[med-svn] [Git][med-team/salmon][master] 19 commits: New upstream version 1.9.0+ds1

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / salmon


Commits:
471a464d by Étienne Mollier at 2022-10-28T18:25:51+02:00
New upstream version 1.9.0+ds1
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aa16855f by Étienne Mollier at 2022-10-28T18:25:51+02:00
routine-update: New upstream version

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218ecbc5 by Étienne Mollier at 2022-10-28T18:25:55+02:00
Update upstream source from tag 'upstream/1.9.0+ds1'

Update to upstream version '1.9.0+ds1'
with Debian dir 82da8a3b43661d5db9dea02400bc3950fda8aa57
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b3c1fa69 by Étienne Mollier at 2022-10-28T18:25:55+02:00
routine-update: Standards-Version: 4.6.1

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94015975 by Étienne Mollier at 2022-10-28T18:26:38+02:00
spelling patch: refresh.

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4768eb61 by Étienne Mollier at 2022-10-28T18:30:25+02:00
use_debian_packaged_libs.patch: refresh.

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38aa0447 by Étienne Mollier at 2022-10-28T18:30:47+02:00
disable-version-check.patch: refresh.

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53b6a1a1 by Étienne Mollier at 2022-10-31T22:17:10+01:00
use_debian_packaged_libs.patch: don't scan for plain tbb.

The oneapi tbb will be used instead.

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8a731d83 by Étienne Mollier at 2022-10-31T22:18:29+01:00
d/external/: bump pufferfish version to support onetbb.

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dc17dc6f by Étienne Mollier at 2022-10-31T22:30:43+01:00
d/external/: update twopaco to fix ftbfs with onetbb.

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e6a9e4a0 by Étienne Mollier at 2022-11-01T14:41:16+01:00
d/external/: update to reflect changes in embedded pufferfish.

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bc37f508 by Étienne Mollier at 2022-11-01T14:41:47+01:00
use_debian_packaged_libs.patch: adjust to missing external assets.

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7df0dd8c by Étienne Mollier at 2022-11-01T14:58:24+01:00
update changelog.

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74739a44 by Étienne Mollier at 2022-11-01T15:04:56+01:00
leave fixme item.

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03656e49 by Étienne Mollier at 2022-11-04T00:10:39+01:00
d/e/p/e/twopaco: upgrade vendored version for onetbb support.

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7c5fedb0 by Étienne Mollier at 2022-11-04T00:11:26+01:00
d/e/pufferfish: upgrade vendored version for onetbb support.

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fdb2f485 by Étienne Mollier at 2022-11-04T00:12:09+01:00
d/e/i/i/pufferfish: upgrade files.

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4267cd8e by Étienne Mollier at 2022-11-04T00:12:51+01:00
use_debian_packaged_libs.patch: adjust to build through.

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19ecb3f0 by Étienne Mollier at 2022-11-04T00:15:33+01:00
update FIXME in changelog.

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26 changed files:

- .drone.yml
- .drone/build.sh
- .drone/test_quant.sh
- CMakeLists.txt
- + CONTRIBUTING.md
- README.md
- current_version.txt
- debian/changelog
- debian/control
- debian/external/install/include/pufferfish/CommonTypes.hpp
- debian/external/install/include/pufferfish/MemChainer.hpp
- debian/external/install/include/pufferfish/MemCollector.hpp
- debian/external/install/include/pufferfish/PairedAlignmentFormatter.hpp
- debian/external/install/include/pufferfish/ProgOpts.hpp
- debian/external/install/include/pufferfish/SAMWriter.hpp
- debian/external/install/include/pufferfish/Util.hpp
- debian/external/install/include/pufferfish/compact_vector/compact_iterator.hpp
- debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp
- + debian/external/install/include/pufferfish/itlib/dynamic_bitset.hpp
- + debian/external/install/include/pufferfish/itlib/expected.hpp
- + debian/external/install/include/pufferfish/itlib/flat_map.hpp
- + debian/external/install/include/pufferfish/itlib/flat_set.hpp
- + debian/external/install/include/pufferfish/itlib/make_ptr.hpp
- + debian/external/install/include/pufferfish/itlib/mem_streambuf.hpp
- + debian/external/install/include/pufferfish/itlib/memory_view.hpp
- + debian/external/install/include/pufferfish/itlib/mutex.hpp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/5a4686dd4a317d7eca724727b1a34e2577bc5904...19ecb3f06d818b14fbda2d0e6e36a3a2b98c4af6

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View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/5a4686dd4a317d7eca724727b1a34e2577bc5904...19ecb3f06d818b14fbda2d0e6e36a3a2b98c4af6
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