class doExit(Exception):
def __init__(self, value):
self.value = value
isGit = os.environ["TEST_SEARCHER"] == "git"
print isGit
try:
ancestryFilename = os.environ["TEST_ANCESTRY"]
testDir = os.environ["TEST_DIR"]
loc = int(os.environ["TEST_LOC"])
f = file(ancestryFilename, "r")
(identifiers, parents) = dagRead.read(f)
f.close()
N = len(parents)
thisDag = dag.dag(parents, N)
t = testDetector.detect(N, 1.0, thisDag, False, loc)
numbers = {}
for i in range(len(identifiers)):
numbers[identifiers[i]] = i
if isGit:
os.system("git rev-parse HEAD >$TEST_DIR/__head__")
where = open(testDir + "/__head__", "r").readline().strip()
where = numbers[where]
else:
where = sys.argv[1]
# You should have received a copy of the GNU General Public License
# along with BBChop. If not, see <http://www.gnu.org/licenses/>.
import randomdag
import random
import dagRead
try:
for test in range(100):
N=random.randint(10,100)
dagDef=randomdag.randomdagTxt(N)
dagDefShuffled=dagDef
random.shuffle(dagDefShuffled)
(dagIds,dagParents)=dagRead.read(dagDefShuffled)
dagCheck=dagDef
for i in range(len(dagDef)):
dagTerm=dagIds[i]
for p in dagParents[i]:
if p>i:
raise "invalidDag"
dagTerm+=' '+dagIds[p]
if dagTerm not in dagCheck:
raise "missing term"
dagCheck=[x for x in dagCheck if x!=dagTerm]
print "test %d passed" %(test)
except:
print "FAILED"
ancFname = testDir + "/anc.txt"
os.environ['TEST_ANCESTRY'] = ancFname
def sysc(cmd):
print cmd,"->"
os.system(cmd)
sysc("mkdir -p "+testDir)
os.environ["TEST_DIR"] = testDir
os.chdir(gitRepo)
os.system("$topdir/interfaces/git/git-bbchop-list "+failVer+" ^"+passVer+" >$TEST_ANCESTRY")
ancFile=open(ancFname,"r")
(identifiers,parents)=dagRead.read(ancFile)
N=len(parents)
gitcmd = "./git "
import pdb
def commonBefore(rev,searcher):
os.environ['TEST_LOC']=str(rev)
os.environ['TEST_SEARCHER']=searcher
sysc("cp /dev/null $TEST_DIR/tries")
def commonAfter(where,rev):
sysc('wc -l $TEST_DIR/tries >$TEST_DIR/count')
count=int(open(testDir+"/count","r").readline().split()[0])
return (where==identifiers[rev],count)
def write(self, sep):
pass
def close(self):
pass
#runner=profiler("profiles/master")
runner = timer("tlog-master-mpmath")
for i in range(1, 10):
fname = "rc" + str(i) + ".anc"
f = file(fname, "r")
(identifiers, parents) = dagRead.read(f)
locations = len(identifiers)
prior = [1 / float(locations) for i in range(locations)]
f.close()
runner.startSet(str(i))
thisDag = runner.run(dag.dag, (parents, len(parents)))
finder = BBChop(prior, 0.9, fakeTest(), likelihoods.singleRateCalc,
thisDag)
runner.run(runFinder, [finder])
runner.write(" ")
#
# You should have received a copy of the GNU General Public License
# along with BBChop. If not, see <http://www.gnu.org/licenses/>.
import randomdag
import random
import dagRead
try:
for test in range(100):
N = random.randint(10, 100)
dagDef = randomdag.randomdagTxt(N)
dagDefShuffled = dagDef
random.shuffle(dagDefShuffled)
(dagIds, dagParents) = dagRead.read(dagDefShuffled)
dagCheck = dagDef
for i in range(len(dagDef)):
dagTerm = dagIds[i]
for p in dagParents[i]:
if p > i:
raise "invalidDag"
dagTerm += ' ' + dagIds[p]
if dagTerm not in dagCheck:
raise "missing term"
dagCheck = [x for x in dagCheck if x != dagTerm]
print "test %d passed" % (test)
except:
print "FAILED"
exit(1)