-03  0:19 ` [bug#58261] [PATCH 10/11] gnu: Add yaehmop-tightbind David Elsing
2022-10-04  7:54   ` Liliana Marie Prikler
2022-10-07 15:12     ` David Elsing
2022-10-07 15:25       ` Liliana Marie Prikler
2022-10-03  0:19 ` [bug#58261] [PATCH 11/11] gnu: Add rdkit David Elsing
2022-10-04  8:13   ` Liliana Marie Prikler
2022-10-07 15:12     ` David Elsing
2022-10-07 15:29       ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 00/13] Add rdkit v2 David Elsing
2022-10-09 10:02   ` Liliana Marie Prikler
2022-10-13 20:58     ` David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 00/15] Add rdkit v3 David Elsing
2022-10-15 14:37     ` bug#58261: " Liliana Marie Prikler
2022-10-17  9:55       ` [bug#58261] " David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 01/15] gnu: Add fast-float David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 02/15] gnu: Add pocketfft-cpp David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 03/15] gnu: Add sajson David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 04/15] gnu: Add cbehave David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 05/15] gnu: Add tinydir David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 06/15] gnu: Add optionparser David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 07/15] gnu: Add sajson-for-gemmi David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 08/15] gnu: Add gemmi David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 09/15] gnu: Add freesasa David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 10/15] gnu: Add maeparser David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 11/15] gnu: Add coordgenlibs David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 12/15] gnu: Add yaehmop David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 13/15] gnu: Add avalon-toolkit David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 14/15] gnu: Add ringdecomposerlib David Elsing
2022-10-13 21:04   ` [bug#58261] [PATCH v3 15/15] gnu: Add rdkit David Elsing
2022-10-07 15:21 ` [bug#58261] [PATCH v2 01/13] gnu: Add fast-float David Elsing
2022-10-09 10:04   ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 02/13] gnu: Add pocketfft David Elsing
2022-10-09 11:42   ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 03/13] gnu: Add sajson David Elsing
2022-10-09 11:46   ` Liliana Marie Prikler
2022-10-13 20:59     ` David Elsing
2022-10-14 21:30       ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 04/13] gnu: Add tinydir David Elsing
2022-10-09 11:48   ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 05/13] gnu: Add optionparser David Elsing
2022-10-07 15:21 ` [bug#58261] [PATCH v2 06/13] gnu: Add gemmi David Elsing
2022-10-09 11:54   ` Liliana Marie Prikler
2022-10-13 21:00     ` David Elsing
2022-10-14 21:32       ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 07/13] gnu: Add freesasa David Elsing
2022-10-07 15:21 ` [bug#58261] [PATCH v2 08/13] gnu: Add maeparser David Elsing
2022-10-07 15:21 ` [bug#58261] [PATCH v2 09/13] gnu: Add coordgenlibs David Elsing
2022-10-09 11:56   ` Liliana Marie Prikler
2022-10-13 21:00     ` David Elsing
2022-10-07 15:21 ` [bug#58261] [PATCH v2 10/13] gnu: Add yaehmop-tightbind David Elsing
2022-10-09 12:02   ` Liliana Marie Prikler
2022-10-13 21:00     ` David Elsing
2022-10-14 21:33       ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 11/13] gnu: Add avalontoolkit David Elsing
2022-10-09 12:06   ` Liliana Marie Prikler
2022-10-13 21:01     ` David Elsing
2022-10-07 15:22 ` [bug#58261] [PATCH v2 12/13] gnu: Add ringdecomposerlib David Elsing
2022-10-07 15:22 ` [bug#58261] [PATCH v2 13/13] gnu: Add rdkit David Elsing
2022-10-09 12:12   ` Liliana Marie Prikler
2022-10-13 21:01     ` David Elsing

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