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sci-biology/cmdock

Program for docking ligands to proteins and nucleic acids

Screenshots

  • cmdock-0.2.0-r3
    ~amd64
    apidoc cpu_flags_x86_sse2 doc test boinc

    View      Download      Browse     License: LGPL-3 ZLIB   
    Overlay: guru
  • cmdock-0.2.0-r2
    ~amd64
    apidoc cpu_flags_x86_sse2 doc test boinc

    View      Download      Browse     License: LGPL-3 ZLIB   
    Overlay: guru

ChangeLog

commit bb0aae8ad3292e932111cb0c52be559a6740b4b8
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Thu Feb 20 18:56:40 2025 +0500

*/*: disable py3.10

Python 3.10 target is scheduled for removal in Gentoo:
https://public-inbox.gentoo.org/gentoo-dev/e6ca9f1f4ababb79ab2a3d005c39b483c3ecef6e.camel@gentoo.org/

Sphinx 8.2.0 already dropped support for CPython 3.10 and PyPy 3.10,
leading to multiple CI failures in ::guru.

We can safely remove this target, because GURU is "experimental" and
does not have stable keywords.

Let's not remove "pypy3" right now because
a) There are not many packages using it.
b) So we can see which packages supported PyPy 3.10, and test them with
PyPy 3.11.

Closes: https://github.com/gentoo/guru/pull/291
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit 716c7719158ce9c31340b35f97e8ca72e423f3a1
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Mon Oct 7 05:25:39 2024 +0500

sci-biology/cmdock: add myself as a maintainer

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit de2cb421545b839fe097d6c04089989d12ed4b23
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Thu Aug 22 05:25:42 2024 +0500

sci-biology/cmdock: fix boinc deps

Add "--wrapper" to "boinc-app_add_deps" call.

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit 1a76004eaaa74e01bdbe8f2afacac8306fbe6d6f
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Tue Jul 9 20:56:46 2024 +0500

sci-biology/cmdock: boinc fixes

* Update cmdline to the upstream current. Particularly, the option that
causes CmDock to get stuck in an infinite loop in 1-5% of runs is
removed.

* Sync with boinc-app.eclass updates.

Closes: https://bugs.gentoo.org/935231
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit e9427f8954a1efb68fa1c95e9e111f226e9500a1
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Tue Jul 9 20:47:57 2024 +0500

sci-biology/cmdock: drop 0.2.0-r0

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit a395a6f2ccebd4bcea65ef71c86abf6c5ee9e8bf
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Sat Jan 20 13:39:36 2024 +0500

Revert "sci-biology/cmdock: make python optional"

This reverts commit d1a766a47405d4cfeced96a49b3bd70f81bd9a94.

Closes: https://bugs.gentoo.org/922486
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit d1a766a47405d4cfeced96a49b3bd70f81bd9a94
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Tue Jan 16 16:12:58 2024 +0500

sci-biology/cmdock: make python optional

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit ec4d1b0c2f5ff10810dc1a0b45c20ade3e9aaf2a
Author: Takuya Wakazono <pastalian46@gmail.com>
Date: Sat Jan 13 12:18:38 2024 +0900

*/*: move {app-doc → app-text}/doxygen

Signed-off-by: Takuya Wakazono <pastalian46@gmail.com>

commit bf5dd7c748cd41b6fa540780d668045d1836db0b
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Tue Jan 9 15:19:33 2024 +0500

sci-biology/cmdock: fix build

Closes: https://bugs.gentoo.org/901345
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit aa759c4c98861c3b3e6b50cc154c76732930eb9f
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Tue Jan 9 14:05:39 2024 +0500

sci-biology/cmdock: drop *really* unused files

Closes: https://bugs.gentoo.org/921229
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit 8f10f75977eefa6285c362170df29351475f1ed7
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Tue Jan 9 14:02:42 2024 +0500

Revert "sci-biology/cmdock: remove unused patches"

This reverts commit 1298cd25348ad37dac19c0838415436a8c18d3f5.

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit 1298cd25348ad37dac19c0838415436a8c18d3f5
Author: Michael Mair-Keimberger <mmk@levelnine.at>
Date: Sat Dec 30 19:16:39 2023 +0100

sci-biology/cmdock: remove unused patches

Signed-off-by: Michael Mair-Keimberger <mmk@levelnine.at>

commit 9945d109525dd5c72a0aeb858ca133883d2b7499
Author: Viorel Munteanu <ceamac@gentoo.org>
Date: Thu Oct 5 17:01:04 2023 +0300

*/*: reassign cybertailor's packages

Signed-off-by: Viorel Munteanu <ceamac@gentoo.org>

commit 12088906c597f38640e866db39c7ba6dea3f5ec0
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Tue May 2 00:45:35 2023 +0500

*/*: drop dead py3.9 impl

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit 1e95f22062b44b3708c09b56fb2334f41c633e2e
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Sat Mar 4 18:56:32 2023 +0500

*/*: update metadata schema uri

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit 5921ae942a5c831957c1d975278befd4d8cb5e28
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Sun Feb 19 10:26:31 2023 +0500

sci-biology/cmdock: drop 0.1.4-r2

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit 43200432ac81cfb799df3a1a62076920d42f8f5a
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Fri Jan 6 10:30:16 2023 +0500

sci-biology/cmdock: add 0.2.0

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit 2c7621909ee00689a9aaf0be8f8c0539d6bcc70a
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Mon Dec 12 16:42:12 2022 +0500

sci-biology/cmdock: update SRC_URI

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit c7742604b7a71c99ce1d96cd72380c5021bb4613
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Mon Dec 12 16:41:07 2022 +0500

sci-biology/cmdock: drop 0.1.3-r1

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit b1a2cd7094d51b66191a84fe23be6d8fde91db1c
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Fri Dec 9 14:32:45 2022 +0500

sci-biology/cmdock: fix docs build

Closes: https://bugs.gentoo.org/884905
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit e41cb6fdcdeee98756bad4f3e77113f2a59db1e1
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Sun Jun 26 00:17:06 2022 +0500

sci-biology/cmdock: set file owner to root

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit d5a3eafb7c0a35e8025e6eb7ef5df2ef0d58e8e1
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Sun Jun 26 00:14:40 2022 +0500

sci-biology/cmdock: fix app_info.xml

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit bec2b834dd663f30d9bc508ee6043959b50fccfb
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Thu Jun 23 00:31:16 2022 +0500

sci-biology/cmdock: boinc fix

See https://www.sidock.si/sidock/forum_thread.php?id=125&postid=1427

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit af0420fb5d5d6d99e31e9f0b8ff9f37033167c60
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Thu Jun 2 09:00:28 2022 +0500

sci-biology/cmdock: fix CPU flags detection

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit 50bb2e29704a88fb6d53a79ed4eda6a064d23c1a
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Thu Nov 25 12:15:21 2021 +0500

sci-biology/cmdock: add 0.1.4

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit ff56baf97e8c8a3551b3a1875d3d480c56782331
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Thu Jul 22 13:12:11 2021 +0500

sci-biology/cmdock: revbump (new eclass)

Also includes a hack to install both sphinx and doxygen docs.
pkgcheck isn't very happy about it, but who cares.

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit 4d7271caedd3ec77361bba7d98772767dfee8b78
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Mon Jul 19 15:55:37 2021 +0500

sci-biology/cmdock: make it prettier, fix perms

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit eb972dae4900efd571efe420cf683200a997d924
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Sun Jun 27 13:51:43 2021 +0500

sci-biology/cmdock: drop obsolete

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit aba20d3142c80878bbc1a3b045f14c849a63cb63
Author: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Date: Sat May 29 18:37:10 2021 +0500

sci-biology/cmdock: add 0.1.3

* revise deps
* fix symlinks
* replace slotting with subslotting

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

commit 832e0124b98de06cdd097aefa69b81aec8f97191
Author: Anna Vyalkova <cyber+gentoo@sysrq.in>
Date: Fri May 21 12:15:58 2021 +0500

sci-biology/cmdock/files: increment <version_num/>

Signed-off-by: Anna Vyalkova <cyber+gentoo@sysrq.in>

commit 08de1b6acdc9e1957c4b1690d683818d7fb6841c
Author: Anna Vyalkova <cyber@sysrq.in>
Date: Fri May 21 02:48:57 2021 +0500

sci-biology/cmdock/files: fix filenames

Signed-off-by: Anna Vyalkova <cyber@sysrq.in>

commit 1883f124c2d77a9648dae60406fb1e956186af04
Author: Anna Vyalkova <cyber@sysrq.in>
Date: Thu May 20 17:26:42 2021 +0500

sci-biology/cmdock: fixes in deps and app_info.xml

1) Python is only used by Sphinx to build documentation
2) Rename app_config.xml to app_info.xml:
https://boinc.berkeley.edu/wiki/Anonymous_platform

Signed-off-by: Anna Vyalkova <cyber@sysrq.in>

commit 745983646dd24ced02f842ce010c431c1b499a45
Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Date: Wed May 19 14:56:19 2021 +0200

sci-biology/cmdock: add missing PYTHON_DEPS

Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

commit 8b0e3834b1db271f7499bfb1721eeb2d74b0907a
Author: Anna Vyalkova <cyber@sysrq.in>
Date: Wed May 19 02:31:09 2021 +0500

sci-biology/cmdock: initial import

Signed-off-by: Anna Vyalkova <cyber@sysrq.in>