gentoo auto-resync : 17:09:2023 - 23:04:24

8 files changed, 37 insertions, 31 deletions

diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.2.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild
index cf12f39f51df..e5c508fd6ca1 100644
--- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.2.ebuild
+++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.5.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 PYTHON_COMPAT=( python3_{9..11} )
 DISTUTILS_USE_PEP517=setuptools
diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest
index 20f6d340c98d..59c53091950e 100644
--- a/sci-chemistry/GromacsWrapper/Manifest
+++ b/sci-chemistry/GromacsWrapper/Manifest
@@ -1,5 +1,5 @@
-DIST GromacsWrapper-0.8.2.tar.gz 1954926 BLAKE2B c05995667f925a7519e07e59519e985693effa2fd511d228d236bff978d05430d422003e1360f9fda26564e40bb69183ae8e9b7334e0427c2b177f019df38a6a SHA512 b8a3e7da43eaabaf0fe12f4c06ff80f018847f9386c16eb66c96b3840c66b79d02ee47e675c08ed81df0ef495261c3b557d64c62caac0e484f661ef6b3a5be73
 DIST GromacsWrapper-0.8.4.tar.gz 1955167 BLAKE2B 59f0301263eefaa4d7c139b34a48172c218a76f0f9488477d6203d9cd732098468dae5a73ff46aa74eb2b4433268c77bc265e506129e4c14a357042453d5f97f SHA512 822edc33c77ca4dbfbc1e4172686744345ed3c0d2305f4b19abab15576a1433bbb3b23b96f637398ad4f72cd5414d96ee531ab4a329d3acb462d90b95437a6a5
-EBUILD GromacsWrapper-0.8.2.ebuild 911 BLAKE2B bb0f003e877d03904ac5bcce4c73c103eb008670491070e593bbda3d5c5471c2cb766b020626c0dbf3f43694321f71b7d16a1a70b92abe6bb5b014f494ae1506 SHA512 c53c908443c871a87386c48195df4f052d0a211a3d16b298e2f82ac2f73e3078a6d2784c17e22f93598d2e0c80cffe31713b13b390600c4d7e036ddea0c0d390
+DIST GromacsWrapper-0.8.5.tar.gz 1958570 BLAKE2B b8f79721a7566117206818144fc7087c4634d7fb71c77abef63dd9565a0655ce6b4a259ea5bf9cb3b5bc13df8f428f58e514f7871192d27a6d463e758e27f4b3 SHA512 8800afdbe92edad35df58e825546797ede1738b9029df0fb57a96e377d7be94f3d21fe1df9d5cb4490d12b984972d63d87e673d3d33af60a7dc8d0453574a5c6
 EBUILD GromacsWrapper-0.8.4.ebuild 911 BLAKE2B 827ac820482bd41895e02a218041fb1668899d7c80e95ee51021a92d6f7fe36452d1012330118266958f8313694b9c655cc32ddf995d62f3b08aad508c912301 SHA512 6d0f23fcc82cfd0097768a98a1d5755fb003437734f2c6ac90ccff21aa8a8c69bac8f7c0dd4803711e249ff66e513b906394394b71313b2a48f9f0bc37b2ce7e
+EBUILD GromacsWrapper-0.8.5.ebuild 911 BLAKE2B 827ac820482bd41895e02a218041fb1668899d7c80e95ee51021a92d6f7fe36452d1012330118266958f8313694b9c655cc32ddf995d62f3b08aad508c912301 SHA512 6d0f23fcc82cfd0097768a98a1d5755fb003437734f2c6ac90ccff21aa8a8c69bac8f7c0dd4803711e249ff66e513b906394394b71313b2a48f9f0bc37b2ce7e
 MISC metadata.xml 483 BLAKE2B 1d8a7e888d8b95bd229ef72894ba02f583e3e3958f9cd5733ab6b466312bac0b0f5a9004135caa37a3ef137e8782fa93ff4bb90f35f31c058d8c528025b193d0 SHA512 70e5dc653ff21a0395b946e5f3548320d2abb8c63ae9f3ce04be6768e20b02ce55a612a2ad12b6c2262529ab753ca9fda02d9bdae7f6ac859bca49bbbad6f75f
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 5156f0811930..b92065d97f52 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest
index 1986c9845998..910723bedde2 100644
--- a/sci-chemistry/chemex/Manifest
+++ b/sci-chemistry/chemex/Manifest
@@ -1,5 +1,5 @@
-DIST chemex-2022.3.4.tar.gz 2845201 BLAKE2B 91a76bdb54857710d482b14e36d24adec8706c385da7300d8cf7189426af28651877d487eb061e26656432575eb711de0e3a92724d1488d99efcdc8a682b59bd SHA512 304af730149a2f6723bbe36c0deafb826392cd571a2b4245bb42e28612ceef3ee2ca989f1909ddc7709081f742a997469565ef7d02994fda8087372f29e1dfe1
 DIST chemex-2022.3.5.tar.gz 2845347 BLAKE2B 29b53ba8afcfd91e4f50119f212557de85d8576474b74d2ad925c8c2adb89397640e7b352b6785dc99a8c4e5007294609640219b2374cbb3144f94c5f9113d96 SHA512 3a92702d105e95e0a7b15e01b839d5982df55477afb98e58f7458a0e87230e94597c01d33c219ae469ed62e4ddaecdb787ae435453d428843d5a612159715d2b
-EBUILD chemex-2022.3.4.ebuild 1250 BLAKE2B e6af845a61c59bc318e985d4e0b335aa526d426ff5186d07455768d2cf03e2ae6cdfd128fad40da16d33c13aba6dee6bf52f18e9eaeca9d2ddf8288312f3366a SHA512 b19b3336e0ac78b877463bc2431fb1daa57d5070444785ca47691cf21174b27277b3c41b49b136c18893a89015caab111edbb65b6a3dd1c90310f96388a85fdd
+DIST chemex-2022.3.6.tar.gz 2843118 BLAKE2B e51b385dbf9e3c42f54f95f9929125e3263e12afa62beab8e5b8eb13e78a4fe9a0fb445f4f6c3cd4aa8e71748732ec58124682daa86be079eed036b78492ca71 SHA512 5c734e1b3ea39e9729bada93dfe5bc55f877b69ba6edd9612f95aab0d31949489582957a14f175646c7e6652644a5a55c26bcd74affc7fecc1e7b9cfdd4ceb63
 EBUILD chemex-2022.3.5.ebuild 1250 BLAKE2B d1f61563a971c3c6795b2d398d71073e1db4cc5cca62a6ffc7d9bd2b22b6517417faddc037369fa545fb7f6493d95f658d850c1319eea4adb8bb51c9109e9df7 SHA512 2b1a3a0ca2eeadc7256efadd15a70bdb6b866da1a26a6c209b42fe6e010e871b675f1f2448a2dfdb8fefcbd9c0e97f54ac757a13fb0d29c03bb93ede9c8be97a
+EBUILD chemex-2022.3.6.ebuild 1240 BLAKE2B 46d4f9fd57f5dbc8ad5b527e8568337cd57d3c03f25581d275e15204e5e2ee2c2224c6e8ada71c8d91aed01128be697987cc808bdfd7d7e3abc5f655eb2abb44 SHA512 814348dc6b404698634ecb33ee3956479dd1c05f91f7ca82e4f8a15776a582dd911e30a2070bff727f2aeae678a609fe2d8b676f107741904886c83315dbeb78
 MISC metadata.xml 300 BLAKE2B a1ad769918094ddbda13ac92462ec69fa469dfcacde1202c653a4aa7443db661ffa5739cd039b6e38b13f0345a2680f276b4e071362106b162c95cd92007b5a8 SHA512 755c273f6bf67f79c388d06d970702a1d4a9f84338f8d889dd9146905c6994621917952225406ffba5bfe1e1b69f0bfd0f471374178b15343f4927af9de49aef
diff --git a/sci-chemistry/chemex/chemex-2022.3.4.ebuild b/sci-chemistry/chemex/chemex-2022.3.6.ebuild
index 3df32b1ac247..81b3e45f7856 100644
--- a/sci-chemistry/chemex/chemex-2022.3.4.ebuild
+++ b/sci-chemistry/chemex/chemex-2022.3.6.ebuild
@@ -4,14 +4,14 @@
 EAPI=8
 
 DISTUTILS_SINGLE_IMPL="yes"
-DISTUTILS_USE_PEP517=poetry
+DISTUTILS_USE_PEP517=pdm-backend
 PYTHON_COMPAT=( python3_{9..11} )
 
 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/refs/tags/v${PV/_p/-dev}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/gbouvignies/ChemEx/archive/refs/tags/${PV/_p/-dev}.tar.gz -> ${P}.tar.gz"
 S="${WORKDIR}/ChemEx-${PV/_p/-dev}"
 
 SLOT="0"
@@ -25,18 +25,19 @@ RESTRICT="test"
 
 RDEPEND="
 	$(python_gen_cond_dep '
-		>=dev-python/asteval-0.9.25[${PYTHON_USEDEP}]
-		>=dev-python/cachetools-5.3.0[${PYTHON_USEDEP}]
-		>=dev-python/lmfit-1.2.0[${PYTHON_USEDEP}]
+		>=dev-python/cachetools-5.3.1[${PYTHON_USEDEP}]
+		>=dev-python/lmfit-1.2.1[${PYTHON_USEDEP}]
 		>=dev-python/matplotlib-3.7.1[${PYTHON_USEDEP}]
-		>=dev-python/numpy-1.24.2[${PYTHON_USEDEP}]
-		>=dev-python/pydantic-1.10.7[${PYTHON_USEDEP}]
-		>=dev-python/rapidfuzz-3.0.0[${PYTHON_USEDEP}]
-		>=dev-python/rich-13.3.4[${PYTHON_USEDEP}]
-		>=dev-python/scipy-1.10.1[${PYTHON_USEDEP}]
+		>=dev-python/numpy-1.25.0[${PYTHON_USEDEP}]
+		>=dev-python/pydantic-2.0.1[${PYTHON_USEDEP}]
+		>=dev-python/rapidfuzz-3.1.1[${PYTHON_USEDEP}]
+		>=dev-python/rich-13.4.2[${PYTHON_USEDEP}]
+		>=dev-python/scipy-1.9.3[${PYTHON_USEDEP}]
 		>=dev-python/tomli-2.0.1[${PYTHON_USEDEP}]
 	')
 "
 DEPEND="${RDEPEND}"
 
 distutils_enable_tests pytest
+
+export PDM_BUILD_SCM_VERSION=${PV}
diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest
index c426121ecf3e..0d3471385728 100644
--- a/sci-chemistry/tinker/Manifest
+++ b/sci-chemistry/tinker/Manifest
@@ -1,4 +1,4 @@
 AUX 8.2.1-openmp.patch 559 BLAKE2B 254a7b5d5d40bec938420527ad77e4ec96b9cee50392137eab3370df35a00a00b9488b5cd95c4e3c52d4904a6093216a782f52c82c2141cd913c6cf10f2fbcc7 SHA512 799b488ddba95ec75c2f5f97bdba10e297cad12d23239354b7d66af47b4e9ef1496e8f6b8a7446f85827a8303105af7552616bc865a4e8114b89d3e6e3302ed6
 DIST tinker-8.2.1.tar.gz 33015410 BLAKE2B 0b7c94662248761459cf9d681056f5cf9c4d669a790a522f23f800bf355235f6a9f392e008b13d14cf1e17d9725abb6512077c24ff7772108d69c9cf35b43e6e SHA512 5039078781d1ce226456882dd95ad15715f1e91829d26efcdb29ceedc213973883699eb6710b0a162a74208809305b7fee734b175139e6df63d0460fe5751ae7
-EBUILD tinker-8.2.1.ebuild 2310 BLAKE2B bec87fef793e09143154b3d22b60dd7532469e87c10a67378b8fd87273b61b577478a7f21622ce6432339f8ca864cb3271aa23a20bb62f46269504d510869cf3 SHA512 9226fc0afc7e7d545376f09cda475f5ed7eda11cddcf099e4ecf4cd62ae478a4def5498a7ff5ebc8d80c32c54783fbb017e482aa322ca9e91f33204c79bd96c4
-MISC metadata.xml 266 BLAKE2B a03b1fcf7148cf43fb829f619c218219bcd4e66c45d12f563113401e3ae0b06cb0df9a8c0af01ea97e21453638d627d420e7df5b9b0d330ef1752253faa8aa32 SHA512 1dc293fa0d0296eba18ac2cbcd57f47ffc6cc822bf0d76e1cc86cb046700201f703d705375b5555b88cbe8780ef3750be05b8f9f8de092693e6d165c1734e049
+EBUILD tinker-8.2.1-r1.ebuild 2387 BLAKE2B 2eec46ab90656d4336f4c130bac95f76aae850ce7bea72ce7ba5fde37897f4345c7ff8e714190dad5279592ad51fae37b5c96190614a67725d6f23c534ca94c3 SHA512 f89dcf18394067c9485fb8a85c8a6bd841bf485f3deb6671ed457e995bf008e6db64206b0903cda9e0e86dd4ffc9253ee2f1f8b469688d044e629c506a5c3abb
+MISC metadata.xml 349 BLAKE2B e2a70d46ddb77f5ea51a0d6d378cdcbe2c897464127bd86c34ec43615588a509ff038e035c24855c305248789eb0708d51d21208d2cc65e8507e4f767172582f SHA512 0cb63aaf7aadd62ea12289936ea25c8f5233c8784af96b71f103794d6bd7e0711b53728a2840f5768df2652c0b19e220b1f35223dbf27fc65f7871b6e3b4c756
diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml
index d4ff1000a775..9bfb6f28bafc 100644
--- a/sci-chemistry/tinker/metadata.xml
+++ b/sci-chemistry/tinker/metadata.xml
@@ -5,4 +5,7 @@
 		<email>sci-chemistry@gentoo.org</email>
 		<name>Gentoo Chemistry Project</name>
 	</maintainer>
+	<upstream>
+		<remote-id type="github">TinkerTools/tinker</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-chemistry/tinker/tinker-8.2.1.ebuild b/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild
index a54f1ecb210d..9964b16b549f 100644
--- a/sci-chemistry/tinker/tinker-8.2.1.ebuild
+++ b/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild
@@ -1,33 +1,34 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
-inherit flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs
+inherit flag-o-matic fortran-2 java-pkg-2 toolchain-funcs
 
 DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM"
-HOMEPAGE="http://dasher.wustl.edu/tinker/"
-SRC_URI="http://dasher.wustl.edu/${PN}/downloads/${P}.tar.gz"
+HOMEPAGE="https://dasher.wustl.edu/tinker/"
+SRC_URI="https://dasher.wustl.edu/${PN}/downloads/${P}.tar.gz"
 
 SLOT="0"
 LICENSE="Tinker"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="examples"
+RESTRICT="mirror"
 
-RDEPEND="
+COMMON_DEPEND="
 	>=sci-libs/fftw-3.2.2-r1[fortran,threads]
 	dev-libs/maloc
 	!sys-apps/bar
 	!dev-util/diffuse
-	>=virtual/jre-1.6
+"
+RDEPEND="${COMMON_DEPEND}
+	>=virtual/jre-1.8:*
 "
 DEPEND="
-	${RDEPEND}
-	>=virtual/jdk-1.6
-	virtual/pkgconfig
+	${COMMON_DEPEND}
+	>=virtual/jdk-1.8:*
 "
-
-RESTRICT="mirror"
+BDEPEND="virtual/pkgconfig"
 
 S="${WORKDIR}"/${PN}/source
 
@@ -39,17 +40,17 @@ pkg_setup() {
 	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
 
 	fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
 }
 
 src_prepare() {
 	sed 's:strip:true:g' -i ../make/Makefile || die
 	[[ $(tc-getFC) =~ "ifort" ]] && eapply "${FILESDIR}"/${PV}-openmp.patch
 	default
+	java-pkg-2_src_prepare
 }
 
 src_compile() {
-	local javalib=
+	local javalib= _omplib _fftwlib
 	for i in $(java-config -g LDPATH | sed 's|:| |g'); do
 		[[ -f ${i}/libjvm.so ]] && javalib=${i}
 	done
@@ -87,6 +88,7 @@ src_compile() {
 }
 
 src_test() {
+	local test
 	cd "${WORKDIR}"/${PN}/test/
 	for test in *.run; do
 		einfo "Testing ${test} ..."