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commit 458e426c3d792ca14dba8643abf27ce0cbe5dd42 Author: Kevin Murray <[email protected]> Date: Sat Feb 6 11:40:48 2016 +0100 Remove .py extension from binary names --- debian/{PartitionFinder.py.1 => PartitionFinder.1} | 31 +++++++++++----------- ...FinderProtein.py.1 => PartitionFinderProtein.1} | 28 +++++++++---------- debian/partitionfinder.install | 4 +-- debian/partitionfinder.lintian-overrides | 2 -- debian/rules | 10 +++++-- 5 files changed, 38 insertions(+), 37 deletions(-) diff --git a/debian/PartitionFinder.py.1 b/debian/PartitionFinder.1 similarity index 83% rename from debian/PartitionFinder.py.1 rename to debian/PartitionFinder.1 index 6af9344..03e704b 100644 --- a/debian/PartitionFinder.py.1 +++ b/debian/PartitionFinder.1 @@ -1,8 +1,8 @@ -.TH USAGE: "1" "November 2015" "PartitionFinder.py" "User Commands" +.TH USAGE: "1" "November 2015" "PartitionFinder" "User Commands" .SH NAME -PartitionFinder.py \- manual page for PartitionFinder.py +PartitionFinder \- detects optimal partitioning schemes for nucleotide alignments .SH SYNOPSIS -.B PartitionFinder.py \/\fR[\fI\,options\/\fR] \fI\,<foldername>\/\fR +.B PartitionFinder \/\fR[\fI\,options\/\fR] \fI\,<foldername>\/\fR .SH DESCRIPTION .IP PartitionFinder and PartitionFinderProtein are designed to discover optimal @@ -22,18 +22,18 @@ partitioning scheme, and the best model for each partiiton .IP Usage Examples: .IP ->python PartitionFinder.py example +>python PartitionFinder example Analyse what is in the 'example' sub\-folder in the current folder. .IP ->python PartitionFinder.py \fB\-v\fR example +>python PartitionFinder \fB\-v\fR example Analyse what is in the 'example' sub\-folder in the current folder, but show all the debug output .IP ->python PartitionFinder.py \fB\-c\fR \fI\,~/data/frogs\/\fP +>python PartitionFinder \fB\-c\fR \fI\,~/data/frogs\/\fP Check the configuration files in the folder data/frogs in the current user's home folder. .IP ->python PartitionFinder.py \fB\-\-force\-restart\fR \fI\,~/data/frogs\/\fP +>python PartitionFinder \fB\-\-force\-restart\fR \fI\,~/data/frogs\/\fP Deletes any data produced by the previous runs (which is in \fI\,~/data/frogs/output\/\fP) and starts afresh .SH OPTIONS @@ -114,7 +114,8 @@ values \fB\-\-rcluster\-percent\fR=\fI\,N\/\fR This defines the proportion of possible schemes that the relaxed clustering algorithm will consider before -it stops looking. The default is 10%.e.g. \fB\-\-rclusterpercent\fR 10.0 +it stops looking. The default is 10%.e.g. +\fB\-\-rclusterpercent\fR 10.0 .TP \fB\-\-rcluster\-max\fR=\fI\,N\/\fR This defines the number of possible schemes that the @@ -130,14 +131,12 @@ they will be merged with other subsets at the end of the algorithm.e.g. \fB\-\-min\-subset\-size\fR 100 .TP \fB\-\-debug\-output\fR=\fI\,REGION\/\fR,REGION,... -(advanced option) Provide a list of debug regions to -output extra information about what the program is -doing. Possible regions are 'all' or any of {subset,su -bset_ops,neighbour,raxml,parser,model_util,results,ent -ropy,alignment,future_stdlib,threadpool,progress,main, -config,pandas,reporter,kmeans,pandas.io.gbq,pandas.io, -analysis_m,util,scheme,submodels,database,analysis,phy -ml,raxml_mode,model_load,phyml_mode}. +(advanced option) Provide a list of debug regions to output extra information +about what the program is doing. Possible regions are 'all' or any of {subset, +subset_ops, neighbour, raxml, parser, model_util, results, entropy, alignment, +future_stdlib, threadpool, progress, main, config, pandas, reporter, kmeans, +pandas.io.gbq, pandas.io, analysis_m, util, scheme, submodels, database, +analysis, phyml, raxml_mode, model_load, phyml_mode}. .TP \fB\-\-all\-states\fR In the k\-means algorithm, only produce subsets which diff --git a/debian/PartitionFinderProtein.py.1 b/debian/PartitionFinderProtein.1 similarity index 84% rename from debian/PartitionFinderProtein.py.1 rename to debian/PartitionFinderProtein.1 index 00d8c09..f5c14d7 100644 --- a/debian/PartitionFinderProtein.py.1 +++ b/debian/PartitionFinderProtein.1 @@ -1,9 +1,9 @@ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.2. -.TH USAGE: "1" "November 2015" "PartitionFinderProtein.py" "User Commands" +.TH USAGE: "1" "November 2015" "PartitionFinderProtein" "User Commands" .SH NAME -PartitionFinderProtein.py \- manual page for PartitionFinderProtein.py +PartitionFinderProtein \- PartitionFinder for protein sequences .SH SYNOPSIS -.B PartitionFinderProtein.py \/\fR[\fI\,options\/\fR] \fI\,<foldername>\/\fR +.B PartitionFinderProtein \/\fR[\fI\,options\/\fR] \fI\,<foldername>\/\fR .SH DESCRIPTION .IP PartitionFinder and PartitionFinderProtein are designed to discover optimal @@ -23,18 +23,18 @@ partitioning scheme, and the best model for each partiiton .IP Usage Examples: .IP ->python PartitionFinderProtein.py example +>python PartitionFinderProtein example Analyse what is in the 'example' sub\-folder in the current folder. .IP ->python PartitionFinderProtein.py \fB\-v\fR example +>python PartitionFinderProtein \fB\-v\fR example Analyse what is in the 'example' sub\-folder in the current folder, but show all the debug output .IP ->python PartitionFinderProtein.py \fB\-c\fR \fI\,~/data/frogs\/\fP +>python PartitionFinderProtein \fB\-c\fR \fI\,~/data/frogs\/\fP Check the configuration files in the folder data/frogs in the current user's home folder. .IP ->python PartitionFinderProtein.py \fB\-\-force\-restart\fR \fI\,~/data/frogs\/\fP +>python PartitionFinderProtein \fB\-\-force\-restart\fR \fI\,~/data/frogs\/\fP Deletes any data produced by the previous runs (which is in \fI\,~/data/frogs/output\/\fP) and starts afresh .SH OPTIONS @@ -131,14 +131,12 @@ they will be merged with other subsets at the end of the algorithm.e.g. \fB\-\-min\-subset\-size\fR 100 .TP \fB\-\-debug\-output\fR=\fI\,REGION\/\fR,REGION,... -(advanced option) Provide a list of debug regions to -output extra information about what the program is -doing. Possible regions are 'all' or any of {subset,su -bset_ops,neighbour,raxml,parser,model_util,results,ent -ropy,alignment,future_stdlib,threadpool,progress,main, -config,pandas,reporter,kmeans,pandas.io.gbq,pandas.io, -analysis_m,util,scheme,submodels,database,analysis,phy -ml,raxml_mode,model_load,phyml_mode}. +(advanced option) Provide a list of debug regions to output extra information +about what the program is doing. Possible regions are 'all' or any of {subset, +subset_ops, neighbour, raxml, parser, model_util, results, entropy, alignment, +future_stdlib, threadpool, progress, main, config, pandas, reporter, kmeans, +pandas.io.gbq, pandas.io, analysis_m, util, scheme, submodels, database, +analysis, phyml, raxml_mode, model_load, phyml_mode}. .TP \fB\-\-all\-states\fR In the k\-means algorithm, only produce subsets which diff --git a/debian/partitionfinder.install b/debian/partitionfinder.install index b4fcb3b..2a052ef 100644 --- a/debian/partitionfinder.install +++ b/debian/partitionfinder.install @@ -1,3 +1,3 @@ -PartitionFinder.py usr/bin -PartitionFinderProtein.py usr/bin +PartitionFinder.py usr/bin/PartionFinder +PartitionFinderProtein.py usr/bin/PartitionFinderProtein partfinder/ usr/lib/python2.7/dist-packages/ diff --git a/debian/partitionfinder.lintian-overrides b/debian/partitionfinder.lintian-overrides deleted file mode 100644 index c3e26ae..0000000 --- a/debian/partitionfinder.lintian-overrides +++ /dev/null @@ -1,2 +0,0 @@ -partitionfinder: script-with-language-extension usr/bin/PartitionFinder.py -partitionfinder: script-with-language-extension usr/bin/PartitionFinderProtein.py diff --git a/debian/rules b/debian/rules index 2a36ff0..02aaaf1 100755 --- a/debian/rules +++ b/debian/rules @@ -3,6 +3,12 @@ %: dh $@ --parallel -overide_dh_auto_build: +override_dh_clean: + dh_clean + rm -f PartitionFinder PartitionFinderProtein + +override_dh_auto_build: dh_python2 - g++ -o partfinder/_tiger.so -fPIC -shared -I/usr/include/python2.7/ -lpython2.7 partfinder/_tiger.cpp + g++ -o partfinder/_tiger.so -fPIC -shared -I/usr/include/python2.7/ -lpython2.7 $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) partfinder/_tiger.cpp + cp PartitionFinder.py PartitionFinder + cp PartitionFinderProtein.py PartitionFinderProtein -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/partitionfinder.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
