[med-svn] [circlator] 04/07: Drop all patches - no longer required

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository circlator.

commit d34111fec99357a4425c7bcfc7ab87f65456b8be
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Aug 15 20:56:34 2016 -0700

    Drop all patches - no longer required
    
    * Upstream no longer caps the pysam version dependency.
    * The spades executable is not called by specifying the python interpreter anymore.
---
 debian/patches/pysam-maxversion.patch | 17 -----------------
 debian/patches/series                 |  2 --
 debian/patches/spades-call.patch      | 18 ------------------
 3 files changed, 37 deletions(-)

diff --git a/debian/patches/pysam-maxversion.patch b/debian/patches/pysam-maxversion.patch
deleted file mode 100644
index a318447..0000000
--- a/debian/patches/pysam-maxversion.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Description: Don't restrict pysam max version
- circlator presumably works with pysam 0.9.0, but blocks it
- because pip has issues installing it.
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: not-needed
-Last-Update: 2016-04-23
---- circlator.orig/setup.py
-+++ circlator/setup.py
-@@ -20,7 +20,7 @@
-     install_requires=[
-         'openpyxl',
-         'pyfastaq >= 3.12.1',
--        'pysam >= 0.8.1, <= 0.8.3',
-+        'pysam >= 0.8.1',
-         'pymummer>=0.7.1',
-     ],
-     license='GPLv3',
diff --git a/debian/patches/series b/debian/patches/series
index fe47d41..e69de29 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +0,0 @@
-spades-call.patch
-pysam-maxversion.patch
diff --git a/debian/patches/spades-call.patch b/debian/patches/spades-call.patch
deleted file mode 100644
index 665b953..0000000
--- a/debian/patches/spades-call.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Description: Fix the way spades is called by circlator
- The wrapper script in the Debian packaged spades fails when called
- as "python2 /usr/bin/spades.py". Our shebang lines handle the interpreter,
- so circlator should only be concerned with calling spades directly.
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: no
-Last-Update: 2016-03-18
---- circlator.orig/circlator/external_progs.py
-+++ circlator/circlator/external_progs.py
-@@ -14,7 +14,7 @@
- # This means we need to explicitly run SPAdes with python2.
- class Spades(program.Program):
-     def exe(self):
--        return 'python2 ' + shutil.which(self.path)
-+        return shutil.which(self.path)
- 
- 
- prog_to_env_var = {

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/circlator.git