[med-svn] [Git][med-team/metaphlan2][master] 2 commits: Compile with Python2 despite _metaphlan2.py is using Python3 syntax (Thanks to…

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / metaphlan2


Commits:
eef9bbe8 by Andreas Tille at 2018-05-28T15:13:14+02:00
Compile with Python2 despite _metaphlan2.py is using Python3 syntax (Thanks to Tony Travis for the patch)

- - - - -
9d9b7df7 by Andreas Tille at 2018-05-28T15:19:13+02:00
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/_metaphlan2.py.patch
- debian/patches/series
- debian/patches/spelling.patch


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,15 @@
-metaphlan2 (2.7.6-1) UNRELEASED; urgency=medium
+metaphlan2 (2.7.6-1) unstable; urgency=medium
 
+  [ Andreas Tille ]
   * New upstream version
   * Point Vcs fields to salsa.debian.org
   * Standards-Version: 4.1.4
   * Avoid privacy breach by referencing remote files from README.html
 
- -- Andreas Tille <tille at debian.org>  Mon, 28 May 2018 07:27:16 +0200
+  [ Tony Travis ]
+  * Compile with Python2 despite _metaphlan2.py is using Python3 syntax
+
+ -- Andreas Tille <tille at debian.org>  Mon, 28 May 2018 15:13:38 +0200
 
 metaphlan2 (2.7.5-1) unstable; urgency=medium
 


=====================================
debian/patches/_metaphlan2.py.patch
=====================================
--- /dev/null
+++ b/debian/patches/_metaphlan2.py.patch
@@ -0,0 +1,42 @@
+Author: Tony Travis <tony.travis at minke-informatics.co.uk>
+Las-Update: Mon, 28 May 2018 01:36:48 +0100
+Origin: https://lists.debian.org/debian-med/2018/05/msg00071.html
+Description: Compile with Python2 despite _metaphlan2.py is using Python3 syntax
+ The "_metaphlan2.py" file contains Python 3 source but the "postinst"
+ script runs "pycompile" on the Python source files. However, "pycompile"
+ only supports Python version 2. The print() function in "_metaphlan2.py"
+ can be imported from the "__future__" library, but Python 2 does not
+ support function annotations: These are optional in Python 3, and are
+ removed from the function definitions in "_metaphlan2.py" by the patch.
+
+--- a/_metaphlan2.py
++++ b/_metaphlan2.py
+@@ -3,7 +3,7 @@
+ # This module defines the functions which run MetaPhlAn2 on
+ # single and paired fastq data.
+ 
+-
++from __future__ import print_function
+ import subprocess as sb
+ from q2_types.per_sample_sequences import SingleLanePerSampleSingleEndFastqDirFmt
+ from q2_types.per_sample_sequences import SingleLanePerSamplePairedEndFastqDirFmt
+@@ -24,8 +24,7 @@ def metaphlan2_helper(raw_data, nproc, i
+     sb.run(cmd, check=True)
+ 
+ 
+-def profile_single_fastq(raw_data: SingleLanePerSampleSingleEndFastqDirFmt,
+-                         nproc: int=1) -> biom.Table:
++def profile_single_fastq(raw_data, nproc=1):
+     output_biom = None
+ 
+     with tempfile.TemporaryDirectory() as tmp_dir:
+@@ -36,8 +35,7 @@ def profile_single_fastq(raw_data: Singl
+     return output_biom
+ 
+ 
+-def profile_paired_fastq(raw_data: SingleLanePerSamplePairedEndFastqDirFmt,
+-                         nproc: int=1) -> biom.Table:
++def profile_paired_fastq(raw_data, nproc=1):
+     output_biom = None
+ 
+     with tempfile.TemporaryDirectory() as tmp_dir:


=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 mpa_dir-is-usr_share_metaphlan2.patch
 spelling.patch
+_metaphlan2.py.patch


=====================================
debian/patches/spelling.patch
=====================================
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -35,7 +35,7 @@ Description: Spelling
                  'file where each clade name is on a line will be read.'
 --- a/metaphlan2.py
 +++ b/metaphlan2.py
-@@ -597,7 +597,7 @@ def read_params(args):
+@@ -595,7 +595,7 @@ def read_params(args):
           default='rel_ab', help =
           "Type of analysis to perform: \n"
           " * rel_ab: profiling a metagenomes in terms of relative abundances\n"



View it on GitLab: https://salsa.debian.org/med-team/metaphlan2/compare/0d7cca03335bdac7213519c2c3804e245da1ec03...9d9b7df7ff658d2e71f92ff93fe919d83ac79dab

-- 
View it on GitLab: https://salsa.debian.org/med-team/metaphlan2/compare/0d7cca03335bdac7213519c2c3804e245da1ec03...9d9b7df7ff658d2e71f92ff93fe919d83ac79dab
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