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From: Alexey Shvetsov <alexxy@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/
Date: Thu, 14 May 2020 14:02:37
Message-Id: 1589464936.e22f74af474679a87dadb2f75dac4b6235105a59.alexxy@gentoo
1 commit: e22f74af474679a87dadb2f75dac4b6235105a59
2 Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
3 AuthorDate: Thu May 14 14:01:51 2020 +0000
4 Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
5 CommitDate: Thu May 14 14:02:16 2020 +0000
6 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e22f74af
7
8 sci-chemistry/gromacs: Use mainstream manual
9
10 Closes: https://bugs.gentoo.org/717890
11 Package-Manager: Portage-2.3.99, Repoman-2.3.22
12 Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
13
14 sci-chemistry/gromacs/Manifest | 3 +
15 sci-chemistry/gromacs/gromacs-2018.8.ebuild | 68 ++--------------------
16 sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild | 80 +++-----------------------
17 sci-chemistry/gromacs/gromacs-2019.6.ebuild | 80 +++-----------------------
18 4 files changed, 25 insertions(+), 206 deletions(-)
19
20 diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
21 index 85ca68f2924..d9068e0f9f0 100644
22 --- a/sci-chemistry/gromacs/Manifest
23 +++ b/sci-chemistry/gromacs/Manifest
24 @@ -3,6 +3,9 @@ DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b
25 DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8
26 DIST gromacs-2020.1.tar.gz 29153989 BLAKE2B b1c0313da945c57c74040c2bcd50495b238b0e131cc4ebecd74ae0d01465b47d732ea456a52a2f9d998cd37e2bfdb93d52bd15177328c4b7a14e6b1d8bc00117 SHA512 130394ec70e5d75ea451e9fa77c4ea2dd4adb0c51cc7663ac8579972bab7a0b75d9143d0eebb21802fc93305deca8831393a8cb3f51b6d01f9477f3dadece037
27 DIST gromacs-2020.2.tar.gz 29144614 BLAKE2B cd20b031dcec32d9a797d66f2679779077910c184702f12f12093d92e8417d42e07bfb17a8fe63e9d29a889d5f57461b5f86e11adfc26635f8d2b5a5df19473a SHA512 348c80fad93b34e6703906fec97c6c2294c0803c326d6145776b732e1c33cd58e0967ddb2ec4799e3583542c09e7a6a015e4d084d60cf97b81b3a92253cca76c
28 +DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5
29 +DIST manual-2019.5.pdf 12702361 BLAKE2B cb80429a59019b190115bf2af689c0df23b0fec6e41a9ebc9eba20977d1b06eed79044c906c41228883767f673140e15d3a5ef947a0c1ec4fe84012089f4fa91 SHA512 baf27961b87e6120c49abc9dc58e25d12a15588b4ac787e1a086748d488692d4a1262229ac66e550d3cca3a6042545fb6ec472a2c98d6a8698b7a18b4397f605
30 +DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb
31 DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
32 DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d SHA512 7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce
33 DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
34
35 diff --git a/sci-chemistry/gromacs/gromacs-2018.8.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
36 index 3e5988a06d2..feaa75c10bf 100644
37 --- a/sci-chemistry/gromacs/gromacs-2018.8.ebuild
38 +++ b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
39 @@ -7,18 +7,10 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
40
41 inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
42
43 -if [[ $PV = *9999* ]]; then
44 - EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
45 - https://gerrit.gromacs.org/gromacs.git
46 - https://github.com/gromacs/gromacs.git
47 - https://repo.or.cz/r/gromacs.git"
48 - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
49 - inherit git-r3
50 -else
51 - SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
52 +SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
53 + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
54 test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
55 - KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
56 -fi
57 +KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
58
59 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
60
61 @@ -49,12 +41,7 @@ CDEPEND="
62 "
63 BDEPEND="${CDEPEND}
64 virtual/pkgconfig
65 - doc? (
66 - app-doc/doxygen
67 - dev-texlive/texlive-latex
68 - dev-texlive/texlive-latexextra
69 - media-gfx/imagemagick
70 - )"
71 + "
72 RDEPEND="${CDEPEND}"
73
74 REQUIRED_USE="
75 @@ -67,9 +54,7 @@ DOCS=( AUTHORS README )
76
77 RESTRICT="!test? ( test )"
78
79 -if [[ ${PV} != *9999 ]]; then
80 - S="${WORKDIR}/${PN}-${PV/_/-}"
81 -fi
82 +S="${WORKDIR}/${PN}-${PV/_/-}"
83
84 pkg_pretend() {
85 [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
86 @@ -77,20 +62,6 @@ pkg_pretend() {
87 die "Please switch to an openmp compatible compiler"
88 }
89
90 -src_unpack() {
91 - if [[ ${PV} != *9999 ]]; then
92 - default
93 - else
94 - git-r3_src_unpack
95 - if use test; then
96 - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
97 - EGIT_BRANCH="${EGIT_BRANCH}" \
98 - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
99 - git-r3_src_unpack
100 - fi
101 - fi
102 -}
103 -
104 src_prepare() {
105 #notes/todos
106 # -on apple: there is framework support
107 @@ -113,27 +84,6 @@ src_prepare() {
108 fi
109
110 DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
111 - # try to create policy for imagemagik
112 - mkdir -p ${HOME}/.config/ImageMagick
113 - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
114 - <?xml version="1.0" encoding="UTF-8"?>
115 - <!DOCTYPE policymap [
116 - <!ELEMENT policymap (policy)+>
117 - !ATTLIST policymap xmlns CDATA #FIXED ''>
118 - <!ELEMENT policy EMPTY>
119 - <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
120 - name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
121 - stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
122 - ]>
123 - <policymap>
124 - <policy domain="coder" rights="read | write" pattern="PS" />
125 - <policy domain="coder" rights="read | write" pattern="PS2" />
126 - <policy domain="coder" rights="read | write" pattern="PS3" />
127 - <policy domain="coder" rights="read | write" pattern="EPS" />
128 - <policy domain="coder" rights="read | write" pattern="PDF" />
129 - <policy domain="coder" rights="read | write" pattern="XPS" />
130 - </policymap>
131 - EOF
132 }
133
134 src_configure() {
135 @@ -176,7 +126,6 @@ src_configure() {
136 -DGMX_OPENMP=$(usex openmp)
137 -DGMX_COOL_QUOTES=$(usex offensive)
138 -DGMX_USE_TNG=$(usex tng)
139 - -DGMX_BUILD_MANUAL=$(usex doc)
140 -DGMX_HWLOC=$(usex hwloc)
141 -DGMX_DEFAULT_SUFFIX=off
142 -DGMX_SIMD="$acce"
143 @@ -238,11 +187,6 @@ src_compile() {
144 einfo "Compiling for ${x} precision"
145 BUILD_DIR="${WORKDIR}/${P}_${x}"\
146 cmake-utils_src_compile
147 - # not 100% necessary for rel ebuilds as available from website
148 - if use doc; then
149 - BUILD_DIR="${WORKDIR}/${P}_${x}"\
150 - cmake-utils_src_compile manual
151 - fi
152 use mpi || continue
153 einfo "Compiling for ${x} precision with mpi"
154 BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
155 @@ -262,7 +206,7 @@ src_install() {
156 BUILD_DIR="${WORKDIR}/${P}_${x}" \
157 cmake-utils_src_install
158 if use doc; then
159 - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
160 + newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
161 fi
162 use mpi || continue
163 BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
164
165 diff --git a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
166 index dab1a95179d..d5258ab6f23 100644
167 --- a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
168 +++ b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
169 @@ -5,22 +5,12 @@ EAPI=7
170
171 CMAKE_MAKEFILE_GENERATOR="ninja"
172
173 -PYTHON_COMPAT=( python2_7 )
174 -
175 -inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils
176 -
177 -if [[ $PV = *9999* ]]; then
178 - EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
179 - https://gerrit.gromacs.org/gromacs.git
180 - https://github.com/gromacs/gromacs.git
181 - https://repo.or.cz/r/gromacs.git"
182 - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
183 - inherit git-r3
184 -else
185 - SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
186 +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
187 +
188 +SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
189 + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
190 test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
191 - KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
192 -fi
193 +KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
194
195 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
196
197 @@ -53,17 +43,7 @@ CDEPEND="
198 "
199 BDEPEND="${CDEPEND}
200 virtual/pkgconfig
201 - doc? (
202 - app-doc/doxygen
203 - $(python_gen_cond_dep '
204 - dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
205 - ')
206 - media-gfx/mscgen
207 - media-gfx/graphviz
208 - dev-texlive/texlive-latex
209 - dev-texlive/texlive-latexextra
210 - media-gfx/imagemagick
211 - )"
212 + "
213 RDEPEND="${CDEPEND}"
214
215 REQUIRED_USE="
216 @@ -77,9 +57,7 @@ DOCS=( AUTHORS README )
217
218 RESTRICT="!test? ( test )"
219
220 -if [[ ${PV} != *9999 ]]; then
221 - S="${WORKDIR}/${PN}-${PV/_/-}"
222 -fi
223 +S="${WORKDIR}/${PN}-${PV/_/-}"
224
225 pkg_pretend() {
226 [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
227 @@ -87,20 +65,6 @@ pkg_pretend() {
228 die "Please switch to an openmp compatible compiler"
229 }
230
231 -src_unpack() {
232 - if [[ ${PV} != *9999 ]]; then
233 - default
234 - else
235 - git-r3_src_unpack
236 - if use test; then
237 - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
238 - EGIT_BRANCH="${EGIT_BRANCH}" \
239 - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests" \
240 - git-r3_src_unpack
241 - fi
242 - fi
243 -}
244 -
245 src_prepare() {
246 #notes/todos
247 # -on apple: there is framework support
248 @@ -123,28 +87,6 @@ src_prepare() {
249 fi
250
251 DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
252 -
253 - # try to create policy for imagemagik
254 - mkdir -p ${HOME}/.config/ImageMagick
255 - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
256 - <?xml version="1.0" encoding="UTF-8"?>
257 - <!DOCTYPE policymap [
258 - <!ELEMENT policymap (policy)+>
259 - !ATTLIST policymap xmlns CDATA #FIXED ''>
260 - <!ELEMENT policy EMPTY>
261 - <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
262 - name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
263 - stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
264 - ]>
265 - <policymap>
266 - <policy domain="coder" rights="read | write" pattern="PS" />
267 - <policy domain="coder" rights="read | write" pattern="PS2" />
268 - <policy domain="coder" rights="read | write" pattern="PS3" />
269 - <policy domain="coder" rights="read | write" pattern="EPS" />
270 - <policy domain="coder" rights="read | write" pattern="PDF" />
271 - <policy domain="coder" rights="read | write" pattern="XPS" />
272 - </policymap>
273 - EOF
274 }
275
276 src_configure() {
277 @@ -194,7 +136,6 @@ src_configure() {
278 -DGMX_OPENMP=$(usex openmp)
279 -DGMX_COOL_QUOTES=$(usex offensive)
280 -DGMX_USE_TNG=$(usex tng)
281 - -DGMX_BUILD_MANUAL=$(usex doc)
282 -DGMX_HWLOC=$(usex hwloc)
283 -DGMX_DEFAULT_SUFFIX=off
284 -DGMX_SIMD="$acce"
285 @@ -259,11 +200,6 @@ src_compile() {
286 einfo "Compiling for ${x} precision"
287 BUILD_DIR="${WORKDIR}/${P}_${x}"\
288 cmake-utils_src_compile
289 - # not 100% necessary for rel ebuilds as available from website
290 - if use doc; then
291 - BUILD_DIR="${WORKDIR}/${P}_${x}"\
292 - cmake-utils_src_compile manual
293 - fi
294 use mpi || continue
295 einfo "Compiling for ${x} precision with mpi"
296 BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
297 @@ -283,7 +219,7 @@ src_install() {
298 BUILD_DIR="${WORKDIR}/${P}_${x}" \
299 cmake-utils_src_install
300 if use doc; then
301 - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
302 + newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
303 fi
304 use mpi || continue
305 BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
306
307 diff --git a/sci-chemistry/gromacs/gromacs-2019.6.ebuild b/sci-chemistry/gromacs/gromacs-2019.6.ebuild
308 index 755bafef447..e8541e9964e 100644
309 --- a/sci-chemistry/gromacs/gromacs-2019.6.ebuild
310 +++ b/sci-chemistry/gromacs/gromacs-2019.6.ebuild
311 @@ -5,22 +5,12 @@ EAPI=7
312
313 CMAKE_MAKEFILE_GENERATOR="ninja"
314
315 -PYTHON_COMPAT=( python2_7 )
316 -
317 -inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils
318 -
319 -if [[ $PV = *9999* ]]; then
320 - EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
321 - https://gerrit.gromacs.org/gromacs.git
322 - https://github.com/gromacs/gromacs.git
323 - https://repo.or.cz/r/gromacs.git"
324 - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
325 - inherit git-r3
326 -else
327 - SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
328 +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
329 +
330 +SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
331 + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
332 test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
333 - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
334 -fi
335 +KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
336
337 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
338
339 @@ -53,17 +43,7 @@ CDEPEND="
340 "
341 BDEPEND="${CDEPEND}
342 virtual/pkgconfig
343 - doc? (
344 - app-doc/doxygen
345 - $(python_gen_cond_dep '
346 - dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
347 - ')
348 - media-gfx/mscgen
349 - media-gfx/graphviz
350 - dev-texlive/texlive-latex
351 - dev-texlive/texlive-latexextra
352 - media-gfx/imagemagick
353 - )"
354 + "
355 RDEPEND="${CDEPEND}"
356
357 REQUIRED_USE="
358 @@ -77,9 +57,7 @@ DOCS=( AUTHORS README )
359
360 RESTRICT="!test? ( test )"
361
362 -if [[ ${PV} != *9999 ]]; then
363 - S="${WORKDIR}/${PN}-${PV/_/-}"
364 -fi
365 +S="${WORKDIR}/${PN}-${PV/_/-}"
366
367 pkg_pretend() {
368 [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
369 @@ -87,20 +65,6 @@ pkg_pretend() {
370 die "Please switch to an openmp compatible compiler"
371 }
372
373 -src_unpack() {
374 - if [[ ${PV} != *9999 ]]; then
375 - default
376 - else
377 - git-r3_src_unpack
378 - if use test; then
379 - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
380 - EGIT_BRANCH="${EGIT_BRANCH}" \
381 - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests" \
382 - git-r3_src_unpack
383 - fi
384 - fi
385 -}
386 -
387 src_prepare() {
388 #notes/todos
389 # -on apple: there is framework support
390 @@ -123,28 +87,6 @@ src_prepare() {
391 fi
392
393 DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
394 -
395 - # try to create policy for imagemagik
396 - mkdir -p ${HOME}/.config/ImageMagick
397 - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
398 - <?xml version="1.0" encoding="UTF-8"?>
399 - <!DOCTYPE policymap [
400 - <!ELEMENT policymap (policy)+>
401 - !ATTLIST policymap xmlns CDATA #FIXED ''>
402 - <!ELEMENT policy EMPTY>
403 - <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
404 - name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
405 - stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
406 - ]>
407 - <policymap>
408 - <policy domain="coder" rights="read | write" pattern="PS" />
409 - <policy domain="coder" rights="read | write" pattern="PS2" />
410 - <policy domain="coder" rights="read | write" pattern="PS3" />
411 - <policy domain="coder" rights="read | write" pattern="EPS" />
412 - <policy domain="coder" rights="read | write" pattern="PDF" />
413 - <policy domain="coder" rights="read | write" pattern="XPS" />
414 - </policymap>
415 - EOF
416 }
417
418 src_configure() {
419 @@ -194,7 +136,6 @@ src_configure() {
420 -DGMX_OPENMP=$(usex openmp)
421 -DGMX_COOL_QUOTES=$(usex offensive)
422 -DGMX_USE_TNG=$(usex tng)
423 - -DGMX_BUILD_MANUAL=$(usex doc)
424 -DGMX_HWLOC=$(usex hwloc)
425 -DGMX_DEFAULT_SUFFIX=off
426 -DGMX_SIMD="$acce"
427 @@ -259,11 +200,6 @@ src_compile() {
428 einfo "Compiling for ${x} precision"
429 BUILD_DIR="${WORKDIR}/${P}_${x}"\
430 cmake-utils_src_compile
431 - # not 100% necessary for rel ebuilds as available from website
432 - if use doc; then
433 - BUILD_DIR="${WORKDIR}/${P}_${x}"\
434 - cmake-utils_src_compile manual
435 - fi
436 use mpi || continue
437 einfo "Compiling for ${x} precision with mpi"
438 BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
439 @@ -283,7 +219,7 @@ src_install() {
440 BUILD_DIR="${WORKDIR}/${P}_${x}" \
441 cmake-utils_src_install
442 if use doc; then
443 - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
444 + newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
445 fi
446 use mpi || continue
447 BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
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