debian/changelog

+bedops (2.4.37+dfsg-2) unstable; urgency=medium
+
+  * Team upload.
+  * Depends: s/python/python3/ + fix shebang lines in Python scripts
+    Closes: #948590
+  * Remove trailing whitespace in debian/changelog
+  * Set upstream metadata fields: Bug-Database, Bug-Submit.
+  * Remove obsolete field Name from debian/upstream/metadata (already
+    present in machine-readable debian/copyright).
+
+ -- Andreas Tille <tille@debian.org>  Sat, 11 Jan 2020 07:24:20 +0100
+
 bedops (2.4.37+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -20,7 +20,7 @@ Package: bedops
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         python,
+         python3,
          tcsh
 Description: high-performance genomic feature operations
  BEDOPS is a suite of tools to address common questions raised in genomic

debian/patches/2to3.patch

@@ -4,10 +4,14 @@ Bug-Debian: https://bugs.debian.org/936197
 Last-Update: 2019-09-13
 ---
 
-Index: bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
-===================================================================
---- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
-+++ bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
+--- a/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
++++ b/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ #
+ #    BEDOPS
 @@ -19,7 +19,7 @@
  #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  #
@@ -17,10 +21,14 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.p
  
  import sys
  import os
-Index: bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py
-===================================================================
---- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-slurm.py
-+++ bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py
+--- a/applications/bed/sort-bed/src/update-sort-bed-slurm.py
++++ b/applications/bed/sort-bed/src/update-sort-bed-slurm.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ #
+ #    BEDOPS
 @@ -19,7 +19,7 @@
  #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  #
@@ -30,10 +38,14 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py
  
  import sys
  import os
-Index: bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
-===================================================================
---- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
-+++ bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
+--- a/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
++++ b/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ #
+ #    BEDOPS
 @@ -19,7 +19,7 @@
  #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  #
@@ -43,10 +55,14 @@ Index: bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
  
  import sys
  import os
-Index: bedops/applications/bed/starch/src/starch-diff.py
-===================================================================
---- bedops.orig/applications/bed/starch/src/starch-diff.py
-+++ bedops/applications/bed/starch/src/starch-diff.py
+--- a/applications/bed/starch/src/starch-diff.py
++++ b/applications/bed/starch/src/starch-diff.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ #
+ #    BEDOPS
 @@ -19,7 +19,7 @@
  #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  #
@@ -79,10 +95,14 @@ Index: bedops/applications/bed/starch/src/starch-diff.py
          uncommon_chromosomes.sort()
          if args.debug: logger.info('Uncommon chromosomes [%s]' % (','.join(uncommon_chromosomes)))        
  
-Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
-===================================================================
---- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
-+++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
+--- a/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
++++ b/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import os, sys, subprocess
+ 
 @@ -10,35 +10,35 @@ chr1_proc = subprocess.Popen([unstarch,
  chr1_proc_out, chr1_proc_err = chr1_proc.communicate()
  chr1_proc_out.strip('\n')
@@ -124,10 +144,14 @@ Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/has
      sys.exit(os.EX_USAGE)
  
  sys.exit(os.EX_OK)
-Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
-===================================================================
---- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
-+++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
+--- a/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
++++ b/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import os, sys, subprocess
+ 
 @@ -10,35 +10,35 @@ chr1_proc = subprocess.Popen([unstarch,
  chr1_proc_out, chr1_proc_err = chr1_proc.communicate()
  chr1_proc_out.strip('\n')
@@ -169,10 +193,8 @@ Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/has
      sys.exit(os.EX_USAGE)
  
  sys.exit(os.EX_OK)
-Index: bedops/docs/conf.py
-===================================================================
---- bedops.orig/docs/conf.py
-+++ bedops/docs/conf.py
+--- a/docs/conf.py
++++ b/docs/conf.py
 @@ -42,8 +42,8 @@ source_suffix = '.rst'
  master_doc = 'index'
  
@@ -232,3 +254,38 @@ Index: bedops/docs/conf.py
  
  # The language of the text. It defaults to the language option
  # or en if the language is not set.
+--- a/applications/bed/starch/test/unsortable_elements/src/isUnsortable.py
++++ b/applications/bed/starch/test/unsortable_elements/src/isUnsortable.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import os, sys, subprocess
+ 
+--- a/tests/starch/generate_random_intervals.sh
++++ b/tests/starch/generate_random_intervals.sh
+@@ -6,7 +6,7 @@ maxLength=$3
+ 
+ # rand=$(od -N 4 -t uL -An /dev/urandom | tr -d " ") && rand=$(($rand % 1234))
+ # rand=$(shuf -i 0-${upperBound} -n ${samples})
+-# rand=$(python -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${upperBound})))")
++# rand=$(python3 -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${upperBound})))")
+ 
+ while IFS='' read -r line || [[ -n "$line" ]]; do
+     chr=`printf "$line" | awk '{ print $1 }'`
+@@ -18,10 +18,10 @@ while IFS='' read -r line || [[ -n "$lin
+         # length=$(od -N 4 -t uL -An /dev/urandom | tr -d " ") && length=$(($length % $maxLength))
+         # start=$(shuf -i 0-${adjustedBound} -n 1)
+         # length=$(shuf -i 0-${maxLength} -n 1)
+-        # start=$(python -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${adjustedBound})))")
+-        # length=$(python -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${maxLength})))")
++        # start=$(python3 -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${adjustedBound})))")
++        # length=$(python3 -S -c "import sys; import random; sys.stdout.write(str(random.randrange(0,${maxLength})))")
+         # stop=$(($start + $length + 1))
+         # echo -e "$chr\t$start\t$stop\tid-$chrN-$sample"
+-        echo $(python -S -c "import sys; import random; start=random.randrange(0,${adjustedBound}); length=random.randrange(0,${maxLength}); stop=start+length+1; sys.stdout.write('${chr}\t%s\t%s\tid-${chrN}-${sample}\n' % (start, stop))") | tr " " "\t"
++        echo $(python3 -S -c "import sys; import random; start=random.randrange(0,${adjustedBound}); length=random.randrange(0,${maxLength}); stop=start+length+1; sys.stdout.write('${chr}\t%s\t%s\tid-${chrN}-${sample}\n' % (start, stop))") | tr " " "\t"
+     done
+-done < "${boundsFn}"
+\ No newline at end of file
++done < "${boundsFn}"

debian/upstream/metadata

@@ -2,14 +2,13 @@ Cite-As: |
   Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.
   BEDOPS: high-performance genomic feature operations
   Bioinformatics (2012) 28 (14): 1919-1920.
-Name: bedops
 Reference:
 - Author: >
     Shane Neph and M. Scott Kuehn and Alex P. Reynolds and Eric Haugen and
     Robert E. Thurman and Audra K. Johnson and Eric Rynes and
     Matthew T. Maurano and Jeff Vierstra and Sean Thomas and
     Richard Sandstrom and Richard Humbert and John A. Stamatoyannopoulos
-   Title: "BEDOPS: high-performance genomic feature operations"
+  Title: 'BEDOPS: high-performance genomic feature operations'
   Publisher: Bioinformatics
   Year: 2012
   Volume: 28
@@ -18,8 +17,7 @@ Reference:
   DOI: 10.1093/bioinformatics/bts277
   PMID: 22576172
   URL: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
-   eprint: "https://academic.oup.com/bioinformatics/article-pdf/\
-    28/14/1919/582641/bts277.pdf"
+  eprint: https://academic.oup.com/bioinformatics/article-pdf/28/14/1919/582641/bts277.pdf
 Registry:
 - Name: bio.tools
   Entry: Bedops
@@ -29,3 +27,5 @@ Registry:
   Entry: SCR_012865
 - Name: conda:bioconda
   Entry: bedops
+Bug-Database: https://github.com/bedops/bedops/issues
+Bug-Submit: https://github.com/bedops/bedops/issues/new