sra-tools: Replace post-install hacks with cmake patches

[Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Nov 18 06:20:01 2024 -0600
Changeset:	908def8a8bd9684ee72ed4e83d04daffd359cb4b

Modified Files:
	sra-tools/Makefile
	sra-tools/distinfo
Added Files:
	sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt
	sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt

Log Message:
sra-tools: Replace post-install hacks with cmake patches

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=908def8a8bd9684ee72ed4e83d04daffd359cb4b

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 sra-tools/Makefile                                 | 12 +++--------
 sra-tools/distinfo                                 |  2 ++
 .../patch-ngs_ngs-python_examples_CMakeLists.txt   | 15 ++++++++++++++
 .../patch-ngs_ngs-sdk_examples_CMakeLists.txt      | 24 ++++++++++++++++++++++
 4 files changed, 44 insertions(+), 9 deletions(-)

diffs:
diff --git a/sra-tools/Makefile b/sra-tools/Makefile
index 328143bdd3..8355239fd7 100644
--- a/sra-tools/Makefile
+++ b/sra-tools/Makefile
@@ -61,16 +61,9 @@ pre-configure:
 	cd ${WRKSRC}/ncbi-vdb/build && cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON ..
 	cd ${WRKSRC}/ncbi-vdb/build && ${MAKE}
 
-# FIXME: Tweak build so moving things around destdir is unnecessary
 post-install:
-	${STRIP} ${DESTDIR}${PREFIX}/bin/*.${PKGVERSION}
-	${STRIP} ${DESTDIR}${PREFIX}/lib/*.${PKGVERSION}
-	${TEST} -e ${DESTDIR}${PREFIX}/share/examples && ${MV} ${DESTDIR}${PREFIX}/share/examples ${DESTDIR}${PREFIX}/share/examples-sratools
-	${MKDIR} ${DESTDIR}${EXAMPLESDIR}
-	${TEST} -e ${DESTDIR}${EXAMPLESDIR}/AlignSliceTest.cpp || ${MV} ${DESTDIR}${PREFIX}/share/examples-sratools/* ${DESTDIR}${EXAMPLESDIR}
-	${RMDIR} ${DESTDIR}${PREFIX}/share/examples-sratools
-	${TEST} -e ${DESTDIR}${PREFIX}/share/examples-python && ${MV} ${DESTDIR}${PREFIX}/share/examples-python ${DESTDIR}${EXAMPLESDIR}/python
-	# FIXME: Can we prevent build from detecting java?
+	${STRIP} ${DESTDIR}${PREFIX}/bin/*.${PKGVERSION_NOREV}
+	${STRIP} ${DESTDIR}${PREFIX}/lib/*.${PKGVERSION_NOREV}
 	${RM} -rf ${DESTDIR}${PREFIX}/jar
 	${RM} -rf ${DESTDIR}${PREFIX}/share/examples-java
 	${RM} -rf ${DESTDIR}${PREFIX}/share/javadoc
@@ -81,6 +74,7 @@ post-install:
 
 .include "../../mk/pthread.buildlink3.mk"
 .include "../../devel/cmake/build.mk"
+.include "../../lang/python/pyversion.mk"
 .include "../../textproc/libxml2/buildlink3.mk"
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../archivers/zstd/buildlink3.mk"
diff --git a/sra-tools/distinfo b/sra-tools/distinfo
index 8a5cc185d5..6b3c4f1642 100644
--- a/sra-tools/distinfo
+++ b/sra-tools/distinfo
@@ -9,4 +9,6 @@ Size (sra-tools-3.1.1.tar.gz) = 45754110 bytes
 SHA1 (patch-build_env.cmake) = 14add56e66e5578fd0d51ce55329285e0981ac4e
 SHA1 (patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c) = f49eb28f8bfeb528c1d7c2e9d184502b9eba273c
 SHA1 (patch-ngs_ngs-java_CMakeLists.txt) = 44b822381fd564d045406cc926f807adae9fbe59
+SHA1 (patch-ngs_ngs-python_examples_CMakeLists.txt) = a8a01d17a27c060c08311ab8571ae10af265781d
+SHA1 (patch-ngs_ngs-sdk_examples_CMakeLists.txt) = 6a4b09afe4b919eeb9bd144635695437e5a3b57f
 SHA1 (patch-tools_external_driver-tool_sratools.cpp) = c490d83f03471e6e8e34b8e88534469ed45b2886
diff --git a/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt b/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt
new file mode 100644
index 0000000000..79f5647cc1
--- /dev/null
+++ b/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Canonicalize python examples dir
+
+--- ngs/ngs-python/examples/CMakeLists.txt.orig	2024-11-18 12:08:54.646596198 +0000
++++ ngs/ngs-python/examples/CMakeLists.txt
+@@ -54,7 +54,7 @@ if( Python3_EXECUTABLE )
+             RunAndDiff( RefTest "SRR1121656" )
+         endif()
+ 
+-        set( INSTALL_DEST ${CMAKE_INSTALL_PREFIX}/share/examples-python )
++        set( INSTALL_DEST ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools/python )
+ 
+         install(FILES ${SOURCES} expected.txt
+             DESTINATION ${INSTALL_DEST} )
diff --git a/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt b/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt
new file mode 100644
index 0000000000..fc6d6467a5
--- /dev/null
+++ b/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt
@@ -0,0 +1,24 @@
+$NetBSD$
+
+# Canonicalize examples dir
+
+--- ngs/ngs-sdk/examples/CMakeLists.txt.orig	2024-11-18 12:10:46.495627136 +0000
++++ ngs/ngs-sdk/examples/CMakeLists.txt
+@@ -62,14 +62,14 @@ if ( SINGLE_CONFIG )
+     install(
+         FILES FragTest.cpp AlignTest.cpp AlignSliceTest.cpp PileupTest.cpp RefTest.cpp DumpReferenceFASTA.cpp
+               expected.txt
+-        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples
++        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools
+     )
+     install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Makefile.install
+-        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples
++        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools
+         RENAME Makefile
+     )
+     install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/README.install
+-        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples
++        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/examples/sra-tools
+         RENAME README.txt
+     )
+ endif()