[med-svn] [Git][med-team/fitgcp][master] 6 commits: Use 2to3 to port to Python3
Andreas Tille
gitlab at salsa.debian.org
Tue Sep 10 09:29:59 BST 2019
Andreas Tille pushed to branch master at Debian Med / fitgcp
Commits:
9cb24d55 by Andreas Tille at 2019-09-10T06:56:59Z
Use 2to3 to port to Python3
- - - - -
9060f655 by Andreas Tille at 2019-09-10T06:57:40Z
Switch Build system to Python3
- - - - -
4a05c6df by Andreas Tille at 2019-09-10T06:58:04Z
debhelper-compat 12
- - - - -
88f0db3e by Andreas Tille at 2019-09-10T06:58:06Z
Standards-Version: 4.4.0
- - - - -
dd371b68 by Andreas Tille at 2019-09-10T06:58:07Z
Secure URI in copyright format
- - - - -
0dd63d0d by Andreas Tille at 2019-09-10T06:59:16Z
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/patches/2to3.patch
- + debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+fitgcp (0.0.20150429-3) unstable; urgency=medium
+
+ * Use 2to3 to port to Python3
+ Closes: #936518
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * Secure URI in copyright format
+
+ -- Andreas Tille <tille at debian.org> Tue, 10 Sep 2019 08:58:14 +0200
+
fitgcp (0.0.20150429-2) unstable; urgency=medium
* debhelper 11
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
dh-python,
- python,
- python-pysam
-Standards-Version: 4.2.0
+ python3,
+ python3-pysam
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/fitgcp
Vcs-Git: https://salsa.debian.org/med-team/fitgcp.git
Homepage: http://sourceforge.net/projects/fitgcp/
@@ -16,10 +16,10 @@ Package: fitgcp
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- ${python:Depends},
- python-scipy,
- python-numpy,
- python-pysam
+ ${python3:Depends},
+ python3-scipy,
+ python3-numpy,
+ python3-pysam
Description: fitting genome coverage distributions with mixture models
Genome coverage, the number of sequencing reads mapped to a position in
a genome, is an insightful indicator of irregularities within sequencing
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: fitGCP
Upstream-Contact: Martin S. Lindner <LindnerM at rki.de>
Source: http://sourceforge.net/projects/fitgcp/files/
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,154 @@
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/936518
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 10 Sep 2019 08:55:27 +0200
+
+--- a/README.txt
++++ b/README.txt
+@@ -1,4 +1,4 @@
+-Help on python script fitGCP.py
++Help on python3 script fitGCP.py
+
+ Fits mixtures of probability distributions to genome coverage profiles using an
+ EM-like iterative algorithm.
+@@ -25,7 +25,7 @@ USAGE:
+ fitGCP runs on the command line. The following command describes the general
+ structure:
+
+-python fitGCP.py [options] NAME
++python3 fitGCP.py [options] NAME
+
+ fitGCP fits mixtures of probability distributions to genome coverage profiles using
+ an EM-like iterative algorithm.
+@@ -76,4 +76,4 @@ Options:
+ distributions.
+ -l, --log Enable logging. Default: False
+ --view Only view the GCP. Do not fit any distribution.
+- Respects cutoff (-c). Default: False
+\ No newline at end of file
++ Respects cutoff (-c). Default: False
+--- a/fitGCP.py
++++ b/fitGCP.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+ """
+ Created on Fri Aug 31 2012 14:05
+
+@@ -31,7 +31,7 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBI
+ usage = """
+ %prog [options] NAME
+
+-Help on python script fitGCP.py
++Help on python3 script fitGCP.py
+
+ Fits mixtures of probability distributions to genome coverage profiles using an
+ EM-like iterative algorithm.
+@@ -60,7 +60,7 @@ import sys
+ import os
+ from collections import namedtuple
+ import time
+-import cPickle
++import pickle
+ from optparse import OptionParser
+ from scipy.special import digamma, betainc
+ from scipy.optimize import newton
+@@ -136,7 +136,7 @@ class NBinom(Distribution):
+
+ if self._use_MOM:
+ if var < mean:
+- print "Warning: var < mean"
++ print("Warning: var < mean")
+ var = 1.01*mean
+ self._p1 = mean**2 / (var - mean)
+ self._p2 = mean / var
+@@ -154,9 +154,9 @@ class NBinom(Distribution):
+ maxiter=10000)
+ self._p2 = (self._p1)/(self._p1+mean)
+ except:
+- print "Warning: MLE for negative binomial failed. Using MOM."
++ print("Warning: MLE for negative binomial failed. Using MOM.")
+ if var < mean:
+- print "Warning: var < mean"
++ print("Warning: var < mean")
+ var = 1.01*mean
+ self._p1 = mean**2 / (var - mean)
+ self._p2 = mean / var
+@@ -216,7 +216,7 @@ class NbTail(TailDistribution):
+ if isinstance(nbinom, NBinom):
+ self._parent = nbinom
+ else:
+- raise(Exception("NbTail must be connected to a NBinom object"))
++ raise Exception
+
+ def pmf(self, x):
+ if np.isscalar(x) and x == 0:
+@@ -253,7 +253,7 @@ class PoissonTail(TailDistribution):
+ if isinstance(poisson, Poisson):
+ self._parent = poisson
+ else:
+- raise(Exception("PoissonTail must be connected to a Poisson object"))
++ raise Exception
+
+ def pmf(self, x):
+ if self._p1 < 1.:
+@@ -338,7 +338,7 @@ class DataSet:
+
+ def read_from_pickle(self,filename):
+ """ read a genome coverage profile from a pickle file. """
+- data = cPickle.load(open(filename,'r'))
++ data = pickle.load(open(filename,'r'))
+
+ self.cov = np.array(data[0],dtype=np.int)
+ self.count = np.array(data[1],dtype=np.int)
+@@ -375,7 +375,7 @@ class DataSet:
+
+ def write_to_pickle(self, filename):
+ """ store dataset in a pickle file. """
+- return cPickle.dump([self.cov, self.count, self.rlen, self.rds,
++ return pickle.dump([self.cov, self.count, self.rlen, self.rds,
+ self.glen, self.fname], open(filename,'w'))
+
+
+@@ -471,7 +471,7 @@ class Logger:
+ def log(self, s, c=True):
+ """ write string s to log file and print to console (if c) """
+ if c:
+- print s
++ print(s)
+ if self.log_file:
+ self.log_file.write(s+'\n')
+
+@@ -585,7 +585,7 @@ if __name__ == "__main__":
+ # load data
+ DS = DataSet()
+ if os.path.exists(name+'.pcl'):
+- print 'found pickle file'
++ print('found pickle file')
+ DS.read_from_pickle(name+'.pcl')
+ else:
+ DS.read_from_sam(name+'.sam')
+@@ -617,7 +617,7 @@ if __name__ == "__main__":
+ # create empty mixture model
+ MM = np.array([])
+ create_plot(DS,MM,name+'.png')
+- print "Wrote GCP plot to file %s."%(name+'.png')
++ print("Wrote GCP plot to file %s."%(name+'.png'))
+ sys.exit(0)
+
+
+@@ -710,7 +710,7 @@ if __name__ == "__main__":
+ # run the iteration, repeatedly update the variables MM and GAMMA
+ t_start = time.time()
+ for i,change,diff in iterative_fitting(DS, MM, GAMMA, options.steps):
+- print i
++ print(i)
+ t_step = time.time() - t_start
+ lg.log(('step#: '+str(i+1)).ljust(20)+'time: '+str(round(t_step,1))+'s'
+ +'\n',False)
+@@ -792,4 +792,4 @@ if __name__ == "__main__":
+ if plot:
+ create_plot(DS,MM,name+'_'+options.dist+'.png')
+
+- print "\nFinished."
++ print("\nFinished.")
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+2to3.patch
=====================================
debian/rules
=====================================
@@ -3,7 +3,7 @@
# DH_VERBOSE := 1
%:
- dh $@ --with python2
+ dh $@ --with python3
override_dh_fixperms:
dh_fixperms
View it on GitLab: https://salsa.debian.org/med-team/fitgcp/compare/0fc0368e04b9adda48dc4cbb3f40873cfc8c91ce...0dd63d0d91fce2e7afc75ef3acd899bbfd8ee847
--
View it on GitLab: https://salsa.debian.org/med-team/fitgcp/compare/0fc0368e04b9adda48dc4cbb3f40873cfc8c91ce...0dd63d0d91fce2e7afc75ef3acd899bbfd8ee847
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