[med-svn] [partitionfinder] 01/13: Remove .py extension from binary names
Kevin Murray
daube-guest at moszumanska.debian.org
Sat Feb 6 19:45:45 UTC 2016
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a commit to branch master
in repository partitionfinder.
commit 458e426c3d792ca14dba8643abf27ce0cbe5dd42
Author: Kevin Murray <spam at kdmurray.id.au>
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
--
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