gentoo auto-resync : 07:08:2024 - 12:37:20

11 files changed, 55 insertions, 16 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index fa838783aca7..24619a314124 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index f11612320ce8..12ada1118c65 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -3,6 +3,6 @@ AUX openbabel-python.cmake 4402 BLAKE2B 36c325a26f9b23c3957db22110628a0a922ad02b
 DIST openbabel-3.1.1_p20210225.tar.gz 36674527 BLAKE2B bb82fc96f704249d211bd86c73de0cf4e7cfe5e2ba5c745aa8b4f6f19583837e2181d85101377810095f6b71fc3b91bf2f6f5636726fc8271c6905f1f8c59e7b SHA512 9ff7cb4acbfad7a9c5c8d0dd8930ac0390d0d0f2758d1a6120009071f47ffe718f92ad620d37f26f196babb14649c52b5eb7bb161c342ef36aec655e0a172de4
 DIST openbabel.jpg 12159 BLAKE2B b701df2b8c29df607dc2bd3997a282aa9a726d56c789ff2db900d33234dc691f76b6af12a4c9ccda4f09984504b863c40c39e8bf91058939996714ede2dd37c7 SHA512 998ea526c8c92f87dd203527fdd9f4e001357e951409209f41ab68e0b730fe12d97f9079c12ca289be413854ea2abcf8bb691ae5af823a6f29d6a590e1a3e2b0
 DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70
-EBUILD openbabel-3.1.1_p20210225-r1.ebuild 7464 BLAKE2B 3c3b12086a4b69c1ccfd92b5da672ff2ec4a1dc161832094d62b049977e0cb8d8717e5999f3138f857efb642a123a64fca804c5a109f69de939686fae9a08bd8 SHA512 0b516f2a8cb7194d2146397c3fc1ef375446d8dd6a29d862ed73e78455e41c0d9a86cdaee7de64cd2d4403dac34b0ec8fee4e68156df7562331d4577c82f411c
-EBUILD openbabel-9999.ebuild 7314 BLAKE2B 4bb03f325ec2876317c4f13d481b2f7738989358bd7707f27f6f650e3e41a9afe758721b4c4929a664eb09f82fbb8da0ba9dba8331f687c36758547345ce2ef0 SHA512 37b58ea4747b79b6dcfc5e5cd69af8f1d37b2a6a1c8bf414116396549094db9e89133b70a944ab3b7668eb9d815c7e4ae9fcff9a877cea85a00911e44682eb0a
+EBUILD openbabel-3.1.1_p20210225-r1.ebuild 7465 BLAKE2B fedf37c6772c62b7d9d6a5c5cc2e89b396cfebe803d34abdd5a1a77248c9f4ce27fdcce42aa2aa625a79d29361d2fd9c31a104a8d4b886fbf63fe84af4e0066d SHA512 0089ac6f89ca13e1999fe440922f0bd864568d61f8cb8dac1519c2b1d2a9b73f278c325ffe177474f678991a4ebe1264baafdd4b419d5eacfebbaccebfd31195
+EBUILD openbabel-9999.ebuild 7465 BLAKE2B fedf37c6772c62b7d9d6a5c5cc2e89b396cfebe803d34abdd5a1a77248c9f4ce27fdcce42aa2aa625a79d29361d2fd9c31a104a8d4b886fbf63fe84af4e0066d SHA512 0089ac6f89ca13e1999fe440922f0bd864568d61f8cb8dac1519c2b1d2a9b73f278c325ffe177474f678991a4ebe1264baafdd4b419d5eacfebbaccebfd31195
 MISC metadata.xml 921 BLAKE2B c0797440e50f813777c4858cc1ce893546d7785e57243318ec7d2c601c6ec2ecb7ec5ab3dbacce960c8b71196eef51ddce07802257fff0d4cba0293f940a773f SHA512 8ee8a50230f374904a9ddaaf7337caf018788ab25a1839dbf5a48b0e5c49ac4e285a1fa759900fa6d993bc220d3586a923ae21158687be971fc51a6c302f12ad
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild
index bdfef2a675e8..fc4d6cab575e 100644
--- a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild
+++ b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225-r1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 WX_GTK_VER=3.2-gtk3
 
 inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils
diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild
index d533ec698acf..fc4d6cab575e 100644
--- a/sci-chemistry/openbabel/openbabel-9999.ebuild
+++ b/sci-chemistry/openbabel/openbabel-9999.ebuild
@@ -3,13 +3,13 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 WX_GTK_VER=3.2-gtk3
 
 inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils
 
 DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="https://openbabel.org/"
+HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
 
 if [[ "${PV}" == *9999* ]]; then
 	inherit git-r3
@@ -17,7 +17,7 @@ if [[ "${PV}" == *9999* ]]; then
 else
 	if [[ "${PV}" == *_p* ]]; then	# eg., openbabel-3.1.1_p20210325
 		# Set to commit hash
-		OPENBABEL_COMMIT=
+		OPENBABEL_COMMIT=08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b
 		SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
 		S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
 	else
@@ -25,7 +25,7 @@ else
 		SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz"
 		S="${WORKDIR}/${PN}-${MY_P}"
 	fi
-	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+	KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 fi
 
 SRC_URI="${SRC_URI}
@@ -80,6 +80,10 @@ RDEPEND="
 	)
 "
 
+PATCHES=(
+	"${FILESDIR}"/openbabel-3.1.1-fix-time-check-cmake.patch
+)
+
 pkg_pretend() {
 	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
 }
diff --git a/sci-chemistry/propka/Manifest b/sci-chemistry/propka/Manifest
index dc5a1eddff6a..2c45708435b7 100644
--- a/sci-chemistry/propka/Manifest
+++ b/sci-chemistry/propka/Manifest
@@ -1,3 +1,5 @@
 DIST propka-3.4.0.gh.tar.gz 363641 BLAKE2B 87f495ba69028593cf3ebf98ed33da0944f7a3833f2d08cae4f0a0b5cbe2f3a67e9812685b896a7d89c88ba25653861f135dbac53dc6df7af426a290bacb3d22 SHA512 2ce431c66374d0692acb7504661caa870ab6460ace3a6478f88c1d46a7bfcd82c748bf153a1ce2ea6d1611bc4bbf2351c4f5149f4578e5f8a9f9ec8385298fe9
+DIST propka-3.5.1.gh.tar.gz 376176 BLAKE2B ef4f5f51a6d08da566aa8dc4d2ec73ca028137031dbe49ca329589fe9ceb7cdda672cac755735a11bed79db1f31be5401b083239214177c2d459207ae998ae29 SHA512 3a9a7fd773700850f14c3ef1cc4ef7614242ea1191001fdca6afd44953486f208cbc067b84752c89e97e82ef6bac5561907b2aeafbee80c4d83cbf3ab443aaa2
 EBUILD propka-3.4.0.ebuild 750 BLAKE2B 811914f17aaa8c9ba8779d4267ecc372c7397394ccf87bb6ea25159759248861da362c13d1e70a991ddd08783c9d4c8c9edb59b99aaac0e253f99935ed2666ee SHA512 e5d23bb7cff54dfc009435da11de8f7e73e2da41e908d4efde1f722a15e2af2d3e5c126fdeb59c5177349a64e6fdeb18cd407a7bd9a6aad3cbeaa3ab6ec04312
+EBUILD propka-3.5.1.ebuild 751 BLAKE2B b3db6aebf5bcf519ae9f248b854d92defe476233d311601ac158763e07ed757ad74542ead5507f7d81de2f356c59efce29f8c501922de544189b51431595b5c8 SHA512 15ff70d3711166276c7b548ebddccf6684942d095fd941e093bd027d55d9bf632c70e50ed045e9a00f8a3ec577927018444c2b38f686c7e772894b01b3d6117d
 MISC metadata.xml 417 BLAKE2B 89fda735965e8ae53eb86dfd438137e7770718b5601d5cd753cce9a03001419e53404dde70fed53d37ccf407265ee387accb26640bb4fce479e01ff141702b70 SHA512 5a9f942fa28e679ee5e1795fddf91661c35c55df79e0d9b742353ad265057ceb030ef15d3bb218ad5e8217c61d462aa09206e261c14dc363e6d6bfc3d20c6500
diff --git a/sci-chemistry/propka/propka-3.5.1.ebuild b/sci-chemistry/propka/propka-3.5.1.ebuild
new file mode 100644
index 000000000000..2c9eb2ee4f27
--- /dev/null
+++ b/sci-chemistry/propka/propka-3.5.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="pKa-value prediction of ionizable groups in protein and protein-ligand complexes"
+HOMEPAGE="https://github.com/jensengroup/propka"
+SRC_URI="https://github.com/jensengroup/propka/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+SLOT="0"
+LICENSE="LGPL-2.1"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+	# Do not install the tests
+	sed -e "/exclude/s:scripts:\', \'tests:g" \
+		-i setup.py || die
+	distutils-r1_python_prepare_all
+}
diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest
index 0d3471385728..46bf0037f904 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-r1.ebuild 2387 BLAKE2B 2eec46ab90656d4336f4c130bac95f76aae850ce7bea72ce7ba5fde37897f4345c7ff8e714190dad5279592ad51fae37b5c96190614a67725d6f23c534ca94c3 SHA512 f89dcf18394067c9485fb8a85c8a6bd841bf485f3deb6671ed457e995bf008e6db64206b0903cda9e0e86dd4ffc9253ee2f1f8b469688d044e629c506a5c3abb
+EBUILD tinker-8.2.1-r1.ebuild 2529 BLAKE2B 3ed97f45a8850f58cc79216127c51acca2d85f78f32e7d753e4e98e7a7bda004373664fe60cdd38f66b12d9f6c79fe70f1f78dd33d9ff27a9cca9373716e66a0 SHA512 cf263a10c4ff53074b4ecaa1c7f4fd936291043b0aafa47af25c371efd5a8b761e349e1d55bd65c03567b9970579996599657bda34bfb431a4918dcd7582defa
 MISC metadata.xml 349 BLAKE2B e2a70d46ddb77f5ea51a0d6d378cdcbe2c897464127bd86c34ec43615588a509ff038e035c24855c305248789eb0708d51d21208d2cc65e8507e4f767172582f SHA512 0cb63aaf7aadd62ea12289936ea25c8f5233c8784af96b71f103794d6bd7e0711b53728a2840f5768df2652c0b19e220b1f35223dbf27fc65f7871b6e3b4c756
diff --git a/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild b/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild
index 9964b16b549f..8689a962c2fd 100644
--- a/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild
+++ b/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -50,6 +50,11 @@ src_prepare() {
 }
 
 src_compile() {
+	# tests fail with weird results under LTO
+	# https://bugs.gentoo.org/878059
+	# https://github.com/TinkerTools/tinker/issues/159
+	filter-lto
+
 	local javalib= _omplib _fftwlib
 	for i in $(java-config -g LDPATH | sed 's|:| |g'); do
 		[[ -f ${i}/libjvm.so ]] && javalib=${i}
diff --git a/sci-chemistry/votca/Manifest b/sci-chemistry/votca/Manifest
index f8eb4f2293fe..adcbcc0ddad3 100644
--- a/sci-chemistry/votca/Manifest
+++ b/sci-chemistry/votca/Manifest
@@ -1,4 +1,4 @@
 DIST votca-2022.1.tar.gz 61692029 BLAKE2B c58023098f596d7c6f301e94883df3e442761b8c1009823ef5a07e788fabb2a0fa572326e0d614f8102104ef5dcec89505da1c911bb703126c123d2a25a2031e SHA512 dda5cbf1835440abd1b0b511275e10e5facfa9f133062ae082cca4f5654e4af0be0b574b87c70004c0d07920519927bac5620b89ce073de9985bdf792f0dd21a
-EBUILD votca-2022.1-r1.ebuild 1871 BLAKE2B 52840f4654fba69077c0950ba5ffee7abb9c4cd0c937bfe3331aa70ec1e0dc44af2309ddba033a660f31d77ade08bd74da90551586d16ceb4d71aa2894a1d7b0 SHA512 ea82eb9c580ff6e5337bf1d96d3c8c716d207d5515df03c466e3a775a89aeba59bc533ee3f047cae23bcefc3653c3a4f98cf752ca4585e7cbe61bab1a6059239
-EBUILD votca-9999.ebuild 1872 BLAKE2B cf72b8d2731e2dd7a11609a760bcdd918579eca872c8ffdc96931220df192d14e535b7a2c4e23861a44a0fa3acd56c5a0e65a324adf9322ecf7d79ebb0916f02 SHA512 7f068a887eb57eba03b83589cb474a5269179233b300f5f3c861a21f9aa40397ed8407cb89046c19f6ea42b89ae51b3b83e43fd73dd9c78952fbbf2aac0127a9
+EBUILD votca-2022.1-r1.ebuild 1872 BLAKE2B 3171180eafc258d421d6f9fdac5220b5421aae74724d8aae06e208c6be05f502e379dfb40800fe8364e445212df600291ef1db9e65c094bd9d704ee88d189b45 SHA512 c8134faa9fa5bd29526470260c0a30d148231d4ef8e460af037f7c2775c969525f9da19633007bc02c4aa68d2ed48cf9570ff134f73f437f004288118d6b7c2c
+EBUILD votca-9999.ebuild 1872 BLAKE2B 3171180eafc258d421d6f9fdac5220b5421aae74724d8aae06e208c6be05f502e379dfb40800fe8364e445212df600291ef1db9e65c094bd9d704ee88d189b45 SHA512 c8134faa9fa5bd29526470260c0a30d148231d4ef8e460af037f7c2775c969525f9da19633007bc02c4aa68d2ed48cf9570ff134f73f437f004288118d6b7c2c
 MISC metadata.xml 465 BLAKE2B 3fe0aa7dbb87cfe5ec1b5d1500dccb087f2f582982ab7d41687675f7ad38ce3eae1c12141ab8a020d467114cc7017da64ceaa65a10bb37f55ff3aed3e113378b SHA512 b204a6c45aea2fc428a0e421cfc22a218e59ef4f9cb8e352bdf8983272c9f28baf2beec4650ca65e8fb640d713dbdb39d2f43b1ccfce8329b0c3669e6b4562c8
diff --git a/sci-chemistry/votca/votca-2022.1-r1.ebuild b/sci-chemistry/votca/votca-2022.1-r1.ebuild
index ad5aa680498e..88d3c6a469fb 100644
--- a/sci-chemistry/votca/votca-2022.1-r1.ebuild
+++ b/sci-chemistry/votca/votca-2022.1-r1.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
-PYTHON_COMPAT=( python3_{9..11} )
+EAPI=8
+PYTHON_COMPAT=( python3_{10..12} )
 
 inherit bash-completion-r1 cmake python-single-r1
 
diff --git a/sci-chemistry/votca/votca-9999.ebuild b/sci-chemistry/votca/votca-9999.ebuild
index 04064219f641..88d3c6a469fb 100644
--- a/sci-chemistry/votca/votca-9999.ebuild
+++ b/sci-chemistry/votca/votca-9999.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
-PYTHON_COMPAT=( python3_{9..10} )
+EAPI=8
+PYTHON_COMPAT=( python3_{10..12} )
 
 inherit bash-completion-r1 cmake python-single-r1
 
@@ -16,7 +16,7 @@ else
 		MY_PV="${PV}"
 	fi
 	SRC_URI="https://github.com/votca/votca/archive/v${MY_PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux"
+	KEYWORDS="amd64 ~x86 ~amd64-linux"
 	S="${WORKDIR}/votca-${MY_PV}"
 fi