[med-svn] [Git][med-team/libvcflib][master] 3 commits: Use 2to3 to port to Python3
Andreas Tille
gitlab at salsa.debian.org
Fri Sep 6 08:22:56 BST 2019
Andreas Tille pushed to branch master at Debian Med / libvcflib
Commits:
34d8c469 by Andreas Tille at 2019-09-06T07:02:28Z
Use 2to3 to port to Python3
- - - - -
26723664 by Andreas Tille at 2019-09-06T07:05:37Z
Use markdown instead of python-markdown
- - - - -
5c94992b by Andreas Tille at 2019-09-06T07:11:52Z
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+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 at 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
=====================================
@@ -0,0 +1,103 @@
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/936930
+Author: Andreas Tille <tille at 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)))
View it on GitLab: https://salsa.debian.org/med-team/libvcflib/compare/988c8c63c12ade6bbc1fe2653c1af9eee4054ac1...5c94992bd9ce95528e72d7ea4aa06d8b28431767
--
View it on GitLab: https://salsa.debian.org/med-team/libvcflib/compare/988c8c63c12ade6bbc1fe2653c1af9eee4054ac1...5c94992bd9ce95528e72d7ea4aa06d8b28431767
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