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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

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    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 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>