science/libcifpp: update 5.1.0.1 → 7.0.4

5 files changed, 52 insertions, 33 deletions

diff --git a/science/dssp/Makefile b/science/dssp/Makefile
index 002bb973b054..2d37a09f2031 100644
--- a/science/dssp/Makefile
+++ b/science/dssp/Makefile
@@ -1,6 +1,7 @@
 PORTNAME=	dssp
 DISTVERSIONPREFIX=	v
 DISTVERSION=	4.4.2
+PORTREVISION=	1
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/science/libcifpp/Makefile b/science/libcifpp/Makefile
index 8f9a6a98a623..c26cbf0ae479 100644
--- a/science/libcifpp/Makefile
+++ b/science/libcifpp/Makefile
@@ -1,9 +1,8 @@
 PORTNAME=	libcifpp
 DISTVERSIONPREFIX=	v
-DISTVERSION=	5.1.0.1
-PORTREVISION=	1
+DISTVERSION=	7.0.4
 CATEGORIES=	science
-MASTER_SITES=	ftp://ftp.wwpdb.org/pub/pdb/data/monomers/:components
+MASTER_SITES=	https://files.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}
@@ -15,6 +14,7 @@ WWW=		https://github.com/PDB-REDO/libcifpp
 LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
+BUILD_DEPENDS=	catch>0:devel/catch
 LIB_DEPENDS=	libboost_iostreams.so:devel/boost-libs
 RUN_DEPENDS=	bash:shells/bash
 
diff --git a/science/libcifpp/distinfo b/science/libcifpp/distinfo
index 308709c237e5..860546baef63 100644
--- a/science/libcifpp/distinfo
+++ b/science/libcifpp/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1689922296
-SHA256 (libcifpp-5.1.0.1/components.cif.gz) = 981c20f825179f073663aeac5b7416d8b851c87caa5bf9e7d885963bfa471ac0
-SIZE (libcifpp-5.1.0.1/components.cif.gz) = 92865675
-SHA256 (libcifpp-5.1.0.1/PDB-REDO-libcifpp-v5.1.0.1_GH0.tar.gz) = ae2cdf7851d1be4ef1fa5bdaf9abbc7d01df9d0935ae8baf9d6335577445d74b
-SIZE (libcifpp-5.1.0.1/PDB-REDO-libcifpp-v5.1.0.1_GH0.tar.gz) = 2242975
+TIMESTAMP = 1722210707
+SHA256 (libcifpp-7.0.4/components.cif.gz) = 09b35f5f7e2841f08a6d3f19fc66e4d422b2a415d08cae5f074723608b997278
+SIZE (libcifpp-7.0.4/components.cif.gz) = 100547781
+SHA256 (libcifpp-7.0.4/PDB-REDO-libcifpp-v7.0.4_GH0.tar.gz) = 324eda2f6874df32671cd984c7249bfae025ca3fe1bfd875cbef35b046408b88
+SIZE (libcifpp-7.0.4/PDB-REDO-libcifpp-v7.0.4_GH0.tar.gz) = 2598838
diff --git a/science/libcifpp/files/patch-CMakeLists.txt b/science/libcifpp/files/patch-CMakeLists.txt
index 4d9aa0eb46cd..cd053e94fecc 100644
--- a/science/libcifpp/files/patch-CMakeLists.txt
+++ b/science/libcifpp/files/patch-CMakeLists.txt
@@ -1,20 +1,38 @@
---- CMakeLists.txt.orig	2023-05-31 13:17:00 UTC
+--- CMakeLists.txt.orig	2024-04-03 12:01:51 UTC
 +++ CMakeLists.txt
-@@ -310,7 +310,7 @@ if(CIFPP_DOWNLOAD_CCD)
+@@ -331,7 +331,7 @@ set(project_headers
+ 	include/cif++/validate.hpp
+ )
+ 
+-add_library(cifpp STATIC)
++add_library(cifpp)
+ add_library(cifpp::cifpp ALIAS cifpp)
+ 
+ target_sources(cifpp
+@@ -395,7 +395,7 @@ if(CIFPP_DOWNLOAD_CCD)
+ 		# to download the gzipped version and decompress it ourselves.
  		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} ${COMPONENTS_CIF}.gz
-@@ -478,7 +478,7 @@ if(CIFPP_INSTALL_UPDATE_SCRIPT)
- 	install(DIRECTORY DESTINATION "${CIFPP_ETC_DIR}/libcifpp/cache-update.d")
+-		if(WIN32 OR GUNZIP STREQUAL "GUNZIP-NOTFOUND")
++		if(FALSE OR WIN32 OR GUNZIP STREQUAL "GUNZIP-NOTFOUND")
+ 			file(
+ 				DOWNLOAD https://files.wwpdb.org/pub/pdb/data/monomers/components.cif
+ 				${COMPONENTS_CIF}
+@@ -405,7 +405,7 @@ if(CIFPP_DOWNLOAD_CCD)
+ 			if(NOT EXISTS "${COMPONENTS_CIF}.gz")
+ 				file(
+ 					DOWNLOAD
+-					https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
++					file://${DISTDIR_FULL}/components.cif.gz
+ 					${COMPONENTS_CIF}.gz
+ 					SHOW_PROGRESS
+ 					STATUS CCD_FETCH_STATUS)
+@@ -557,7 +557,7 @@ if(CIFPP_INSTALL_UPDATE_SCRIPT)
  
- 	# a config to, to make it complete
--	if(NOT EXISTS "${CIFPP_ETC_DIR}/libcifpp.conf")
-+	if(TRUE OR NOT EXISTS "${CIFPP_ETC_DIR}/libcifpp.conf")
- 		file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf [[# Uncomment the next line to enable automatic updates
- # update=true
- ]])
+ 	# a config file, to make it complete
+ 	# install(DIRECTORY DESTINATION "${CMAKE_INSTALL_LOCALSTATEDIR}/libcifpp")
+-	if(NOT EXISTS "${CMAKE_INSTALL_SYSCONFDIR}/libcifpp.conf")
++	if(TRUE OR NOT EXISTS "${CMAKE_INSTALL_SYSCONFDIR}/libcifpp.conf")
+ 		file(
+ 			WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf
+ 			[[# Uncomment the next line to enable automatic updates
diff --git a/science/libcifpp/pkg-plist b/science/libcifpp/pkg-plist
index c28a15a76e9a..1238023be915 100644
--- a/science/libcifpp/pkg-plist
+++ b/science/libcifpp/pkg-plist
@@ -1,4 +1,5 @@
-etc/libcifpp.conf
+etc/cron.weekly/update-libcifpp-data
+%%ETCDIR%%.conf
 include/cif++.hpp
 include/cif++/atom_type.hpp
 include/cif++/category.hpp
@@ -16,10 +17,10 @@ include/cif++/iterator.hpp
 include/cif++/matrix.hpp
 include/cif++/model.hpp
 include/cif++/parser.hpp
+include/cif++/pdb.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
@@ -27,14 +28,13 @@ 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/cmake/cifpp/cifpp-config-version.cmake
+lib/cmake/cifpp/cifpp-config.cmake
+lib/cmake/cifpp/cifpp-targets-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/cifpp/cifpp-targets.cmake
 lib/libcifpp.so
-lib/libcifpp.so.5
-lib/libcifpp.so.5.1.0.1
-libdata/pkgconfig/libcifpp.pc
+lib/libcifpp.so.7.0
+lib/libcifpp.so.7.0.4
 %%DATADIR%%/components.cif
 %%DATADIR%%/mmcif_ddl.dic
 %%DATADIR%%/mmcif_ma.dic