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@debian.org>  Tue, 08 Oct 2019 18:17:07 +0200
 

debian/patches/python3.patch

+Author: Andreas Tille <tille@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/upstream/metadata

@@ -37,3 +37,4 @@ Registry:
   Entry: OMICS_01502
 - Name: bio.tools
   Entry: Spades
+Repository: https://github.com/ablab/spades