[med-svn] [Git][med-team/libsonlib][master] Attempt to fix import issues with python tests
Shayan Doust
gitlab at salsa.debian.org
Fri Jun 26 17:33:55 BST 2020
Shayan Doust pushed to branch master at Debian Med / libsonlib
Commits:
5145d390 by Shayan Doust at 2020-06-26T17:33:28+01:00
Attempt to fix import issues with python tests
- - - - -
1 changed file:
- debian/patches/2to3.patch
Changes:
=====================================
debian/patches/2to3.patch
=====================================
@@ -4,33 +4,15 @@ Description: Port to Python3
--- libsonlib.orig/treeTest.py
+++ libsonlib/treeTest.py
-@@ -7,16 +7,16 @@
- import unittest
- import random
-
--from tree import remodelTreeRemovingRoot
--from tree import binaryTree_depthFirstNumbers
--from tree import mapTraversalIDsBetweenTrees
--from tree import BinaryTree
--from bioio import printBinaryTree
--from bioio import newickTreeParser
--from misc import close
--from tree import moveRoot
--from tree import calculateDupsAndLossesByReconcilingTrees
--from tree import calculateProbableRootOfGeneTree
-+from .tree import remodelTreeRemovingRoot
-+from .tree import binaryTree_depthFirstNumbers
-+from .tree import mapTraversalIDsBetweenTrees
-+from .tree import BinaryTree
-+from .bioio import printBinaryTree
-+from .bioio import newickTreeParser
-+from .misc import close
-+from .tree import moveRoot
-+from .tree import calculateDupsAndLossesByReconcilingTrees
-+from .tree import calculateProbableRootOfGeneTree
- from sonLib.bioio import TestStatus
+@@ -17,7 +17,7 @@
+ from tree import moveRoot
+ from tree import calculateDupsAndLossesByReconcilingTrees
+ from tree import calculateProbableRootOfGeneTree
+-from sonLib.bioio import TestStatus
++from bioio import TestStatus
class TestCase(unittest.TestCase):
+
@@ -29,29 +29,29 @@
unittest.TestCase.tearDown(self)
@@ -110,29 +92,19 @@ Description: Port to Python3
geneTree = getRandomTree()
--- libsonlib.orig/allTests.py
+++ libsonlib/allTests.py
-@@ -5,16 +5,16 @@
- #Released under the MIT license, see LICENSE.txt
- import unittest
-
--import bioioTest
--import cigarsTest
--import treeTest
--import kvdbTest
-+from . import bioioTest
-+from . import cigarsTest
-+from . import treeTest
-+from . import kvdbTest
- import socket
- try:
- import networkx as NX
- networkx_installed = True
-- import nxtreeTest
-- import nxnewickTest
-+ from . import nxtreeTest
-+ from . import nxnewickTest
+@@ -18,9 +18,9 @@
except ImportError:
networkx_installed = False
+-from sonLib.bioio import system
+-from sonLib.bioio import parseSuiteTestOptions
+-from sonLib.bioio import getLogLevelString
++from bioio import system
++from bioio import parseSuiteTestOptions
++from bioio import getLogLevelString
+
+
+ class TestCase(unittest.TestCase):
--- libsonlib.orig/sonLib_daemonize.py
+++ libsonlib/sonLib_daemonize.py
@@ -66,7 +66,7 @@
@@ -146,15 +118,20 @@ Description: Port to Python3
if pid > 0:
--- libsonlib.orig/nxnewick.py
+++ libsonlib/nxnewick.py
-@@ -14,7 +14,7 @@
+@@ -13,11 +13,11 @@
+ import math
import random
from string import whitespace as ws
- from sonLib.misc import close
--import bioio
-+from . import bioio
+-from sonLib.misc import close
++from misc import close
+ import bioio
import networkx as NX
from optparse import OptionParser
- from sonLib.nxtree import NXTree
+-from sonLib.nxtree import NXTree
++from nxtree import NXTree
+
+
+ class NXNewick(object):
@@ -187,15 +187,15 @@
parser.parseFile(args[0])
NX.drawing.nx_agraph.write_dot(parser.nxTree.nxDg, args[1])
@@ -179,17 +156,6 @@ Description: Port to Python3
if __name__ == '__main__':
--- libsonlib.orig/bioio.py
+++ libsonlib/bioio.py
-@@ -16,8 +16,8 @@
- import shutil
- from argparse import ArgumentParser
- from optparse import OptionParser, OptionContainer, OptionGroup
--from tree import BinaryTree
--from misc import close
-+from .tree import BinaryTree
-+from .misc import close
- import subprocess
- import array
- import string
@@ -421,14 +421,14 @@
def getRandomAlphaNumericString(length=10):
"""Returns a random alpha numeric string of the given length.
@@ -350,58 +316,15 @@ Description: Port to Python3
#########################################################
--- libsonlib.orig/bioioTest.py
+++ libsonlib/bioioTest.py
-@@ -11,32 +11,32 @@
- import random
- import math
+@@ -33,7 +33,7 @@
+ from bioio import PairwiseAlignment
+ from bioio import getRandomPairwiseAlignment
--from bioio import getTempFile
--from bioio import getTempDirectory
--from bioio import TempFileTree
--from bioio import getRandomAlphaNumericString
-+from .bioio import getTempFile
-+from .bioio import getTempDirectory
-+from .bioio import TempFileTree
-+from .bioio import getRandomAlphaNumericString
-
--from bioio import fastaRead
--from bioio import fastaWrite
--from bioio import fastqRead
--from bioio import fastqWrite
--from bioio import getRandomSequence
-+from .bioio import fastaRead
-+from .bioio import fastaWrite
-+from .bioio import fastqRead
-+from .bioio import fastqWrite
-+from .bioio import getRandomSequence
-
--from bioio import pWMRead
--from bioio import pWMWrite
-+from .bioio import pWMRead
-+from .bioio import pWMWrite
-
--from bioio import newickTreeParser
--from bioio import printBinaryTree
-+from .bioio import newickTreeParser
-+from .bioio import printBinaryTree
-
--from bioio import cigarRead
--from bioio import cigarWrite
--from bioio import PairwiseAlignment
--from bioio import getRandomPairwiseAlignment
-+from .bioio import cigarRead
-+from .bioio import cigarWrite
-+from .bioio import PairwiseAlignment
-+from .bioio import getRandomPairwiseAlignment
-
- from sonLib.bioio import TestStatus
-
--from bioio import system
--from bioio import logger
-+from .bioio import system
-+from .bioio import logger
+-from sonLib.bioio import TestStatus
++from bioio import TestStatus
- class TestCase(unittest.TestCase):
-
+ from bioio import system
+ from bioio import logger
@@ -61,12 +61,12 @@
#########################################################
@@ -537,24 +460,17 @@ Description: Port to Python3
unittest.main()
--- libsonlib.orig/cigarsTest.py
+++ libsonlib/cigarsTest.py
-@@ -10,12 +10,12 @@
- import sys
- import random
-
--from bioio import getTempFile
-+from .bioio import getTempFile
-
--from bioio import cigarRead
--from bioio import cigarWrite
--from bioio import getRandomPairwiseAlignment
--from bioio import system
-+from .bioio import cigarRead
-+from .bioio import cigarWrite
-+from .bioio import getRandomPairwiseAlignment
-+from .bioio import system
- from sonLib.bioio import TestStatus
- from sonLib.bioio import logger
+@@ -16,8 +16,8 @@
+ from bioio import cigarWrite
+ from bioio import getRandomPairwiseAlignment
+ from bioio import system
+-from sonLib.bioio import TestStatus
+-from sonLib.bioio import logger
++from bioio import TestStatus
++from bioio import logger
+ class TestCase(unittest.TestCase):
+
@@ -36,9 +36,9 @@
"""
tempFile = getTempFile()
@@ -570,6 +486,15 @@ Description: Port to Python3
keepProbs = random.random() > 0.5
--- libsonlib.orig/tree.py
+++ libsonlib/tree.py
+@@ -10,7 +10,7 @@
+ import math
+ import random
+
+-from sonLib.misc import close
++from misc import close
+ #import bioio
+
+ #########################################################
@@ -69,7 +69,7 @@
return mid+1, leafNo+1
traverse(binaryTree)
@@ -786,24 +711,6 @@ Description: Port to Python3
def fn4(newTree):
if newTree.internal:
fn4(newTree.left)
-@@ -596,7 +596,7 @@
- """
- Node is mid order number
- """
-- import bioio
-+ from . import bioio
- assert root.traversalID.mid != node
- hash = {}
- def fn(bT):
-@@ -632,7 +632,7 @@
- """
- Removes the old root and places the new root at the mid point along the given branch
- """
-- import bioio
-+ from . import bioio
- if root.traversalID.mid == branch:
- return bioio.newickTreeParser(bioio.printBinaryTree(root, True))
- def fn2(tree, seq):
@@ -703,7 +703,7 @@
if nodes.issubset(a[speciesTree.right.traversalID.mid]):
return fn2(nodes, speciesTree.right)
@@ -850,3 +757,53 @@ Description: Port to Python3
${binPath}/sonLib_daemonize.py : sonLib_daemonize.py cP
cp sonLib_daemonize.py ${binPath}/sonLib_daemonize.py
+--- libsonlib.orig/kvdbTest.py
++++ libsonlib/kvdbTest.py
+@@ -10,7 +10,7 @@
+ import sys
+ import socket
+
+-from sonLib.bioio import system
++from bioio import system
+
+ class TestCase(unittest.TestCase):
+
+--- libsonlib.orig/misc.py
++++ libsonlib/misc.py
+@@ -21,7 +21,7 @@
+ """
+ function for finding external location
+ """
+- import sonLib.bioio
++ import bioio
+ i = os.path.abspath(sonLib.bioio.__file__)
+ return os.path.split(os.path.split(os.path.split(i)[0])[0])[0]
+
+--- libsonlib.orig/nxnewickTest.py
++++ libsonlib/nxnewickTest.py
+@@ -9,9 +9,9 @@
+ import re
+ from string import whitespace as ws
+
+-from sonLib.nxnewick import NXNewick
+-from sonLib.bioio import TestStatus
+-from sonLib.bioio import logger
++from nxnewick import NXNewick
++from bioio import TestStatus
++from bioio import logger
+
+ class TestCase(unittest.TestCase):
+
+--- libsonlib.orig/nxtreeTest.py
++++ libsonlib/nxtreeTest.py
+@@ -9,8 +9,8 @@
+ import copy
+
+ import networkx as NX
+-from sonLib.nxtree import NXTree
+-from sonLib.bioio import TestStatus
++from nxtree import NXTree
++from bioio import TestStatus
+
+ class TestCase(unittest.TestCase):
+
View it on GitLab: https://salsa.debian.org/med-team/libsonlib/-/commit/5145d390a8cde350f916a0e40804d405cae6f684
--
View it on GitLab: https://salsa.debian.org/med-team/libsonlib/-/commit/5145d390a8cde350f916a0e40804d405cae6f684
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