[75633] trunk/dports/python
mmoll at macports.org
mmoll at macports.org
Tue Feb 1 19:10:04 PST 2011
Revision: 75633
http://trac.macports.org/changeset/75633
Author: mmoll at macports.org
Date: 2011-02-01 19:10:03 -0800 (Tue, 01 Feb 2011)
Log Message:
-----------
python/py2[567]-biopython: enable mmCIF parser, add dependency on flex, closes #27919
Modified Paths:
--------------
trunk/dports/python/py25-biopython/Portfile
trunk/dports/python/py26-biopython/Portfile
trunk/dports/python/py27-biopython/Portfile
Added Paths:
-----------
trunk/dports/python/py25-biopython/files/
trunk/dports/python/py25-biopython/files/patch-setup.diff
trunk/dports/python/py26-biopython/files/
trunk/dports/python/py26-biopython/files/patch-setup.diff
trunk/dports/python/py27-biopython/files/
trunk/dports/python/py27-biopython/files/patch-setup.diff
Modified: trunk/dports/python/py25-biopython/Portfile
===================================================================
--- trunk/dports/python/py25-biopython/Portfile 2011-02-02 01:06:01 UTC (rev 75632)
+++ trunk/dports/python/py25-biopython/Portfile 2011-02-02 03:10:03 UTC (rev 75633)
@@ -6,6 +6,7 @@
name py25-biopython
version 1.56
+revision 1
categories python science
maintainers mww openmaintainer
platforms darwin
@@ -20,9 +21,10 @@
checksums md5 19e6481e7724b7dadb1c9d0b956c9b77 \
sha1 d33dda23adb148cf4ae0fa5eb37f7396b26c856f \
rmd160 a1c2b0daa4a881052b5e300c59293b8896240f2c
-
+patchfiles patch-setup.diff
depends_lib-append port:py25-numpy \
- port:py25-reportlab
+ port:py25-reportlab \
+ port:flex
build.env CFLAGS=-I${python.include}
Added: trunk/dports/python/py25-biopython/files/patch-setup.diff
===================================================================
--- trunk/dports/python/py25-biopython/files/patch-setup.diff (rev 0)
+++ trunk/dports/python/py25-biopython/files/patch-setup.diff 2011-02-02 03:10:03 UTC (rev 75633)
@@ -0,0 +1,23 @@
+--- setup.py.orig 2011-01-10 16:10:04.000000000 -0500
++++ setup.py 2011-01-10 16:23:44.000000000 -0500
+@@ -303,13 +303,13 @@
+ 'Bio/trie.c'],
+ include_dirs=["Bio"]
+ ),
+-#Commented out due to the build dependency on flex, see Bug 2619
+-# Extension('Bio.PDB.mmCIF.MMCIFlex',
+-# ['Bio/PDB/mmCIF/lex.yy.c',
+-# 'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
+-# include_dirs=["Bio"],
+-# libraries=["fl"]
+-# ),
++# Commented out due to the build dependency on flex, see Bug 2619
++ Extension('Bio.PDB.mmCIF.MMCIFlex',
++ ['Bio/PDB/mmCIF/lex.yy.c',
++ 'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
++ include_dirs=["Bio"],
++ libraries=["fl"]
++ ),
+ Extension('Bio.Nexus.cnexus',
+ ['Bio/Nexus/cnexus.c']
+ ),
Modified: trunk/dports/python/py26-biopython/Portfile
===================================================================
--- trunk/dports/python/py26-biopython/Portfile 2011-02-02 01:06:01 UTC (rev 75632)
+++ trunk/dports/python/py26-biopython/Portfile 2011-02-02 03:10:03 UTC (rev 75633)
@@ -6,6 +6,7 @@
name py26-biopython
version 1.56
+revision 1
categories python science
maintainers mmoll openmaintainer
platforms darwin
@@ -20,9 +21,10 @@
checksums md5 19e6481e7724b7dadb1c9d0b956c9b77 \
sha1 d33dda23adb148cf4ae0fa5eb37f7396b26c856f \
rmd160 a1c2b0daa4a881052b5e300c59293b8896240f2c
-
+patchfiles patch-setup.diff
depends_lib-append port:py26-numpy \
- port:py26-reportlab
+ port:py26-reportlab \
+ port:flex
build.env CFLAGS=-I${python.include}
Added: trunk/dports/python/py26-biopython/files/patch-setup.diff
===================================================================
--- trunk/dports/python/py26-biopython/files/patch-setup.diff (rev 0)
+++ trunk/dports/python/py26-biopython/files/patch-setup.diff 2011-02-02 03:10:03 UTC (rev 75633)
@@ -0,0 +1,23 @@
+--- setup.py.orig 2011-01-10 16:10:04.000000000 -0500
++++ setup.py 2011-01-10 16:23:44.000000000 -0500
+@@ -303,13 +303,13 @@
+ 'Bio/trie.c'],
+ include_dirs=["Bio"]
+ ),
+-#Commented out due to the build dependency on flex, see Bug 2619
+-# Extension('Bio.PDB.mmCIF.MMCIFlex',
+-# ['Bio/PDB/mmCIF/lex.yy.c',
+-# 'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
+-# include_dirs=["Bio"],
+-# libraries=["fl"]
+-# ),
++# Commented out due to the build dependency on flex, see Bug 2619
++ Extension('Bio.PDB.mmCIF.MMCIFlex',
++ ['Bio/PDB/mmCIF/lex.yy.c',
++ 'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
++ include_dirs=["Bio"],
++ libraries=["fl"]
++ ),
+ Extension('Bio.Nexus.cnexus',
+ ['Bio/Nexus/cnexus.c']
+ ),
Modified: trunk/dports/python/py27-biopython/Portfile
===================================================================
--- trunk/dports/python/py27-biopython/Portfile 2011-02-02 01:06:01 UTC (rev 75632)
+++ trunk/dports/python/py27-biopython/Portfile 2011-02-02 03:10:03 UTC (rev 75633)
@@ -6,6 +6,7 @@
name py27-biopython
version 1.56
+revision 1
categories python science
maintainers mmoll openmaintainer
platforms darwin
@@ -20,9 +21,10 @@
checksums md5 19e6481e7724b7dadb1c9d0b956c9b77 \
sha1 d33dda23adb148cf4ae0fa5eb37f7396b26c856f \
rmd160 a1c2b0daa4a881052b5e300c59293b8896240f2c
-
+patchfiles patch-setup.diff
depends_lib-append port:py27-numpy \
- port:py27-reportlab
+ port:py27-reportlab \
+ port:flex
build.env CFLAGS=-I${python.include}
Added: trunk/dports/python/py27-biopython/files/patch-setup.diff
===================================================================
--- trunk/dports/python/py27-biopython/files/patch-setup.diff (rev 0)
+++ trunk/dports/python/py27-biopython/files/patch-setup.diff 2011-02-02 03:10:03 UTC (rev 75633)
@@ -0,0 +1,23 @@
+--- setup.py.orig 2011-01-10 16:10:04.000000000 -0500
++++ setup.py 2011-01-10 16:23:44.000000000 -0500
+@@ -303,13 +303,13 @@
+ 'Bio/trie.c'],
+ include_dirs=["Bio"]
+ ),
+-#Commented out due to the build dependency on flex, see Bug 2619
+-# Extension('Bio.PDB.mmCIF.MMCIFlex',
+-# ['Bio/PDB/mmCIF/lex.yy.c',
+-# 'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
+-# include_dirs=["Bio"],
+-# libraries=["fl"]
+-# ),
++# Commented out due to the build dependency on flex, see Bug 2619
++ Extension('Bio.PDB.mmCIF.MMCIFlex',
++ ['Bio/PDB/mmCIF/lex.yy.c',
++ 'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
++ include_dirs=["Bio"],
++ libraries=["fl"]
++ ),
+ Extension('Bio.Nexus.cnexus',
+ ['Bio/Nexus/cnexus.c']
+ ),
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