Gentoo Archives: gentoo-commits

From: Anna Vyalkova <cyber+gentoo@×××××.in>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/files/, sci-biology/cmdock/
Date: Thu, 01 Jul 2021 05:08:31
Message-Id: 1625115505.eb972dae4900efd571efe420cf683200a997d924.cybertailor@gentoo
1 commit: eb972dae4900efd571efe420cf683200a997d924
2 Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
3 AuthorDate: Sun Jun 27 08:51:43 2021 +0000
4 Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
5 CommitDate: Thu Jul 1 04:58:25 2021 +0000
6 URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=eb972dae
7
8 sci-biology/cmdock: drop obsolete
9
10 Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
11
12 sci-biology/cmdock/Manifest | 1 -
13 sci-biology/cmdock/cmdock-0.1.2.ebuild | 74 ----------------------
14 sci-biology/cmdock/cmdock-0.1.3.ebuild | 13 ++--
15 sci-biology/cmdock/files/app_info_0.1.2.xml | 66 -------------------
16 sci-biology/cmdock/files/app_info_0.1.3.xml | 58 -----------------
17 .../cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 14 ----
18 .../cmdock/files/cmdock-boinc_job_0.1.2.xml | 10 ---
19 .../cmdock/files/cmdock-boinc_job_0.1.3.xml | 10 ---
20 8 files changed, 4 insertions(+), 242 deletions(-)
21
22 diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
23 index c20f5e305..84968a8f8 100644
24 --- a/sci-biology/cmdock/Manifest
25 +++ b/sci-biology/cmdock/Manifest
26 @@ -1,2 +1 @@
27 -DIST cmdock-v0.1.2.tar.gz 13394195 BLAKE2B bd377b6a953d1e38b527da4eda36aee7a634e9f0c400487d4092ae1939589890038fc90052d8bddb25457dd027fa929acd50e836d65bd5994af89116f4c770a7 SHA512 90d4114a10dde99d34cd7ea4b28399da744cc295adebb10f1f9771b59841cd13e07cae5218643c90dd2847cdb014867ab795649a3d1883396a3609c3344b8226
28 DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454 SHA512 d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22
29
30 diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.2.ebuild
31 deleted file mode 100644
32 index 00934f81c..000000000
33 --- a/sci-biology/cmdock/cmdock-0.1.2.ebuild
34 +++ /dev/null
35 @@ -1,74 +0,0 @@
36 -# Copyright 2021 Gentoo Authors
37 -# Distributed under the terms of the GNU General Public License v2
38 -
39 -EAPI=7
40 -
41 -PYTHON_COMPAT=( python3_{7..10} pypy3 )
42 -DOCS_BUILDER="sphinx"
43 -DOCS_AUTODOC=0
44 -DOCS_DIR="docs"
45 -inherit python-any-r1 docs meson
46 -
47 -DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
48 -HOMEPAGE="https://gitlab.com/Jukic/cmdock"
49 -SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz"
50 -S="${WORKDIR}/${PN}-v${PV}"
51 -
52 -LICENSE="LGPL-3"
53 -SLOT="0/${PV}"
54 -KEYWORDS="~amd64"
55 -IUSE="boinc"
56 -
57 -RDEPEND="
58 - dev-lang/perl
59 - boinc? ( sci-misc/boinc-wrapper )
60 -"
61 -BDEPEND="
62 - dev-cpp/eigen:3
63 - dev-cpp/pcg-cpp
64 - dev-libs/cxxopts
65 -"
66 -
67 -src_prepare() {
68 - default
69 - sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die
70 -}
71 -
72 -src_configure() {
73 - # very weird directory layout
74 - local emesonargs=(
75 - --prefix="${EPREFIX}/opt/cmdock-${PV}"
76 - )
77 - meson_src_configure
78 -}
79 -
80 -src_compile() {
81 - meson_src_compile
82 - docs_compile
83 -}
84 -
85 -src_install() {
86 - meson_src_install
87 -
88 - if use boinc ; then
89 - insinto /var/lib/boinc/projects/www.sidock.si_sidock
90 - newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
91 - doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
92 - doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml"
93 -
94 - dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}
95 - dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}
96 - fi
97 -}
98 -
99 -pkg_postinst() {
100 - if use boinc ; then
101 - touch /var/lib/boinc/projects/www.sidock.si_sidock/docking_out.sd || die
102 - elog
103 - elog "The easiest way to do something useful with this application"
104 - elog "is to attach it to SiDock@home BOINC project."
105 - elog
106 - elog "- Master URL: https://sidock.si/sidock/"
107 - elog "- Invitation code: Crunch_4Science"
108 - fi
109 -}
110
111 diff --git a/sci-biology/cmdock/cmdock-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild
112 index c4a2da7b4..e42b1f253 100644
113 --- a/sci-biology/cmdock/cmdock-0.1.3.ebuild
114 +++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild
115 @@ -1,9 +1,9 @@
116 # Copyright 2021 Gentoo Authors
117 # Distributed under the terms of the GNU General Public License v2
118
119 -EAPI=7
120 +EAPI=8
121
122 -PYTHON_COMPAT=( python3_{7..10} pypy3 )
123 +PYTHON_COMPAT=( python3_{8..10} pypy3 )
124 DOCS_BUILDER="sphinx"
125 DOCS_AUTODOC=0
126 DOCS_DIR="docs"
127 @@ -26,14 +26,13 @@ RDEPEND="
128 BDEPEND="
129 dev-cpp/eigen:3
130 dev-cpp/indicators
131 - dev-cpp/pcg-cpp
132 + >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
133 dev-libs/cxxopts
134 "
135
136 src_prepare() {
137 default
138 rm -r include/indicators || die
139 - sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die
140 }
141
142 src_configure() {
143 @@ -55,13 +54,9 @@ src_install() {
144 if use boinc ; then
145 insinto /var/lib/boinc/projects/www.sidock.si_sidock
146 newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
147 - doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
148 doins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml"
149 - newins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" cmdock-boinc-zip_job_${PV}.xml
150
151 - dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}
152 - dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV}
153 - dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}
154 + dosym -r /usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV}
155 fi
156 }
157
158
159 diff --git a/sci-biology/cmdock/files/app_info_0.1.2.xml b/sci-biology/cmdock/files/app_info_0.1.2.xml
160 deleted file mode 100644
161 index f7575656b..000000000
162 --- a/sci-biology/cmdock/files/app_info_0.1.2.xml
163 +++ /dev/null
164 @@ -1,66 +0,0 @@
165 -<app_info>
166 -<app>
167 - <name>cmdock-boinc</name>
168 - <user_friendly_name>CurieMarieDock on BOINC</user_friendly_name>
169 -</app>
170 -<app>
171 - <name>cmdock-boinc-zip</name>
172 - <user_friendly_name>CurieMarieDock on BOINC + zipped input</user_friendly_name>
173 -</app>
174 -
175 -<file_info>
176 - <name>cmdock-wrapper_0.1.2</name>
177 - <executable/>
178 -</file_info>
179 -<file_info>
180 - <name>cmdock-boinc-zip_wrapper_0.1.2</name>
181 - <executable/>
182 -</file_info>
183 -
184 -<file_info>
185 - <name>cmdock-boinc_job_0.1.2.xml</name>
186 -</file_info>
187 -<file_info>
188 - <name>cmdock-boinc-zip_job_0.1.2.xml</name>
189 -</file_info>
190 -<file_info>
191 - <name>docking_out.sd</name>
192 -</file_info>
193 -
194 -<app_version>
195 - <app_name>cmdock-boinc</app_name>
196 - <version_num>102</version_num>
197 - <file_ref>
198 - <file_name>cmdock-wrapper_0.1.2</file_name>
199 - <main_program/>
200 - </file_ref>
201 - <file_ref>
202 - <file_name>cmdock-boinc_job_0.1.2.xml</file_name>
203 - <open_name>job.xml</open_name>
204 - <copy_file/>
205 - </file_ref>
206 - <file_ref>
207 - <file_name>docking_out.sd</file_name>
208 - <open_name>docking_out.sd</open_name>
209 - <copy_file/>
210 - </file_ref>
211 -</app_version>
212 -<app_version>
213 - <app_name>cmdock-boinc-zip</app_name>
214 - <version_num>204</version_num>
215 - <file_ref>
216 - <file_name>cmdock-boinc-zip_wrapper_0.1.2</file_name>
217 - <main_program/>
218 - </file_ref>
219 - <file_ref>
220 - <file_name>cmdock-boinc-zip_job_0.1.2.xml</file_name>
221 - <open_name>job.xml</open_name>
222 - <copy_file/>
223 - </file_ref>
224 - <file_ref>
225 - <file_name>docking_out.sd</file_name>
226 - <open_name>docking_out.sd</open_name>
227 - <copy_file/>
228 - </file_ref>
229 -</app_version>
230 -</app_info>
231
232 diff --git a/sci-biology/cmdock/files/app_info_0.1.3.xml b/sci-biology/cmdock/files/app_info_0.1.3.xml
233 index 5c901eba8..162ad0c05 100644
234 --- a/sci-biology/cmdock/files/app_info_0.1.3.xml
235 +++ b/sci-biology/cmdock/files/app_info_0.1.3.xml
236 @@ -1,61 +1,21 @@
237 <app_info>
238 -<app>
239 - <name>cmdock-boinc</name>
240 - <user_friendly_name>CurieMarieDock on BOINC</user_friendly_name>
241 -</app>
242 -<app>
243 - <name>cmdock-boinc-zip</name>
244 - <user_friendly_name>CurieMarieDock on BOINC + zipped input</user_friendly_name>
245 -</app>
246 <app>
247 <name>cmdock-boinc-zcp</name>
248 <user_friendly_name>CurieMarieDock on BOINC + zipped input, checkpoints and progress bar</user_friendly_name>
249 </app>
250
251 -<file_info>
252 - <name>cmdock-wrapper_0.1.3</name>
253 - <executable/>
254 -</file_info>
255 <file_info>
256 <name>cmdock-boinc-zcp_wrapper_0.1.3</name>
257 <executable/>
258 </file_info>
259 -<file_info>
260 - <name>cmdock-boinc-zip_wrapper_0.1.3</name>
261 - <executable/>
262 -</file_info>
263
264 -<file_info>
265 - <name>cmdock-boinc_job_0.1.3.xml</name>
266 -</file_info>
267 <file_info>
268 <name>cmdock-boinc-zcp_job_0.1.3.xml</name>
269 </file_info>
270 -<file_info>
271 - <name>cmdock-boinc-zip_job_0.1.3.xml</name>
272 -</file_info>
273 <file_info>
274 <name>docking_out.sd</name>
275 </file_info>
276
277 -<app_version>
278 - <app_name>cmdock-boinc</app_name>
279 - <version_num>103</version_num>
280 - <file_ref>
281 - <file_name>cmdock-wrapper_0.1.3</file_name>
282 - <main_program/>
283 - </file_ref>
284 - <file_ref>
285 - <file_name>cmdock-boinc_job_0.1.3.xml</file_name>
286 - <open_name>job.xml</open_name>
287 - <copy_file/>
288 - </file_ref>
289 - <file_ref>
290 - <file_name>docking_out.sd</file_name>
291 - <open_name>docking_out.sd</open_name>
292 - <copy_file/>
293 - </file_ref>
294 -</app_version>
295 <app_version>
296 <app_name>cmdock-boinc-zcp</app_name>
297 <version_num>100</version_num>
298 @@ -74,22 +34,4 @@
299 <copy_file/>
300 </file_ref>
301 </app_version>
302 -<app_version>
303 - <app_name>cmdock-boinc-zip</app_name>
304 - <version_num>300</version_num>
305 - <file_ref>
306 - <file_name>cmdock-boinc-zip_wrapper_0.1.3</file_name>
307 - <main_program/>
308 - </file_ref>
309 - <file_ref>
310 - <file_name>cmdock-boinc-zip_job_0.1.3.xml</file_name>
311 - <open_name>job.xml</open_name>
312 - <copy_file/>
313 - </file_ref>
314 - <file_ref>
315 - <file_name>docking_out.sd</file_name>
316 - <open_name>docking_out.sd</open_name>
317 - <copy_file/>
318 - </file_ref>
319 -</app_version>
320 </app_info>
321
322 diff --git a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
323 deleted file mode 100644
324 index a11f1fe9b..000000000
325 --- a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
326 +++ /dev/null
327 @@ -1,14 +0,0 @@
328 -<job_desc>
329 - <task>
330 - <application>/opt/cmdock-0.1.2/build/cmdock</application>
331 - <stdout_filename>docking_log</stdout_filename>
332 - <command_line>-c -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
333 - <checkpoint_filename>docking_out.chk</checkpoint_filename>
334 - <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv>
335 - <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv>
336 - <setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv>
337 - </task>
338 - <unzip_input>
339 - <zipfilename>ligands.zip</zipfilename>
340 - </unzip_input>
341 -</job_desc>
342
343 diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
344 deleted file mode 100644
345 index c670b677e..000000000
346 --- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
347 +++ /dev/null
348 @@ -1,10 +0,0 @@
349 -<job_desc>
350 - <task>
351 - <application>/opt/cmdock-0.1.2/build/cmdock</application>
352 - <stdout_filename>docking_log</stdout_filename>
353 - <command_line>-r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
354 - <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv>
355 - <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv>
356 - <setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv>
357 - </task>
358 -</job_desc>
359
360 diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
361 deleted file mode 100644
362 index 6082dc8fe..000000000
363 --- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
364 +++ /dev/null
365 @@ -1,10 +0,0 @@
366 -<job_desc>
367 - <task>
368 - <application>/opt/cmdock-0.1.3/build/cmdock</application>
369 - <stdout_filename>docking_log</stdout_filename>
370 - <command_line>-r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
371 - <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv>
372 - <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv>
373 - <setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv>
374 - </task>
375 -</job_desc>