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authorV3n3RiX <venerix@koprulu.sector>2021-10-20 10:22:14 +0100
committerV3n3RiX <venerix@koprulu.sector>2021-10-20 10:22:14 +0100
commit46eedbedafdb0040c37884982d4c775ce277fb7b (patch)
treedb33a91259730be84999e13a8d8168c799f50ac0 /sci-chemistry
parente23a08d0c97a0cc415aaa165da840b056f93c997 (diff)
gentoo resync : 20.10.2021
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/Manifest.gzbin10838 -> 10833 bytes
-rw-r--r--sci-chemistry/chemex/Manifest4
-rw-r--r--sci-chemistry/chemex/chemex-2018.10.3.ebuild40
-rw-r--r--sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild46
-rw-r--r--sci-chemistry/dssp/Manifest2
-rw-r--r--sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild2
-rw-r--r--sci-chemistry/gromacs/Manifest6
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.3.ebuild15
-rw-r--r--sci-chemistry/gromacs/gromacs-2021.9999.ebuild15
-rw-r--r--sci-chemistry/gromacs/gromacs-9999.ebuild15
10 files changed, 77 insertions, 68 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index a0b7688fa224..9179b0b9fb77 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
Binary files differ
diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest
index e4c35fa87574..fd297d8394a5 100644
--- a/sci-chemistry/chemex/Manifest
+++ b/sci-chemistry/chemex/Manifest
@@ -1,5 +1,5 @@
-DIST chemex-2018.10.3.tar.gz 546696 BLAKE2B d283cfb94118686f1974780249641e0ea6f86cdb854c4a256897e361a300a94506813a5035ee2f300fca13263e8452b77e7a0817436cbd620ba16d801a541af7 SHA512 784bd03b354724d6aa52d663c6f661f865d4ef7ca345573bc8aae9ef63e5dbb3e65abba364de3ff441b78adfa588344c718809c5880b3fc70d8ed24be06a0826
DIST chemex-2021.4.0_p2.tar.gz 2384471 BLAKE2B 1eb609c4e4ad9ac0f7cac8ab523e72e8ab9c12d40671fd598cd26b8de2a3d6e68dfdcaee9202521fc583068f591377842b3e7b9f0e1f95e6cba8da9b0c6d63a4 SHA512 568072eaf0d1c666de2aedacc50cd98da15631e0ef15ba60414be671ac97a50967e5b4d6d00340b1263f730b3a803ccc8995fbb86cfc47517b9521c9920641c8
-EBUILD chemex-2018.10.3.ebuild 1007 BLAKE2B 9b231e246e6401185db827f7cc808be6c1955a569f00b156b7b3ef43645cb51596865551df05c176bfa916128dd40953d933a54e7c10548c37fb08acbb8fb62c SHA512 82f4719818573b63cbdc8d7ffac0968204357f705655e327df0866ea6296c03fb38b8b05133b301fb88fdbaec693814c55c6fea935f7dc4a507eeee5fe0493f3
+DIST chemex-2021.4.0_p4.tar.gz 2387888 BLAKE2B 26b4467756ba1b31775c554906a2ce09556e1fb99dd2ff294620a12b92246f441a2daa07e6bad7cedf903bd18e6ecc0613b6473f54d27d89ed9117ddc6a27269 SHA512 7d93f213317e4cb5a987c0b3cfcce146fb02a15ac9efbde74f9d3fc56a5e86c89ca6b606f45013bf08ed10f3de17cc72fa010ce0e42c5cb746119ede0ce4d38f
EBUILD chemex-2021.4.0_p2.ebuild 1184 BLAKE2B a7ab020a416e46f232ce5b9bd140d7af6c925b8e0da5b2dfe629e7f50533692700c183cf1068be6fa0cee7cd3141eee6f684a936fea9b034f0a68b8f0f080358 SHA512 06067c09038bcc2629ac272a5005acd1f11fce5014ceb2fb9eb8fa9f7c6d900d9ccdc07a90e54fde11e5399baed2b12def1facdfaf7e929e603e6c334b463a04
+EBUILD chemex-2021.4.0_p4.ebuild 1279 BLAKE2B dc10ef290d4dac75119a4b215da0b1fea01cbfc7558c6fc78f46801ec5cb0514d6d2ae7cbd58028ce4da2903109d25b0fd02637d4b3a6570b819696fc4c15348 SHA512 faaa7006bd9ee86684de6afaceb25695c63dc1514abb21201172c0338068abf0787ae67c935b12e10dcacac2c30652f513458c9f6e0284d94b1b57b53dc7e310
MISC metadata.xml 217 BLAKE2B f8189b02494f180dac078dcd5c275d3c795f20f360f8b172c66065a2d937e396b24b8631bba4cd8567d60285ce89fc77b9539f2233bf33899c820613c48c33ba SHA512 f0c9e5b3d281fecd21b1e23a6f44c94c1c0b3220de46a177d35932111b7f1ab4399061c42833ac1ee9bd0324b139fc8db66e0d2890224d607bd3be38ae469be9
diff --git a/sci-chemistry/chemex/chemex-2018.10.3.ebuild b/sci-chemistry/chemex/chemex-2018.10.3.ebuild
deleted file mode 100644
index 19f50cce7be7..000000000000
--- a/sci-chemistry/chemex/chemex-2018.10.3.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-DISTUTILS_SINGLE_IMPL="yes"
-DISTUTILS_USE_SETUPTOOLS=rdepend
-PYTHON_COMPAT=( python3_{8..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data"
-HOMEPAGE="https://github.com/gbouvignies/chemex"
-SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- $(python_gen_cond_dep '
- >=dev-python/asteval-0.9.11[${PYTHON_USEDEP}]
- >=dev-python/lmfit-0.9.11[${PYTHON_USEDEP}]
- >=dev-python/matplotlib-1.1[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/setuptools_scm[${PYTHON_USEDEP}]
- >=dev-python/scipy-0.11[${PYTHON_USEDEP}]
- ')
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
-
-S="${WORKDIR}/ChemEx-${PV}"
-
-src_prepare() {
- export SETUPTOOLS_SCM_PRETEND_VERSION="${PV}"
- distutils-r1_src_prepare
-}
diff --git a/sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild b/sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild
new file mode 100644
index 000000000000..3a331d48eba7
--- /dev/null
+++ b/sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+DISTUTILS_SINGLE_IMPL="yes"
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+
+inherit distutils-r1
+
+DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data"
+HOMEPAGE="https://github.com/gbouvignies/chemex"
+SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV/_p/-dev}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64"
+IUSE="test"
+
+#RESTRICT="!test? ( test )"
+# FIXME: Restrict until we figure out how to run tests properly, bug #815079
+RESTRICT="test"
+
+RDEPEND="
+ $(python_gen_cond_dep '
+ >=dev-python/asteval-0.9.25[${PYTHON_USEDEP}]
+ >=dev-python/jsonschema-4.1.0[${PYTHON_USEDEP}]
+ >=dev-python/lmfit-1.0.3[${PYTHON_USEDEP}]
+ >=dev-python/matplotlib-3.4.3[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.21.2[${PYTHON_USEDEP}]
+ dev-python/setuptools_scm[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.7.0[${PYTHON_USEDEP}]
+ >=dev-python/tomlkit-0.7.2[${PYTHON_USEDEP}]
+ >=dev-python/tqdm-4.61.1[${PYTHON_USEDEP}]
+ ')
+"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests pytest
+
+S="${WORKDIR}/ChemEx-${PV/_p/-dev}"
+
+src_prepare() {
+ export SETUPTOOLS_SCM_PRETEND_VERSION="${PV}"
+ distutils-r1_src_prepare
+}
diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest
index ba167e11628e..cd68455be0ea 100644
--- a/sci-chemistry/dssp/Manifest
+++ b/sci-chemistry/dssp/Manifest
@@ -8,6 +8,6 @@ DIST dssp-4.0.3.tar.gz 122872 BLAKE2B f88c330370645b4bd4e89656ad676e443a33c38d78
EBUILD dssp-2.2.1-r2.ebuild 962 BLAKE2B 4badf2ae8647aab9c5e359d9e0763d051388afe3bf5763c8eeb99cb21b30283d72ace619f1b65c5ee248c42f8264cb31c2c1c079f75eacda1568cc4352cec5e3 SHA512 4a599b6e7cd068175bd89f4ea948ad1267df783c240ab46d3c6109bf3f2853de714ecf1e5776722309688599f28af545287fe5cb98d8b7a5f46d319df953b926
EBUILD dssp-2.2.1-r3.ebuild 880 BLAKE2B 057a862fbc9ff19fbf487f9df0faf661a7db5406c28e6cb91d5e38dfaa2e9d24eead9ba78d4e92b5b5022e2be5c69b30ff6c386aeac8160062b5f7f35b449889 SHA512 747ac74fd95400759569e657db85c3dc5c5a7ee0753761bc4b4927f4d119d168f0d5dcbd9ca16f37486358e7117e773d812034fb07953aae88c63ac1e706f8f7
EBUILD dssp-3.0.11.ebuild 825 BLAKE2B 020ea517127ffc1167cbff3a9362e5ff255b25664769ef2ac8f7f3060e34e0bec29e965df46e65bab8943cbf5fb11175d70b1b9f9e7d71bdbf92a4c54a903367 SHA512 b81dbe1cb9f7b66c5268485dc262bb705b12d250e2ec778c80fddbc584a38e36b64cb93e92385c178fdeca0e593c45ce25aef16480bfa9eb230bdd2b8a82fa53
-EBUILD dssp-4.0.1_p20210831.ebuild 849 BLAKE2B 0d6089c63608b85c98f67136cfd275098272985f689ac0e6338c7ee6cd158a851901815d0dab988a2ab65ff63a1bfbcd689577daa98c2c91bc04c95f2a95420b SHA512 35d5e67754a7a7b3d3021c16d57d1b4e5c8a2316606b7ebed08bb543e647794d87b64e4ba04db3d86d34f13999e04af08b4df8cbe4d8d5843c1f3f26c491b0b0
+EBUILD dssp-4.0.1_p20210831.ebuild 854 BLAKE2B 0900056de41489970920f7bc190df755478a719ee19d9afcc9bfcebd666e0e6abe3bc03ce93a6ce5b4c426401f4243114e576a7eba4b84a84ea63c0c73f1f78e SHA512 4d2deb26d537014238592d7062b7d9ad6ce3350d09c9e422c47f70df7c9320235e141e05290635b63d66c65aebc8c964604b9269bf423bf09a2e90e87e70015f
EBUILD dssp-4.0.3.ebuild 769 BLAKE2B 406a817ed8545b7b85524cd36a0f7016b75639a0dd15971639eba0e55a2eb78b68817d0892149d8b6781d6b4ed9a767d7e508d236023a1bd16663fc289bc6399 SHA512 2dbd1aa4e76d6bc58a42ed4dc848c7e87afd3079d5f2bd21652288b38ef7ad0d5c5804a52532e33cd2519652d3a94cc2f9fc462e8488aee42309edb2a40dc156
MISC metadata.xml 217 BLAKE2B f8189b02494f180dac078dcd5c275d3c795f20f360f8b172c66065a2d937e396b24b8631bba4cd8567d60285ce89fc77b9539f2233bf33899c820613c48c33ba SHA512 f0c9e5b3d281fecd21b1e23a6f44c94c1c0b3220de46a177d35932111b7f1ab4399061c42833ac1ee9bd0324b139fc8db66e0d2890224d607bd3be38ae469be9
diff --git a/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild b/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild
index a5e5af9c7424..ca051ca5a0d2 100644
--- a/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild
+++ b/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild
@@ -13,7 +13,7 @@ S="${WORKDIR}/${PN}-${COMMIT}"
LICENSE="BSD-2"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE=""
BDEPEND="
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 11c5547a7590..ceeb952dad3e 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -23,7 +23,7 @@ EBUILD gromacs-2019.6.ebuild 7264 BLAKE2B 6196f750a81562c82f1004ba3e4be05193aa91
EBUILD gromacs-2020.4.ebuild 10134 BLAKE2B efc77b2cb0981ebf3f90fbe531d54020be2e82b464dace3ab8d07d41cae060c5e073a8a3f641b4bb0431ec2717a5f990a2a6f08ceed6a805bde82742b9eba487 SHA512 f7af8d31c43abe23b9c92ce6afd0dbea4219fe48dad3d91bf19f50f80a520cb0ab98949d4f2653679de751853755e793fd0e84ad73ebf13bef17fc255d693001
EBUILD gromacs-2020.6.ebuild 10137 BLAKE2B e5f058493f7757ffcff53c892445a3ea2dd15ebb83bbd7fd186a56d85e785be75277e8329487a182d27e23f7756b02618c227ef40c2aaf0243f2a1fbeda232c6 SHA512 37df9d310ab597ce4bb69bd3d77ec20d4b6e0b825b341e5fe78b139164fd02a43b5e3d012530fd9a62500d4a63d2efa05fcbc1219ef5edcb93bf232d563af821
EBUILD gromacs-2021.2.ebuild 10361 BLAKE2B 925ad220aa14d1e0ec8ad0bc2a1b5f887c2dc7e3e419ef54b009026fa8dd251ef91821acd82e12a3126a065d709dde9a9df14f026323373d0b2909b750795b50 SHA512 15e159486ff136633fc6de6f32a5efd14b7d7276197db7bd0e83dfdf8c57ecc2374c8021783726de9b0d99512ccb8f0980506ceb53cdaaee1cecd847a699caf0
-EBUILD gromacs-2021.3.ebuild 10269 BLAKE2B 90f318b96a6a5a4ce24753d6ea610dabe2cbd59670db5f4ee61c9d9b282fd79e6db0d2e758834fdb563c8c3b27876f63c619306f8c25a669ac9fa8153d71b0fc SHA512 7eaeff9d5468e3c51d7277b18588250aedae6c5c023793c91f0d9583608c85ee11da6278e293a0597d29ea408b7a86d17448c118f7f52c6b575be9ec137b4d5a
-EBUILD gromacs-2021.9999.ebuild 10271 BLAKE2B 59d6173d1c82cfa1c084528edf2e9cf9bab8e6eefb5e3cc7c05fc43654c7be9463a24cd62a8c764afcddb9fe29fad2643cf60222608f0cdbe72eedd6c41337f2 SHA512 8434cfaf918264c8ad1e0c87f2876c6531a70d330c1205378ac65f537a562e2a72208cffca41bc85773ff1f2eb73653a4c5b1cb992f007c03bab125aa13ae4f6
-EBUILD gromacs-9999.ebuild 10271 BLAKE2B 59d6173d1c82cfa1c084528edf2e9cf9bab8e6eefb5e3cc7c05fc43654c7be9463a24cd62a8c764afcddb9fe29fad2643cf60222608f0cdbe72eedd6c41337f2 SHA512 8434cfaf918264c8ad1e0c87f2876c6531a70d330c1205378ac65f537a562e2a72208cffca41bc85773ff1f2eb73653a4c5b1cb992f007c03bab125aa13ae4f6
+EBUILD gromacs-2021.3.ebuild 10288 BLAKE2B 051f7c792d1138cbf14b0c2986d51216650e852ff72e99eaba599710f0b101345c83cb3a513c0a4949fb402ed0ff19f6ff7459134e521107741e6fa122691365 SHA512 a8612408e6beae5bde8d13749086721696c2a3d7620e5fd259d35bc17b3e843031ac682394fcdad37898fcaf77492a2dc7f0fc6de9426aad31849ff03c5f57de
+EBUILD gromacs-2021.9999.ebuild 10290 BLAKE2B 5253608d15b6230ef26d8d795367efe86223c15731470893232abd9f2c657774f1fc63ed884450402344c692cf31f441b72aa34fee703089f0fab218f430c2e3 SHA512 10a06dab21f41a9866fd7871251009a93f02e1510ba297c2434c14b237be01744aeca7e3163667b74c992b4c485c50219212aed7979672ae61917025fd187e1b
+EBUILD gromacs-9999.ebuild 10290 BLAKE2B 5253608d15b6230ef26d8d795367efe86223c15731470893232abd9f2c657774f1fc63ed884450402344c692cf31f441b72aa34fee703089f0fab218f430c2e3 SHA512 10a06dab21f41a9866fd7871251009a93f02e1510ba297c2434c14b237be01744aeca7e3163667b74c992b4c485c50219212aed7979672ae61917025fd187e1b
MISC metadata.xml 1224 BLAKE2B dc6de7f135e5cbd7bdb94bc630d3c7344f5f5387305ada4f3f0fd3f027f9fa4e2c5e44120c8eab8e983fcda314680ac3d140ab61873ab21b839f912a52b21dde SHA512 d036cffac5fd3c4b8d26efdee0f4b4db8d3520f771754a0859f8e99f64d558795b6cab1efba1d4f1700027707a05a724ae96a7e257434d3894ef5fa6eed7ccba
diff --git a/sci-chemistry/gromacs/gromacs-2021.3.ebuild b/sci-chemistry/gromacs/gromacs-2021.3.ebuild
index e77091aa53d1..12b437ed37ee 100644
--- a/sci-chemistry/gromacs/gromacs-2021.3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.3.ebuild
@@ -161,17 +161,18 @@ src_prepare() {
src_configure() {
local mycmakeargs_pre=( ) extra fft_opts=( )
+ local acce="AUTO"
if use custom-cflags; then
#go from slowest to fastest acceleration
- local acce="None"
+ acce="None"
if (use amd64 || use x86); then
- use cpu_flags_x86_sse2 && acce="SSE2"
- use cpu_flags_x86_sse4_1 && acce="SSE4.1"
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
- use cpu_flags_x86_avx && acce="AVX_256"
- use cpu_flags_x86_avx2 && acce="AVX2_256"
- use cpu_flags_x86_avx512f && acce="AVX_512"
+ use cpu_flags_x86_sse2 && acce="SSE2"
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+ use cpu_flags_x86_avx && acce="AVX_256"
+ use cpu_flags_x86_avx2 && acce="AVX2_256"
+ use cpu_flags_x86_avx512f && acce="AVX_512"
elif (use arm); then
use cpu_flags_arm_neon && acce="ARM_NEON"
elif (use arm64); then
diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
index ebd3a798340c..ac7420b81358 100644
--- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
@@ -161,17 +161,18 @@ src_prepare() {
src_configure() {
local mycmakeargs_pre=( ) extra fft_opts=( )
+ local acce="AUTO"
if use custom-cflags; then
#go from slowest to fastest acceleration
- local acce="None"
+ acce="None"
if (use amd64 || use x86); then
- use cpu_flags_x86_sse2 && acce="SSE2"
- use cpu_flags_x86_sse4_1 && acce="SSE4.1"
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
- use cpu_flags_x86_avx && acce="AVX_256"
- use cpu_flags_x86_avx2 && acce="AVX2_256"
- use cpu_flags_x86_avx512f && acce="AVX_512"
+ use cpu_flags_x86_sse2 && acce="SSE2"
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+ use cpu_flags_x86_avx && acce="AVX_256"
+ use cpu_flags_x86_avx2 && acce="AVX2_256"
+ use cpu_flags_x86_avx512f && acce="AVX_512"
elif (use arm); then
use cpu_flags_arm_neon && acce="ARM_NEON"
elif (use arm64); then
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index ebd3a798340c..ac7420b81358 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -161,17 +161,18 @@ src_prepare() {
src_configure() {
local mycmakeargs_pre=( ) extra fft_opts=( )
+ local acce="AUTO"
if use custom-cflags; then
#go from slowest to fastest acceleration
- local acce="None"
+ acce="None"
if (use amd64 || use x86); then
- use cpu_flags_x86_sse2 && acce="SSE2"
- use cpu_flags_x86_sse4_1 && acce="SSE4.1"
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
- use cpu_flags_x86_avx && acce="AVX_256"
- use cpu_flags_x86_avx2 && acce="AVX2_256"
- use cpu_flags_x86_avx512f && acce="AVX_512"
+ use cpu_flags_x86_sse2 && acce="SSE2"
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+ use cpu_flags_x86_avx && acce="AVX_256"
+ use cpu_flags_x86_avx2 && acce="AVX2_256"
+ use cpu_flags_x86_avx512f && acce="AVX_512"
elif (use arm); then
use cpu_flags_arm_neon && acce="ARM_NEON"
elif (use arm64); then
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-22 21:06:34 +0000