[med-svn] [Git][med-team/sra-sdk][master] 9 commits: Attempt Architecture: any for sra-toolkit (modulo B-D availability).
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Mon Nov 14 03:32:41 GMT 2022
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
a14c60e4 by Aaron M. Ucko at 2022-11-11T09:30:31-05:00
Attempt Architecture: any for sra-toolkit (modulo B-D availability).
This setting matches architecture-dependent NGS packages'; if it
doesn't work out, we'll want to rein them all in for simplicity.
- - - - -
ef60057b by Aaron M. Ucko at 2022-11-11T09:46:37-05:00
Honor ${misc:Depends} for libngs-java per Lintian.
- - - - -
46ea311e by Aaron M. Ucko at 2022-11-11T17:10:40-05:00
reflect_code_donations.patch (new): Drop stray copyright statements.
Clean up stray licenseless copyright statements per consultation with
upstream (as quoted in the patch's header).
- - - - -
66aa8644 by Aaron M. Ucko at 2022-11-13T18:22:01-05:00
debian/copyright: Reflect a full inventory
... including convenience copies of several third-party libraries for
which it would be good to substitute existing packages at some point.
- - - - -
508580c9 by Aaron M. Ucko at 2022-11-13T22:21:43-05:00
d/rules: Refrain from shipping .gitignore files alongside examples.
- - - - -
62b321e8 by Aaron M. Ucko at 2022-11-13T22:21:43-05:00
debian/rules: Clean up after tests (offline ones, anyway).
- - - - -
5ed6598c by Aaron M. Ucko at 2022-11-13T22:21:43-05:00
(debian/).gitignore (new): Ignore build and (offline) test results.
- - - - -
cc105f17 by Aaron M. Ucko at 2022-11-13T22:21:43-05:00
routine-update: Remove trailing whitespace in debian/changelog
- - - - -
fc558e81 by Aaron M. Ucko at 2022-11-13T22:22:29-05:00
Finalize sra-sdk 3.0.0+dfsg-1 for experimental.
- - - - -
8 changed files:
- + .gitignore
- + debian/.gitignore
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/reflect_code_donations.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
.gitignore
=====================================
@@ -0,0 +1,3 @@
+obj-x86_64-linux-gnu
+test/copycat/actual
+test/fastq-loader/tmp.kfg
=====================================
debian/.gitignore
=====================================
@@ -0,0 +1,16 @@
+*.debhelper
+*.substvars
+.debhelper
+.javahelper_clean
+debhelper-build-stamp
+files
+lib*-dev
+lib*[0-9]
+libngs-java
+libngs-java-doc
+libngs-java-doc.doc-base.javadoc
+libngs-jni
+libngs-jni.links
+python3-ngs
+sra-toolkit
+tmp
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-sra-sdk (3.0.0+dfsg-1) UNRELEASED; urgency=medium
+sra-sdk (3.0.0+dfsg-1) experimental; urgency=medium
[ Andreas Tille ]
* New upstream version
@@ -9,7 +9,7 @@ sra-sdk (3.0.0+dfsg-1) UNRELEASED; urgency=medium
* debian/control:
- Account for consolidation of ngs-sdk (albeit with some intervening
changes, notably library restructuring); take the opportunity to add
- a -java-doc package.
+ a -java-doc package.0
- Let python3-ngs bypass libncbi-ngs-dev and use libncbi-ngs3 directly.
- Drop build dependency on libvdb-sqlite-dev, now internal to sra-sdk.
* debian/libngs-java-doc.javadoc: Enable javadoc installation.
@@ -50,17 +50,33 @@ sra-sdk (3.0.0+dfsg-1) UNRELEASED; urgency=medium
* 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/).gitignore (new): Ignore build and (offline) test results.
+ * debian/control:
+ - Make python3-ngs (safely!) Architecture: all too.
+ - Attempt Architecture: any for sra-toolkit (modulo B-D availability).
+ This setting matches architecture-dependent NGS packages'; if it
+ doesn't work out, we'll want to rein them all in for simplicity.
+ - Honor ${misc:Depends} for libngs-java per Lintian.
+ * debian/copyright: Reflect a full inventory, including convenience
+ copies of several third-party libraries for which it would be good to
+ substitute existing packages at some point.
* debian/patches/label_online_tests (new): Label tests that involve data
retrieval as "online".
+ * debian/patches/reflect_code_donations.patch (new): Clean up stray
+ licenseless copyright statements per consultation with upstream (as
+ quoted in the patch's header).
* 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.
+ * debian/rules:
+ - Skip tests labeled "online" to avoid breaking on
+ autobuilders, which require builds to work fully offline.
+ - Refrain from shipping .gitignore files alongside examples.
+ - Clean up after tests (offline ones, anyway).
+ * Remove trailing whitespace in debian/changelog (routine-update)
- -- Aaron M. Ucko <ucko at debian.org> Sun, 16 Oct 2022 22:45:04 -0400
+ -- Aaron M. Ucko <ucko at debian.org> Sun, 13 Nov 2022 22:22:28 -0500
sra-sdk (2.11.3+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -33,7 +33,7 @@ Homepage: https://github.com/ncbi/sra-tools/
Rules-Requires-Root: no
Package: sra-toolkit
-Architecture: amd64
+Architecture: any
Depends: ${shlibs:Depends},
libncbi-wvdb2 (>= 2.10.6+dfsg-3~),
${misc:Depends}
@@ -167,6 +167,7 @@ Multi-Arch: foreign
Architecture: all
Section: java
Depends: ${java:Depends},
+ ${misc:Depends},
libngs-jni (>= ${source:Version}),
libngs-jni (<< ${source:Version}.1~)
Recommends: ${java:Recommends}
=====================================
debian/copyright
=====================================
@@ -68,3 +68,172 @@ License: unrestricted
Comment:
The test data files contained in the archive are a data set prepared from
original SRAs with accession numbers SRR6650398, SRR2042184 and SRR7032226.
+
+Files: ngs/ngs-sdk/language/java/jni*.h ngs/ncbi/ngs-jni/jni*.h
+Copyright: 1996, Netscape Communications Corporation
+ 2006, Oracle and/or its affiliates
+License: GPL-2
+ This code is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License version 2 only, as
+ published by the Free Software Foundation. Oracle designates this
+ particular file as subject to the "Classpath" exception as provided
+ by Oracle in the LICENSE file that accompanied this code.
+ .
+ This code is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ version 2 for more details (a copy is included in the LICENSE file that
+ accompanied this code).
+ .
+ You should have received a copy of the GNU General Public License version
+ 2 along with this work; if not, write to the Free Software Foundation,
+ Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ .
+ Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ or visit www.oracle.com if you need additional information or have any
+ questions.
+ .
+ We used part of Netscape's Java Runtime Interface (JRI) as the starting
+ point of our design and implementation.
+
+Files: tools/driver-tool/utf8proc/*
+Copyright: 2009, 2013 Public Software Group e. V., Berlin, Germany
+ 2014-2018 Steven G. Johnson, Jiahao Chen, Tony Kelman,
+ Jonas Fonseca, and other contributors
+License: Expat
+
+Files: tools/driver-tool/utf8proc/data/data_generator.rb
+Copyright: 1991-2007 Unicode, Inc.
+License: Unicode
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of the Unicode data files and any associated documentation (the "Data
+ Files") or Unicode software and any associated documentation (the
+ "Software") to deal in the Data Files or Software without restriction,
+ including without limitation the rights to use, copy, modify, merge,
+ publish, distribute, and/or sell copies of the Data Files or Software, and
+ to permit persons to whom the Data Files or Software are furnished to do
+ so, provided that (a) the above copyright notice(s) and this permission
+ notice appear with all copies of the Data Files or Software, (b) both the
+ above copyright notice(s) and this permission notice appear in associated
+ documentation, and (c) there is clear notice in each modified Data File or
+ in the Software as well as in the documentation associated with the Data
+ File(s) or Software that the data or software has been modified.
+ .
+ THE DATA FILES AND SOFTWARE ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY
+ KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF
+ THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR HOLDERS
+ INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL INDIRECT OR
+ CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
+ USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+ TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
+ PERFORMANCE OF THE DATA FILES OR SOFTWARE.
+ .
+ Except as contained in this notice, the name of a copyright holder shall
+ not be used in advertising or otherwise to promote the sale, use or other
+ dealings in these Data Files or Software without prior written
+ authorization of the copyright holder.
+
+Files: tools/fastq-loader/fastq-tokens.h
+ tools/fastq-loader/zz_fastq-grammar.?
+ tools/vcf-loader/zz_vcf-grammar.?
+Copyright: 1984, 1989-1990, 2000-2015, 2018-2020 Free Software Foundation, Inc.
+License: GPL-3+
+
+Files: tools/sharq/CLI11.hpp
+Copyright: 2017-2020 University of Cincinnati
+ (developed by Henry Schreiner under NSF AWARD 1414736)
+License: BSD-3-clause-CLI11
+ Redistribution and use in source and binary forms of CLI11, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ 1. Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ 3. Neither the name of the copyright holder nor the names of its contributors
+ may be used to endorse or promote products derived from this software without
+ specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: tools/sharq/bm/*
+Copyright: 2002-2021 Anatoliy Kuznetsov (anatoliy_kuznetsov at yahoo.com)
+License: Apache-2
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+ .
+ http://www.apache.org/licenses/LICENSE-2.0
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ .
+ For more information please visit: http://bitmagic.io
+ .
+ On Debian systems you can find a copy of the Apache License, version
+ 2.0, at /usr/share/common-licenses/Apache-2.0.
+
+Files: tools/sharq/hash/*
+Copyright: 2017-2020 Mike Tzou (Chocobo1)
+License: GPL-3+
+
+Files: tools/sharq/hash/gsl/*
+Copyright: 2015 Microsoft Corporation
+License: Expat
+
+Files: tools/sharq/json.hpp
+Copyright: 2008-2009 Bjoern Hoehrmann <bjoern at hoehrmann.de>
+ 2009 Florian Loitsch
+ 2013-2021 Niels Lohmann <http://nlohmann.me>
+License: Expat
+
+Files: tools/sharq/spdlog/*
+Copyright: 2015-2021, Gabi Melman & spdlog contributors.
+License: Expat
+
+License: Expat
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the "Software"),
+ to deal in the Software without restriction, including without limitation
+ the rights to use, copy, modify, merge, publish, distribute, sublicense,
+ and/or sell copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE.
+
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ On Debian systems you can find a copy of the GNU General Public
+ License version 3 at /usr/share/common-licenses/GPL-3.
=====================================
debian/patches/reflect_code_donations.patch
=====================================
@@ -0,0 +1,139 @@
+Author: Aaron M. Ucko <ucko at debian.org>
+LastChanged: Fri, 11 Nov 2022 17:02:26 -0500
+Description: Drop author-waived copyright claims
+ From: Rodarmer, Kurt Sr. (NIH/NLM/NCBI) [C] <rodarmer at ncbi.nlm.nih.gov>
+ Sent: Friday, November 11, 2022 16:36
+ To: Ucko, Aaron (NIH/NLM/NCBI) [E] <ucko at ncbi.nlm.nih.gov>
+ Cc: Durbrow, Kenneth (NIH/NLM/NCBI) [C] <durbrowk at ncbi.nlm.nih.gov>
+ Subject: Re: SRA driver-tool log-{db,pro*}.?pp license?
+ .
+ These appear to be in the master branch from several years ago. I
+ donated some code to VDB as a starting point for the driver tool, but
+ the copyright did not get removed for some reason.
+ .
+ As I said, I went through the repo and it appears to be absent from
+ the engineering branch. It should just be cleaned up to remove any
+ such copyright statement, since I donated the code to NCBI.
+ .
+ Kurt
+
+Index: b/tools/driver-tool/log-db.cpp
+===================================================================
+--- a/tools/driver-tool/log-db.cpp
++++ b/tools/driver-tool/log-db.cpp
+@@ -1,9 +1,29 @@
+-/*
+-
+- tools.common.log-db
+-
+- copyright: (C) 2014-2017 Rodarmer, Inc. All Rights Reserved
+-
++/* ===========================================================================
++ *
++ * PUBLIC DOMAIN NOTICE
++ * National Center for Biotechnology Information
++ *
++ * This software/database is a "United States Government Work" under the
++ * terms of the United States Copyright Act. It was written as part of
++ * the author's official duties as a United States Government employee and
++ * thus cannot be copyrighted. This software/database is freely available
++ * to the public for use. The National Library of Medicine and the U.S.
++ * Government have not placed any restriction on its use or reproduction.
++ *
++ * Although all reasonable efforts have been taken to ensure the accuracy
++ * and reliability of the software and data, the NLM and the U.S.
++ * Government do not and cannot warrant the performance or results that
++ * may be obtained by using this software or data. The NLM and the U.S.
++ * Government disclaim all warranties, express or implied, including
++ * warranties of performance, merchantability or fitness for any particular
++ * purpose.
++ *
++ * Please cite the author in any work or product based on this material.
++ *
++ * ===========================================================================
++ *
++ * tools.common.log-db
++ *
+ */
+
+ #include "logging.hpp"
+Index: b/tools/driver-tool/log-protocol.hpp
+===================================================================
+--- a/tools/driver-tool/log-protocol.hpp
++++ b/tools/driver-tool/log-protocol.hpp
+@@ -1,9 +1,29 @@
+-/*
+-
+- tools.common.log-protocol
+-
+- copyright: (C) 2015-2018 Rodarmer, Inc. All Rights Reserved
+-
++/* ===========================================================================
++ *
++ * PUBLIC DOMAIN NOTICE
++ * National Center for Biotechnology Information
++ *
++ * This software/database is a "United States Government Work" under the
++ * terms of the United States Copyright Act. It was written as part of
++ * the author's official duties as a United States Government employee and
++ * thus cannot be copyrighted. This software/database is freely available
++ * to the public for use. The National Library of Medicine and the U.S.
++ * Government have not placed any restriction on its use or reproduction.
++ *
++ * Although all reasonable efforts have been taken to ensure the accuracy
++ * and reliability of the software and data, the NLM and the U.S.
++ * Government do not and cannot warrant the performance or results that
++ * may be obtained by using this software or data. The NLM and the U.S.
++ * Government disclaim all warranties, express or implied, including
++ * warranties of performance, merchantability or fitness for any particular
++ * purpose.
++ *
++ * Please cite the author in any work or product based on this material.
++ *
++ * ===========================================================================
++ *
++ * tools.common.log-protocol
++ *
+ */
+
+ #ifndef _hpp_tools_common_log_protocol_
+Index: b/tools/driver-tool/log-proxy.cpp
+===================================================================
+--- a/tools/driver-tool/log-proxy.cpp
++++ b/tools/driver-tool/log-proxy.cpp
+@@ -1,9 +1,29 @@
+-/*
+-
+- tools.common.log-proxy
+-
+- copyright: (C) 2015-2018 Rodarmer, Inc. All Rights Reserved
+-
++/* ===========================================================================
++ *
++ * PUBLIC DOMAIN NOTICE
++ * National Center for Biotechnology Information
++ *
++ * This software/database is a "United States Government Work" under the
++ * terms of the United States Copyright Act. It was written as part of
++ * the author's official duties as a United States Government employee and
++ * thus cannot be copyrighted. This software/database is freely available
++ * to the public for use. The National Library of Medicine and the U.S.
++ * Government have not placed any restriction on its use or reproduction.
++ *
++ * Although all reasonable efforts have been taken to ensure the accuracy
++ * and reliability of the software and data, the NLM and the U.S.
++ * Government do not and cannot warrant the performance or results that
++ * may be obtained by using this software or data. The NLM and the U.S.
++ * Government disclaim all warranties, express or implied, including
++ * warranties of performance, merchantability or fitness for any particular
++ * purpose.
++ *
++ * Please cite the author in any work or product based on this material.
++ *
++ * ===========================================================================
++ *
++ * tools.common.log-proxy
++ *
+ */
+
+ #include "logging.hpp"
=====================================
debian/patches/series
=====================================
@@ -33,3 +33,4 @@ fix_javadoc_build.patch
use_soversions.patch
use_stock_magic.patch
label_online_tests.patch
+reflect_code_donations.patch
=====================================
debian/rules
=====================================
@@ -33,6 +33,8 @@ override_dh_auto_clean:
rm -rf ngs/ngs-sdk/$(DEB_HOST_MULTIARCH)
rm -rf ngs/ngs-python/build
+ rm -rf test/*/actual test/fastq-loader/tmp.kfg
+
-rm debian/libngs-jni.links
override_dh_auto_configure:
@@ -116,6 +118,10 @@ override_dh_install:
find debian -name "*.pyc" -delete
find debian -type d -name __pycache__ | xargs rm -rf
+override_dh_installexamples:
+ dh_installexamples
+ find debian/*/ -name .gitignore -delete
+
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
cd obj-$(DEB_HOST_MULTIARCH) && \
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/5c4e86ea9f6fae83f1f029e756fc1d9fbfa01a98...fc558e816c8d16662097d845e18af76184519ea3
--
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/5c4e86ea9f6fae83f1f029e756fc1d9fbfa01a98...fc558e816c8d16662097d845e18af76184519ea3
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