gentoo auto-resync : 25:04:2023 - 18:13:05

5 files changed, 28 insertions, 70 deletions

diff --git a/sci-libs/libcifpp/Manifest b/sci-libs/libcifpp/Manifest
index 91a010374a9c..a8b2682e395e 100644
--- a/sci-libs/libcifpp/Manifest
+++ b/sci-libs/libcifpp/Manifest
@@ -1,10 +1,5 @@
-DIST components-2.0.4.cif.gz 81445161 BLAKE2B 80d538109a716af0273d109151a434e68cc1be16dc3a21653a4b78dd9719c93f59259146a6e980fbab4484a6b41d32064a276566411e23bf56b0a42b6dacf408 SHA512 a154305f1d3ba2df24ca3859b0a7d1a81cae79c927a708a531bee1689b0b65752fd68032d12335afa4b6b2f5969e003365abd49bed729d740c0f3055328f08ad
-DIST components-3.0.0.cif.gz 82114845 BLAKE2B 9934110efb9848e8b71e75173bf9c8cfeec1daeef45648296dbcc41641308b9c4e6ff2ef16d86b44ebdb0a200fe6f2a8f13dadac1cce4d8ea2a2961927bf4c94 SHA512 625478378d236ec46130d83545c1b0fbdfb5e9cada3834ac14d4b052e9e460e73523e4438b3356a78d64f569e12cd4c13439b5de56462a10d5c11d0de09d52b8
-DIST libcifpp-2.0.4.tar.gz 960402 BLAKE2B 4650478b187ece13d38c0a5f13c94e6098e3271088a7dd19d72645d52d085304a463387f9d1b1edacbcd03a051b32fbf2384e3287d5ff4835091f2eae2fe2805 SHA512 f4a6b126b376b245d399508e9bc360bcf0451e6bd3cad3127567dd95afb1965c8eb764bb9b0bf26be26695fc5636e509709bdbc9f8c9a00939d049c1634dcae0
-DIST libcifpp-3.0.0.tar.gz 950896 BLAKE2B 8aad3ebea5cc82c2615b6dc6a8a50654375dd9f58ff6c27306bf1415d9658f29f196c5ea9bf0e4f913400b3eba48f19bc11dd97c84b59cf2df94f87afb06d5b7 SHA512 507abed829e4d5194eb22fe73d261295a9814577d7bc53743731e7a1ccb032f763f4bfa0e1b23665d52fabbfa38baca20e6373c14db029705427b6fa773df976
+AUX libcifpp-5.0.8-missing-include.patch 553 BLAKE2B 0bcda2161396c3a863f2b4bc0074ac1298c57fa67cdc7771c05bd56b99e8d88a2124dc361aeef99e4fe2aa06f8ba1af9bccd4f2c20c90ac3a8e8fcd0f211d6fc SHA512 deb17752ac3bf005e8936ab5894f0b5ca3eb8fcb59a41dff511111b0eddf88ff983504629888904ceaca17826710609add09e0075bf5c8726767d2a8589b1e90
 DIST libcifpp-5.0.8-components.cif.gz 89984770 BLAKE2B d42147d4da56589ac30de9fc3cdacd43e036f548eebf80a19d878c4bf0be535578eec6b78625e1ba60db53090ce5e4b9a3e59b06705f208b660fb2e37e79d1c2 SHA512 5f9705714816656aa910b571d77966926d66b2724136119857138975f8be5bb2e889e0c9b28ef1340a72857afb5831dba529b96e8dfc796f739e24b0dcab0424
 DIST libcifpp-5.0.8.tar.gz 1873629 BLAKE2B 07257a898b1253995880fea9b416b3a7681122b544f8397d353fda4069c33f4a6c2d5cf2210983acf68dc56cb27a20d780461c7c2485a445855e7b45cccd326d SHA512 4ea67fa4a93218fe96289de95591faa9411508e41e308f4ff470033fb0deb4029a86eafb7ba9295807fe3b350e8cc9f2267f7735ee8b1dbb431ee0275db2b8cc
-EBUILD libcifpp-2.0.4-r1.ebuild 734 BLAKE2B 98776f8cdb01d30fc71a59b859ac0b5a336a79771fdf0f5b953fec5b1e932745f2ed10e26f707c9ba18479546a382acc123b7f45565a6b7fc5cbfe6aea6c524f SHA512 92882477bdd15718a78a980bf00cce6b7271fc9db5d405da95a747ec0ff1b45f797949673ce0799c3a281c17c40f1fd800e24e46ce676f4038699cce692a8954
-EBUILD libcifpp-3.0.0.ebuild 738 BLAKE2B e4577178cba7b208e9dde896997a131729031f916a3b9c67be5d83b8bc9b6e689940959ea132e27d399e6b9be5f3d7faae1b84de8445477c81385967013feb31 SHA512 849c3b2f65fc540bae1dd22cd4c39538728c34f5312c2dab94d9102fe9b59f0a903c60128dfba6bb791bcee5762f1d3a428f61f5190bea582a191012f35707c9
-EBUILD libcifpp-5.0.8.ebuild 870 BLAKE2B fa9206b2a876c9a6ed7b2f47059c2bdec6e81f8663257acadffe13a460d3c4235ebab513809820fcb8c7b875a6ae2351df3485d8fa2d2b1f6b935f768db8b34e SHA512 7cd7303f6925f6574959104244427ae9a7853140e6511d14c23d83c90de12ac803655893aa8af308fff1b7e345b10fe6826b07136f9ed06b5483cb1f892e1366
+EBUILD libcifpp-5.0.8.ebuild 975 BLAKE2B 7e001c18b1feea681575f3c4b60b07602cd270295a8b16ee722f01fdf46e4f04d53e5b5748c64341c6d01969ddd2258f0beb513c96c93f6933eab6d07169f26e SHA512 a3a32d9f577a550abf60b0eef1500ecc5bd56af880bc9f1d8777709320ad485e83727a9f2d3e7069b552b803206245f8fbe56189a5ee43489a33f88d8a821b4a
 MISC metadata.xml 299 BLAKE2B 88091a7fbc350db0c22800bcd0de80ec406f7b8a0187b29d8660978384179f8194f7aa794bf0bd3b3f4ab68ac662ca62479319e218d2622e2a3e470653848251 SHA512 e6bc610ae1cf40584ba3067ece0c0c85d08ad0bbb99f5ecd8281c41b04ff932db838926a6ff238794ff46eb8035eb57c750e088bd3f164180952a9e597544e14
diff --git a/sci-libs/libcifpp/files/libcifpp-5.0.8-missing-include.patch b/sci-libs/libcifpp/files/libcifpp-5.0.8-missing-include.patch
new file mode 100644
index 000000000000..26735e003f4d
--- /dev/null
+++ b/sci-libs/libcifpp/files/libcifpp-5.0.8-missing-include.patch
@@ -0,0 +1,21 @@
+From 0f03fc31e058da4b66f16a67e7674fba1b85ca80 Mon Sep 17 00:00:00 2001
+From: "Maarten L. Hekkelman" <maarten@hekkelman.com>
+Date: Wed, 19 Apr 2023 09:22:32 +0200
+Subject: [PATCH] added required include
+
+---
+ include/cif++/text.hpp | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/include/cif++/text.hpp b/include/cif++/text.hpp
+index 9da9ab9..00f33c1 100644
+--- a/include/cif++/text.hpp
++++ b/include/cif++/text.hpp
+@@ -30,6 +30,7 @@
+ 
+ #include <charconv>
+ #include <cmath>
++#include <cstdint>
+ #include <limits>
+ #include <set>
+ #include <sstream>
diff --git a/sci-libs/libcifpp/libcifpp-2.0.4-r1.ebuild b/sci-libs/libcifpp/libcifpp-2.0.4-r1.ebuild
deleted file mode 100644
index 70d19261a89d..000000000000
--- a/sci-libs/libcifpp/libcifpp-2.0.4-r1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake
-
-DESCRIPTION="Code to work with mmCIF and PDB files"
-HOMEPAGE="https://github.com/PDB-REDO/libcifpp"
-SRC_URI="
-	https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz
-	ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz -> components-${PV}.cif.gz
-"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND="dev-libs/boost:="
-RDEPEND="${DEPEND}"
-
-src_configure() {
-	cp "${WORKDIR}"/components-${PV}.cif data/components.cif || die
-
-	local mycmakeargs=(
-		-DBUILD_SHARED_LIBS=ON
-		-DCIFPP_BUILD_TESTS="$(usex test)"
-	)
-	cmake_src_configure
-}
diff --git a/sci-libs/libcifpp/libcifpp-3.0.0.ebuild b/sci-libs/libcifpp/libcifpp-3.0.0.ebuild
deleted file mode 100644
index 32bb52f339bb..000000000000
--- a/sci-libs/libcifpp/libcifpp-3.0.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit cmake
-
-DESCRIPTION="Code to work with mmCIF and PDB files"
-HOMEPAGE="https://github.com/PDB-REDO/libcifpp"
-SRC_URI="
-	https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz
-	ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz -> components-${PV}.cif.gz
-"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND="dev-libs/boost:="
-RDEPEND="${DEPEND}"
-
-src_configure() {
-	cp "${WORKDIR}"/components-${PV}.cif data/components.cif || die
-
-	local mycmakeargs=(
-		-DBUILD_SHARED_LIBS=ON
-		-DCIFPP_BUILD_TESTS="$(usex test)"
-	)
-	cmake_src_configure
-}
diff --git a/sci-libs/libcifpp/libcifpp-5.0.8.ebuild b/sci-libs/libcifpp/libcifpp-5.0.8.ebuild
index 856007e7bd81..b468bb36559f 100644
--- a/sci-libs/libcifpp/libcifpp-5.0.8.ebuild
+++ b/sci-libs/libcifpp/libcifpp-5.0.8.ebuild
@@ -22,6 +22,11 @@ RESTRICT="!test? ( test )"
 DEPEND="dev-libs/boost:="
 RDEPEND="${DEPEND}"
 
+PATCHES=(
+	# https://github.com/PDB-REDO/libcifpp/issues/40
+	"${FILESDIR}/${P}-missing-include.patch"
+)
+
 src_configure() {
 	cp "${WORKDIR}"/${P}-components.cif data/components.cif || die