gentoo resync : 17.06.2021

6 files changed, 94 insertions, 2 deletions

diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz
index a4aad804b50c..d8e29a514148 100644
--- a/sci-mathematics/Manifest.gz
+++ b/sci-mathematics/Manifest.gz
diff --git a/sci-mathematics/giac/Manifest b/sci-mathematics/giac/Manifest
index 22ffbbdd0aed..aa834378eb82 100644
--- a/sci-mathematics/giac/Manifest
+++ b/sci-mathematics/giac/Manifest
@@ -1,5 +1,6 @@
 AUX giac-1.6.0-pari-2.11.patch 783 BLAKE2B f173015006fef4a9f8176965f923664f11b0b05151b126cf74a5bccf5036e1fd3aa97f12fd91808fab7fe23a3194e6a4a7a9f12be5b69a5dfda5aedec8a0117c SHA512 56102439f05f0e27bda49f1e9803bbba7921c87eab383fc2f068ccca6ef598f11e35d00f5a737076a6a41df08ef9065e567cb84030ba6ea928520f371d51b9ed
 AUX giac-1.7.0.1-gsl_lapack.patch 2912 BLAKE2B b0f9f05126316b9b76d5f1a5ad737cc88ecbc71dc450ef714f6da323128d9c945ada9d658c73647987f84638498aa4d3bbef49062424ab63b53c76defc127902 SHA512 14bfcb04e5a23933cfa4635789bf02f6d6e6a528c167504678b3d2ecb38f135d0c05583712005fe53afd7696cc9ebee5dc3ab90cac056d75bd43be786075b011
-DIST giac_1.7.0-5.tar.gz 82481999 BLAKE2B b322c7008fc6fd687ef11355d3c1dfe48abdbbff6415968d4476dd7760e03f5d174e2ab88f87d638a77c16762d977b5e211b54a71529cf65af0ad4c7d6d16403 SHA512 39e0d1fca0497365ddebe9eba871bbcff790cbcb33f2a61bfbf0e018f300d7429eee7d97a446f0cbb45f2e8abe3af4ed77e3c58a74e919b9f907959f270df355
-EBUILD giac-1.7.0.5.ebuild 4194 BLAKE2B 007f9fa8fa746b612de657f745823c9136b493ad605f401345d841297e9b2744c7ca3803f2a1a448e1f24d732471561eade99bd56da5d4ee256c50e82b64bb39 SHA512 6cab89d4980088f43a53ae130070e25c7a4d1c2181d7f72faa8e8cfdfb29c0d8fe6e451016de787c1275b4c960b256479199da85c963e40a58d2c99ad32d9eca
+AUX giac-1.7.0.13-xcas-desktop.patch 890 BLAKE2B 31e33a52fdcb70c610edf21f046d112df3702e1d4f635cd4956bbe17d928839c9a0a87cb5ba5d6aeff94213b482ce22bd497d1d258aaa8abd6d8fc0116031f15 SHA512 269c733edc899051fc3de23021c322a3099499dfeb559ab1cada0964258a91a9735e620b480560226e5a3b492f2f5654062ee9c2c5479ae9789b012e7a5055ca
+DIST giac_1.7.0-13.tar.gz 86447065 BLAKE2B 4d91e83608f7ec376d133c2784ffce99447a9dd78b5c8582b81a0aae0b8ac59eec4db3ee4a8bcb39202c777c300178a181f2dc2ac74ab445ddba2f3efa0ecb1b SHA512 99fff7ce5117fd8c106601ead03679805d529fe12d5372cdd4ae54824aa6fdcbdaaa1a62ea1153391a1a65af8970e38fca7d95ca9983755ff06053f1d8b6d65a
+EBUILD giac-1.7.0.13.ebuild 4243 BLAKE2B 4274b4dcb6752d1a033f6561ea3bed336db5e2e606463946ac109e0e9aa6c3530b981fea631a9257236a0de0d4e874b1028a969564185b05a8917cebc9480610 SHA512 1bd27ea2ef3f44eb4b3a9337a61baa37191668a3f2ff9dc6478a942aa77478b838085dfb1f4e711318066c76fb26a51555f549590e3840374eb6a022875a5319
 MISC metadata.xml 1314 BLAKE2B c38eadb22de3e64b39e144c8dd2e2c359b88ea7910390ea6044af9f8f83a6db08cb4f0142d1217ddd0f4ff051f2bb94f846a789adc521d02d4c704763da1c50a SHA512 7554640bd7ab2b2c1cb77d492d044d419b178497f8b5a6165168f4c3ab0c421121e98b0f0f25d3d10479a8fcd6635f28cfdae4562d6e0b5143b541155f697077
diff --git a/sci-mathematics/giac/files/giac-1.7.0.13-xcas-desktop.patch b/sci-mathematics/giac/files/giac-1.7.0.13-xcas-desktop.patch
new file mode 100644
index 000000000000..bc542b0a615c
--- /dev/null
+++ b/sci-mathematics/giac/files/giac-1.7.0.13-xcas-desktop.patch
@@ -0,0 +1,33 @@
+From 51fa4502039ec09d4a9e1d6b2fa73e5a1f789f94 Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Tue, 15 Jun 2021 08:31:06 -0400
+Subject: [PATCH 1/1] xcas.desktop: fix "Version" field.
+
+The "Version" field in a desktop file refers to the version of the
+specification, not the version of the software it launches:
+
+  https://specifications.freedesktop.org/desktop-entry-spec
+
+This issue has already been fixed upstream:
+
+  https://xcas.univ-grenoble-alpes.fr/forum/viewtopic.php?f=3&t=2716
+
+and will be part of the next release.
+---
+ xcas.desktop | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/xcas.desktop b/xcas.desktop
+index 9e1b648..fad99cd 100644
+--- a/xcas.desktop
++++ b/xcas.desktop
+@@ -1,5 +1,5 @@
+ [Desktop Entry]
+-Version=1.7
++Version=1.0
+ Keywords=computer algebra system;CAS;
+ Keywords[fr]=calcul formel;CAS;
+ Name=Xcas
+-- 
+2.31.1
+
diff --git a/sci-mathematics/giac/giac-1.7.0.5.ebuild b/sci-mathematics/giac/giac-1.7.0.13.ebuild
index 8dcab375adc8..2d6ab4387bf3 100644
--- a/sci-mathematics/giac/giac-1.7.0.5.ebuild
+++ b/sci-mathematics/giac/giac-1.7.0.13.ebuild
@@ -49,6 +49,7 @@ BDEPEND="dev-tex/hevea
 PATCHES=(
 	"${FILESDIR}/${PN}-1.7.0.1-gsl_lapack.patch"
 	"${FILESDIR}/${PN}-1.6.0-pari-2.11.patch"
+	"${FILESDIR}/${PN}-1.7.0.13-xcas-desktop.patch"
 )
 
 REQUIRED_USE="test? ( gui )"
diff --git a/sci-mathematics/nauty/Manifest b/sci-mathematics/nauty/Manifest
index 4fb5b5add61b..dbb4beab0ae2 100644
--- a/sci-mathematics/nauty/Manifest
+++ b/sci-mathematics/nauty/Manifest
@@ -1,5 +1,6 @@
 DIST nauty-popcnt.patch 56034 BLAKE2B 838858a0decf9323217f6b8d7b200b0158db9a02efd278a5d3cf7392ac2201e901b36b963f3f30ca6070fd0ddfa70577a442b795b09fec0d457d33649c6e93c6 SHA512 4931440b6178cb668997539ac2991f0d04758b8750668d4477cb8a456640640c5bb71c2858e423a4ad812e3401151834366e04693bf9a5ecc5ccc211d2e4229c
 DIST nauty26r7.tar.gz 1660659 BLAKE2B d1d6774dd65cbdb906727324b5008bb962d54d16f99afe68f643f62ab2e7fe297a7cb4ef59b5f50c72c7e59fa9ff8ef2c82f4a77764c7f076b90e8171c7f1370 SHA512 60a724264b43b48338c17240c3cf7156f408267f1b2df995ea7b5ab9fa48852cb11057e83178a364ca028d80dc9124ca9b38cdac34e150a995475140d07c8af6
 DIST nauty_2.6r7+ds-1.debian.tar.xz 30328 BLAKE2B 009d64aa2042f814e55238ff83bde4d205925922c13a46213b933ec0f6364ed9a86aeabc7b4c22fdb717bd3ee7efdf794f3f2637cd08d7921e61cee99e73cf9a SHA512 fadde6a767e43048980842415207613ffeaa38d021fbf6a3f26a4bbe6877a92ddf5950094de517edd0f924deeacc8dec1d6a7334123c2a87d15befcc3876bc63
+EBUILD nauty-2.6.7-r1.ebuild 1526 BLAKE2B c3ffeaa04617b7d18d2c18c5264930b6cd3b67db184770cbc34dfaa1b63e8c3496bc2d45f3922965e041a3929e53443da15c84762ac8b4132c8f320d5971a7da SHA512 191f12019f2d3016b6154d9f41a652bdebcbc0ab1cfdc57bc17a77bba4876434dc1b0950777cf4ec556997c82b3897964cb9ff635b8b5b485350a86791e56be0
 EBUILD nauty-2.6.7.ebuild 1469 BLAKE2B 31dbd03617b358b4881f866c7b0c0863aa808c58433120c215886f23439896fff8f05e4df3e635473a4400a54fea53084cc81a949bc9eb732397d73775e1c831 SHA512 b9d7e3d17636c716e53658b590d37aaf4ed09219fed46b975cbd9ee1d36c17c1c57c3ce430b13f6125baf094e8f748072313c53e63c1e9249f081afe3f535f9b
 MISC metadata.xml 545 BLAKE2B dc773d4acdd458e7dbe5bc8744c847d9ae04eaedff901e4daa1f78cefcd261f158f54d916dcf054f7ba348b3c9d555d6542a421c3cc1ed1feda1276bd798064d SHA512 19b48e8150e6776f4c51f80cc0b4d468cbb320a9468dfe298debe21177e13a2c9a41d7ef2a24b54c5e7986231402f72d7db19c6c8b075ae9a3f103c040dd9262
diff --git a/sci-mathematics/nauty/nauty-2.6.7-r1.ebuild b/sci-mathematics/nauty/nauty-2.6.7-r1.ebuild
new file mode 100644
index 000000000000..3bbf8f7251b1
--- /dev/null
+++ b/sci-mathematics/nauty/nauty-2.6.7-r1.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+MY_PV1=$(ver_rs 2 'r')
+MY_PV=$(ver_rs 1 '' $(ver_rs 2 'r'))
+
+DESCRIPTION="Computing automorphism groups of graphs and digraphs"
+HOMEPAGE="https://pallini.di.uniroma1.it/"
+DEBIAN_PATCH_VERSION="1"
+SRC_URI="http://cs.anu.edu.au/~bdm/${PN}/${PN}${MY_PV}.tar.gz
+	mirror://debian/pool/main/${PN:0:1}/${PN}/${PN}_${MY_PV1}+ds-${DEBIAN_PATCH_VERSION}.debian.tar.xz
+	http://pkgs.fedoraproject.org/cgit/rpms/nauty.git/plain/nauty-popcnt.patch"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+DEPEND="dev-libs/gmp:0
+	sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}${MY_PV}"
+DOCS=( schreier.txt config.txt formats.txt changes24-26.txt )
+PATCHES=(
+	"${WORKDIR}"/debian/patches/upstream-lintian-spelling-error.patch
+	"${WORKDIR}"/debian/patches/upstream-fix-gt_numorbits.patch
+	"${WORKDIR}"/debian/patches/upstream-fix-include-extern.patch
+	"${WORKDIR}"/debian/patches/upstream-zlib-blisstog_c.patch
+	"${WORKDIR}"/debian/patches/upstream-C2help2man.patch
+	"${WORKDIR}"/debian/patches/upstream-autotoolization.patch
+	"${WORKDIR}"/debian/patches/system-preprocessing-examples.patch
+	"${DISTDIR}"/nauty-popcnt.patch
+)
+
+src_prepare() {
+	default
+	rm makefile || die
+	eautoreconf
+}
+
+src_configure() {
+	econf --disable-static --enable-runtime-popcnt --enable-tls
+}
+
+src_install() {
+	default
+
+	# remove .la file
+	find "${ED}" -name '*.la' -delete || die
+}