gentoo resync : 06.04.2022

9 files changed, 131 insertions, 103 deletions

diff --git a/sci-visualization/Manifest.gz b/sci-visualization/Manifest.gz
index f254757a73a3..0755bf1f0ad9 100644
--- a/sci-visualization/Manifest.gz
+++ b/sci-visualization/Manifest.gz
diff --git a/sci-visualization/gnuplot/Manifest b/sci-visualization/gnuplot/Manifest
index ab94a34a47db..3a7e5c59a578 100644
--- a/sci-visualization/gnuplot/Manifest
+++ b/sci-visualization/gnuplot/Manifest
@@ -4,6 +4,6 @@ AUX gnuplot-5.5-no-picins.patch 830 BLAKE2B 8e0a303ff5306f3afa07a585b220fe654404
 DIST gnuplot-5.4.2.tar.gz 5640202 BLAKE2B 42bdbe569a4dcd9e65010aff3d0b7428f1c3485bc64429ac0f2c4f157d43c4d640aa2b191430428ec01cb289bd1d43eb95b4167b5b9d236002d54e48b45c0a2a SHA512 e69ca74335cdd69c6013a254ac785dc67cc82713308460971cf6e0a66438716d8892a37344611d1841563efbc4b2b8c5692c13c7b06cff4f30f8d43e2ddfd7d4
 DIST gnuplot-5.4.3.tar.gz 5656008 BLAKE2B 44745bfc23f3c9f2d27499e0c1430ac32d7995fd12210d83996b87cd989cfdeca75848f0407ce25271f86b866405e726a56523c88a80a476015423cafb32b501 SHA512 fc35ab68a992acc8e35402c89cb7704c0efe117ec1fb272739d4378289d6c5a2e8f4b747b339fca916e559453547f2405863fb52038576883f0d5643a7220b5e
 EBUILD gnuplot-5.4.2-r1.ebuild 5130 BLAKE2B 5e10a5250dc13e34a7962c12a4280880e15eb2801ef176d161483c609d2bd05f089ecd4c794b4f7066c9d132f2ad56e33d1ada15a2550951a337fa46d861a2d7 SHA512 37e8bb451c4f3ec5dda87d2e6e0e1bd242cf7ca06c5d0d5a3a24c0c1b8b0ecdd4843cef9befe12918e43d6166f7cc8f7054c120684ac9f3d53c6448a87eb336a
-EBUILD gnuplot-5.4.3.ebuild 5006 BLAKE2B 0bd5ddf7501896c951fa066cb5aa413cbc84005840b782a142c160d523c62e4b33516c1868804ce4b31150955eb898797a4262b8fe38e4a05526964fe7c04d3e SHA512 32320f7bf94d6817a0dce1f79513b18a87bb4fae1700c32e85d122249007ea3e4642f9dc9646f345f2c00dedf9045ecf9580493d905da8e6c915b0988cdb8bfe
+EBUILD gnuplot-5.4.3.ebuild 5005 BLAKE2B d5a18d94757be9cfa1c04f80ad549ef8d239a1b885a8a71e0389a4a58db2168b9269445e42f84f9ade8b2e779f073c958a29b483c5facd55b8f9513d32ec91f5 SHA512 9fd714a3226d87bccf24c2e61ceb7dfc32ef91f5c18cf430b94df68ddee265f8044792f4319148b2235691ed5af2ea13d4ee542f82f9845b0ea3876f5bb85bc2
 EBUILD gnuplot-5.5.9999-r1.ebuild 5004 BLAKE2B 50c97333406cb28a5a14405190815e8629dd69028da084ab3cef4720ba3be4b6e12e1382428c60a98e57d3013fabc2d74763239923c05860a59f88bcb5f70844 SHA512 df00dca2a95c77c21a75a68bd925401a6739b5666dd9b120ed133c73379be97fec81307f5e9f6584034520a4a64bc314155e8baefabcaa36024e66a45cff1749
 MISC metadata.xml 1070 BLAKE2B 92ac6f016dedc1ee0aced2792c735e692efac0b0c045b7119d6f2268ed9a7ee3c2437a4038ff45799670265e01f74d8470e3c0abf45b35980a4e761fcd802d19 SHA512 04100f29255dd4d3caf3c81a39f7d6f8ad341598e89555219ba054e980484da00835c2226f35a2b63ec5f27238a97003c7bdac28ca504aed68af0fad737beb8a
diff --git a/sci-visualization/gnuplot/gnuplot-5.4.3.ebuild b/sci-visualization/gnuplot/gnuplot-5.4.3.ebuild
index e95661e51f3a..d077fa69781f 100644
--- a/sci-visualization/gnuplot/gnuplot-5.4.3.ebuild
+++ b/sci-visualization/gnuplot/gnuplot-5.4.3.ebuild
@@ -20,7 +20,7 @@ if [[ -z ${PV%%*9999} ]]; then
 else
 	MY_P="${P/_/.}"
 	SRC_URI="mirror://sourceforge/gnuplot/${MY_P}.tar.gz"
-	KEYWORDS="~alpha amd64 ~arm arm64 ~hppa ~ia64 ppc ppc64 ~riscv ~s390 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris ~x64-solaris ~x86-solaris"
+	KEYWORDS="~alpha amd64 arm arm64 ~hppa ~ia64 ppc ppc64 ~riscv ~s390 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris ~x64-solaris ~x86-solaris"
 fi
 
 S="${WORKDIR}/${MY_P}"
diff --git a/sci-visualization/gwyddion/Manifest b/sci-visualization/gwyddion/Manifest
index 44e9287bde99..50486de12148 100644
--- a/sci-visualization/gwyddion/Manifest
+++ b/sci-visualization/gwyddion/Manifest
@@ -1,4 +1,7 @@
 AUX gwyddion-2.56-automagic.patch 1522 BLAKE2B c760f952221ee4cd2e36572bef682ca45b8adbc962c63b9664d02bdc2a3fca405b9d58fed7a18a53da89eb6577cba93e17dd713598897629a10eba0e2c2f4bd9 SHA512 4e3a4761d1858803a6b35bd66c0516fd4ac733be7337298bd56454bde9253685b3622ea47a8759a3f512fb6c13a95ae3efb834cc9d9160608f85c3c26fd1e7d0
+AUX gwyddion-2.60-automagic.patch 1552 BLAKE2B c106acfee1e00d8a4ade965cddab943bc79c246503fb51e53d20ba6a3b8b0a76cc433b75e867d448d7622ef190f1f54225b0f45be3860d32672397090be619d9 SHA512 50eca983c81bb14c33415e3ad69bf2e18be4a88fb674537dc335d8aa9986edb1baa962f7a4eead41d70b54828729165d413387c64696a0f4e1aa9ad49675afb0
 DIST gwyddion-2.56.tar.xz 4645620 BLAKE2B f4f2ce2bf119a24c3e1919b14db409a81ad286ef2242918f356d2b4c56b498f41cbafa03a136eac5d87b4905529e06982694f19bdf30933454e94d34526962c3 SHA512 cf4a40367ea5b0a671c5df70123ef93f6aecc25322af7eb05e4f32d40e54d9b0d48ddd1df9f2589c468eb511ada3f3ef409603c1513de33ba2482078a9415eae
+DIST gwyddion-2.60.tar.xz 4973404 BLAKE2B 6ded40f34bfcd70db2e897abc1f07b070aca78e08c90661ee4fe281d19f16337ca81b5a4e2adaeb29e1870e8194eb77976910a54248842c8474864065d64defd SHA512 e568df77ef580aaedfcdd1f746a78f3ca93676a07a331fc6e70f997780bb403d1c3967aa93440c7fa1f010bd01f5376700c869a38dacaf1f98b075c4c950cf54
 EBUILD gwyddion-2.56.ebuild 1646 BLAKE2B 56173da9c59cff136b908ae5a1eac7767199a73a3fa09c2b1a5480cc9d5d191ba7604e731a1b0c43b2f65f19a0580481efe91742cdb0581645c43215daf8768c SHA512 1205b0dc85fd5c418089555b3a31ab555576ff91fcddfe925595e29a2f31de2d529269aa7092eb80e9a0995e4a0627dc19edbc6de88e58b35ab1e209c1b8e6da
-MISC metadata.xml 939 BLAKE2B 35e2419838c00caf4449307f3a033712e5f49738ab539cddc328bb86b6a6238ca7f0fce5c9815ec15ee74e9880639085a4cb79ded39eeade8291c29aced0a8db SHA512 bba0f5c8c8f7405fe2ff8bf9ddcb41d673dfc49a677cbe29047dd2d3a70c427fafc979c0e39ca4f12cdce9305953ecd588789a7640a91d4b48685b3c30efa8f4
+EBUILD gwyddion-2.60.ebuild 1940 BLAKE2B 20b7359a3232946696773dcdfd7ae65857638a970045632dc39516d32564e578d9d511d5ba64e6d8c953cf41d0df5e7c225027a4482eaf78c318c6d858c037bf SHA512 968338bb87644350ebf7240896cf0cd8fbbad643fe60719f43fa482e2499ebb163e2aa796c8d8d64d745159f123d972f4d0525d6c6f66be170b3d2b5dffc8cfb
+MISC metadata.xml 1152 BLAKE2B c3ab652b26ed500c74d53dd479fe33a3647749478881f79780f360a551bcd262a1652a0e96de7b9bc6ef5d694f40387926b919515c879c8aeb5e2275fe807583 SHA512 8ab81680f6e02090d84f1e43d05c459ae9856b4195341718080b5e8e41a4c722933c6258fb69ddb1c5b7f087356c80d35f8d4fb259c0cb5dabe2636a79b2c64e
diff --git a/sci-visualization/gwyddion/files/gwyddion-2.60-automagic.patch b/sci-visualization/gwyddion/files/gwyddion-2.60-automagic.patch
new file mode 100644
index 000000000000..ac68ac0a2861
--- /dev/null
+++ b/sci-visualization/gwyddion/files/gwyddion-2.60-automagic.patch
@@ -0,0 +1,35 @@
+diff --git a/configure.ac b/configure.ac
+index 5a7465a..cc5a54d 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -660,11 +660,13 @@ AM_CONDITIONAL([HAVE_CXX],[test "x$have_cxx" != xno])
+ #############################################################################
+ # OpenEXR 2.x+
+ # Optional.  Used for HDR greyscale OpenEXR pixmap import/export.
+-enable_exr=$have_cxx
+-PKG_CHECK_MODULES(EXR, [OpenEXR >= 2.0],
++GWY_WITH([exr],,[build with OpenEXR support])
++if test "x$enable_exr" != "xno" && "x$have_cxx" != "xno"; then
++  PKG_CHECK_MODULES(EXR, [OpenEXR],
+                   [AC_DEFINE(HAVE_EXR,1,
+                             [Define if we have the OpenEXR 2.x+ package.])],
+                   [enable_exr=no])
++fi
+ AM_CONDITIONAL([HAVE_EXR],[test "x$enable_exr" != xno])
+ 
+ #############################################################################
+@@ -679,10 +681,13 @@ AM_CONDITIONAL([HAVE_HDF5],[test "x$enable_hdf5" != xno])
+ #############################################################################
+ # CFITSIO
+ # Optional.  Used for FITS image import.
+-PKG_CHECK_MODULES(CFITSIO, [cfitsio],
++GWY_WITH([cfitsio],,[build with cfitsio support])
++if test "x$enable_cfitsio" != "xno"; then
++  PKG_CHECK_MODULES(CFITSIO, [cfitsio],
+                   [AC_DEFINE(HAVE_CFITSIO,1,
+                             [Define if we have the cfitsio package.])],
+                   [enable_cfitsio=no])
++fi
+ AM_CONDITIONAL([HAVE_CFITSIO],[test "x$enable_cfitsio" != xno])
+ 
+ #############################################################################
diff --git a/sci-visualization/gwyddion/gwyddion-2.60.ebuild b/sci-visualization/gwyddion/gwyddion-2.60.ebuild
new file mode 100644
index 000000000000..4680d9f429f2
--- /dev/null
+++ b/sci-visualization/gwyddion/gwyddion-2.60.ebuild
@@ -0,0 +1,84 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools xdg
+
+DESCRIPTION="Framework for Scanning Mode Microscopy data analysis"
+HOMEPAGE="http://gwyddion.net/"
+SRC_URI="http://gwyddion.net/download/${PV}/${P}.tar.xz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="bzip2 doc fits jansson hdf5 nls openexr openmp perl ruby sourceview unique xml X zlib"
+
+RDEPEND="
+	>=dev-libs/glib-2.32
+	dev-libs/libzip
+	media-libs/libpng:0=
+	>=sci-libs/fftw-3.1:3.0=[openmp?]
+	virtual/libiconv
+	virtual/libintl
+	x11-libs/cairo
+	>=x11-libs/gtk+-2.18:2
+	x11-libs/libXmu
+	x11-libs/pango
+	bzip2? ( app-arch/bzip2 )
+	fits? ( sci-libs/cfitsio[bzip2?] )
+	jansson? ( dev-libs/jansson )
+	hdf5? ( sci-libs/hdf5[zlib?] )
+	openexr? ( media-libs/openexr:= )
+	perl? ( dev-lang/perl:= )
+	ruby? ( dev-ruby/narray )
+	unique? ( dev-libs/libunique:3 )
+	sourceview? ( x11-libs/gtksourceview:2.0 )
+	xml? ( dev-libs/libxml2:2 )
+	zlib? ( sys-libs/zlib )
+"
+
+DEPEND="${RDEPEND}"
+BDEPEND="
+	virtual/pkgconfig
+	doc? ( dev-util/gtk-doc )
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-2.60-automagic.patch"
+)
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+# There are python bindings (--enable-pygwy) but they are py2 only
+# 3D opengl rendering requires deprecated GTK-2 x11-libs/gtkglext
+src_configure() {
+	# hack for bug 741840
+	use doc && export GTK_DOC_PATH=/usr/share/gtk-doc
+
+	econf \
+		--disable-rpath \
+		--without-kde4-thumbnailer \
+		$(use_enable doc gtk-doc) \
+		$(use_enable openmp) \
+		$(use_enable nls) \
+		--disable-pygwy \
+		--without-python \
+		$(use_with bzip2) \
+		$(use_with fits cfitsio) \
+		$(use_with hdf5) \
+		$(use_with jansson) \
+		$(use_with perl) \
+		$(use_with ruby) \
+		$(use_with openexr exr) \
+		--without-gl \
+		$(use_with sourceview gtksourceview) \
+		$(use_with unique) \
+		$(use_with xml libxml2) \
+		$(use_with X x) \
+		$(use_with zlib) \
+		--with-zip=libzip
+}
diff --git a/sci-visualization/gwyddion/metadata.xml b/sci-visualization/gwyddion/metadata.xml
index 7749445d7975..7259dfaa2d64 100644
--- a/sci-visualization/gwyddion/metadata.xml
+++ b/sci-visualization/gwyddion/metadata.xml
@@ -23,5 +23,11 @@
     <flag name="fits">
       Enable FITS image import via <pkg>sci-libs/cfitsio</pkg>
     </flag>
+    <flag name="jansson">
+      Enable JSON data manipulation via <pkg>dev-libs/jansson</pkg>
+    </flag>
+    <flag name="unique">
+      Enable remote control backend via <pkg>dev-libs/libunique</pkg>
+    </flag>
   </use>
 </pkgmetadata>
diff --git a/sci-visualization/scidavis/Manifest b/sci-visualization/scidavis/Manifest
index 6bc21d33150c..ab5b4711e6af 100644
--- a/sci-visualization/scidavis/Manifest
+++ b/sci-visualization/scidavis/Manifest
@@ -1,7 +1,5 @@
 AUX scidavis-muparser.patch 2299 BLAKE2B 9ba9e99c838c4fe8c767b8cbfdb9ce93202a8d539039993552a6da2590a28b7acd27f891b6e251ee9bb063a0010d52fa419807ab2a515e633ebd32ea8179877d SHA512 44841cac0f111687ffe38e322c8fb25139f5529321eb4609a8a7821e0ee3bba832f61fe9f6b0e42f28f4571898468de83274d36bbdfc57c97ed227426244c103
 AUX scidavis-qwtplot3d.patch 453 BLAKE2B 774cae5c148944cb4c0a85965431031296b9f846b1154620e39cca0c6ec4ba8645e84bfccbcca051334f11ba301f3aa1bb6a4d6110cec57dc9cb881fd4fa0d85 SHA512 95a778670c8540a150e52317a95f8ff8211bc0cdaf10280f84bf2c5365f7b803cd56b46760a56db75ba29289ebf53abf9d803d0bb78cf55c0426059bb994b584
-DIST scidavis-2.4.0_p20211117.tar.gz 9248921 BLAKE2B e14d4a270ab0b7221b3e21762c4547e5d64930ddc72bf085d72d02e4756cc4c82f38b438f90dc472a05837d059650ea3718e100ad8c56762e990b11f571fce31 SHA512 f3fba2569d5ba79be1b10ffe4ed242f7a4df81fb4561388fcdb9461404ab966b21ecfdaa001518b5139eeef319e3c979109e2889d9268b07dad9c3cec970999b
 DIST scidavis-2.7.tar.gz 11765155 BLAKE2B 10e218472893cd19fe3fb6ebef0116c37167b10b1535e6d39b3eb0f6e2f9a537a75c8da5648dae41b77add089d57cafea640d0c7f4dca459c5a9ef2cc24bff18 SHA512 8063d9f5fb29f824e0183d8902dfe9a8310b6041664ac2189765953088968136f3d72fd04f667d8dfce0ede16e17593e3351f5593d70e73705f1b737bf90b4de
-EBUILD scidavis-2.4.0_p20211117.ebuild 2211 BLAKE2B e0c6796817df8c47712ec8d09739116e6252d5379f77d90263968809298fe382c9f3fb1ec4d88872c0f85dcbd0a3a00bc6cb0893a64cba3a49bc38926184f2bb SHA512 a27456b517479b96713b9c06a67e05d6034c796ccffd8e44c8371c9aa6c5fd601a6cf430ee5810f8a0d9b706d9e80dba3d0e7fb481d7636bef3acbc5ba254c85
 EBUILD scidavis-2.7.ebuild 2104 BLAKE2B c342b5e17575d5e2cb3f583c67d35c814b47dc5ef87d7648fc8078436205ec8b1ecd2db06de26cd20cfe3ae6b31abeb3fc044daddec3b746181d2a5c3da7b751 SHA512 d98a5bf780411ca6601162c6652a6af5058b265a70ba0261120df7420e6b7605d5d47c86b005ef528fcfcf0684ce02ee2593e907b04e6e5b19f3c32c46f59b0f
 MISC metadata.xml 1085 BLAKE2B e02c4b1a7fa0eecbdb26db3cd577a06591b557678e91598c5e84a4dfec87c215e5758ca67a438331bef33265b6a0f1441141b6711b05c7e496f7e5feebca9954 SHA512 e33807092bd789cdc11819a0d56d9d39fcb7065d870d47ef1f20254e75f6f85a299ca4fe9c3dae50c53a90d9fe730cb9062c8b0cf8e09c4a46e449bff655181a
diff --git a/sci-visualization/scidavis/scidavis-2.4.0_p20211117.ebuild b/sci-visualization/scidavis/scidavis-2.4.0_p20211117.ebuild
deleted file mode 100644
index 83ff296ac304..000000000000
--- a/sci-visualization/scidavis/scidavis-2.4.0_p20211117.ebuild
+++ /dev/null
@@ -1,98 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DOCS_BUILDER="doxygen"
-DOCS_DEPEND="media-gfx/graphviz"
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit python-single-r1 cmake docs virtualx xdg
-
-COMMIT="acc11c507631dc89db90c8777bab53b814620b4c"
-
-DESCRIPTION="Application for Scientific Data Analysis and Visualization"
-HOMEPAGE="http://scidavis.sourceforge.net/ https://github.com/SciDAVis/scidavis/"
-SRC_URI="https://github.com/SciDAVis/scidavis/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN}-${COMMIT}"
-
-LICENSE="GPL-2+ ZLIB"
-KEYWORDS="~amd64"
-SLOT="0"
-
-IUSE="doc +muparser origin python test"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-# requires network
-RESTRICT="test"
-PROPERTIES="test_network"
-
-RDEPEND="
-	muparser? ( dev-cpp/muParser )
-	dev-qt/qtcore:5
-	dev-qt/qtgui:5
-	dev-qt/qtnetwork:5
-	dev-qt/qtopengl:5
-	dev-qt/qtprintsupport:5
-	dev-qt/qtwidgets:5
-	dev-qt/qtxml:5
-	sci-libs/gsl:=
-	sys-libs/zlib[minizip]
-	x11-libs/qwt:5
-	x11-libs/qwtplot3d
-	origin? ( sci-libs/liborigin )
-	python? (
-		${PYTHON_DEPS}
-		$(python_gen_cond_dep '
-			>=dev-python/PyQt5-5.15.6[${PYTHON_USEDEP}]
-			dev-python/PyQt5-sip[${PYTHON_USEDEP}]
-			>=dev-python/sip-6:5[${PYTHON_USEDEP}]
-		')
-	)
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-qt/linguist-tools:5
-	test? (
-		dev-libs/unittest++
-		dev-cpp/gtest
-	)
-"
-
-PATCHES=(
-	"${FILESDIR}/${PN}-muparser.patch"
-	"${FILESDIR}/${PN}-qwtplot3d.patch"
-)
-
-src_prepare() {
-	cmake_src_prepare
-
-	# Remove things which are packaged elsewhere
-	rm -r 3rdparty/qwt5-qt5 3rdparty/qwtplot3d 3rdparty/liborigin || die
-
-	# OF has been renamed in Gentoo https://bugs.gentoo.org/383179
-	# Note this is *not* packaged in sys-libs/zlib[minizip] because
-	# this file resides in the test directory in upstream zlib
-	sed -i -r 's:\<(O[FN])\>:_Z_\1:g' 3rdparty/minigzip/minigzip.c || die
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DSCRIPTING_MUPARSER=$(usex muparser)
-		-DSCRIPTING_PYTHON=$(usex python)
-		-DPYTHON_SCRIPTDIR="$(python_get_scriptdir)"
-		-DORIGIN_IMPORT=$(usex origin)
-		-DBUILD_TESTS=$(usex test)
-	)
-	cmake_src_configure
-}
-
-src_compile() {
-	cmake_src_compile
-	docs_compile
-}
-
-src_test() {
-	virtx cmake_src_test
-}