From nobody Tue Jul 30 02:02:12 2024 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4WXz4h55gQz5SQkH; Tue, 30 Jul 2024 02:02:12 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4WXz4h39cyz4T3W; Tue, 30 Jul 2024 02:02:12 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1722304932; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=ZaUs9DSv39tbue38mWxt50d7QThCWI6DUvD/GC6XMTI=; b=gcnt3Pp4KQsWKGUEJDow8SmdnD+SWm/QP9UUbsoPcde/mLywYpdBMZiQgZXj8sDED+xh4Y BGhEM5GVi2zzb9QmM0BZ2IUWN+ZzYMqAoSR+ZLvSBVlejrM6tJ8q3cs9jbOVJC67QnfQ1w +cW6wf9zrJsD3QljPVL9otFfGmoglKj3C59vSrq310ejcrSQ9wJ/eBM/uqNiILJMWbwW/w OJo3gFos0lwqms2adUasfhdwGCdGVvEP0oMgffwQ1nekqzSbMT3K/JFDCKI5kFmU+MOSfR 9Luwr8/27LfAeNWBwQQprn6NDo5sfPaDaS9V+G/xqeFi7o3yOrvFzxz+TYLx0Q== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1722304932; a=rsa-sha256; cv=none; b=Q/uDzG8DCF3B3bAoCx4Imsuc2QWl5v2rUDliAU1K5EJI4pNGQAukDoOyDThTB3o1EB9fCy qw1ME9aFAeEXYaSYVK/GMmUAAvT0UZu3A+frtsPvb5n0ndy5KZov0CG5OkWswztoBfKtyk 0b8Zm0wf2wmIJEwDWdrke3E0YTkeyjGMHPc7PHq6IknMdm9zreiJj8SjYRHjjNofoBbBT6 CTfws4/ji56R2qKEkCZm4xUgi4iCgBpNAALwO1fbkj6FVE2KgQiAWCJaX8i+7fs3bALoW9 MHDQTu+Gn187u/NTakvVud0CioEOSbJAIaCviMQH00GOF4hyBMf3eyEC3hnHKQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1722304932; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=ZaUs9DSv39tbue38mWxt50d7QThCWI6DUvD/GC6XMTI=; b=r8bjWKzUfhRxHgSgIZlay9KzHfdWGZpPD1mb2bLJXmx3qwd6BLF+WrtNuZowCcJQPG+O5e IW/6dIMfMlW7s/oGRSC0jFZw1TCIyR+3LmvvcoJMny7eC9aEQReg1B8ms6tZB8XoY1fBnh Gbr8njVWeR63cqROoYR3LCQdOvx08qeerFU19dJIYfSqR8PEOKZ9uft3xn06NZzZYdZWc5 AVIkr1cr3oQiKrSijSYPWQOLyyT8Qkn7cM14lrOrrixVdB/J+fpaTZDwGa9B3e0TyKlkNY KjQDjPPhx4mIgtxzAMJsPQwu0DVfnpXbWoXgBPGF2bhuYq5DUpuIeD49ou/B5w== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4WXz4h2p7fzyg8; Tue, 30 Jul 2024 02:02:12 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 46U22CiP070375; Tue, 30 Jul 2024 02:02:12 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 46U22CDs070372; Tue, 30 Jul 2024 02:02:12 GMT (envelope-from git) Date: Tue, 30 Jul 2024 02:02:12 GMT Message-Id: <202407300202.46U22CDs070372@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: b4d3bbb5d136 - main - science/libcifpp: update 5.1.0.1 =?utf-8?Q?=E2=86=92?= 7.0.4 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: b4d3bbb5d136aaf50530e1233ea1355d8a8f19c7 Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=b4d3bbb5d136aaf50530e1233ea1355d8a8f19c7 commit b4d3bbb5d136aaf50530e1233ea1355d8a8f19c7 Author: Yuri Victorovich AuthorDate: 2024-07-29 19:22:11 +0000 Commit: Yuri Victorovich CommitDate: 2024-07-30 02:01:57 +0000 science/libcifpp: update 5.1.0.1 → 7.0.4 --- science/dssp/Makefile | 1 + science/libcifpp/Makefile | 6 ++-- science/libcifpp/distinfo | 10 +++--- science/libcifpp/files/patch-CMakeLists.txt | 50 ++++++++++++++++++++--------- science/libcifpp/pkg-plist | 18 +++++------ 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