[med-svn] [Git][med-team/spades][debian/stretch-backports] 51 commits: New upstream version 3.13.0+dfsg

[Andreas Tille]

Andreas Tille pushed to branch debian/stretch-backports at Debian Med / spades


Commits:
67452d60 by Andreas Tille at 2018-10-16T18:45:31Z
New upstream version 3.13.0+dfsg
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827aee0c by Andreas Tille at 2018-10-16T18:45:36Z
Update upstream source from tag 'upstream/3.13.0+dfsg'

Update to upstream version '3.13.0+dfsg'
with Debian dir 0768d131941f4e8144c7690f47cd52076e696ede
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c2d2816c by Andreas Tille at 2018-10-16T18:45:36Z
New upstream version

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29f8a294 by Andreas Tille at 2018-10-16T18:59:27Z
Adapt patches

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f15cc256 by Andreas Tille at 2018-10-16T19:45:06Z
Upstream has removed dipspades

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52e4cb3d by Andreas Tille at 2018-10-16T20:05:06Z
Remove some more dipspades references

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80a7ae0f by Andreas Tille at 2018-10-16T20:07:33Z
Really remove all dipspades references

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be18902a by Andreas Tille at 2018-10-16T20:23:08Z
Upload to unstable

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0f9831fe by Michael R. Crusoe at 2019-01-17T11:20:08Z
restore bundled jemalloc

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e1e4b751 by Michael R. Crusoe at 2019-01-17T11:21:14Z
New upstream version 3.13.0+dfsg2
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7040094c by Michael R. Crusoe at 2019-01-17T11:21:22Z
Update upstream source from tag 'upstream/3.13.0+dfsg2'

Update to upstream version '3.13.0+dfsg2'
with Debian dir a6b95c5dd1db70925d6ad61004cd3a3d9d6c1620
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5e5971a3 by Michael R. Crusoe at 2019-01-17T11:28:51Z
restore bundled jemalloc part 2

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69116e78 by Michael R. Crusoe at 2019-01-17T15:43:33Z
Pull releases from GitHib.

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0ad9955c by Michael R. Crusoe at 2019-01-17T15:43:34Z
Standards-Version: 4.3.0 (no changes needed)

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5e3dfc55 by Michael R. Crusoe at 2019-01-17T15:46:45Z
Install README.md to /usr/share/doc/spades/

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4ba8e0c5 by Michael R. Crusoe at 2019-01-17T15:54:56Z
upload to unstable

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e709085c by Michael R. Crusoe at 2019-01-17T18:13:22Z
Also remove jemalloc from (build-)depends.

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2e3b2cfb by Andreas Tille at 2019-10-08T15:39:30Z
Fix watch file

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365d0ad3 by Andreas Tille at 2019-10-08T15:41:16Z
Moved packaging to Python3

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5937a0b3 by Andreas Tille at 2019-10-08T16:17:07Z
New upstream version

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05939cac by Andreas Tille at 2019-10-08T16:17:09Z
New upstream version 3.13.1
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d3f6d486 by Andreas Tille at 2019-10-08T16:17:30Z
Update upstream source from tag 'upstream/3.13.1'

Update to upstream version '3.13.1'
with Debian dir 6e303cab55c3681c9ae6371ba96d9f210790afde
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b1626032 by Andreas Tille at 2019-10-08T16:17:31Z
debhelper-compat 12

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5da42bf6 by Andreas Tille at 2019-10-08T17:41:13Z
Standards-Version: 4.4.1

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89bd17cf by Andreas Tille at 2019-10-08T17:54:04Z
All original code was moved to subdir assembler - reflect this move in quilt patches

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e4717a4a by Andreas Tille at 2019-10-08T18:27:23Z
Respect move to dir assembler

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95087a4a by Andreas Tille at 2019-11-12T15:27:17Z
Move source package lintian overrides to debian/source.

Fixes lintian: package-uses-deprecated-source-override-location
See https://lintian.debian.org/tags/package-uses-deprecated-source-override-location.html for more details.

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4740e25f by Andreas Tille at 2019-11-12T15:27:23Z
Set upstream metadata fields: Repository.
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533d1e6e by Andreas Tille at 2019-11-12T16:11:40Z
Make sure Python3 interpreter is used in scripts

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2a1a3c6d by Andreas Tille at 2019-11-12T17:57:21Z
Specify yaml loader

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54bc9d00 by Andreas Tille at 2019-11-12T18:12:30Z
Hopefully fix

  File "/build/spades-3.13.1/install_spades/../../share/spades/spades_pipeline/spades_logic.
    for src, target in replacements.iteritems():
AttributeError: 'dict' object has no attribute 'iteritems'

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9207cab9 by Andreas Tille at 2019-11-12T18:13:25Z
Build-Depends: s/python-all-dev/python3-dev/

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3b3309c0 by Andreas Tille at 2019-11-13T13:24:53Z
Fix pyyaml patch

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639914be by Andreas Tille at 2019-11-13T13:25:13Z
Fix Python3 patch

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68470522 by Andreas Tille at 2019-11-13T14:32:17Z
More yaml.load issues fixed

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0c6e72d1 by Andreas Tille at 2019-11-13T15:29:31Z
Fix location of docs

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6cd83d99 by Andreas Tille at 2019-11-17T18:35:46Z
Fix changelog creation

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14ca7cff by Andreas Tille at 2019-11-17T18:40:44Z
New upstream version 3.13.1+dfsg
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3e3bdaeb by Andreas Tille at 2019-11-17T22:30:40Z
Drop ioncommunity and webvis dir from source which has compressed JS but its not used in the binary package

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f1ec307f by Andreas Tille at 2019-11-17T22:31:25Z
New upstream version 3.13.1+dfsg
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4e682ce0 by Andreas Tille at 2019-11-18T10:18:53Z
Adapt to new file locations

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89b1e879 by Andreas Tille at 2019-11-18T10:19:29Z
New upstream version 3.13.1+dfsg
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84e500a0 by Andreas Tille at 2019-11-18T10:19:38Z
Update upstream source from tag 'upstream/3.13.1+dfsg'

Update to upstream version '3.13.1+dfsg'
with Debian dir 4c0a5468bd150dffa327b94735c6892128fcea9a
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2dd0d58b by Andreas Tille at 2019-11-18T13:21:18Z
Lots of more python to python3 conversions

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c224015a by Andreas Tille at 2019-11-18T14:33:14Z
Integer division in Python3

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927512e6 by Andreas Tille at 2019-11-18T15:03:15Z
Upload to unstable

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f24b7807 by Andreas Tille at 2019-11-22T09:48:29Z
Depends: python3-distutils

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9b2cb3ca by Andreas Tille at 2019-11-22T09:48:54Z
Upload to unstable

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768be6ee by Andreas Tille at 2019-11-24T20:00:07Z
Merge tag 'debian/3.13.1+dfsg-2' into debian/stretch-backports

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46034a86 by Andreas Tille at 2019-11-24T20:01:45Z
Rebuild for stretch-backports-sloppy

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ca6d9c2b by Andreas Tille at 2019-11-27T14:30:17Z
Stretch has python3-distutils-extra

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30 changed files:

- + .gitignore
- − LICENSE
- − README
- + README.md
- − VERSION
- + assembler/.gitignore
- GPLv2.txt → assembler/GPLv2.txt
- + assembler/LICENSE
- + assembler/VERSION
- + assembler/changelog.html
- + assembler/changer_of_K.py
- + assembler/compare_saves.sh
- + assembler/configs/.gitignore
- configs/cap/gaf.info → assembler/configs/cap/gaf.info
- configs/cclean/config.info → assembler/configs/cclean/config.info
- configs/corrector/corrector.info → assembler/configs/corrector/corrector.info
- configs/corrector/log.properties → assembler/configs/corrector/log.properties
- configs/debruijn/careful_mda_mode.info → assembler/configs/debruijn/careful_mda_mode.info
- configs/debruijn/careful_mode.info → assembler/configs/debruijn/careful_mode.info
- + assembler/configs/debruijn/config.info
- configs/debruijn/construction.info → assembler/configs/debruijn/construction.info
- configs/debruijn/detail_info_printer.info → assembler/configs/debruijn/detail_info_printer.info
- configs/debruijn/distance_estimation.info → assembler/configs/debruijn/distance_estimation.info
- configs/debruijn/large_genome_mode.info → assembler/configs/debruijn/large_genome_mode.info
- + assembler/configs/debruijn/log.properties
- configs/debruijn/mda_mode.info → assembler/configs/debruijn/mda_mode.info
- configs/debruijn/meta_mode.info → assembler/configs/debruijn/meta_mode.info
- configs/debruijn/moleculo_mode.info → assembler/configs/debruijn/moleculo_mode.info
- + assembler/configs/debruijn/pe_params.info
- configs/debruijn/plasmid_mode.info → assembler/configs/debruijn/plasmid_mode.info


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/spades/compare/77e69f048847fc0f6efa9678664ae8955e104fef...ca6d9c2bcd8cc26273c0de26b1d6c7c9d5733c29

-- 
View it on GitLab: https://salsa.debian.org/med-team/spades/compare/77e69f048847fc0f6efa9678664ae8955e104fef...ca6d9c2bcd8cc26273c0de26b1d6c7c9d5733c29
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