[med-svn] [hyphy] 01/04: Imported Upstream version 2.2.6+dfsg

[Andreas Tille]

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

tille pushed a commit to branch master
in repository hyphy.

commit 04ec654bce3b6f0a032cfc19e3cf94860ac08b1d
Author: Andreas Tille <tille at debian.org>
Date:   Tue Sep 22 17:00:36 2015 +0200

    Imported Upstream version 2.2.6+dfsg
---
 .gitattributes                                         | 1 +
 res/SubstitutionModels/Codon/MG94_REV_3x4.mdl copy     | 0
 res/TemplateBatchFiles/BranchSiteREL.bf                | 4 ++--
 res/TemplateBatchFiles/PairwiseDNDS.bf                 | 0
 res/TemplateBatchFiles/QuickSelectionDetectionMF.bf    | 3 ++-
 res/TemplateBatchFiles/dNdSDistributionComparisonMF.bf | 0
 src/lib/setup.py                                       | 6 ++++--
 7 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..6c7c54c
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1 @@
+*.bf linguist-language=HyPhy
diff --git a/res/SubstitutionModels/Codon/MG94_REV_3x4.mdl copy b/res/SubstitutionModels/Codon/MG94_REV_3x4.mdl copy
deleted file mode 100644
index e69de29..0000000
diff --git a/res/TemplateBatchFiles/BranchSiteREL.bf b/res/TemplateBatchFiles/BranchSiteREL.bf
index 92ae3a4..cb67d11 100644
--- a/res/TemplateBatchFiles/BranchSiteREL.bf
+++ b/res/TemplateBatchFiles/BranchSiteREL.bf
@@ -354,7 +354,7 @@ for (k = 0; k < totalBranchCount; k+=1) {
     Optimize                      (res, stepupLF);
     
     test_IC = getIC (res[1][0], current_parameter_count + 2 + doSynRateVariation, sample_size);
-    fprintf 					  (stdout, "\n[PHASE 1] Branch ", local_branch_name, " log(L) = ", Format(res[1][0],8,3), ", IC = ", Format (test_IC,8,3), "\n\t2 rate clases\n\t");
+    fprintf 					  (stdout, "\n[PHASE 1] Branch ", local_branch_name, " log(L) = ", Format(res[1][0],8,3), ", IC = ", Format (test_IC,8,3), "\n\t2 rate classes\n\t");
     printNodeDesc ("mixtureTree.`local_branch_name`", 2);
     
     while (test_IC < current_IC || oldBSREL && accepted_rates_count < 3 || useExistingModelSpec && tree_info_map[local_branch_name] > accepted_rates_count) {
@@ -400,7 +400,7 @@ for (k = 0; k < totalBranchCount; k+=1) {
         
         Optimize                      (res, stepupLF);
         test_IC = getIC (res[1][0], current_parameter_count + 2 + doSynRateVariation, sample_size);
-        fprintf 					  (stdout, "\n[PHASE 1] Branch ", local_branch_name, " log(L) = ", res[1][0], ", IC = ", test_IC, "\n\t", accepted_rates_count+1, " rate clases\n\t");
+        fprintf 					  (stdout, "\n[PHASE 1] Branch ", local_branch_name, " log(L) = ", res[1][0], ", IC = ", test_IC, "\n\t", accepted_rates_count+1, " rate classes\n\t");
         printNodeDesc ("mixtureTree.`local_branch_name`", accepted_rates_count + 1);
 
     }
diff --git a/res/TemplateBatchFiles/PairwiseDNDS.bf b/res/TemplateBatchFiles/PairwiseDNDS.bf
deleted file mode 100644
index e69de29..0000000
diff --git a/res/TemplateBatchFiles/QuickSelectionDetectionMF.bf b/res/TemplateBatchFiles/QuickSelectionDetectionMF.bf
index 6fdfec8..530c9f1 100644
--- a/res/TemplateBatchFiles/QuickSelectionDetectionMF.bf
+++ b/res/TemplateBatchFiles/QuickSelectionDetectionMF.bf
@@ -58,7 +58,8 @@ if (cOptions == 0) {
 	ExecuteAFile("SGEmulator_MF.bf");
 }
 else { // FEL 
-    pValue = prompt_for_a_value ("Significance level for Likelihood Ratio Tests",0.1,0,1,0)
+
+  pValue = prompt_for_a_value ("Significance level for Likelihood Ratio Tests",0.1,0,1,0);
 					
 	SHORT_MPI_RETURN = 1;
 	FEL_RUN_TIMER    = Time(1);
diff --git a/res/TemplateBatchFiles/dNdSDistributionComparisonMF.bf b/res/TemplateBatchFiles/dNdSDistributionComparisonMF.bf
deleted file mode 100644
index e69de29..0000000
diff --git a/src/lib/setup.py b/src/lib/setup.py
index cf17360..3bad511 100644
--- a/src/lib/setup.py
+++ b/src/lib/setup.py
@@ -28,6 +28,7 @@ coreSrcPath = path.join(srcPath, 'core')
 newSrcPath = path.join(srcPath, 'new')
 guiSrcPath = path.join(srcPath, 'gui')
 prefFile = [path.join(guiSrcPath, 'preferences.cpp')]
+
 if sys.version_info >= (3,0,0):
     swigFile = [path.join(scriptPath, 'SWIGWrappers', 'THyPhy_py3.cpp')]
 else:
@@ -48,11 +49,12 @@ includePaths += [linkPath, contribPath, sqlitePath]
 define_macros = [('__HYPHY_64__', None)] if '64' in architecture()[0] else []
 
 # openmp on Mac OS X Lion is broken
-openmp = ['-fopenmp'] if mac_ver()[0] < '10.7.0' else []
+major, minor, patch = mac_ver()[0].split('.')
+openmp = ['-fopenmp'] if int(major) < 10 or (int(major) == 10 and int(minor) < 7) else []
 
 setup(
     name = 'HyPhy',
-    version = '0.1',
+    version = '0.1.1',
     description = 'HyPhy package interface library',
     author = 'Sergei L Kosakovsky Pond',
     author_email = 'spond at ucsd.edu',

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