biology/pbcopper: Upgrade to 0.4.1 release

In preparation for biology/unanimity upgrade

5 files changed, 26 insertions, 38 deletions

diff --git a/biology/pbcopper/Makefile b/biology/pbcopper/Makefile
index f02f7ade599c..19f84985b50c 100644
--- a/biology/pbcopper/Makefile
+++ b/biology/pbcopper/Makefile
@@ -1,8 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	pbcopper
-DISTVERSION=	g20180413
-PORTREVISION=	3
+DISTVERSION=	0.4.1 # Test with biology/unanimity before upgrading!
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -13,17 +12,17 @@ LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
 LIB_DEPENDS=	libboost_regex.so:devel/boost-libs
 
-USES=		cmake compiler:c++14-lang
-# Although there are a couple releases, git describe --tags does not work
-# so we cannot use the usual USE_GITHUB tools here.
+# Meson needs BOOST_ROOT=${LOCALBASE}
+# https://github.com/mesonbuild/meson/issues/2239
+USES=		compiler:c++14-lang localbase meson
+USE_LDCONFIG=	yes
 USE_GITHUB=	yes
 GH_ACCOUNT=	PacificBiosciences
-GH_TAGNAME=	17ef457a0dbe1894a8d17af7ddba01a6261bf117
 
-do-install:
-	${INSTALL_DATA} ${BUILD_WRKSRC}/lib/*.a ${STAGEDIR}${PREFIX}/lib
-	cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include
-	${MV} ${STAGEDIR}${PREFIX}/include/meson.build \
-		${STAGEDIR}${PREFIX}/include/pbcopper
+post-install:
+	${RLN} ${STAGEDIR}${PREFIX}/lib/libpbcopper.so.${PORTVERSION} \
+		${STAGEDIR}${PREFIX}/lib/libpbcopper.so.0.4
+	${RLN} ${STAGEDIR}${PREFIX}/lib/libpbcopper.so.${PORTVERSION} \
+		${STAGEDIR}${PREFIX}/lib/libpbcopper.so.0
 
 .include <bsd.port.mk>
diff --git a/biology/pbcopper/distinfo b/biology/pbcopper/distinfo
index 4ee86047d81b..fafecefe146c 100644
--- a/biology/pbcopper/distinfo
+++ b/biology/pbcopper/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1524500014
-SHA256 (PacificBiosciences-pbcopper-g20180413-17ef457a0dbe1894a8d17af7ddba01a6261bf117_GH0.tar.gz) = 13f006d53334a0538657e0ba5c6e02f811f1901cd25fce220fc9011726ffe23f
-SIZE (PacificBiosciences-pbcopper-g20180413-17ef457a0dbe1894a8d17af7ddba01a6261bf117_GH0.tar.gz) = 3033636
+TIMESTAMP = 1550453144
+SHA256 (PacificBiosciences-pbcopper-0.4.1_GH0.tar.gz) = 4c8daf6c1a6efe3860a16fb5b6111ebe65221423254819f3a68a400d0a984fcd
+SIZE (PacificBiosciences-pbcopper-0.4.1_GH0.tar.gz) = 3095846
diff --git a/biology/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake b/biology/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake
deleted file mode 100644
index 56eb84971d36..000000000000
--- a/biology/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake
+++ /dev/null
@@ -1,21 +0,0 @@
---- cmake/pbcopper-gitsha1.cmake.orig	2018-03-16 16:16:38 UTC
-+++ cmake/pbcopper-gitsha1.cmake
-@@ -5,16 +5,15 @@ endif()
- set(__find_git_sha1 YES)
- 
- function(find_git_sha1 _GIT_SHA1)
--    find_package(Git QUIET REQUIRED)
-     execute_process(COMMAND
--        "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=*"
-+        echo ce9a4b6
-         WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
-         RESULT_VARIABLE res
-         OUTPUT_VARIABLE out
-         ERROR_QUIET
-         OUTPUT_STRIP_TRAILING_WHITESPACE)
-     if (NOT res EQUAL 0)
--        message(FATAL_ERROR "Could not determine git sha1 via `git describe --always --dirty=*`")
-+        message(FATAL_ERROR "Could not determine git sha1")
-     endif()
-     set(${_GIT_SHA1} "${out}" PARENT_SCOPE)
- endfunction()
diff --git a/biology/pbcopper/files/patch-meson__options.txt b/biology/pbcopper/files/patch-meson__options.txt
new file mode 100644
index 000000000000..6d50fa2bf1da
--- /dev/null
+++ b/biology/pbcopper/files/patch-meson__options.txt
@@ -0,0 +1,7 @@
+--- meson_options.txt.orig	2019-02-17 22:34:29 UTC
++++ meson_options.txt
+@@ -1,3 +1,3 @@
+ option('build-examples', type : 'boolean', value : true,  description : 'Build pbcopper examples')
+ option('build-docs',     type : 'boolean', value : false, description : 'Build pbcopper docs')
+-option('tests',          type : 'boolean', value : true,  description : 'Enable dependencies required for testing')
++option('tests',          type : 'boolean', value : false,  description : 'Enable dependencies required for testing')
diff --git a/biology/pbcopper/pkg-plist b/biology/pbcopper/pkg-plist
index 0c9352560b76..92caf488a25f 100644
--- a/biology/pbcopper/pkg-plist
+++ b/biology/pbcopper/pkg-plist
@@ -1,4 +1,5 @@
 include/pbcopper/PbcopperConfig.h
+include/pbcopper/PbcopperMakeUnique.h
 include/pbcopper/align/Seed.h
 include/pbcopper/align/Seeds.h
 include/pbcopper/align/internal/Seed-inl.h
@@ -23,7 +24,6 @@ include/pbcopper/cli/toolcontract/ResolvedToolContract.h
 include/pbcopper/cli/toolcontract/ResourceType.h
 include/pbcopper/cli/toolcontract/Task.h
 include/pbcopper/cli/toolcontract/TaskType.h
-include/pbcopper/cli/toolcontract/internal/Config-inl.h
 include/pbcopper/cli/toolcontract/internal/Driver-inl.h
 include/pbcopper/cli/toolcontract/internal/InputFileType-inl.h
 include/pbcopper/cli/toolcontract/internal/OutputFileType-inl.h
@@ -48,7 +48,6 @@ include/pbcopper/json/JSON.h
 include/pbcopper/json/internal/json.hpp
 include/pbcopper/logging/Logging.h
 include/pbcopper/logging/internal/Logging-inl.h
-include/pbcopper/meson.build
 include/pbcopper/parallel/FireAndForget.h
 include/pbcopper/parallel/WorkQueue.h
 include/pbcopper/qgram/Index.h
@@ -72,4 +71,8 @@ include/pbcopper/utility/internal/FileUtils-inl.h
 include/pbcopper/utility/internal/Stopwatch-inl.h
 include/pbcopper/utility/internal/StringUtils-inl.h
 include/pbcopper/utility/internal/SystemInfo-inl.h
-lib/libpbcopper.a
+lib/libpbcopper.so
+lib/libpbcopper.so.0
+lib/libpbcopper.so.0.4
+lib/libpbcopper.so.0.4.1
+libdata/pkgconfig/pbcopper.pc