mbox series

[bug#58261,v2,00/13] Add rdkit v2.

Message ID 20221007152148.32591-1-david.elsing@posteo.net
Headers show
Series Add rdkit v2. | expand

Message

David Elsing Oct. 7, 2022, 3:21 p.m. UTC
Thanks a lot for your comments, they are very helpful!
Sorry about the descriptions, I took them mostly from upstream. :)
Are they still too short?

I still have the following problems:
* The tests of tinydir contain a bundled fork of cbehave which uses a
  (bundled) copy of rlutil, so I left them disabled for now.
* Building the documentation of yaehmop with pdflatex is not reproducible even
  though I set FORCE_SOURCE_DATE=1. Is it even necessary to build the
  documentation?
* Using @abbr in the description does not work (I also did not find it in any
  other package).

Greetings,
David

David Elsing (13):
  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 avalontoolkit.
  gnu: Add ringdecomposerlib.
  gnu: Add rdkit.

 gnu/packages/chemistry.scm                    | 713 ++++++++++++++++++
 gnu/packages/cpp.scm                          | 232 ++++++
 .../patches/gemmi-fix-sajson-types.patch      |  11 +
 .../rdkit-cmake-external-dependencies.patch   | 102 +++
 .../patches/sajson-build-with-gcc10.patch     |  45 ++
 .../sajson-for-gemmi-build-with-gcc10.patch   |  45 ++
 .../sajson-for-gemmi-numbers-as-strings.patch | 195 +++++
 7 files changed, 1343 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-build-with-gcc10.patch
 create mode 100644 gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch
 create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch

Comments

Liliana Marie Prikler Oct. 9, 2022, 10:02 a.m. UTC | #1
Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> Thanks a lot for your comments, they are very helpful!
> Sorry about the descriptions, I took them mostly from upstream. :)
> Are they still too short?
I don't think we can magically poof good descriptions into existence
when upstreams don't provide them.  That being said, it's best to clean
up whatever's there.  Changing descriptions is a lowball issue, though,
I (or another committer) can do so as we're upstreaming it.

> I still have the following problems:
> * The tests of tinydir contain a bundled fork of cbehave which uses a
>   (bundled) copy of rlutil, so I left them disabled for now.
I mentioned this in a reply to another message already, but the idea
would be to 1. try to use upstream versions or 2. try to package the
bundles. 

> * Building the documentation of yaehmop with pdflatex is not
> reproducible even
>   though I set FORCE_SOURCE_DATE=1. Is it even necessary to build the
>   documentation?
Maybe pdftrailerid can help you?  You could also try to convert the
documentation into a reproducible format -- e.g. using pandoc.

> * Using @abbr in the description does not work (I also did not find
> it in any
>   other package).
My bad, that should be @acronym.

Cheers
David Elsing Oct. 13, 2022, 8:58 p.m. UTC | #2
Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
>> Thanks a lot for your comments, they are very helpful!
>> Sorry about the descriptions, I took them mostly from upstream. :)
>> Are they still too short?
> I don't think we can magically poof good descriptions into existence
> when upstreams don't provide them.  That being said, it's best to clean
> up whatever's there.  Changing descriptions is a lowball issue, though,
> I (or another committer) can do so as we're upstreaming it.
>
>> I still have the following problems:
>> * The tests of tinydir contain a bundled fork of cbehave which uses a
>>   (bundled) copy of rlutil, so I left them disabled for now.
> I mentioned this in a reply to another message already, but the idea
> would be to 1. try to use upstream versions or 2. try to package the
> bundles. 
I noticed that there was only one test anyway, so I just made a patch to
run it with the upstream version (which was last updated in 2013).
>
>> * Building the documentation of yaehmop with pdflatex is not
>> reproducible even
>>   though I set FORCE_SOURCE_DATE=1. Is it even necessary to build the
>>   documentation?
> Maybe pdftrailerid can help you?  You could also try to convert the
> documentation into a reproducible format -- e.g. using pandoc.
It worked with \pdfsuppressptexinfo=-1. :)
>
>> * Using @abbr in the description does not work (I also did not find
>> it in any
>>   other package).
> My bad, that should be @acronym.
Ok thanks!
>
> Cheers