[med-svn] [Git][med-team/sra-sdk][master] 4 commits: debian/changelog: Document Pierre Gruet's welcome contributions.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Mon Oct 17 03:47:11 BST 2022
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
65002c11 by Aaron M. Ucko at 2022-10-16T22:31:21-04:00
debian/changelog: Document Pierre Gruet's welcome contributions.
- - - - -
da7affbc by Aaron M. Ucko at 2022-10-16T22:33:37-04:00
use_stock_magic.patch (new): Let copycat use the stock magic db
... in /usr/share/misc.
- - - - -
7ddcf8ed by Aaron M. Ucko at 2022-10-16T22:40:19-04:00
Label and exclude online tests for autobuilders' sake.
* debian/patches/label_online_tests (new): Label tests that involve data
retrieval as "online".
* debian/rules: Skip tests labeled "online" to avoid breaking on
autobuilders, which require builds to work fully offline.
- - - - -
5c4e86ea by Aaron M. Ucko at 2022-10-16T22:45:05-04:00
debian/control: Make python3-ngs (safely!) Architecture: all too.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/label_online_tests.patch
- debian/patches/series
- + debian/patches/use_stock_magic.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -36,7 +36,31 @@ sra-sdk (3.0.0+dfsg-1) UNRELEASED; urgency=medium
- Extend bin deversioning to *+ (i.e., kar+).
* debian/salsa-ci.yml: Use ncbi-vdb's aptly repo to get 3.x for now.
- -- Aaron M. Ucko <ucko at debian.org> Tue, 11 Oct 2022 22:34:52 -0400
+ [ Pierre Gruet ]
+ * debian/control:
+ - Add missing build dependencies on liblzma-dev and libsam-extract-dev.
+ - Mark libngs-java as Architecture: all; loosen its dependencies on
+ libncbi-ngs-dev slightly to account for possible binNMUs.
+ - Introduce a libngs-jni package, on which libngs-java can and will
+ depend in lieu of libncbi-ngs-dev (or patching source to support
+ using libncbi-ngs3 directly).
+ * debian/libngs-java-doc.lintian-overrides: Override complaints about
+ javadoc-embedded jQuery per the discussion starting at
+ https://lists.debian.org/debian-java/2018/06/msg00020.html.
+ * debian/libngs-jni.links.in: Provide a general formula for libngs-jni's
+ central symlink.
+ * debian/rules: Add logic to fill in the specifics.
+
+ [ Aaron M. Ucko ]
+ * debian/control: Make python3-ngs (safely!) Architecture: all too.
+ * debian/patches/label_online_tests (new): Label tests that involve data
+ retrieval as "online".
+ * debian/patches/use_stock_magic.patch (new): Let copycat use the stock
+ magic-number database in /usr/share/misc.
+ * debian/rules: Skip tests labeled "online" to avoid breaking on
+ autobuilders, which require builds to work fully offline.
+
+ -- Aaron M. Ucko <ucko at debian.org> Sun, 16 Oct 2022 22:45:04 -0400
sra-sdk (2.11.3+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -229,11 +229,12 @@ Description: Next Generation Sequencing language Bindings (Java documentation)
Documentation for the Java bindings.
Package: python3-ngs
-Architecture: any
+Architecture: all
Section: python
Depends: ${python3:Depends},
${misc:Depends},
- libncbi-ngs3 (= ${binary:Version})
+ libncbi-ngs3 (>= ${source:Version}),
+ libncbi-ngs3 (<< ${source:Version}.1~)
Description: Next Generation Sequencing language Bindings (Python3 bindings)
NGS is a new, domain-specific API for accessing reads, alignments and
pileups produced from Next Generation Sequencing. The API itself is
=====================================
debian/patches/label_online_tests.patch
=====================================
@@ -0,0 +1,285 @@
+Index: b/ngs/ngs-sdk/examples/CMakeLists.txt
+===================================================================
+--- a/ngs/ngs-sdk/examples/CMakeLists.txt
++++ b/ngs/ngs-sdk/examples/CMakeLists.txt
+@@ -43,6 +43,7 @@ add_executable( DumpReferenceFASTA DumpR
+
+ if ( NOT WIN32 )
+ add_test( NAME SlowTest_NGS_Run_and_diff COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/run_and_diff.sh ${BINDIR} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(SlowTest_NGS_Run_and_diff PROPERTIES LABELS "online")
+ endif()
+
+ if ( SINGLE_CONFIG )
+Index: b/ngs/ngs-java/examples/CMakeLists.txt
+===================================================================
+--- a/ngs/ngs-java/examples/CMakeLists.txt
++++ b/ngs/ngs-java/examples/CMakeLists.txt
+@@ -51,6 +51,8 @@ if ( Java_FOUND )
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ COMMAND_EXPAND_LISTS
+ )
++ set_tests_properties(Test_NgsJavaExamples_${TestName}
++ PROPERTIES LABELS "online")
+ endmacro()
+
+ RunAndDiff( FragTest "ERR225922 10000 2" )
+Index: b/ngs/ngs-python/examples/CMakeLists.txt
+===================================================================
+--- a/ngs/ngs-python/examples/CMakeLists.txt
++++ b/ngs/ngs-python/examples/CMakeLists.txt
+@@ -42,6 +42,7 @@ if( Python3_EXECUTABLE )
+ set_tests_properties( Test_NgsPythonExamples_${TestName}
+
+ PROPERTIES ENVIRONMENT "NGS_PY_DOWNLOAD_LIBRARY=0;PYTHONUSERBASE=${PythonUserBase};NGS_PY_LIBRARY_PATH=${LIBDIR}" DEPENDS Test_NGS_Python_install
++ LABELS "online"
+ )
+ endmacro()
+
+Index: b/test/align/CMakeLists.txt
+===================================================================
+--- a/test/align/CMakeLists.txt
++++ b/test/align/CMakeLists.txt
+@@ -36,3 +36,4 @@ add_executable( test-estimator pileup_es
+ include_directories( ${CMAKE_SOURCE_DIR} )
+ target_link_libraries( test-estimator ncbi-ngs-c++ ngs-c++ ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} )
+ add_test( NAME SlowTest_Align_estimator COMMAND test-estimator WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++set_tests_properties(SlowTest_Align_estimator PROPERTIES LABELS "online")
+Index: b/test/kar/CMakeLists.txt
+===================================================================
+--- a/test/kar/CMakeLists.txt
++++ b/test/kar/CMakeLists.txt
+@@ -29,6 +29,7 @@ if ( NOT WIN32 )
+ ${CMAKE_COMMAND} -E env ${CONFIGTOUSE}=/
+ bash -c "./kar-ntest.sh ${DIRTOTEST}/kar ${DIRTOTEST}/prefetch"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(Test_Kar PROPERTIES LABELS "online")
+
+ else()
+ #TODO: make run on Windows
+Index: b/test/kdbmeta/CMakeLists.txt
+===================================================================
+--- a/test/kdbmeta/CMakeLists.txt
++++ b/test/kdbmeta/CMakeLists.txt
+@@ -26,6 +26,7 @@ if ( NOT WIN32 )
+ add_test( NAME Test_Kdbmeta
+ COMMAND bash -c "${DIRTOTEST}/kdbmeta SRR053325 > /dev/null"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(Test_Kdbmeta PROPERTIES LABELS "online")
+ else()
+ #TODO: make run on Windows
+ endif()
+Index: b/test/kget/CMakeLists.txt
+===================================================================
+--- a/test/kget/CMakeLists.txt
++++ b/test/kget/CMakeLists.txt
+@@ -38,8 +38,10 @@ if ( NOT WIN32 )
+ COMMAND diff-vs-wget.sh ${DIRTOTEST}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
+
++ set_tests_properties(Test_Kget SlowTest_Kget_DiffVsWget
++ PROPERTIES LABELS "online")
+ else()
+ #TODO: make run on Windows
+ endif()
+
+-endif()
+\ No newline at end of file
++endif()
+Index: b/test/ngs-java/CMakeLists.txt
+===================================================================
+--- a/test/ngs-java/CMakeLists.txt
++++ b/test/ngs-java/CMakeLists.txt
+@@ -79,5 +79,6 @@ if ( Java_FOUND )
+ COMMAND ${Java_JAVA_EXECUTABLE} -cp "${CLASSPATH}" "-Djava.library.path=${LIBPATH}" ${VARS} org.junit.runner.JUnitCore ngs_test_CSRA1
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ )
++ set_tests_properties(SlowTest_NgsJava_CSRA1 PROPERTIES LABELS "online")
+
+ endif()
+Index: b/test/ngs-pileup/CMakeLists.txt
+===================================================================
+--- a/test/ngs-pileup/CMakeLists.txt
++++ b/test/ngs-pileup/CMakeLists.txt
+@@ -31,6 +31,7 @@ set( NGS_PILEUP_LIBS
+ ${COMMON_LIBS_READ}
+ )
+ AddExecutableTest( Test_Ngs_Pileup "test-ngs-pileup.cpp" "${NGS_PILEUP_LIBS}" )
++set_tests_properties(Test_Ngs_Pileup PROPERTIES LABELS "online")
+
+ if( NOT WIN32 )
+
+@@ -42,47 +43,56 @@ if( NOT WIN32 )
+ add_test( NAME Test_Ngs_Pileup_2
+ COMMAND ./runtestcase.sh ${BINDIR} ${CMAKE_CURRENT_SOURCE_DIR} 2.0 SRR1166393
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(Test_Ngs_Pileup_2 PROPERTIES LABELS "online")
+
+ # Illumina
+ add_test( NAME Test_Ngs_Pileup_3
+ COMMAND ./runtestcase.sh ${BINDIR} ${CMAKE_CURRENT_SOURCE_DIR} 3.0 ERR334733
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(Test_Ngs_Pileup_3 PROPERTIES LABELS "online")
+
+ add_test( NAME Test_Ngs_Pileup_4
+ COMMAND ./runtestcase.sh ${BINDIR} ${CMAKE_CURRENT_SOURCE_DIR} 4.0 SRR1068006
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(Test_Ngs_Pileup_4 PROPERTIES LABELS "online")
+
+ # ABSOLID REF_ROWS=36172
+ add_test( NAME SlowTest_Ngs_Pileup_5
+ COMMAND ./runtestcase.sh ${BINDIR} ${CMAKE_CURRENT_SOURCE_DIR} 5.0 SRR619510
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(SlowTest_Ngs_Pileup_5 PROPERTIES LABELS "online")
+
+ #TODO: fix
+ # SEC_ROWS=198
+ # add_test( NAME Test_Ngs_Pileup_6
+ # COMMAND ./runtestcase.sh ${BINDIR} ${CMAKE_CURRENT_SOURCE_DIR} 6.0 SRR1251988
+ # WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ # set_tests_properties(Test_Ngs_Pileup_6 PROPERTIES LABELS "online")
+
+ # ION_TORRENT
+ add_test( NAME Test_Ngs_Pileup_7
+ COMMAND ./runtestcase.sh ${BINDIR} ${CMAKE_CURRENT_SOURCE_DIR} 7.0 SRR1186012
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(Test_Ngs_Pileup_7 PROPERTIES LABELS "online")
+
+ #TODO: fix
+ # COMPLETE_GENOMICS
+ # add_test( NAME Test_Ngs_Pileup_8.1
+ # COMMAND ./runtestcase.sh ${BINDIR} ${CMAKE_CURRENT_SOURCE_DIR} 8.1 SRR556739 -r chrY
+ # WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ # set_tests_properties(Test_Ngs_Pileup_8.1 PROPERTIES LABELS "online")
+
+ #TODO: fix
+ # COMPLETE_GENOMICS, circular reference
+ # add_test( NAME Test_Ngs_Pileup_8.2
+ # COMMAND ./runtestcase.sh ${BINDIR} ${CMAKE_CURRENT_SOURCE_DIR} 8.2 SRR556739 -r chrM
+ # WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ # set_tests_properties(Test_Ngs_Pileup_8.2 PROPERTIES LABELS "online")
+
+ #:19900-20022
+ add_test( NAME Test_Ngs_Pileup_9
+ COMMAND ./runtestcase.sh ${BINDIR} ${CMAKE_CURRENT_SOURCE_DIR} 9.0 SRR341578 -r NC_011752.1
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(Test_Ngs_Pileup_9 PROPERTIES LABELS "online")
+
+-endif()
+\ No newline at end of file
++endif()
+Index: b/test/ngs-python/CMakeLists.txt
+===================================================================
+--- a/test/ngs-python/CMakeLists.txt
++++ b/test/ngs-python/CMakeLists.txt
+@@ -33,6 +33,7 @@ if( Python3_EXECUTABLE )
+ PROPERTIES
+ DEPENDS Test_NGS_Python_install
+ ENVIRONMENT "NGS_PY_DOWNLOAD_LIBRARY=0;PYTHONUSERBASE=${PythonUserBase};NGS_PY_LIBRARY_PATH=${LIBDIR};LD_LIBRARY_PATH=${NCBI_VDB_LIBDIR}"
++ LABELS "online"
+ )
+ elseif( WIN32 )
+ add_test( NAME SlowTest_NgsPython
+@@ -44,6 +45,7 @@ if( Python3_EXECUTABLE )
+ PROPERTIES
+ DEPENDS Test_NGS_Python_install
+ ENVIRONMENT "NGS_PY_DOWNLOAD_LIBRARY=0;PYTHONUSERBASE=${PythonUserBase};NGS_PY_LIBRARY_PATH=${BINDIR}"
++ LABELS "online"
+ )
+ endif()
+ endif()
+Index: b/test/prefetch/CMakeLists.txt
+===================================================================
+--- a/test/prefetch/CMakeLists.txt
++++ b/test/prefetch/CMakeLists.txt
+@@ -36,22 +36,31 @@ if ( NOT WIN32 )
+ add_test( NAME Test_Prefetch_urls_and_accs
+ COMMAND perl urls_and_accs.pl ${DIRTOTEST} ${BINDIR}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(Test_Prefetch_urls_and_accs
++ PROPERTIES LABELS "online")
+
+ add_test( NAME Test_Prefetch_out_dir_and_file
+ COMMAND perl out_dir_and_file.pl ${DIRTOTEST} ${BINDIR}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(Test_Prefetch_out_dir_and_file
++ PROPERTIES LABELS "online")
+
+ add_test( NAME SlowTest_Prefetch
+ COMMAND
+ ${CMAKE_COMMAND} -E env ${CONFIGTOUSE}=/
+ bash -c "sh runtests.sh ${CMAKE_BINARY_DIR}/test-bin/SlowTest_Prefetch ${DIRTOTEST}"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(SlowTest_Prefetch PROPERTIES LABELS "online")
+
+ add_test( NAME SlowTest_Prefetch_1GB
+ COMMAND perl ncbi1GB.pl ${BINDIR}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ # Trivially succeeds in the absence of Aspera ascp, but any
++ # meaningful testing would require online resources regardless.
++ set_tests_properties(SlowTest_Prefetch_1GB PROPERTIES LABELS "online")
+
+ add_test( NAME SlowTest_Prefetch_vdbcache
+ COMMAND perl vdbcache.pl ${BINDIR}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++ set_tests_properties(SlowTest_Prefetch_vdbcache PROPERTIES LABELS "online")
+ endif()
+Index: b/test/sra-pileup/CMakeLists.txt
+===================================================================
+--- a/test/sra-pileup/CMakeLists.txt
++++ b/test/sra-pileup/CMakeLists.txt
+@@ -41,4 +41,5 @@ if ( NOT WIN32 AND Python3_EXECUTABLE )
+ bash -c "./runtests-slow.sh ${DIRTOTEST} ${Python3_EXECUTABLE}"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ )
++ set_tests_properties(SlowTest_SraPileup PROPERTIES LABELS "online")
+ endif()
+Index: b/test/sra-stat/CMakeLists.txt
+===================================================================
+--- a/test/sra-stat/CMakeLists.txt
++++ b/test/sra-stat/CMakeLists.txt
+@@ -35,4 +35,7 @@ if ( NOT WIN32 )
+ add_test( NAME SlowTest_Sra_stat
+ COMMAND test-sra-stat-slow.sh ${DIRTOTEST}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
+-endif()
+\ No newline at end of file
++
++ set_tests_properties(Test_Sra_stat SlowTest_Sra_stat
++ PROPERTIES LABELS "online")
++endif()
+Index: b/test/srapath/CMakeLists.txt
+===================================================================
+--- a/test/srapath/CMakeLists.txt
++++ b/test/srapath/CMakeLists.txt
+@@ -41,4 +41,5 @@ if ( NOT WIN32 )
+ bash -c "./test-srapath.sh ${DIRTOTEST}"
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ )
+-endif()
+\ No newline at end of file
++ set_tests_properties(Test_Srapath PROPERTIES LABELS "online")
++endif()
+Index: b/test/vdb-diff/CMakeLists.txt
+===================================================================
+--- a/test/vdb-diff/CMakeLists.txt
++++ b/test/vdb-diff/CMakeLists.txt
+@@ -40,4 +40,8 @@ if( NOT WIN32 )
+ add_test( NAME Test_VDB_Diff_Check_failure
+ COMMAND test_failure.sh "${DIRTOTEST}" ${ACCESSION}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
++
++ set_tests_properties(
++ Test_VDB_Diff_Check_success Test_VDB_Diff_Check_failure
++ PROPERTIES LABELS "online")
+ endif()
+\ No newline at end of file
+Index: b/test/vdb-dump/CMakeLists.txt
+===================================================================
+--- a/test/vdb-dump/CMakeLists.txt
++++ b/test/vdb-dump/CMakeLists.txt
+@@ -46,4 +46,5 @@ if ( NOT WIN32 )
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ )
+
++ set_tests_properties(Test_Vdb_dump PROPERTIES LABELS "online")
+ endif()
=====================================
debian/patches/series
=====================================
@@ -31,3 +31,5 @@ use_debian_packaged_compression_libs.patch
link_magic_dynamically.patch
fix_javadoc_build.patch
use_soversions.patch
+use_stock_magic.patch
+label_online_tests.patch
=====================================
debian/patches/use_stock_magic.patch
=====================================
@@ -0,0 +1,14 @@
+--- a/tools/copycat/ccfileformat.c
++++ b/tools/copycat/ccfileformat.c
+@@ -189,9 +189,11 @@ rc_t CCFileFormatMake (CCFileFormat ** p
+ KConfigRelease ( kfg );
+ if ( rc == 0 )
+ {
++#if 0
+ char magicpath[1024];
+ size_t num_writ;
+ rc = string_printf ( magicpath, sizeof ( magicpath ), &num_writ, "%S/magic", bindir );
++#endif
+ StringWhack ( bindir );
+ if ( rc == 0 )
+ {
=====================================
debian/rules
=====================================
@@ -118,7 +118,8 @@ override_dh_install:
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- dh_auto_test --no-parallel -- -k
+ cd obj-$(DEB_HOST_MULTIARCH) && \
+ ctest --force-new-ctest-process --verbose -j1 -LE online
endif
override_dh_prep:
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/97b0d00bf2cb070ae76eae4a9b0a9ce61587c885...5c4e86ea9f6fae83f1f029e756fc1d9fbfa01a98
--
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/97b0d00bf2cb070ae76eae4a9b0a9ce61587c885...5c4e86ea9f6fae83f1f029e756fc1d9fbfa01a98
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