[med-svn] [Git][med-team/libsonlib][master] 4 commits: Revert "Attempt to fix python test files"
Shayan Doust
gitlab at salsa.debian.org
Fri Jun 26 17:00:58 BST 2020
Shayan Doust pushed to branch master at Debian Med / libsonlib
Commits:
627ba4c5 by Shayan Doust at 2020-06-26T16:59:46+01:00
Revert "Attempt to fix python test files"
This reverts commit 154c65c815d20a5e236d864b5a6998885e148236.
- - - - -
44af7a8f by Shayan Doust at 2020-06-26T16:59:58+01:00
Revert "Fix separator issue due to previous commit"
This reverts commit e5ad017b3617f348a112f99744bde80fed3c85e5.
- - - - -
7060f5af by Shayan Doust at 2020-06-26T17:00:08+01:00
Revert "Move test scripts and binaries into a volatile location within debian/tests/"
This reverts commit 9c872ba3b24f0a7070628d74f3817f965a16df38.
- - - - -
34be65f6 by Shayan Doust at 2020-06-26T17:00:40+01:00
Revert "Comment out test within Makefile (we want to run these tests within autopkgtest in the future)"
This reverts commit 74cbe8742cc70e884506f22744ab5b03dc477301.
- - - - -
4 changed files:
- debian/libsonlib-dev.install
- debian/patches/2to3.patch
- debian/patches/fix_test.patch
- debian/rules
Changes:
=====================================
debian/libsonlib-dev.install
=====================================
@@ -1,4 +1,5 @@
#!/usr/bin/dh-exec
#include/*.h usr/include/sonlib
-lib/* usr/lib/${DEB_HOST_MULTIARCH}
\ No newline at end of file
+lib/* usr/lib/${DEB_HOST_MULTIARCH}
+bin/* usr/bin
=====================================
debian/patches/2to3.patch
=====================================
@@ -4,15 +4,33 @@ Description: Port to Python3
--- libsonlib.orig/treeTest.py
+++ libsonlib/treeTest.py
-@@ -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
+@@ -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
class TestCase(unittest.TestCase):
-
@@ -29,29 +29,29 @@
unittest.TestCase.tearDown(self)
@@ -92,19 +110,29 @@ Description: Port to Python3
geneTree = getRandomTree()
--- libsonlib.orig/allTests.py
+++ libsonlib/allTests.py
-@@ -18,9 +18,9 @@
+@@ -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
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 @@
@@ -118,20 +146,15 @@ Description: Port to Python3
if pid > 0:
--- libsonlib.orig/nxnewick.py
+++ libsonlib/nxnewick.py
-@@ -13,11 +13,11 @@
- import math
+@@ -14,7 +14,7 @@
import random
from string import whitespace as ws
--from sonLib.misc import close
-+from misc import close
- import bioio
+ from sonLib.misc import close
+-import bioio
++from . import bioio
import networkx as NX
from optparse import OptionParser
--from sonLib.nxtree import NXTree
-+from nxtree import NXTree
-
-
- class NXNewick(object):
+ from sonLib.nxtree import NXTree
@@ -187,15 +187,15 @@
parser.parseFile(args[0])
NX.drawing.nx_agraph.write_dot(parser.nxTree.nxDg, args[1])
@@ -327,15 +350,58 @@ Description: Port to Python3
#########################################################
--- libsonlib.orig/bioioTest.py
+++ libsonlib/bioioTest.py
-@@ -33,7 +33,7 @@
- from bioio import PairwiseAlignment
- from bioio import getRandomPairwiseAlignment
+@@ -11,32 +11,32 @@
+ import random
+ import math
--from sonLib.bioio import TestStatus
-+from bioio import TestStatus
+-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 bioio import system
- from bioio import logger
+ class TestCase(unittest.TestCase):
+
@@ -61,12 +61,12 @@
#########################################################
@@ -471,17 +537,24 @@ Description: Port to Python3
unittest.main()
--- libsonlib.orig/cigarsTest.py
+++ libsonlib/cigarsTest.py
-@@ -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
+@@ -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
- class TestCase(unittest.TestCase):
-
@@ -36,9 +36,9 @@
"""
tempFile = getTempFile()
@@ -497,15 +570,6 @@ 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)
@@ -722,6 +786,24 @@ 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)
@@ -768,42 +850,3 @@ 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/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):
-
=====================================
debian/patches/fix_test.patch
=====================================
@@ -17,7 +17,7 @@ Description: Somehow the test suite was non-functional. Fix some PATHs here
test : all
- PYTHONPATH=.. PATH=../../bin:$$PATH python3 allTests.py --testLength=SHORT --logLevel=CRITICAL
-+ #PYTHONPATH=$(CURDIR)/src:$(CURDIR)/src/sonLib PATH=$(CURDIR)/bin:$$PATH python3 allTests.py --testLength=SHORT --logLevel=CRITICAL
++ PYTHONPATH=$(CURDIR)/src:$(CURDIR)/src/sonLib PATH=$(CURDIR)/bin:$$PATH python3 allTests.py --testLength=SHORT --logLevel=CRITICAL
${binPath}/sonLib_daemonize.py : sonLib_daemonize.py cP
cp sonLib_daemonize.py ${binPath}/sonLib_daemonize.py
=====================================
debian/rules
=====================================
@@ -21,12 +21,5 @@ endif
override_dh_install:
dh_install
- mkdir -p debian/libsonlib-dev/usr/include/sonlib \
- debian/tests/sonlib-test
+ mkdir -p debian/libsonlib-dev/usr/include/sonlib
mv debian/libsonlib-dev/usr/lib/*/*.h debian/libsonlib-dev/usr/include/sonlib
- cp -rf bin/ debian/tests/sonlib-test
- cp -f *Test*.py debian/tests/sonlib-test
-
-override_dh_clean:
- dh_clean
- rm -rf debian/tests/sonlib-test
View it on GitLab: https://salsa.debian.org/med-team/libsonlib/-/compare/154c65c815d20a5e236d864b5a6998885e148236...34be65f64aea44b31bff2df96a7f315cf3981022
--
View it on GitLab: https://salsa.debian.org/med-team/libsonlib/-/compare/154c65c815d20a5e236d864b5a6998885e148236...34be65f64aea44b31bff2df96a7f315cf3981022
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