[med-svn] [Git][med-team/transdecoder][master] 6 commits: Use 2to3 to port from Python2 to Python3

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / transdecoder


Commits:
483b43b4 by Andreas Tille at 2020-01-10T12:03:01+01:00
Use 2to3 to port from Python2 to Python3

- - - - -
86f127aa by Andreas Tille at 2020-01-10T12:03:28+01:00
Depends: python3

- - - - -
da52634e by Andreas Tille at 2020-01-10T12:04:37+01:00
routine-update: debhelper-compat 12

- - - - -
ee5837e9 by Andreas Tille at 2020-01-10T12:04:44+01:00
routine-update: Standards-Version: 4.4.1

- - - - -
585dd9de by Andreas Tille at 2020-01-10T12:04:54+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
- - - - -
d1ab1efb by Andreas Tille at 2020-01-10T12:21:17+01:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+transdecoder (5.0.1-3) unstable; urgency=medium
+
+  * Use 2to3 to port from Python2 to Python3
+    Closes: #945719
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+
+ -- Andreas Tille <tille at debian.org>  Fri, 10 Jan 2020 12:04:54 +0100
+
 transdecoder (5.0.1-2) unstable; urgency=medium
 
   * Point Vcs fields to salsa.debian.org


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -4,9 +4,9 @@ Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                liburi-perl
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/transdecoder
 Vcs-Git: https://salsa.debian.org/med-team/transdecoder.git
 Homepage: https://transdecoder.github.io/
@@ -17,7 +17,7 @@ Depends: ${misc:Depends},
          ${perl:Depends},
          liburi-perl,
          r-base-core,
-         python
+         python3
 Description: find coding regions within RNA transcript sequences
  TransDecoder identifies candidate coding regions within transcript sequences,
  such as those generated by de novo RNA-Seq transcript assembly using Trinity,


=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,41 @@
+Description: Use 2to3 to port from Python2 to Python3
+Bug-Debian: https://bugs.debian.org/945719
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 10 Jan 2020 12:00:47 +0100
+
+--- a/util/misc/get_FP_FN_scores.py
++++ b/util/misc/get_FP_FN_scores.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import os, sys, re
+ 
+--- a/util/misc/plot_indiv_seq_likelihood_profile.py
++++ b/util/misc/plot_indiv_seq_likelihood_profile.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import os,sys
+ import re
+@@ -39,9 +39,9 @@ def main():
+         score_vec.sort()
+ 
+     if args.cumsum:
+-        plt.plot(range(1,len(score_vec)+1), np.cumsum(score_vec), marker ='o')
++        plt.plot(list(range(1,len(score_vec)+1)), np.cumsum(score_vec), marker ='o')
+     else:
+-        plt.plot(range(1,len(score_vec)+1), score_vec, marker ='+')
++        plt.plot(list(range(1,len(score_vec)+1)), score_vec, marker ='+')
+     
+     
+     plt.show()
+--- a/util/misc/select_TD_orfs.py
++++ b/util/misc/select_TD_orfs.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import sys, os, re
+ import collections


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 fix-whatis
 reproducible-sample_data.patch
+2to3.patch


=====================================
debian/upstream/metadata
=====================================
@@ -1,9 +1,13 @@
 Registry:
- - Name: OMICtools
-   Entry: OMICS_10852
- - Name: SciCrunch
-   Entry: NA
- - Name: bio.tools
-   Entry: NA
- - Name: conda:bioconda
-   Entry: transdecoder
+- Name: OMICtools
+  Entry: OMICS_10852
+- Name: SciCrunch
+  Entry: NA
+- Name: bio.tools
+  Entry: NA
+- Name: conda:bioconda
+  Entry: transdecoder
+Bug-Database: https://github.com/TransDecoder/Transdecoder/issues
+Bug-Submit: https://github.com/TransDecoder/Transdecoder/issues/new
+Repository: https://github.com/TransDecoder/Transdecoder.git
+Repository-Browse: https://github.com/TransDecoder/Transdecoder



View it on GitLab: https://salsa.debian.org/med-team/transdecoder/compare/d20e0b3109d70efe743cbda7aa26cf0c8396ea37...d1ab1efbc3d407ec6797455b64962678a00f68e5

-- 
View it on GitLab: https://salsa.debian.org/med-team/transdecoder/compare/d20e0b3109d70efe743cbda7aa26cf0c8396ea37...d1ab1efbc3d407ec6797455b64962678a00f68e5
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