unofficial mirror of guix-patches@gnu.org 
 help / color / mirror / code / Atom feed
From: David Elsing <david.elsing@posteo.net>
To: 58261@debbugs.gnu.org
Cc: David Elsing <david.elsing@posteo.net>
Subject: [bug#58261] [PATCH v2 00/13] Add rdkit v2.
Date: Fri,  7 Oct 2022 15:21:37 +0000	[thread overview]
Message-ID: <20221007152148.32591-1-david.elsing@posteo.net> (raw)
In-Reply-To: <cover.1664725832.git.david.elsing@posteo.net>

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

-- 
2.37.0





  parent reply	other threads:[~2022-10-07 16:15 UTC|newest]

Thread overview: 87+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
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 ` David Elsing [this message]
2022-10-09 10:02   ` [bug#58261] [PATCH v2 00/13] Add rdkit v2 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

Reply instructions:

You may reply publicly to this message via plain-text email
using any one of the following methods:

* Save the following mbox file, import it into your mail client,
  and reply-to-all from there: mbox

  Avoid top-posting and favor interleaved quoting:
  https://en.wikipedia.org/wiki/Posting_style#Interleaved_style

  List information: https://guix.gnu.org/

* Reply using the --to, --cc, and --in-reply-to
  switches of git-send-email(1):

  git send-email \
    --in-reply-to=20221007152148.32591-1-david.elsing@posteo.net \
    --to=david.elsing@posteo.net \
    --cc=58261@debbugs.gnu.org \
    /path/to/YOUR_REPLY

  https://kernel.org/pub/software/scm/git/docs/git-send-email.html

* If your mail client supports setting the In-Reply-To header
  via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line before the message body.
Code repositories for project(s) associated with this public inbox

	https://git.savannah.gnu.org/cgit/guix.git

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).