Revision: 75633 http://trac.macports.org/changeset/75633 Author: mmoll@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'] + ),