[med-svn] [falconkit] 01/02: Make the v0.1 scripts work with the compiled extension

[Afif Elghraoui]

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

afif-guest pushed a commit to branch master
in repository falconkit.

commit 4310a4a902c1ef283c059c2335732c444a1a14b3
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sat Dec 19 22:02:59 2015 -0800

    Make the v0.1 scripts work with the compiled extension
---
 debian/patches/adjust-extension-name.patch | 29 ++++++++++++++++++++++
 debian/patches/python-multiarch.patch      | 40 ++++++++++++++++++++++++++++++
 debian/patches/series                      |  2 ++
 3 files changed, 71 insertions(+)

diff --git a/debian/patches/adjust-extension-name.patch b/debian/patches/adjust-extension-name.patch
new file mode 100644
index 0000000..0b6d893
--- /dev/null
+++ b/debian/patches/adjust-extension-name.patch
@@ -0,0 +1,29 @@
+Description: Adjust the name of the compiled extension for new version
+ The extension's name has changed from "falcon" to "ext_falcon".
+ The v0.1 scripts are not maintained anymore, so did not account
+ for this.
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: no
+Last-Update: 2015-12-19
+--- falconkit.orig/src/py_scripts_v0.1/falcon_sense.py
++++ falconkit/src/py_scripts_v0.1/falcon_sense.py
+@@ -45,7 +45,7 @@
+ 
+ module_path = falcon_kit.__path__[0]
+ 
+-falcon = CDLL(os.path.join(module_path, "falcon.so"))
++falcon = CDLL(os.path.join(module_path, "ext_falcon.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_v0.1/falcon_utgcns.py
++++ falconkit/src/py_scripts_v0.1/falcon_utgcns.py
+@@ -45,7 +45,7 @@
+ 
+ module_path = falcon_kit.__path__[0]
+ 
+-falcon = CDLL(os.path.join(module_path, "falcon.so"))
++falcon = CDLL(os.path.join(module_path, "ext_falcon.so"))
+ """
+ consensus_data * generate_utg_consensus( char ** input_seq, 
+                            seq_coor_t *offset,
diff --git a/debian/patches/python-multiarch.patch b/debian/patches/python-multiarch.patch
new file mode 100644
index 0000000..d66a639
--- /dev/null
+++ b/debian/patches/python-multiarch.patch
@@ -0,0 +1,40 @@
+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_v0.1/falcon_sense.py
++++ falconkit/src/py_scripts_v0.1/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, "ext_falcon.so"))
++falcon = CDLL(
++    module_path+os.path.sep+"ext_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_v0.1/falcon_utgcns.py
++++ falconkit/src/py_scripts_v0.1/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, "ext_falcon.so"))
++falcon = CDLL(
++    module_path + os.path.sep + "ext_falcon." + sysconfig.get_config_var('MULTIARCH') + ".so")
+ """
+ consensus_data * generate_utg_consensus( char ** input_seq, 
+                            seq_coor_t *offset,
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..145e692
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+adjust-extension-name.patch
+python-multiarch.patch

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