[med-svn] [falconkit] 07/09: Drop incompatible patches and rules

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository falconkit.

commit ed8a5e8bdde36c9d4ae568c2e5bf75b4bffcf7db
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Tue Mar 8 23:32:35 2016 -0800

    Drop incompatible patches and rules
---
 debian/docs                            |  1 -
 debian/patches/add-shebang-lines.patch | 12 ------
 debian/patches/python-multiarch.patch  | 77 ----------------------------------
 debian/patches/series                  |  2 -
 debian/rules                           |  5 ---
 5 files changed, 97 deletions(-)

diff --git a/debian/docs b/debian/docs
index eedc49d..b43bf86 100644
--- a/debian/docs
+++ b/debian/docs
@@ -1,2 +1 @@
 README.md
-doc/*.md
diff --git a/debian/patches/add-shebang-lines.patch b/debian/patches/add-shebang-lines.patch
deleted file mode 100644
index bd934d5..0000000
--- a/debian/patches/add-shebang-lines.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-Description: Add shebang lines to executable scripts
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: no
-Last-Update: 2015-12-20
---- falconkit.orig/src/py_scripts/falcon_dedup.py
-+++ falconkit/src/py_scripts/falcon_dedup.py
-@@ -1,3 +1,5 @@
-+#!/usr/bin/python
-+
- import subprocess
- from pbcore.io import FastaReader
- 
diff --git a/debian/patches/python-multiarch.patch b/debian/patches/python-multiarch.patch
deleted file mode 100644
index a1a157b..0000000
--- a/debian/patches/python-multiarch.patch
+++ /dev/null
@@ -1,77 +0,0 @@
-Description: Account for multiarch component in module path name
- Some of the scripts encode the path to the compiled module. The
- original code does not take into account Debian's multiarch renaming.
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: not-needed
-Last-Update: 2015-12-19
---- falconkit.orig/src/py_scripts/falcon_sense.py
-+++ falconkit/src/py_scripts/falcon_sense.py
-@@ -41,11 +41,13 @@
- import sys
- from multiprocessing import Pool
- import os
-+import sysconfig
- import falcon_kit
- 
- module_path = falcon_kit.__path__[0]
- 
--falcon = CDLL(os.path.join(module_path, "falcon.so"))
-+falcon = CDLL(
-+    module_path+os.path.sep+"falcon."+sysconfig.get_config_var('MULTIARCH')+".so")
- 
- falcon.generate_consensus.argtypes = [ POINTER(c_char_p), c_uint, c_uint, c_uint, c_uint, c_uint, c_double ]
- falcon.generate_consensus.restype = POINTER(falcon_kit.ConsensusData)
---- falconkit.orig/src/py_scripts/falcon_utgcns.py
-+++ falconkit/src/py_scripts/falcon_utgcns.py
-@@ -41,11 +41,13 @@
- import sys
- from multiprocessing import Pool
- import os
-+import sysconfig
- import falcon_kit
- 
- module_path = falcon_kit.__path__[0]
- 
--falcon = CDLL(os.path.join(module_path, "falcon.so"))
-+falcon = CDLL(
-+    module_path + os.path.sep + "falcon." + sysconfig.get_config_var('MULTIARCH') + ".so")
- """
- consensus_data * generate_utg_consensus( char ** input_seq, 
-                            seq_coor_t *offset,
---- falconkit.orig/src/py/falcon_kit.py
-+++ falconkit/src/py/falcon_kit.py
-@@ -39,6 +39,8 @@
- 
- from ctypes import *
- import os
-+import sysconfig
-+multiarch = sysconfig.get_config_var('MULTIARCH')
- module_path = os.path.split(__file__)[0]
- 
- 
-@@ -66,7 +68,7 @@
-     _fields_ = [ ("sequence", c_char_p),
-                  ("eff_cov", POINTER(c_uint)) ]
- 
--kup = CDLL(os.path.join(module_path, "kmer_lookup.so"))
-+kup = CDLL(os.path.join(module_path, "kmer_lookup."+multiarch+".so"))
- 
- kup.allocate_kmer_lookup.argtypes =  [seq_coor_t] 
- kup.allocate_kmer_lookup.restype = POINTER(KmerLookup)
-@@ -121,14 +123,14 @@
-                  ("t_aln_str", c_char_p)]
- 
- 
--DWA = CDLL(os.path.join(module_path, "DW_align.so"))
-+DWA = CDLL(os.path.join(module_path, "DW_align."+multiarch+".so"))
- DWA.align.argtypes = [ POINTER(c_char), c_long, POINTER(c_char), c_long, c_long, c_int ] 
- DWA.align.restype = POINTER(Alignment)
- DWA.free_alignment.argtypes = [POINTER(Alignment)]
- 
- 
- 
--falcon = CDLL(os.path.join(module_path,"falcon.so"))
-+falcon = CDLL(os.path.join(module_path,"falcon."+multiarch+".so"))
- 
- falcon.generate_consensus.argtypes = [POINTER(c_char_p), c_uint, c_uint, c_uint, c_uint, c_uint, c_double  ]
- falcon.generate_consensus.restype = POINTER(ConsensusData)
diff --git a/debian/patches/series b/debian/patches/series
index bf91044..e69de29 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +0,0 @@
-add-shebang-lines.patch
-python-multiarch.patch
diff --git a/debian/rules b/debian/rules
index a7cfaed..7eed105 100755
--- a/debian/rules
+++ b/debian/rules
@@ -22,8 +22,3 @@ override_dh_link:
 	$(call link-man,falconkit,falconkit.1,$$script.1); \
 	done
 	dh_link
-
-override_dh_fixperms:
-	chmod -x debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples/HBAR.cfg
-	chmod -x debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples/test_data/*.fofn
-	dh_fixperms

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