git: b1acd3f15930 - main - science/libcifpp: Update 4.2.2 -> 5.0.3

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=b1acd3f159303eefaa81d77f196cfea38ca70426

commit b1acd3f159303eefaa81d77f196cfea38ca70426
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2022-11-13 19:12:47 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2022-11-13 23:12:27 +0000

    science/libcifpp: Update 4.2.2 -> 5.0.3
---
 science/libcifpp/Makefile                   | 18 ++++++++--
 science/libcifpp/distinfo                   |  8 +++--
 science/libcifpp/files/patch-CMakeLists.txt | 11 ++++++
 science/libcifpp/pkg-plist                  | 52 ++++++++++++++++++-----------
 4 files changed, 64 insertions(+), 25 deletions(-)

diff --git a/science/libcifpp/Makefile b/science/libcifpp/Makefile
index f65f7e4af785..ef1a1b079566 100644
--- a/science/libcifpp/Makefile
+++ b/science/libcifpp/Makefile
@@ -1,7 +1,11 @@
 PORTNAME=	libcifpp
 DISTVERSIONPREFIX=	v
-DISTVERSION=	4.2.2
+DISTVERSION=	5.0.3
 CATEGORIES=	science
+MASTER_SITES=	ftp://ftp.wwpdb.org/pub/pdb/data/monomers/:components
+DISTFILES=	components.cif.gz:components
+DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}
+EXTRACT_ONLY=	${GH_ACCOUNT}-${GH_PROJECT}-${DISTVERSIONFULL}_GH0${EXTRACT_SUFX}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Library to manipulate mmCIF and PDB files
@@ -11,14 +15,22 @@ LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 LIB_DEPENDS=	libboost_iostreams.so:devel/boost-libs
+RUN_DEPENDS=	bash:shells/bash
 
-USES=		cmake:testing compiler:c++17-lang
+USES=		cmake:testing compiler:c++17-lang shebangfix
 USE_LDCONFIG=	yes
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	PDB-REDO
 
+SHEBANG_FILES=	tools/update-libcifpp-data.in
+
 CMAKE_ON=	BUILD_SHARED_LIBS
-CMAKE_TESTING_ON=	CIFPP_BUILD_TESTS
+CMAKE_ARGS=	-DDISTDIR_FULL=${DISTDIR}/${DIST_SUBDIR}
+CMAKE_TESTING_ON=	ENABLE_TESTING
+
+post-install:
+	@cd ${STAGEDIR}${PREFIX} && \
+		${RM} -r var etc/libcifpp etc/periodic
 
 .include <bsd.port.mk>
diff --git a/science/libcifpp/distinfo b/science/libcifpp/distinfo
index eb335874d309..46fe6b941fc3 100644
--- a/science/libcifpp/distinfo
+++ b/science/libcifpp/distinfo
@@ -1,3 +1,5 @@
-TIMESTAMP = 1664847727
-SHA256 (PDB-REDO-libcifpp-v4.2.2_GH0.tar.gz) = 458050db52416866033b5557939bc9221bce84f9ffe95cfe1680548db9b2ba39
-SIZE (PDB-REDO-libcifpp-v4.2.2_GH0.tar.gz) = 1274530
+TIMESTAMP = 1668337095
+SHA256 (libcifpp-5.0.3/components.cif.gz) = 941b2cac1137a95fcf7bb5237fc2dd0d86628e003bc484d38aa27cea2b33f551
+SIZE (libcifpp-5.0.3/components.cif.gz) = 88204196
+SHA256 (libcifpp-5.0.3/PDB-REDO-libcifpp-v5.0.3_GH0.tar.gz) = 600af7c29fe25d60c0dd9ae06191c5db2b587dedecde983ee3472e5d9eee1c0c
+SIZE (libcifpp-5.0.3/PDB-REDO-libcifpp-v5.0.3_GH0.tar.gz) = 1869491
diff --git a/science/libcifpp/files/patch-CMakeLists.txt b/science/libcifpp/files/patch-CMakeLists.txt
new file mode 100644
index 000000000000..1ba47658f564
--- /dev/null
+++ b/science/libcifpp/files/patch-CMakeLists.txt
@@ -0,0 +1,11 @@
+--- CMakeLists.txt.orig	2022-11-13 18:41:37 UTC
++++ CMakeLists.txt
+@@ -285,7 +285,7 @@ if(CIFPP_DOWNLOAD_CCD)
+ 		find_program(GUNZIP gunzip)
+ 
+ 		if(GUNZIP)
+-			file(DOWNLOAD ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz ${COMPONENTS_CIF}.gz
++			file(DOWNLOAD file://${DISTDIR_FULL}/components.cif.gz ${COMPONENTS_CIF}.gz
+ 				SHOW_PROGRESS)
+ 			add_custom_command(OUTPUT ${COMPONENTS_CIF}
+ 				COMMAND ${GUNZIP} ${COMPONENTS_CIF}.gz
diff --git a/science/libcifpp/pkg-plist b/science/libcifpp/pkg-plist
index 71557f19e2a8..e7a050083ee0 100644
--- a/science/libcifpp/pkg-plist
+++ b/science/libcifpp/pkg-plist
@@ -1,26 +1,40 @@
-include/cif++/AtomType.hpp
-include/cif++/BondMap.hpp
-include/cif++/Cif++.hpp
-include/cif++/Cif++Export.hpp
-include/cif++/Cif2PDB.hpp
-include/cif++/CifParser.hpp
-include/cif++/CifUtils.hpp
-include/cif++/CifValidator.hpp
-include/cif++/Compound.hpp
-include/cif++/PDB2Cif.hpp
-include/cif++/PDB2CifRemark3.hpp
-include/cif++/Point.hpp
-include/cif++/Secondary.hpp
-include/cif++/Structure.hpp
-include/cif++/Symmetry.hpp
-include/cif++/TlsParser.hpp
+etc/libcifpp.conf
+include/cif++.hpp
+include/cif++/atom_type.hpp
+include/cif++/category.hpp
+include/cif++/compound.hpp
+include/cif++/condition.hpp
+include/cif++/datablock.hpp
+include/cif++/dictionary_parser.hpp
+include/cif++/file.hpp
+include/cif++/format.hpp
+include/cif++/forward_decl.hpp
+include/cif++/gzio.hpp
+include/cif++/item.hpp
+include/cif++/iterator.hpp
+include/cif++/list.hpp
+include/cif++/model.hpp
+include/cif++/parser.hpp
+include/cif++/pdb/cif2pdb.hpp
+include/cif++/pdb/io.hpp
+include/cif++/pdb/pdb2cif.hpp
+include/cif++/pdb/pdb2cif_remark_3.hpp
+include/cif++/pdb/tls.hpp
+include/cif++/point.hpp
+include/cif++/row.hpp
+include/cif++/symmetry.hpp
+include/cif++/text.hpp
+include/cif++/utilities.hpp
+include/cif++/validate.hpp
 lib/cmake/cifpp/cifppConfig.cmake
 lib/cmake/cifpp/cifppConfigVersion.cmake
 lib/cmake/cifpp/cifppTargets-%%CMAKE_BUILD_TYPE%%.cmake
 lib/cmake/cifpp/cifppTargets.cmake
 lib/libcifpp.so
-lib/libcifpp.so.4
-lib/libcifpp.so.4.2.2
+lib/libcifpp.so.5
+lib/libcifpp.so.5.0.3
 libdata/pkgconfig/libcifpp.pc
+%%DATADIR%%/components.cif
 %%DATADIR%%/mmcif_ddl.dic
-%%DATADIR%%/mmcif_pdbx_v50.dic
+%%DATADIR%%/mmcif_ma.dic
+%%DATADIR%%/mmcif_pdbx.dic