bug#58261: closed ([PATCH 00/11] Add rdkit.)

[GNU bug Tracking System]

Your message dated Sat, 15 Oct 2022 16:37:27 +0200
with message-id <d7500c15de3f502785c9825e938ab8cc4d3f8861.camel@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.

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58261: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=58261
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> --- Begin Message ---
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>
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> Subject: 
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> [PATCH 00/11] Add rdkit.
>
>
>
>
> Date: 
>
> Sun,  2 Oct 2022 22:55:26 +0000
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>
>
>
> 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
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [PATCH v3 00/15] Add rdkit v3.
>
>
>
>
> Date: 
>
> Sat, 15 Oct 2022 16:37:27 +0200
>
>
>
>
> User-agent: 
>
> Evolution 3.46.0 
>
>
>
>
> 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
>
>
> --- End Message ---