debian/changelog

+libvcflib (1.0.0+dfsg-2) unstable; urgency=medium
+
+  * Use 2to3 to port to Python3
+    Closes: #936930
+  * Use markdown instead of python-markdown
+
+ -- Andreas Tille <tille@debian.org>  Fri, 06 Sep 2019 09:05:48 +0200
+
 libvcflib (1.0.0+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
                dh-exec,
-               python-markdown,
+               markdown,
                libtabixpp-dev,
                libbz2-dev,
                libdisorder-dev,
@@ -71,7 +71,7 @@ Package: libvcflib-tools
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         python,
+         python3,
          r-base-core,
          r-cran-plyr,
          r-cran-ggplot2,

debian/patches/2to3.patch

+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/936930
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 05 Sep 2019 17:07:24 +0200
+
+--- a/README.md
++++ b/README.md
+@@ -108,7 +108,7 @@ vcflib provides a variety of functions f
+  * **Classify variants** by annotations in the INFO field using a self-organizing map ([vcfsom](#vcfsom)); **re-estimate their quality** given known variants.
+ 
+ 
+-A number of "helper" perl and python scripts (e.g. vcf2bed.py, vcfbiallelic) further extend functionality.
++A number of "helper" perl and python3 scripts (e.g. vcf2bed.py, vcfbiallelic) further extend functionality.
+ 
+ In practice, users are encouraged to drive the utilities in the library in a streaming fashion, using pipes, to fully utilize resources on multi-core systems during interactive work.  Piping provides a convenient method to interface with other libraries (vcf-tools, BedTools, GATK, htslib, bcftools, freebayes) which interface via VCF files, allowing the composition of an immense variety of processing functions.
+ 
+@@ -135,7 +135,7 @@ To build, use Make:
+     % make
+ 
+ Executables are built into the ./bin directory in the repository.
+-A number of shell, perl, python, and R scripts already reside there.
++A number of shell, perl, python3, and R scripts already reside there.
+ This makes installation easy, as users can add vcflib/bin to their path, or copy the contained executables to a directory already in their path.
+ 
+ 
+--- a/scripts/vcf2bed.py
++++ b/scripts/vcf2bed.py
+@@ -1,5 +1,5 @@
+-#!/usr/bin/env python
+-from __future__ import print_function
++#!/usr/bin/python3
++
+ import sys
+ 
+ for line in sys.stdin:
+--- a/scripts/vcf2sqlite.py
++++ b/scripts/vcf2sqlite.py
+@@ -1,5 +1,5 @@
+-#!/usr/bin/env python
+-from __future__ import print_function
++#!/usr/bin/python3
++
+ import sys
+ import re
+ import sqlite3
+@@ -93,7 +93,7 @@ for line in sys.stdin:
+                 pair = pair.split("=")
+                 key = pair[0]
+                 value = pair[1]
+-                if not infonumbers.has_key(key):
++                if key not in infonumbers:
+                     continue
+                 if infonumbers[key] == -1:
+                     values = value.split(",")
+@@ -105,7 +105,7 @@ for line in sys.stdin:
+         ordered_insertion = []
+         for field in sorted_fields:
+             value = "null"
+-            if info_values.has_key(field):
++            if field in info_values:
+                 value = info_values[field]
+                 if infotypes[field] == "String":
+                     value = "\'" + value + "\'"
+--- a/scripts/vcfclearid
++++ b/scripts/vcfclearid
+@@ -1,5 +1,5 @@
+-#!/usr/bin/env python
+-from __future__ import print_function
++#!/usr/bin/python3
++
+ import sys
+ 
+ for line in sys.stdin:
+--- a/scripts/vcfclearinfo
++++ b/scripts/vcfclearinfo
+@@ -1,5 +1,5 @@
+-#!/usr/bin/env python
+-from __future__ import print_function
++#!/usr/bin/python3
++
+ import sys
+ 
+ for line in sys.stdin:
+--- a/scripts/vcffirstheader
++++ b/scripts/vcffirstheader
+@@ -1,5 +1,5 @@
+-#!/usr/bin/env python
+-from __future__ import print_function
++#!/usr/bin/python3
++
+ import sys
+ 
+ header=True
+--- a/scripts/vcfnulldotslashdot
++++ b/scripts/vcfnulldotslashdot
+@@ -1,5 +1,5 @@
+-#!/usr/bin/env python
+-from __future__ import print_function, division
++#!/usr/bin/python3
++
+ import sys
+ import math
+ 

debian/patches/series

@@ -14,3 +14,4 @@ dont_link_pthread
 override_version
 hardening-flags
 spelling
+2to3.patch

debian/rules

@@ -19,7 +19,7 @@ override_dh_clean:
 
 override_dh_auto_build:
 	dh_auto_build
-	markdown_py -f README.html README.md
+	markdown README.md > README.html
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))