[med-svn] [Git][med-team/spades][master] 3 commits: Move source package lintian overrides to debian/source.

Andreas Tille gitlab at salsa.debian.org
Tue Nov 12 16:12:00 GMT 2019 


Andreas Tille pushed to branch master at Debian Med / spades


Commits:
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.

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

- - - - -


5 changed files:

- debian/changelog
- + debian/patches/python3.patch
- debian/patches/series
- debian/source.lintian-overrides → debian/source/lintian-overrides
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -6,6 +6,9 @@ spades (3.13.1-1) UNRELEASED; urgency=medium
   * New upstream version
   * debhelper-compat 12
   * Standards-Version: 4.4.1
+  * Move source package lintian overrides to debian/source.
+  * Set upstream metadata fields: Repository.
+  * Make sure Python3 interpreter is used in scripts
 
  -- Andreas Tille <tille at debian.org>  Tue, 08 Oct 2019 18:17:07 +0200
 


=====================================
debian/patches/python3.patch
=====================================
@@ -0,0 +1,338 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 12 Nov 2019 17:11:17 +0100
+Description: Make sure Python3 interpreter is used in scripts
+
+--- a/assembler/changer_of_K.py
++++ b/assembler/changer_of_K.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import os
+ import shutil
+--- a/assembler/spades.py
++++ b/assembler/spades.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/spades_init.py
++++ b/assembler/spades_init.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/spades_pipeline/easy_align.py
++++ b/assembler/src/spades_pipeline/easy_align.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import os
+ import sys
+ 
+--- a/assembler/src/spades_pipeline/process_cfg.py
++++ b/assembler/src/spades_pipeline/process_cfg.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py
++++ b/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/truspades.py
++++ b/assembler/truspades.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/projects/mts/scripts/bin_profiles.py
++++ b/assembler/src/projects/mts/scripts/bin_profiles.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ from __future__ import (print_function)
+ 
+ import pandas
+--- a/assembler/src/spades_pipeline/hammer_logic.py
++++ b/assembler/src/spades_pipeline/hammer_logic.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/spades_pipeline/options_storage.py
++++ b/assembler/src/spades_pipeline/options_storage.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/spades_pipeline/run_contig_breaker.py
++++ b/assembler/src/spades_pipeline/run_contig_breaker.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/spades_pipeline/truspades/break_by_coverage.py
++++ b/assembler/src/spades_pipeline/truspades/break_by_coverage.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/projects/mts/scripts/split_bins.py
++++ b/assembler/src/projects/mts/scripts/split_bins.py
+@@ -1,5 +1,4 @@
+-#!/usr/bin/env python
+-from __future__ import print_function
++#!/usr/bin/python3
+ 
+ from operator import itemgetter
+ import os
+--- a/assembler/src/spades_pipeline/spades_logic.py
++++ b/assembler/src/spades_pipeline/spades_logic.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/spades_pipeline/truspades/reference_construction.py
++++ b/assembler/src/spades_pipeline/truspades/reference_construction.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/test/cap/tests/synthetic/test_generator.py
++++ b/assembler/src/test/cap/tests/synthetic/test_generator.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/projects/mts/scripts/choose_samples.py
++++ b/assembler/src/projects/mts/scripts/choose_samples.py
+@@ -1,5 +1,4 @@
+-#!/usr/bin/env python
+-from __future__ import (print_function)
++#!/usr/bin/python3
+ 
+ import argparse
+ from operator import itemgetter
+--- a/assembler/src/projects/mts/scripts/clusters2csv.py
++++ b/assembler/src/projects/mts/scripts/clusters2csv.py
+@@ -1,5 +1,4 @@
+-#!/usr/bin/env python
+-from __future__ import print_function
++#!/usr/bin/python3
+ import sys
+ 
+ from Bio import SeqIO
+--- a/assembler/src/projects/mts/scripts/combine_contigs.py
++++ b/assembler/src/projects/mts/scripts/combine_contigs.py
+@@ -1,5 +1,4 @@
+-#!/usr/bin/env python
+-from __future__ import print_function
++#!/usr/bin/python3
+ import sys
+ import os
+ import os.path
+--- a/assembler/src/projects/mts/scripts/multi_stats.py
++++ b/assembler/src/projects/mts/scripts/multi_stats.py
+@@ -1,5 +1,4 @@
+-#!/usr/bin/env python
+-from __future__ import (print_function)
++#!/usr/bin/python3
+ 
+ import argparse
+ import os
+--- a/assembler/src/spades_pipeline/support.py
++++ b/assembler/src/spades_pipeline/support.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015-2016 Saint Petersburg State University
+--- a/assembler/src/projects/mts/scripts/cut_fasta.py
++++ b/assembler/src/projects/mts/scripts/cut_fasta.py
+@@ -1,7 +1,6 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ """Cut up fasta file in non-overlapping or overlapping parts of equal length.
+ """
+-from __future__ import print_function
+ import argparse
+ import sys
+ from Bio import SeqIO
+--- a/assembler/src/projects/mts/scripts/bhtsne.py
++++ b/assembler/src/projects/mts/scripts/bhtsne.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ '''
+ A simple Python wrapper for the bh_tsne binary that makes it easier to use it
+--- a/assembler/src/projects/mts/scripts/choose_bins.py
++++ b/assembler/src/projects/mts/scripts/choose_bins.py
+@@ -1,5 +1,4 @@
+-#!/usr/bin/env python
+-from __future__ import (print_function)
++#!/usr/bin/python3
+ 
+ import re
+ import sys
+--- a/assembler/src/projects/mts/scripts/subsample.py
++++ b/assembler/src/projects/mts/scripts/subsample.py
+@@ -1,5 +1,4 @@
+-#!/usr/bin/env python
+-from __future__ import (print_function)
++#!/usr/bin/python3
+ 
+ import argparse
+ import gzip
+--- a/assembler/src/projects/mts/multirun.py
++++ b/assembler/src/projects/mts/multirun.py
+@@ -1,5 +1,4 @@
+-#!/usr/bin/env python
+-from __future__ import (print_function)
++#!/usr/bin/python3
+ 
+ import argparse
+ import os
+--- a/assembler/src/projects/mts/scripts/contig_name_filter.py
++++ b/assembler/src/projects/mts/scripts/contig_name_filter.py
+@@ -1,5 +1,4 @@
+-#!/usr/bin/env python
+-from __future__ import print_function
++#!/usr/bin/python3
+ 
+ import sys
+ from Bio import SeqIO
+--- a/assembler/src/projects/mts/scripts/gather_stats.py
++++ b/assembler/src/projects/mts/scripts/gather_stats.py
+@@ -1,5 +1,4 @@
+-#!/usr/bin/env python
+-from __future__ import (print_function)
++#!/usr/bin/python3
+ 
+ import argparse
+ from collections import OrderedDict
+--- a/assembler/src/tools/misc/copyrighter.py
++++ b/assembler/src/tools/misc/copyrighter.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/misc/datasets_converter.py
++++ b/assembler/src/tools/misc/datasets_converter.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/misc/datasets_info2yaml_converter.py
++++ b/assembler/src/tools/misc/datasets_info2yaml_converter.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/misc/sv_simulator.py
++++ b/assembler/src/tools/misc/sv_simulator.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/crop/crop_bfaecium.py
++++ b/assembler/src/tools/reads_utils/crop/crop_bfaecium.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/projects/mts/mts.py
++++ b/assembler/src/projects/mts/mts.py
+@@ -1,5 +1,4 @@
+-#!/usr/bin/env python
+-from __future__ import (print_function)
++#!/usr/bin/python3
+ 
+ import argparse
+ import subprocess
+--- a/assembler/src/tools/misc/assembler_runner/runner.py
++++ b/assembler/src/tools/misc/assembler_runner/runner.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/misc/txt2gff.py
++++ b/assembler/src/tools/misc/txt2gff.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/reads_utils/ideal_by_fasta.py
++++ b/assembler/src/tools/reads_utils/ideal_by_fasta.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/truseq/quast_all.py
++++ b/assembler/src/tools/truseq/quast_all.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/misc/datasets_info_cleaner.py
++++ b/assembler/src/tools/misc/datasets_info_cleaner.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University
+--- a/assembler/src/tools/spades_pipeline/spades_download_binary.py
++++ b/assembler/src/tools/spades_pipeline/spades_download_binary.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ ############################################################################
+ # Copyright (c) 2015 Saint Petersburg State University


=====================================
debian/patches/series
=====================================
@@ -18,3 +18,4 @@
 fix-bool-cast
 spelling
 gcc7.patch
+python3.patch


=====================================
debian/source.lintian-overrides → debian/source/lintian-overrides
=====================================


=====================================
debian/upstream/metadata
=====================================
@@ -1,39 +1,40 @@
 Reference:
- - Author: >
+- Author: >
     Anton Bankevich and Sergey Nurk and Dmitry Antipov and Alexey
     A. Gurevich and Mikhail Dvorkin and Alexander S. Kulikov and Valery
     M. Lesin and Sergey I. Nikolenko and Son Pham and Andrey D. Prjibelski
     and Alexey V. Pyshkin and Alexander V. Sirotkin and Nikolay Vyahhi
     and Glenn Tesler and Max A. Alekseyev and Pavel A. Pevzner
-   Title: >
+  Title: >
     SPAdes: A New Genome Assembly Algorithm and Its Applications to
     Single-Cell Sequencing
-   Journal: Journal of Computational Biology
-   Year: 2012
-   Volume: 19
-   Number: 5
-   Pages: 455-477
-   DOI: 10.1089/cmb.2012.0021
-   PMID: 22506599
-   URL: http://online.liebertpub.com/doi/abs/10.1089/cmb.2012.0021
-   eprint: http://online.liebertpub.com/doi/pdfplus/10.1089/cmb.2012.0021
- - Author: >
+  Journal: Journal of Computational Biology
+  Year: 2012
+  Volume: 19
+  Number: 5
+  Pages: 455-477
+  DOI: 10.1089/cmb.2012.0021
+  PMID: 22506599
+  URL: http://online.liebertpub.com/doi/abs/10.1089/cmb.2012.0021
+  eprint: http://online.liebertpub.com/doi/pdfplus/10.1089/cmb.2012.0021
+- Author: >
     Sergey Nurk and Anton Bankevich and Dmitry Antipov and Alexey Gurevich
     and Anton Korobeynikov and Alla Lapidus and Andrey Prjibelsky and
     Alexey Pyshkin and Alexander Sirotkin and Yakov Sirotkin and Ramunas
     Stepanauskas and Jeffrey McLean and Roger Lasken and Scott Clingenpeel
     and Tanja Woyke and Glenn Tesler and Max Alekseyev and Pavel Pevzner
-   Title: Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads
-   Journal: Lecture Notes in Computer Science
-   Year: 2013
-   Volume: 7821
-   Pages: 158-170
-   DOI: 10.1007/978-3-642-37195-0_13
-   URL: http://link.springer.com/chapter/10.1007%2F978-3-642-37195-0_13
+  Title: Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads
+  Journal: Lecture Notes in Computer Science
+  Year: 2013
+  Volume: 7821
+  Pages: 158-170
+  DOI: 10.1007/978-3-642-37195-0_13
+  URL: http://link.springer.com/chapter/10.1007%2F978-3-642-37195-0_13
 Registry:
- - Name: SciCrunch
-   Entry: SCR_000131
- - Name: OMICtools
-   Entry: OMICS_01502
- - Name: bio.tools
-   Entry: Spades
+- Name: SciCrunch
+  Entry: SCR_000131
+- Name: OMICtools
+  Entry: OMICS_01502
+- Name: bio.tools
+  Entry: Spades
+Repository: https://github.com/ablab/spades



View it on GitLab: https://salsa.debian.org/med-team/spades/compare/e4717a4a8786577e154a6af8d1f6a4a17e8f2573...533d1e6ed64dde7804e75a149d1eb45661081e2a

-- 
View it on GitLab: https://salsa.debian.org/med-team/spades/compare/e4717a4a8786577e154a6af8d1f6a4a17e8f2573...533d1e6ed64dde7804e75a149d1eb45661081e2a
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