[med-svn] [Git][med-team/python-deeptools][master] Fixed more paths to python

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / python-deeptools


Commits:
5eb159fc by Steffen Möller at 2019-08-09T19:59:56Z
Fixed more paths to python

- - - - -


2 changed files:

- debian/patches/python2to3_for_executables.patch
- debian/rules


Changes:

=====================================
debian/patches/python2to3_for_executables.patch
=====================================
@@ -212,3 +212,263 @@ Index: python-deeptools-3.3.0/bin/plotProfile
  #-*- coding: utf-8 -*-
  
  import deeptools.misc
+Index: python-deeptools-3.3.0/deeptools/plotPCA.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/plotPCA.py
++++ python-deeptools-3.3.0/deeptools/plotPCA.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import sys
+Index: python-deeptools-3.3.0/deeptools/SES_scaleFactor.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/SES_scaleFactor.py
++++ python-deeptools-3.3.0/deeptools/SES_scaleFactor.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import os
+Index: python-deeptools-3.3.0/deeptools/alignmentSieve.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/alignmentSieve.py
++++ python-deeptools-3.3.0/deeptools/alignmentSieve.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import argparse
+ import pysam
+ import os
+Index: python-deeptools-3.3.0/deeptools/bamCompare.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/bamCompare.py
++++ python-deeptools-3.3.0/deeptools/bamCompare.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import argparse  # to parse command line arguments
+Index: python-deeptools-3.3.0/deeptools/bamCoverage.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/bamCoverage.py
++++ python-deeptools-3.3.0/deeptools/bamCoverage.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ # own tools
+Index: python-deeptools-3.3.0/deeptools/bamPEFragmentSize.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/bamPEFragmentSize.py
++++ python-deeptools-3.3.0/deeptools/bamPEFragmentSize.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import argparse
+Index: python-deeptools-3.3.0/deeptools/bigwigCompare.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/bigwigCompare.py
++++ python-deeptools-3.3.0/deeptools/bigwigCompare.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ import argparse  # to parse command line arguments
+ import sys
+Index: python-deeptools-3.3.0/deeptools/computeGCBias.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/computeGCBias.py
++++ python-deeptools-3.3.0/deeptools/computeGCBias.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import time
+Index: python-deeptools-3.3.0/deeptools/computeMatrix.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/computeMatrix.py
++++ python-deeptools-3.3.0/deeptools/computeMatrix.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import argparse
+Index: python-deeptools-3.3.0/deeptools/computeMatrixOperations.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/computeMatrixOperations.py
++++ python-deeptools-3.3.0/deeptools/computeMatrixOperations.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import deeptools.heatmapper as heatmapper
+ import deeptoolsintervals.parse as dti
+ import numpy as np
+Index: python-deeptools-3.3.0/deeptools/correctGCBias.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/correctGCBias.py
++++ python-deeptools-3.3.0/deeptools/correctGCBias.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import os
+Index: python-deeptools-3.3.0/deeptools/deepBlue.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/deepBlue.py
++++ python-deeptools-3.3.0/deeptools/deepBlue.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ try:
+     # python 2
+     import xmlrpclib
+Index: python-deeptools-3.3.0/deeptools/deeptools_list_tools.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/deeptools_list_tools.py
++++ python-deeptools-3.3.0/deeptools/deeptools_list_tools.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import argparse
+Index: python-deeptools-3.3.0/deeptools/estimateReadFiltering.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/estimateReadFiltering.py
++++ python-deeptools-3.3.0/deeptools/estimateReadFiltering.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import argparse
+ import sys
+ 
+Index: python-deeptools-3.3.0/deeptools/getScaleFactor.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/getScaleFactor.py
++++ python-deeptools-3.3.0/deeptools/getScaleFactor.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import numpy as np
+Index: python-deeptools-3.3.0/deeptools/multiBamSummary.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/multiBamSummary.py
++++ python-deeptools-3.3.0/deeptools/multiBamSummary.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import os
+Index: python-deeptools-3.3.0/deeptools/multiBigwigSummary.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/multiBigwigSummary.py
++++ python-deeptools-3.3.0/deeptools/multiBigwigSummary.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import sys
+Index: python-deeptools-3.3.0/deeptools/plotCorrelation.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/plotCorrelation.py
++++ python-deeptools-3.3.0/deeptools/plotCorrelation.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import sys
+Index: python-deeptools-3.3.0/deeptools/plotCoverage.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/plotCoverage.py
++++ python-deeptools-3.3.0/deeptools/plotCoverage.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import os
+Index: python-deeptools-3.3.0/deeptools/plotEnrichment.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/plotEnrichment.py
++++ python-deeptools-3.3.0/deeptools/plotEnrichment.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import sys
+Index: python-deeptools-3.3.0/deeptools/plotFingerprint.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/plotFingerprint.py
++++ python-deeptools-3.3.0/deeptools/plotFingerprint.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import numpy as np
+Index: python-deeptools-3.3.0/deeptools/plotHeatmap.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/plotHeatmap.py
++++ python-deeptools-3.3.0/deeptools/plotHeatmap.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ from __future__ import division
+ 
+Index: python-deeptools-3.3.0/deeptools/plotProfile.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/plotProfile.py
++++ python-deeptools-3.3.0/deeptools/plotProfile.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ 
+Index: python-deeptools-3.3.0/deeptools/writeBedGraph_bam_and_bw.py
+===================================================================
+--- python-deeptools-3.3.0.orig/deeptools/writeBedGraph_bam_and_bw.py
++++ python-deeptools-3.3.0/deeptools/writeBedGraph_bam_and_bw.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ import os
+Index: python-deeptools-3.3.0/scripts/convertChromsBigWig.py
+===================================================================
+--- python-deeptools-3.3.0.orig/scripts/convertChromsBigWig.py
++++ python-deeptools-3.3.0/scripts/convertChromsBigWig.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import sys
+ import pyBigWig
+Index: python-deeptools-3.3.0/scripts/split_bed_into_multiple_files.py
+===================================================================
+--- python-deeptools-3.3.0.orig/scripts/split_bed_into_multiple_files.py
++++ python-deeptools-3.3.0/scripts/split_bed_into_multiple_files.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ """


=====================================
debian/rules
=====================================
@@ -10,9 +10,10 @@ export PYBUILD_NAME=deeptools
 #	 PYTHONPATH=$(CURDIR)/debian/python3-deeptools/usr/lib/python3/dist-packages:/usr/lib/python3/dist-packages nosetests3 -x
 
 override_dh_auto_test:
-	 python3 -m unittest discover -v
+	 #python3 -m unittest discover -v
+	 PYTHONPATH=$(CURDIR) nosetests3 -x -v -s deeptools
 
 override_dh_auto_clean:
 	dh_auto_clean
-	rm -rf .pytest_cache
+	rm -rf .pytest_cache deeptools/__pycache__
 



View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/commit/5eb159fc9d93d5970abc8e23a9879de6e1aa3d43

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View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/commit/5eb159fc9d93d5970abc8e23a9879de6e1aa3d43
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