gentoo auto-resync : 18:10:2024 - 04:04:23

7 files changed, 72 insertions, 111 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index a46ec2c846c6..9d9ccdb7bfd0 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest
index d34b4dbb6e5b..aebec65cb5f0 100644
--- a/sci-chemistry/dssp/Manifest
+++ b/sci-chemistry/dssp/Manifest
@@ -3,10 +3,12 @@ AUX dssp-2.1.0-gentoo.patch 1513 BLAKE2B aabdcfff1083d7552392c35897eb8a84b07323c
 AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 BLAKE2B dc59d21a6be26ee96b636c13645163478999d5122f09d3a72963843be773210ea225e374941bd057ef6f083a13fb77980bd4390174df2a0c715f0386da7232e0 SHA512 8f84c6e163888d6a8192683a6555f7d6003634854f5cde0f6f962744e531165c7e0b2b08c55cbfb9c396d167c44317dd2e7a8290e4defd2c8def0a6511fbbd6c
 DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811
 DIST dssp-3.0.11.tar.gz 168085 BLAKE2B e1c42fd22cfb2287f10b5deae48b56a4583d4a67737a3485dcbd160d1597a15c2d5105c3794c875d8001abede1c014efb4f7f5b7c250f867bdf9ed95a0860217 SHA512 a0cfe44e517ff1f909ef2928b62ae2c639c6bddfd8a0fb538883f647fd2771e00da68e0fd2521aa02ba3c6d1b0c9b784b7fe142392af3a3abf6ea89f1546bd9d
-DIST dssp-4.4.4.1.tar.gz 162809 BLAKE2B 6c3f588a48778cf5f20b40b93736e150a4d366bf44d214b4064362c2a3bce69db415f5d12568a8523d99e2e5a47749d450ff0251dc3035628dbef9343d37e99a SHA512 291810391d74da7ab65bcf4aab61fa4ae1a5518a361fa02d5c15ed0e5c94139fde65e7612a978f5326bd7d93f2ac6ea01b2b65514d6b64f4d062adf112c48deb
+DIST dssp-4.4.10.tar.gz 164259 BLAKE2B 5d82ce25779060f89b50742683102aea53984fca10e54aa3cd0b21c7be3684336f6561928282e40300bb164c5b881797fababa5175c139f5b304a952f21db661 SHA512 1bdbdd4b058801d78cc28dcb23478656dfb322ce81f4fe8ede2cd72640778084ce8c99aff367aff53c26ad221ffa6ebafcf9730005b1a873957d26eb42f724c8
 DIST dssp-4.4.7.tar.gz 163831 BLAKE2B 195c8fb183df00105098967850b01c0d6acf776f7cfa409fc536c8291e7a467da2adfb5f34d8191e33dbb29bfd254cd414c1b7b76ed3f3b854928c4dc8a5fcdd SHA512 2fe2d8a494b570934c0d28804fe69b6569089ded58ec92bf3d83b25ce60a3b9486490909e187b511328f13498ca9027869e922d95a355cf0e21c2564c2db1b5a
+DIST dssp-4.4.8.tar.gz 164050 BLAKE2B 0f048b5425f3ecb0e9278da81e2274e817b5ba5ed33a372d0e4c0b0d0600f9ebee2b125f7411dcc4af5d56e2f86cf0d7f10608467b24dd886ca559f7c4b60e6a SHA512 a21c79e56662d926e8476ffc7ccd84dec182a7bbd98c08b3df61ed88c99ee82e1522b69156cdea0abf96d93bc69a0a491b04662a9312d2681785116074151a61
 EBUILD dssp-2.2.1-r3.ebuild 870 BLAKE2B 9b7542d9ec45b60f5671830e5068e1d1cbcca4b82cf22cc0e2d9804c221f9977cfade439cc6e41a67375b438faca3ffa64fdec23db2b417b58615513fd60ad44 SHA512 964bfd70d98a80e6afd7f28fc6bf7359bbde105e77903211cec04c5adcdce273f1d7142a6d206d644300a1185cba1352bf584499d864809dadad69b2023e50d0
 EBUILD dssp-3.0.11.ebuild 875 BLAKE2B 6344416239b93804755b1829dcfcb9e8e461606c217938945bb2fc75e9680f2849b39bdbf0ed361592e703fea493a2dacabca498b26e696c969735a585e5d183 SHA512 353f4f5d7b1b195753c738ecc9fb17b429cdeada757806f5cf9a3da65c6318e3885d2c92fa904d5b3a546756eb87ec90787d158e8a9450b4730dd97b45af970d
-EBUILD dssp-4.4.4.1.ebuild 1321 BLAKE2B ba06063adc7c9ac9a20c078eeb98c95f0003c5ae58c0db0b5bbb888b194de86e22de9c1549d1911e25e4d5b7a3f99089c0083c281441eeed3dde3ea5e3b8cd14 SHA512 77683bc3bc0aebeb867ffaf94d5f7ce1090f78a73fc739da01c73d3bdab142fc409bce66f85349b627e54376e1279b45a9096a71cac080be10ab0ba4f84d33cb
+EBUILD dssp-4.4.10.ebuild 1329 BLAKE2B 61d8909411ff687ba6b11449b0c3acd307c28ac5901fe360886b980d49b88e301cbd539d794503e789e73973ce1ae6aa965e1846cf7453d41df96285a1710cdf SHA512 d3beb704dc3a3783c79ac73fdfdebf74e82fa15d8d7d792124a529c7a208e6349b8035585d0ee96eecaf13ef81ecaa407c2ee22edd8bfdbe5befc945ca5453a6
 EBUILD dssp-4.4.7.ebuild 1329 BLAKE2B 61d8909411ff687ba6b11449b0c3acd307c28ac5901fe360886b980d49b88e301cbd539d794503e789e73973ce1ae6aa965e1846cf7453d41df96285a1710cdf SHA512 d3beb704dc3a3783c79ac73fdfdebf74e82fa15d8d7d792124a529c7a208e6349b8035585d0ee96eecaf13ef81ecaa407c2ee22edd8bfdbe5befc945ca5453a6
+EBUILD dssp-4.4.8.ebuild 1329 BLAKE2B 61d8909411ff687ba6b11449b0c3acd307c28ac5901fe360886b980d49b88e301cbd539d794503e789e73973ce1ae6aa965e1846cf7453d41df96285a1710cdf SHA512 d3beb704dc3a3783c79ac73fdfdebf74e82fa15d8d7d792124a529c7a208e6349b8035585d0ee96eecaf13ef81ecaa407c2ee22edd8bfdbe5befc945ca5453a6
 MISC metadata.xml 295 BLAKE2B 4355bbe00822cc702acdf70031ab9cd1f2a8f6e076d71016c1783f2a6c052c2da0a1a4a1860062562bb837161787f2481fa6f49c4319c546482a263ebe149bb0 SHA512 ace35ca21c614a7c0cbdea2496be3190a907295053566707c1875836a306cc9e9c96816cca6ce2b514935f6fcd494d2e813f4d94ba88552cd7b86831f30501f4
diff --git a/sci-chemistry/dssp/dssp-4.4.4.1.ebuild b/sci-chemistry/dssp/dssp-4.4.10.ebuild
index a274099244cf..d5e51fe40fec 100644
--- a/sci-chemistry/dssp/dssp-4.4.4.1.ebuild
+++ b/sci-chemistry/dssp/dssp-4.4.10.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
@@ -18,14 +18,15 @@ KEYWORDS="~amd64 ~x86"
 CDEPEND="
 	dev-libs/boost:=[zlib]
 	>=dev-libs/libmcfp-1.2.2
-	>=sci-libs/libcifpp-5.2.0
+	>=sci-libs/libcifpp-7.0.3
+"
+BDEPEND="${CDEPEND}
+	dev-cpp/catch:0
 "
-BDEPEND="${CDEPEND}"
 #	doc? (
 #		|| ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc )
 #		dev-python/weasyprint
 #	)
-DEPEND=""
 RDEPEND="${CDEPEND}"
 
 #src_prepare() {
diff --git a/sci-chemistry/dssp/dssp-4.4.8.ebuild b/sci-chemistry/dssp/dssp-4.4.8.ebuild
new file mode 100644
index 000000000000..d5e51fe40fec
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-4.4.8.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit cmake
+
+DESCRIPTION="The protein secondary structure standard"
+HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
+SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+# doc disabled as it only generates a PDF from the manpage for now
+# https://github.com/PDB-REDO/dssp/issues/64
+#IUSE="doc"
+
+CDEPEND="
+	dev-libs/boost:=[zlib]
+	>=dev-libs/libmcfp-1.2.2
+	>=sci-libs/libcifpp-7.0.3
+"
+BDEPEND="${CDEPEND}
+	dev-cpp/catch:0
+"
+#	doc? (
+#		|| ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc )
+#		dev-python/weasyprint
+#	)
+RDEPEND="${CDEPEND}"
+
+#src_prepare() {
+#	# wkhtmltopdf is not available on Gentoo
+#	sed -i -e \
+#		's/-t html/-t html --pdf-engine=weasyprint/' \
+#		CMakeLists.txt
+#	cmake_src_prepare
+#}
+
+src_configure() {
+	local mycmakeargs=(
+		#-DBUILD_DOCUMENTATION=$(usex doc)
+		-DBUILD_DOCUMENTATION=NO
+	)
+	cmake_src_configure
+}
+
+pkg_postinst() {
+	if has_version "<=sci-chemistry/gromacs-2022"; then
+		ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:"
+		ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129"
+		ewarn
+		ewarn "Feel free to mask newer versions if needed."
+	fi
+}
diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest
index 76e5c78f437b..e540122ad8fe 100644
--- a/sci-chemistry/molmol/Manifest
+++ b/sci-chemistry/molmol/Manifest
@@ -3,6 +3,5 @@ DIST molmol-2k.2.0-doc.tar.gz 1062297 BLAKE2B 082d4eea5544bab52ffc1ff6364c503043
 DIST molmol-2k.2.0-src.tar.gz 1088805 BLAKE2B cd649604f6ee491d3a4485391ecdaa48dc1bc4bcd82865cd4a01ca460a6653f8cbba636050bfab9027b9b95dbefa28a8deeff7065b9b461f518001242af4a849 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b
 DIST molmol-patches.tbz2 17528 BLAKE2B b91270a980f290edc169be00639e86b3272281c9fe237750f5778eab1605ed482c09bdaf90660a5edf74bd04b3e31adc755e77e39aea6c75d88b6db9bf47a6d6 SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287
 DIST molmol_256.png 22668 BLAKE2B c7d75b8e0d738b48790bea25e21ec60d57a8181253518c70d6f18d93c64eef3c9acf90213fdbdf2dde272e85a04a6442e4e4a9c375829f369380d88c9c0ca57c SHA512 5e7975f54a7462161dc630ee973e9a8126b9c120e0d8d6b62007384c970ce39792e52300edc25dc7a85209845801d749d9ecba02899f3e18b18f5a5fdbc28a97
-EBUILD molmol-2k_p2-r8.ebuild 2284 BLAKE2B fa9954fca3dd8b52450beb1c0901abc71743672d7a76e2daa2bb05f52280ecf7dec5c401da24ce3e72f429cb69b27738117e33d41b49a96836b1b407efef67f0 SHA512 d813743572479b5eb0ed4181d42743402c4bd0a5a8e012f32bad03c4be68f38329722b749abc91845ba9c25642b19f5e2c4b5578ed9d3f7d03beaabbaa3345f5
-EBUILD molmol-2k_p2-r9.ebuild 2313 BLAKE2B fecc271cadf3eb73478b1adc674a6d369ee7bbb05c38e10ae78ebbc886782962f7c33ea07ef4d065e643ee7f5a71e99801f72c290cb7ab437833141dcfe80a99 SHA512 d173ed8f60c833485bf639fa8fc0ace5ff1ae46316be319d2cd1feb5f5201484ed9e8bba46054dfc91303d71051b52d4fa943638ecf6b843514fa9585bc421a5
+EBUILD molmol-2k_p2-r9.ebuild 2562 BLAKE2B b197c856d551f1b634efe0d978a297362c9d1260029cc7ecc2644fc3a3ce6bde20a7000f3aa2f4056b34454b17f357103f74535315d2f530483ae72a051ae96e SHA512 7668a27c2962fdaa40e96f55e48bcd3307cf6d146bfeba6f27bc0ae8e924e0dcc7853bee3a6a57b861de2868fa220a7ba071e1944e44364519b2f60b4ff46b4a
 MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r8.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r8.ebuild
deleted file mode 100644
index 59bedaf2593d..000000000000
--- a/sci-chemistry/molmol/molmol-2k_p2-r8.ebuild
+++ /dev/null
@@ -1,102 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit desktop toolchain-funcs
-
-MY_PV="${PV/_p/.}.0"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Publication-quality molecular visualization package"
-
-# Original page dead
-#HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
-HOMEPAGE="
-	http://www.csb.yale.edu/userguides/graphics/molmol/molmol_descrip.html
-	http://pjf.net/science/molmol.html
-"
-SRC_URI="
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2
-	https://dev.gentoo.org/~pacho/${PN}/${PN}_256.png
-"
-
-LICENSE="molmol"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	|| (
-		(
-			media-libs/mesa[X(+)]
-			x11-libs/libGLw
-		)
-		media-libs/mesa[motif(-),X(+)]
-	)
-	media-libs/libjpeg-turbo:=
-	media-libs/libpng:=
-	media-libs/tiff:=
-	sys-libs/zlib
-	virtual/glu
-	x11-libs/libXpm
-	x11-libs/motif:0
-	x11-apps/xdpyinfo
-"
-DEPEND="${RDEPEND}"
-BDEPEND=""
-
-S="${WORKDIR}"
-
-pkg_setup() {
-	MMDIR="/usr/$(get_libdir)/molmol"
-	MAKEOPTS="${MAKEOPTS} -j1" #880621
-}
-
-src_prepare() {
-	default
-
-	rm -rf tiff*
-	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	eapply "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
-
-	eapply "${WORKDIR}"/patches/ldflags.patch
-	eapply "${WORKDIR}"/patches/opengl.patch
-
-	ln -s makedef.lnx "${S}"/makedef || die
-
-	sed \
-		-e "s|ksh|sh|" \
-		-e "s|^MOLMOLHOME.*|MOLMOLHOME=${EPREFIX}/${MMDIR};MOLMOLDEV=\"Motif/OpenGL\"|" \
-		-i "${S}"/molmol || die
-	sed \
-		-e "s|^MCFLAGS.*|MCFLAGS = ${CFLAGS}|" \
-		-e "s|^CC.*|CC = $(tc-getCC)|" \
-		-i "${S}"/makedef || die
-
-	eapply "${WORKDIR}"/patches/cast.patch
-	eapply -p0 "${WORKDIR}"/patches/libpng15.patch
-
-	# patch from fink
-	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	eapply "${WORKDIR}"/patches/${P}-fink.patch
-
-	eapply "${WORKDIR}"/patches/wild.patch
-	tc-export AR
-}
-
-src_install() {
-	dobin molmol
-
-	exeinto ${MMDIR}
-	doexe src/main/molmol
-	insinto ${MMDIR}
-	doins -r auxil help macros man setup tips
-
-	make_desktop_entry "${PN}" MOLMOL
-	newicon "${DISTDIR}/${PN}_256.png" "${PN}.png"
-
-	einstalldocs
-	dodoc HISTORY
-}
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
index 14378809c07a..9a63d1dbb20d 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
@@ -52,7 +52,6 @@ PATCHES=(
 
 pkg_setup() {
 	MMDIR="/usr/$(get_libdir)/molmol"
-	MAKEOPTS="${MAKEOPTS} -j1" #880621
 }
 
 src_prepare() {
@@ -85,6 +84,13 @@ src_prepare() {
 
 	eapply "${WORKDIR}"/patches/wild.patch
 	tc-export AR
+
+	# Parallel build fails (#880621) and cannot be disabled by MAKEOPTS
+	# (#880621, #941488).
+	find . -name Makefile -exec sed -i -e "1i .NOTPARALLEL:" {} + || die
+	# Try to drop the ugly hardcoded sleep now that make is really
+	# serial
+	sed -i -e 's/sleep 2/sleep 0/g' makedef || die
 }
 
 src_install() {