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 <[email protected]> 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 = '[email protected]', -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/hyphy.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
