[med-svn] [Git][med-team/sra-sdk][master] 12 commits: Give up on ineffective before_script.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Fri Jan 20 23:00:59 GMT 2023
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
002f7cab by Aaron M. Ucko at 2023-01-19T21:47:16-05:00
Give up on ineffective before_script.
- - - - -
45e4d0d9 by Aaron M. Ucko at 2023-01-19T21:48:44-05:00
debian/rules: Skip rpaths, not needed even for libhdf5.
- - - - -
4520dd3d by Aaron M. Ucko at 2023-01-19T21:54:02-05:00
debian/not-installed: Refresh.
* Correct location of explicitly tagged lib*-static.a.
* Drop spurious entries (with hardcoded amd64 paths, no less).
- - - - -
bdf381f4 by Aaron M. Ucko at 2023-01-19T21:56:14-05:00
Limit architecture-dependent packages to amd64 and arm64.
The only other architecture ncbi-vdb supports is x32, but these tools
require a 64-bit address space.
- - - - -
d9cfe21c by Aaron M. Ucko at 2023-01-20T17:49:44-05:00
Link libngs-c++ against all internal dependencies
... via a new fix_ngs-c++-underlinkage patch. Hold off for now on
linking against libncbi-vdb, though anyone looking to substitute
libncbi-wvdb would need to contrive to supply a suitable definition of
KDBManagerMakeRead.
- - - - -
6f0725a7 by Aaron M. Ucko at 2023-01-20T17:50:51-05:00
link_vdb_dynamically.patch: Extend prior to building tests again.
Additionally cover makeinputs, from tools/loaders/general-loader/test.
(All other tests were already OK at this point.)
- - - - -
dab8a5c5 by Aaron M. Ucko at 2023-01-20T17:51:32-05:00
label_online_tests.patch: Extend as needed.
All existing labels confirmed to remain appropriate.
- - - - -
18e8eb66 by Aaron M. Ucko at 2023-01-20T17:54:07-05:00
d/rules: Explicitly enable tests, disabled by default these days.
- - - - -
c0626459 by Aaron M. Ucko at 2023-01-20T17:54:35-05:00
Update test cleanup logic to allow for build area reuse.
- - - - -
020a4233 by Aaron M. Ucko at 2023-01-20T17:55:01-05:00
.gitignore: Update patterns corresponding to test output.
- - - - -
f29e7194 by Aaron M. Ucko at 2023-01-20T17:55:44-05:00
debian/salsa-ci.yml: Retire remaining customizations.
- - - - -
e256ccbe by Aaron M. Ucko at 2023-01-20T17:57:36-05:00
Finalize sra-sdk 3.0.3+dfsg-2, back to unstable.
- - - - -
10 changed files:
- .gitignore
- debian/changelog
- debian/control
- debian/not-installed
- + debian/patches/fix_ngs-c++-underlinkage.patch
- debian/patches/label_online_tests.patch
- debian/patches/link_vdb_dynamically.patch
- debian/patches/series
- debian/rules
- debian/salsa-ci.yml
Changes:
=====================================
.gitignore
=====================================
@@ -1,5 +1,6 @@
ngs/ngs-python/dist
ngs/ngs-python/ngs.egg-info
obj-*
-test/copycat/actual
-test/fastq-loader/tmp.kfg
+test/external/vdb-dump/actual
+test/external/vdb-dump/data
+tmp.kfg
=====================================
debian/changelog
=====================================
@@ -1,17 +1,35 @@
-sra-sdk (3.0.3+dfsg-2) UNRELEASED; urgency=medium
+sra-sdk (3.0.3+dfsg-2) unstable; urgency=medium
- * NOT RELEASED YET.
- * debian/control: Drop vestigial versioned dependency on libncbi-wvdb2.
+ * Upload to unstable.
+ * .gitignore: Update patterns corresponding to test output.
+ * debian/control:
+ - Drop vestigial versioned dependency on libncbi-wvdb2.
+ - Limit architecture-dependent packages to amd64 and arm64. The only
+ other architecture ncbi-vdb supports is x32, but these tools require
+ a 64-bit address space.
+ * debian/not-installed: Refresh.
+ - Correct location of explicitly tagged lib*-static.a.
+ - Drop spurious entries (with hardcoded amd64 paths, no less).
+ * debian/patches/fix_ngs-c++-underlinkage.patch (new): Link libngs-c++
+ against all internal dependencies. Hold off for now on linking
+ against libncbi-vdb, though anyone looking to substitute libncbi-wvdb
+ would need to contrive to supply a suitable definition of
+ KDBManagerMakeRead.
+ * debian/patches/label_online_tests.patch: Extend as needed. All
+ existing labels confirmed to remain appropriate.
+ * debian/patches/link_vdb_dynamically.patch: Extend prior to building
+ tests again. To wit, additionally cover makeinputs, from
+ tools/loaders/general-loader/test. (All other tests were already OK at
+ this point.)
* debian/patches/prefer_dynamic_libraries.patch: Comment out upstream
logic that favored static linkage.
- * debian/salsa-ci.yml:
- - Pull in experimental ncbi-vdb via a RELEASE variable rather than a
- before_script. The new approach is simpler, and with any luck will
- apply to autopkgtest and/or piuparts.
- - Reinstate a before_script to favor experimental ncbi-vdb-data (by
- pinning a higher preference on it).
-
- -- Aaron M. Ucko <ucko at debian.org> Thu, 19 Jan 2023 20:24:06 -0500
+ * debian/rules:
+ - Skip rpaths, not needed even for libhdf5.
+ - Explicitly enable tests, disabled by default these days.
+ - Update test cleanup logic to allow for build area reuse.
+ * debian/salsa-ci.yml: Retire remaining customizations.
+
+ -- Aaron M. Ucko <ucko at debian.org> Fri, 20 Jan 2023 17:57:36 -0500
sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium
=====================================
debian/control
=====================================
@@ -33,7 +33,7 @@ Homepage: https://github.com/ncbi/sra-tools/
Rules-Requires-Root: no
Package: sra-toolkit
-Architecture: any
+Architecture: amd64 arm64
Depends: ${shlibs:Depends},
${misc:Depends}
Recommends: med-config
@@ -82,7 +82,7 @@ Description: utilities for the NCBI Sequence Read Archive
Package: libngs-c++3
Multi-Arch: same
-Architecture: any
+Architecture: amd64 arm64
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
@@ -101,7 +101,7 @@ Description: Next Generation Sequencing language Bindings (C++ runtime)
Package: libngs-c++-dev
Multi-Arch: same
-Architecture: any
+Architecture: amd64 arm64
Section: libdevel
Depends: ${misc:Depends},
libngs-c++3 (= ${binary:Version})
@@ -124,7 +124,7 @@ Description: Next Generation Sequencing language Bindings (C++ development)
Package: libncbi-ngs3
Multi-Arch: same
-Architecture: any
+Architecture: amd64 arm64
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
@@ -143,7 +143,7 @@ Description: Next Generation Sequencing language Bindings (full runtime)
Package: libncbi-ngs-dev
Multi-Arch: same
-Architecture: any
+Architecture: amd64 arm64
Section: libdevel
Depends: ${misc:Depends},
libncbi-ngs3 (= ${binary:Version}),
@@ -190,7 +190,7 @@ Description: Next Generation Sequencing language Bindings (Java bindings)
Package: libngs-jni
Multi-Arch: same
-Architecture: any
+Architecture: amd64 arm64
Section: java
Depends: ${shlibs:Depends},
libncbi-ngs3 (= ${binary:Version}),
=====================================
debian/not-installed
=====================================
@@ -1,11 +1,4 @@
usr/jar/*.jar
-usr/lib/x86_64-linux-gnu
-usr/lib64/lib*-static.a
+usr/lib/*/lib*ngs*-static.a
usr/share/examples*
usr/share/javadoc/ngs-doc
-usr/sra-tools/linux/gcc/x86_64/rel/bin/*
-usr/sra-tools/linux/gcc/x86_64/rel/ilib/*
-usr/sra-tools/linux/gcc/x86_64/rel/obj/shared/*
-usr/sra-tools/linux/gcc/x86_64/rel/obj/test/*/*
-usr/sra-tools/linux/gcc/x86_64/rel/obj/tools/*/*
-usr/sra-tools/linux/gcc/x86_64/rel/test-bin/*
=====================================
debian/patches/fix_ngs-c++-underlinkage.patch
=====================================
@@ -0,0 +1,12 @@
+Index: b/ngs/ngs-sdk/CMakeLists.txt
+===================================================================
+--- a/ngs/ngs-sdk/CMakeLists.txt
++++ b/ngs/ngs-sdk/CMakeLists.txt
+@@ -52,6 +52,7 @@ endif()
+
+ # Merging NGS_SDK_TARGETS with NCBI_NGS_TARGETS for ngs-sdk lib to contain all necessary functions for python and java to import (VDB-4713)
+ set(NGS_SDK_TARGETS ${NGS_SDK_TARGETS} ${NCBI_NGS_TARGETS})
++set(NGS_CPP_TARGETS ${NGS_CPP_TARGETS} ${NCBI_NGS_TARGETS})
+
+ if( SINGLE_CONFIG OR WIN32 )
+ include( CMakeLists.posix.txt )
=====================================
debian/patches/label_online_tests.patch
=====================================
@@ -289,3 +289,126 @@ Index: b/test/external/vdb-dump/CMakeLists.txt
+ set_tests_properties(Test_Vdb_dump PROPERTIES LABELS "online")
endif()
+Index: b/libs/ngs-vdb/test/CMakeLists.txt
+===================================================================
+--- a/libs/ngs-vdb/test/CMakeLists.txt
++++ b/libs/ngs-vdb/test/CMakeLists.txt
+@@ -70,32 +70,39 @@ add_test ( NAME Test_Ngs COMMAND test-ng
+ add_executable ( test-ngs_sra ngstest_sra.cpp )
+ target_link_libraries ( test-ngs_sra ${TEST_LIBS})
+ add_test ( NAME Test_Ngs_Sra COMMAND test-ngs_sra WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
++set_tests_properties( Test_Ngs_Sra PROPERTIES LABELS online )
+
+ add_executable ( test-ngs_sradb ngstest_sradb.cpp )
+ target_link_libraries ( test-ngs_sradb ${TEST_LIBS})
+ add_test ( NAME Test_Ngs_SraDb COMMAND test-ngs_sradb WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
++set_tests_properties( Test_Ngs_SraDb PROPERTIES LABELS online )
+
+ add_executable ( test-ngs_csra1 ngstest_csra1.cpp )
+ target_link_libraries ( test-ngs_csra1 ${TEST_LIBS})
+ add_test ( NAME SlowTest_Ngs_Csra1 COMMAND test-ngs_csra1 WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-set_tests_properties( SlowTest_Ngs_Csra1 PROPERTIES ENVIRONMENT "NCBI_VDB_QUALITY=R" )
++set_tests_properties( SlowTest_Ngs_Csra1 PROPERTIES
++ ENVIRONMENT "NCBI_VDB_QUALITY=R" LABELS online )
+
+ add_executable ( test-ngs_csra1_readcollection ngstest_csra1_readcollection.cpp )
+ target_link_libraries ( test-ngs_csra1_readcollection ${TEST_LIBS})
+ add_test ( NAME Test_Ngs_Csra1_ReadCollection COMMAND test-ngs_csra1_readcollection WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
++set_tests_properties( Test_Ngs_Csra1_ReadCollection PROPERTIES LABELS online )
+
+ add_executable ( test-ngs_csra1_refwin ngstest_csra1_refwin.cpp )
+ target_link_libraries ( test-ngs_csra1_refwin ${TEST_LIBS})
+ add_test ( NAME SlowTest_Ngs_Csra1_RefWin COMMAND test-ngs_csra1_refwin WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-set_tests_properties( SlowTest_Ngs_Csra1_RefWin PROPERTIES ENVIRONMENT "NCBI_VDB_QUALITY=R" )
++set_tests_properties( SlowTest_Ngs_Csra1_RefWin PROPERTIES
++ ENVIRONMENT "NCBI_VDB_QUALITY=R" LABELS online )
+
+ add_executable ( test-ngs_csra1_pileup ngstest_csra1_pileup.cpp )
+ target_link_libraries ( test-ngs_csra1_pileup ${TEST_LIBS})
+ add_test ( NAME SlowTest_Ngs_Csra1_Pileup COMMAND test-ngs_csra1_pileup WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
++set_tests_properties( SlowTest_Ngs_Csra1_Pileup PROPERTIES LABELS online )
+
+ add_executable ( test-ngs_reference ngstest_reference.cpp )
+ target_link_libraries ( test-ngs_reference ${TEST_LIBS})
+ add_test ( NAME SlowTest_Ngs_Reference COMMAND test-ngs_reference WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
++set_tests_properties( SlowTest_Ngs_Reference PROPERTIES LABELS online )
+
+
+ add_executable ( test-fragmentblob ngstest_fragmentblob.cpp )
+@@ -103,14 +110,17 @@ target_link_libraries ( test-fragmentblo
+ add_test ( NAME SlowTest_Ngs_FragmentBlob COMMAND test-fragmentblob WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+ # SlowTest_Ngs_FragmentBlob requires MakeDB to be run first
+ set_property(TEST SlowTest_Ngs_FragmentBlob PROPERTY FIXTURES_REQUIRED MakeDB)
++set_tests_properties( SlowTest_Ngs_FragmentBlob PROPERTIES LABELS online )
+
+ add_executable ( test-referenceblob ngstest_referenceblob.cpp )
+ target_link_libraries ( test-referenceblob ${TEST_LIBS})
+ add_test ( NAME Test_Ngs_ReferenceBlob COMMAND test-referenceblob WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
++set_tests_properties( Test_Ngs_ReferenceBlob PROPERTIES LABELS online )
+
+ add_executable ( test-byteblob ngstest_byteblob.cpp )
+ target_link_libraries ( test-byteblob ${TEST_LIBS})
+ add_test ( NAME Test_Ngs_ByteBlob COMMAND test-byteblob WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
++set_tests_properties( Test_Ngs_ByteBlob PROPERTIES LABELS online )
+
+ #-------------------------------------------------------------------------------
+ # tests for the NGS C++ APIs
+@@ -118,20 +128,24 @@ add_test ( NAME Test_Ngs_ByteBlob COMMAN
+ add_executable ( test-ngs_sra_c++ SRAtest.cpp )
+ target_link_libraries ( test-ngs_sra_c++ ${TEST_LIBS})
+ add_test ( NAME Test_Ngs_CPP_Sra COMMAND test-ngs_sra_c++ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
++set_tests_properties( Test_Ngs_CPP_Sra PROPERTIES LABELS online )
+
+ add_executable ( test-ngs_sradb_c++ SRADBtest.cpp )
+ target_link_libraries ( test-ngs_sradb_c++ ${TEST_LIBS})
+ add_test ( NAME Test_Ngs_CPP_SraDb COMMAND test-ngs_sradb_c++ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
++set_tests_properties( Test_Ngs_CPP_SraDb PROPERTIES LABELS online )
+
+ add_executable ( test-ngs_csra1_c++ CSRA1test.cpp )
+ target_link_libraries ( test-ngs_csra1_c++ ${TEST_LIBS})
+ add_test ( NAME SlowTest_Ngs_CPP_CSRA1 COMMAND test-ngs_csra1_c++ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-set_tests_properties( SlowTest_Ngs_CPP_CSRA1 PROPERTIES ENVIRONMENT "NCBI_VDB_QUALITY=R" )
++set_tests_properties( SlowTest_Ngs_CPP_CSRA1 PROPERTIES
++ ENVIRONMENT "NCBI_VDB_QUALITY=R" LABELS online )
+
+ add_executable ( test-ngs_csra1pileup++ CSRA1PileupTest.cpp )
+ target_link_libraries ( test-ngs_csra1pileup++ ${TEST_LIBS})
+ add_test ( NAME SlowTest_Ngs_CPP_CSRA1Pileup COMMAND test-ngs_csra1pileup++ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-set_tests_properties( SlowTest_Ngs_CPP_CSRA1Pileup PROPERTIES ENVIRONMENT "NCBI_VDB_QUALITY=R" )
++set_tests_properties( SlowTest_Ngs_CPP_CSRA1Pileup PROPERTIES
++ ENVIRONMENT "NCBI_VDB_QUALITY=R" LABELS online )
+
+ #-------------------------------------------------------------------------------
+ # tests for this library, ngs-vdb
+@@ -146,4 +160,5 @@ target_link_libraries ( test-ngs-vdb
+ )
+
+ add_test ( NAME SlowTest_NgsVdbWhiteBox COMMAND test-ngs-vdb )
++set_tests_properties( SlowTest_NgsVdbWhiteBox PROPERTIES LABELS online )
+
+Index: b/test/external/ngs/testy-the-bear/CMakeLists.txt
+===================================================================
+--- a/test/external/ngs/testy-the-bear/CMakeLists.txt
++++ b/test/external/ngs/testy-the-bear/CMakeLists.txt
+@@ -30,6 +30,6 @@ if( NOT WIN32 )
+ COMMAND runtestcase.sh "${TESTBINDIR}/testy-the-bear" "1" "0"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
+ set_tests_properties( SlowTest_testy-the-bear
+- PROPERTIES ENVIRONMENT "NCBI_VDB_QUALITY=R"
++ PROPERTIES ENVIRONMENT "NCBI_VDB_QUALITY=R" LABELS online
+ )
+ endif()
+Index: b/tools/external/sra-search/test/CMakeLists.txt
+===================================================================
+--- a/tools/external/sra-search/test/CMakeLists.txt
++++ b/tools/external/sra-search/test/CMakeLists.txt
+@@ -73,7 +73,9 @@ add_executable ( test-searchblock
+ # white box tests
+ add_test ( NAME SearchBlockWhiteBox COMMAND test-searchblock )
+ add_test ( NAME SraSearchWhiteBox COMMAND test-sra-search )
++set_tests_properties( SraSearchWhiteBox PROPERTIES LABELS online )
+ add_test ( NAME SlowTest_SraSearchWhiteBox COMMAND test-sra-search-slow )
++set_tests_properties( SlowTest_SraSearchWhiteBox PROPERTIES LABELS online )
+
+ # command line tests
+ if ( NOT WIN32)
=====================================
debian/patches/link_vdb_dynamically.patch
=====================================
@@ -20,3 +20,16 @@ Index: b/build/env.cmake
endif()
if( WIN32 )
+Index: b/tools/loaders/general-loader/test/CMakeLists.txt
+===================================================================
+--- a/tools/loaders/general-loader/test/CMakeLists.txt
++++ b/tools/loaders/general-loader/test/CMakeLists.txt
+@@ -66,7 +66,7 @@ add_executable ( makeinputs
+ )
+ target_link_libraries ( makeinputs
+ general-writer
+- ncbi-vdb-static
++ ncbi-vdb
+ )
+
+ if ( NOT WIN32)
=====================================
debian/patches/series
=====================================
@@ -35,3 +35,4 @@ use_soversions.patch
label_online_tests.patch
# reflect_code_donations.patch
prefer_dynamic_libraries.patch
+fix_ngs-c++-underlinkage.patch
=====================================
debian/rules
=====================================
@@ -34,14 +34,21 @@ override_dh_auto_clean:
rm -rf ngs/ngs-python/build ngs/ngs-python/dist
rm -rf ngs/ngs-python/ngs.egg-info
- rm -rf test/*/actual test/fastq-loader/tmp.kfg
+ find test tools -name actual -type d | xargs -rt rm -rf
+ rm -rf ngs/ngs-*/examples/actual/*
+ rm -fv test/*/*/tmp.kfg
+ rm -rf libs/ngs-vdb/test/data/SparseFragmentBlobs
+ rm -rf test/external/vdb-dump/data test/loaders/bam-load/out.sra
+ find tools/loaders/general-loader/test -name input | xargs -rt rm -rf
+ rm -f ngs/ngs-sdk/examples/actual.txt
-rm debian/libngs-jni.links
override_dh_auto_configure:
dh_auto_configure -- -DVDB_LIBDIR=/usr/lib/${DEB_HOST_MULTIARCH} \
-DVDB_INCDIR=/usr/include/ncbi-vdb -DBUILD_TOOLS_LOADERS=ON \
- -DBUILD_TOOLS_INTERNAL=ON -DBUILD_TOOLS_TEST_TOOLS=ON
+ -DBUILD_TOOLS_INTERNAL=ON -DBUILD_TOOLS_TEST_TOOLS=ON \
+ -DCMAKE_SKIP_RPATH=ON -DTOOLS_ONLY=OFF
KFG_INC = /usr/include/ncbi-vdb/kfg/ncbi
KFG_DEST = debian/sra-toolkit/etc/ncbi
=====================================
debian/salsa-ci.yml
=====================================
@@ -2,10 +2,3 @@
include:
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
-before_script:
- - 'echo "Package: ncbi-vdb-data" | tee /etc/apt/preferences.d/exp-data'
- - 'echo "Pin: release a=experimental" | tee -a /etc/apt/preferences.d/exp-data'
- - 'echo "Pin-Priority: 999" | tee -a /etc/apt/preferences.d/exp-data'
- - apt-get update
-variables:
- RELEASE: 'experimental'
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/3aac5e632a5641ffca698d6df5d799e1b053469d...e256ccbec8ae099d418b11286348faee40007be7
--
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/3aac5e632a5641ffca698d6df5d799e1b053469d...e256ccbec8ae099d418b11286348faee40007be7
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