toil 5.12.0__py3-none-any.whl → 6.1.0a1__py3-none-any.whl

toil/test/src/autoDeploymentTest.py

@@ -3,13 +3,13 @@ import subprocess
 import time
 from contextlib import contextmanager
 
+from toil.exceptions import FailedJobsException
 from toil.lib.iterables import concat
 from toil.test import (ApplianceTestSupport,
                        needs_local_appliance,
                        needs_mesos,
                        slow)
 from toil.version import exactPython
-from toil.exceptions import FailedJobsException
 
 logger = logging.getLogger(__name__)
 
@@ -207,28 +207,28 @@ class AutoDeploymentTest(ApplianceTestSupport):
 
     def testDeferralWithConcurrentEncapsulation(self):
         """
-        Ensure that the following DAG succeeds:
-
-                      ┌───────────┐
-                      │ Root (W1) │
-                      └───────────┘
-                            │
-                 ┌──────────┴─────────┐
-                 ▼                    ▼
-        ┌────────────────┐ ┌────────────────────┐
-        │ Deferring (W2) │ │ Encapsulating (W3) │═══════════════╗
-        └────────────────┘ └────────────────────┘               ║
-                                      │                         ║
-                                      ▼                         ▼
-                            ┌───────────────────┐      ┌────────────────┐
-                            │ Encapsulated (W3) │      │ Follow-on (W6) │
-                            └───────────────────┘      └────────────────┘
-                                      │                         │
-                              ┌───────┴────────┐                │
-                              ▼                ▼                ▼
-                      ┌──────────────┐ ┌──────────────┐ ┌──────────────┐
-                      │ Dummy 1 (W4) │ │ Dummy 2 (W5) │ │  Last (W6)   │
-                      └──────────────┘ └──────────────┘ └──────────────┘
+        Ensure that the following DAG succeeds::
+
+                          ┌───────────┐
+                          │ Root (W1) │
+                          └───────────┘
+                                │
+                     ┌──────────┴─────────┐
+                     ▼                    ▼
+            ┌────────────────┐ ┌────────────────────┐
+            │ Deferring (W2) │ │ Encapsulating (W3) │═══════════════╗
+            └────────────────┘ └────────────────────┘               ║
+                                          │                         ║
+                                          ▼                         ▼
+                                ┌───────────────────┐      ┌────────────────┐
+                                │ Encapsulated (W3) │      │ Follow-on (W6) │
+                                └───────────────────┘      └────────────────┘
+                                          │                         │
+                                  ┌───────┴────────┐                │
+                                  ▼                ▼                ▼
+                          ┌──────────────┐ ┌──────────────┐ ┌──────────────┐
+                          │ Dummy 1 (W4) │ │ Dummy 2 (W5) │ │  Last (W6)   │
+                          └──────────────┘ └──────────────┘ └──────────────┘
 
         The Wn numbers denote the worker processes that a particular job is run in. `Deferring`
         adds a deferred function and then runs for a long time. The deferred function will be
@@ -313,28 +313,28 @@ class AutoDeploymentTest(ApplianceTestSupport):
 
     def testDeferralWithFailureAndEncapsulation(self):
         """
-        Ensure that the following DAG succeeds:
-
-                      ┌───────────┐
-                      │ Root (W1) │
-                      └───────────┘
-                            │
-                 ┌──────────┴─────────┐
-                 ▼                    ▼
-        ┌────────────────┐ ┌────────────────────┐
-        │ Deferring (W2) │ │ Encapsulating (W3) │═══════════════════════╗
-        └────────────────┘ └────────────────────┘                       ║
-                                      │                                 ║
-                                      ▼                                 ▼
-                            ┌───────────────────┐              ┌────────────────┐
-                            │ Encapsulated (W3) │════════════╗ │ Follow-on (W7) │
-                            └───────────────────┘            ║ └────────────────┘
-                                      │                      ║
-                               ┌──────┴──────┐               ║
-                               ▼             ▼               ▼
-                        ┌────────────┐┌────────────┐ ┌──────────────┐
-                        │ Dummy (W4) ││ Dummy (W5) │ │ Trigger (W6) │
-                        └────────────┘└────────────┘ └──────────────┘
+        Ensure that the following DAG succeeds::
+
+                          ┌───────────┐
+                          │ Root (W1) │
+                          └───────────┘
+                                │
+                     ┌──────────┴─────────┐
+                     ▼                    ▼
+            ┌────────────────┐ ┌────────────────────┐
+            │ Deferring (W2) │ │ Encapsulating (W3) │═══════════════════════╗
+            └────────────────┘ └────────────────────┘                       ║
+                                          │                                 ║
+                                          ▼                                 ▼
+                                ┌───────────────────┐              ┌────────────────┐
+                                │ Encapsulated (W3) │════════════╗ │ Follow-on (W7) │
+                                └───────────────────┘            ║ └────────────────┘
+                                          │                      ║
+                                   ┌──────┴──────┐               ║
+                                   ▼             ▼               ▼
+                            ┌────────────┐┌────────────┐ ┌──────────────┐
+                            │ Dummy (W4) ││ Dummy (W5) │ │ Trigger (W6) │
+                            └────────────┘└────────────┘ └──────────────┘
 
         `Trigger` causes `Deferring` to crash. `Follow-on` runs next, detects `Deferring`'s
         left-overs and runs the deferred function. `Follow-on` is an instance of `Job` and the

toil/test/src/busTest.py

@@ -15,17 +15,17 @@
 import logging
 import os
 from threading import Thread, current_thread
-from typing import Optional
 
 from toil.batchSystems.abstractBatchSystem import BatchJobExitReason
-from toil.bus import JobCompletedMessage, JobIssuedMessage, MessageBus, replay_message_bus
+from toil.bus import (JobCompletedMessage,
+                      JobIssuedMessage,
+                      MessageBus,
+                      replay_message_bus)
 from toil.common import Toil
-from toil.job import Job
 from toil.exceptions import FailedJobsException
+from toil.job import Job
 from toil.test import ToilTest, get_temp_file
 
-
-
 logger = logging.getLogger(__name__)
 
 class MessageBusTest(ToilTest):

toil/test/src/checkpointTest.py

@@ -12,9 +12,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from toil.exceptions import FailedJobsException
 from toil.job import Job
 from toil.jobStores.abstractJobStore import NoSuchFileException
-from toil.exceptions import FailedJobsException
 from toil.test import ToilTest, slow
 
 
@@ -82,7 +82,7 @@ class CheckRetryCount(Job):
 
     def run(self, fileStore):
         retryCount = self.getNumRetries(fileStore)
-        fileStore.logToMaster(str(retryCount))
+        fileStore.log_to_leader(str(retryCount))
         if retryCount < self.numFailuresBeforeSuccess:
             self.addChild(AlwaysFail())
 

toil/test/src/deferredFunctionTest.py

@@ -20,8 +20,8 @@ from uuid import uuid4
 
 import psutil
 
-from toil.job import Job
 from toil.exceptions import FailedJobsException
+from toil.job import Job
 from toil.lib.threading import cpu_count
 from toil.test import ToilTest, slow
 

toil/test/src/fileStoreTest.py

@@ -29,14 +29,18 @@ from uuid import uuid4
 import pytest
 
 from toil.common import Toil
+from toil.exceptions import FailedJobsException
 from toil.fileStores import FileID
 from toil.fileStores.cachingFileStore import (CacheUnbalancedError,
                                               IllegalDeletionCacheError)
 from toil.job import Job
 from toil.jobStores.abstractJobStore import NoSuchFileException
-from toil.exceptions import FailedJobsException
 from toil.realtimeLogger import RealtimeLogger
-from toil.test import ToilTest, needs_aws_ec2, needs_google_project, needs_google_storage, slow
+from toil.test import (ToilTest,
+                       needs_aws_ec2,
+                       needs_google_project,
+                       needs_google_storage,
+                       slow)
 
 # Some tests take too long on the AWS jobstore and are unquitable for CI.  They can be
 # be run during manual tests by setting this to False.
@@ -397,6 +401,7 @@ class hidden:
             self.options.caching = True
 
         @slow
+        @pytest.mark.xfail(reason="Cannot succeed in time on small CI runners")
         def testExtremeCacheSetup(self):
             """
             Try to create the cache with bad worker active and then have 10 child jobs try to run in
@@ -472,7 +477,15 @@ class hidden:
             # the cache hence this test is redundant (caching will be free).
             if not self.options.jobStore.startswith(('aws', 'google')):
                 workDirDev = os.stat(self.options.workDir).st_dev
-                jobStoreDev = os.stat(os.path.dirname(self.options.jobStore)).st_dev
+                if self.options.jobStore.startswith("file:"):
+                    # Before #4538, options.jobStore would have the raw path while the Config object would prepend the
+                    # filesystem to the path (/path/to/file vs file:/path/to/file)
+                    # The options namespace and the Config object now have the exact same behavior
+                    # which means parse_jobstore will be called with argparse rather than with the config object
+                    # so remove the prepended file: scheme
+                    jobStoreDev = os.stat(os.path.dirname(self.options.jobStore[5:])).st_dev
+                else:
+                    jobStoreDev = os.stat(os.path.dirname(self.options.jobStore)).st_dev
                 if workDirDev == jobStoreDev:
                     self.skipTest('Job store and working directory are on the same filesystem.')
 
@@ -633,6 +646,8 @@ class hidden:
 
             Attempting to get the file from the jobstore should not fail.
             """
+            print("Testing")
+            logger.debug("Testing testing 123")
             self.options.retryCount = 0
             self.options.logLevel = 'DEBUG'
             A = Job.wrapJobFn(self._adjustCacheLimit, newTotalMB=1024, disk='1G')
@@ -655,20 +670,20 @@ class hidden:
             :param fileMB: File Size
             :return: Job store file ID for second written file
             """
-            job.fileStore.logToMaster('Double writing a file into job store')
+            job.fileStore.log_to_leader('Double writing a file into job store')
             work_dir = job.fileStore.getLocalTempDir()
             with open(os.path.join(work_dir, str(uuid4())), 'wb') as testFile:
                 testFile.write(os.urandom(fileMB * 1024 * 1024))
 
-            job.fileStore.logToMaster('Writing copy 1 and discarding ID')
+            job.fileStore.log_to_leader('Writing copy 1 and discarding ID')
             job.fileStore.writeGlobalFile(testFile.name)
-            job.fileStore.logToMaster('Writing copy 2 and saving ID')
+            job.fileStore.log_to_leader('Writing copy 2 and saving ID')
             fsID = job.fileStore.writeGlobalFile(testFile.name)
-            job.fileStore.logToMaster(f'Copy 2 ID: {fsID}')
+            job.fileStore.log_to_leader(f'Copy 2 ID: {fsID}')
 
             hidden.AbstractCachingFileStoreTest._readFromJobStoreWithoutAssertions(job, fsID)
 
-            job.fileStore.logToMaster('Writing copy 3 and returning ID')
+            job.fileStore.log_to_leader('Writing copy 3 and returning ID')
             return job.fileStore.writeGlobalFile(testFile.name)
 
         @staticmethod
@@ -680,7 +695,7 @@ class hidden:
             :param fsID: Job store file ID for the read file
             :return: None
             """
-            job.fileStore.logToMaster('Reading the written file')
+            job.fileStore.log_to_leader('Reading the written file')
             job.fileStore.readGlobalFile(fsID)
 
         # writeGlobalFile tests
@@ -794,8 +809,7 @@ class hidden:
             """
             Write a local file to the job store (hence adding a copy to cache), then have 10 jobs
             read it. Assert cached file size never goes up, assert unused job
-            required disk space is always:
-                   (a multiple of job reqs) - (number of current file readers * filesize).
+            required disk space is always ``(a multiple of job reqs) - (number of current file readers * filesize)``.
             At the end, assert the cache shows unused job-required space = 0.
             """
             self._testMultipleJobsReadGlobalFileFunction(cacheHit=True)
@@ -805,8 +819,7 @@ class hidden:
             """
             Write a non-local file to the job store(hence no cached copy), then have 10 jobs read
             it. Assert cached file size never goes up, assert unused job
-            required disk space is always:
-                   (a multiple of job reqs) - (number of current file readers * filesize).
+            required disk space is always ``(a multiple of job reqs) - (number of current file readers * filesize)``.
             At the end, assert the cache shows unused job-required space = 0.
             """
             self._testMultipleJobsReadGlobalFileFunction(cacheHit=False)
@@ -834,7 +847,10 @@ class hidden:
                 jobs[i].addChild(B)
             Job.Runner.startToil(A, self.options)
             with open(x.name) as y:
-                assert int(y.read()) > 2
+                # At least one job at a time should have been observed.
+                # We can't actually guarantee that any of our jobs will
+                # see each other currently running.
+                assert int(y.read()) > 1
 
         @staticmethod
         def _multipleFileReader(job, diskMB, fsID, maxWriteFile):
@@ -1121,7 +1137,7 @@ class hidden:
             """
 
             # Make sure we actually have the disk size we are supposed to
-            job.fileStore.logToMaster('Job is running with %d bytes of disk, %d requested' % (job.disk, jobDisk))
+            job.fileStore.log_to_leader('Job is running with %d bytes of disk, %d requested' % (job.disk, jobDisk))
             assert job.disk == jobDisk, 'Job was scheduled with %d bytes but requested %d' % (job.disk, jobDisk)
 
             cls = hidden.AbstractCachingFileStoreTest
@@ -1187,7 +1203,7 @@ class hidden:
                 try:
                     job.fileStore.deleteLocalFile(fileToDelete)
                 except IllegalDeletionCacheError:
-                    job.fileStore.logToMaster('Detected a deleted file %s.' % fileToDelete)
+                    job.fileStore.log_to_leader('Detected a deleted file %s.' % fileToDelete)
                     os.rename(tempfile, outfile)
                 else:
                     # If we are processing the write test, or if we are testing the immutably read

toil/test/src/helloWorldTest.py

@@ -24,7 +24,7 @@ class HelloWorldTest(ToilTest):
 
 class HelloWorld(Job):
     def __init__(self):
-        Job.__init__(self,  memory=100000, cores=2, disk="3G")
+        Job.__init__(self,  memory=100000, cores=1, disk="3G")
 
     def run(self, fileStore):
         fileID = self.addChildJobFn(childFn, cores=1, memory="1M", disk="3G").rv()

toil/test/src/importExportFileTest.py

@@ -18,9 +18,9 @@ import stat
 import uuid
 
 from toil.common import Toil
+from toil.exceptions import FailedJobsException
 from toil.fileStores import FileID
 from toil.job import Job
-from toil.exceptions import FailedJobsException
 from toil.test import ToilTest, slow
 
 

toil/test/src/jobDescriptionTest.py

@@ -13,7 +13,8 @@
 # limitations under the License.
 
 import os
-from argparse import ArgumentParser
+
+from configargparse import ArgumentParser
 
 from toil.common import Toil
 from toil.job import Job, JobDescription, TemporaryID

toil/test/src/jobServiceTest.py

@@ -24,9 +24,9 @@ from unittest import skipIf
 import pytest
 
 from toil.batchSystems.singleMachine import SingleMachineBatchSystem
+from toil.exceptions import FailedJobsException
 from toil.job import Job
 from toil.leader import DeadlockException
-from toil.exceptions import FailedJobsException
 from toil.lib.retry import retry_flaky_test
 from toil.test import ToilTest, get_temp_file, slow
 

toil/test/src/jobTest.py

@@ -20,8 +20,8 @@ import unittest
 import pytest
 
 from toil.common import Toil
-from toil.job import Job, JobFunctionWrappingJob, JobGraphDeadlockException
 from toil.exceptions import FailedJobsException
+from toil.job import Job, JobFunctionWrappingJob, JobGraphDeadlockException
 from toil.test import ToilTest, get_temp_file, slow
 
 logger = logging.getLogger(__name__)
@@ -37,15 +37,15 @@ class JobTest(ToilTest):
     @slow
     def testStatic(self):
         r"""
-        Create a DAG of jobs non-dynamically and run it. DAG is:
+        Create a DAG of jobs non-dynamically and run it. DAG is::
 
-        A -> F
-        \-------
-        B -> D  \
-         \       \
-          ------- C -> E
+            A -> F
+            \-------
+            B -> D  \
+             \       \
+              ------- C -> E
 
-        Follow on is marked by ->
+        Follow on is marked by ``->``
         """
         outFile = get_temp_file(rootDir=self._createTempDir())
         try:
@@ -81,15 +81,15 @@ class JobTest(ToilTest):
 
     def testStatic2(self):
         r"""
-        Create a DAG of jobs non-dynamically and run it. DAG is:
+        Create a DAG of jobs non-dynamically and run it. DAG is::
 
-        A -> F
-        \-------
-        B -> D  \
-         \       \
-          ------- C -> E
+            A -> F
+            \-------
+            B -> D  \
+             \       \
+              ------- C -> E
 
-        Follow on is marked by ->
+        Follow on is marked by ``->``
         """
         outFile = get_temp_file(rootDir=self._createTempDir())
         try:
@@ -269,7 +269,7 @@ class JobTest(ToilTest):
         identifies leaf vertices incorrectly
 
         Test verification of new checkpoint jobs being leaf verticies,
-        starting with the following baseline workflow:
+        starting with the following baseline workflow::
 
             Parent
               |
@@ -291,7 +291,7 @@ class JobTest(ToilTest):
                               omits the workflow root job
 
         Test verification of a new checkpoint job being leaf vertex,
-        starting with a baseline workflow of a single, root job:
+        starting with a baseline workflow of a single, root job::
 
             Root # Checkpoint=True
 
@@ -623,7 +623,7 @@ class JobTest(ToilTest):
         return True
 
 def simpleJobFn(job, value):
-    job.fileStore.logToMaster(value)
+    job.fileStore.log_to_leader(value)
 
 def fn1Test(string, outputFile):
     """

toil/test/src/miscTests.py

@@ -16,12 +16,14 @@ import logging
 import os
 import random
 import sys
-import tempfile
 from uuid import uuid4
 
 from toil.common import getNodeID
 from toil.lib.exceptions import panic, raise_
-from toil.lib.io import AtomicFileCreate, atomic_install, atomic_tmp_file
+from toil.lib.io import (AtomicFileCreate,
+                         atomic_install,
+                         atomic_tmp_file,
+                         mkdtemp)
 from toil.lib.misc import CalledProcessErrorStderr, call_command
 from toil.test import ToilTest, slow
 
@@ -63,7 +65,7 @@ class MiscTests(ToilTest):
         files = {}
         # Create a random directory structure
         for i in range(0,10):
-            directories.append(tempfile.mkdtemp(dir=random.choice(directories), prefix='test'))
+            directories.append(mkdtemp(dir=random.choice(directories), prefix='test'))
         # Create 50 random file entries in different locations in the directories. 75% of the time
         # these are fresh files of size [1, 10] MB and 25% of the time they are hard links to old
         # files.

toil/test/src/promisedRequirementTest.py

@@ -48,7 +48,7 @@ class hidden:
                                      cores=1, memory='1M', disk='1M')
                 values = Job.Runner.startToil(root, self.getOptions(tempDir))
                 maxValue = max(values)
-                self.assertEqual(maxValue, self.cpuCount // coresPerJob)
+                self.assertLessEqual(maxValue, self.cpuCount // coresPerJob)
 
         @slow
         @retry_flaky_test(prepare=[batchSystemTest.hidden.AbstractBatchSystemJobTest.tearDown,
@@ -74,7 +74,7 @@ class hidden:
                                                 disk='1M'))
                 Job.Runner.startToil(root, self.getOptions(tempDir))
                 _, maxValue = batchSystemTest.getCounters(counterPath)
-                self.assertEqual(maxValue, self.cpuCount // coresPerJob)
+                self.assertLessEqual(maxValue, self.cpuCount // coresPerJob)
 
         def getOptions(self, tempDir, caching=True):
             options = super().getOptions(tempDir)
@@ -194,7 +194,7 @@ def logDiskUsage(job, funcName, sleep=0):
     :return: job function's disk usage
     """
     diskUsage = job.disk
-    job.fileStore.logToMaster(f'{funcName}: {diskUsage}')
+    job.fileStore.log_to_leader(f'{funcName}: {diskUsage}')
     time.sleep(sleep)
     return diskUsage
 

toil/test/src/realtimeLoggerTest.py

@@ -57,7 +57,7 @@ class MessageDetector(logging.StreamHandler):
 
 class LogTest(Job):
     def __init__(self):
-        Job.__init__(self, memory=100000, cores=2, disk='3G')
+        Job.__init__(self, memory=100000, cores=1, disk='3G')
 
     def run(self, fileStore):
         RealtimeLogger.info('This should be logged at info level')

toil/test/src/resourceTest.py

@@ -209,7 +209,7 @@ class ResourceTest(ToilTest):
         """
 
         def script():
-            import argparse
+            from configargparse import ArgumentParser
 
             from toil.common import Toil
             from toil.job import Job
@@ -218,7 +218,7 @@ class ResourceTest(ToilTest):
                 pass
 
             if __name__ == '__main__':
-                parser = argparse.ArgumentParser()
+                parser = ArgumentParser()
                 Job.Runner.addToilOptions(parser)
                 options = parser.parse_args()
                 job = Job.wrapFn(fn, memory='10M', cores=0.1, disk='10M')

toil/test/src/restartDAGTest.py

@@ -19,8 +19,8 @@ import shutil
 import signal
 
 from toil.common import Toil
-from toil.job import Job
 from toil.exceptions import FailedJobsException
+from toil.job import Job
 from toil.test import ToilTest, slow
 
 logger = logging.getLogger(__name__)

toil/test/src/resumabilityTest.py

@@ -14,17 +14,17 @@
 
 import os
 
+from toil.exceptions import FailedJobsException
 from toil.job import Job
 from toil.jobStores.abstractJobStore import NoSuchFileException
-from toil.exceptions import FailedJobsException
 from toil.test import ToilTest, slow
 
 
-@slow
 class ResumabilityTest(ToilTest):
     """
     https://github.com/BD2KGenomics/toil/issues/808
     """
+    @slow
     def test(self):
         """
         Tests that a toil workflow that fails once can be resumed without a NoSuchJobException.
@@ -53,6 +53,34 @@ class ResumabilityTest(ToilTest):
             # store ID: n/t/jobwbijqL failed with exit value 1"
             self.assertTrue("failed with exit value" not in logString)
 
+    def test_chaining(self):
+        """
+        Tests that a job which is chained to and fails can resume and succeed.
+        """
+
+        options = Job.Runner.getDefaultOptions(self._getTestJobStorePath())
+        options.logLevel = "DEBUG"
+        options.retryCount = 0
+        tempDir = self._createTempDir()
+        options.logFile = os.path.join(tempDir, "log.txt")
+
+        root = Job.wrapJobFn(chaining_parent)
+
+        with self.assertRaises(FailedJobsException):
+            # This one is intended to fail.
+            Job.Runner.startToil(root, options)
+
+        with open(options.logFile, 'r') as f:
+            log_content = f.read()
+            # Make sure we actually did do chaining
+            assert "Chaining from" in log_content
+
+        # Because of the chaining, the problem we are looking for is the job
+        # with the root ID not being able to load the body of a job with a
+        # different ID. That doesn't look like a job deleted despite failure.
+        options.restart = True
+        Job.Runner.startToil(root, options)
+
 def parent(job):
     """
     Set up a bunch of dummy child jobs, and a bad job that needs to be
@@ -62,6 +90,12 @@ def parent(job):
         job.addChildJobFn(goodChild)
     job.addFollowOnJobFn(badChild)
 
+def chaining_parent(job):
+    """
+    Set up a failing job to chain to.
+    """
+    job.addFollowOnJobFn(badChild)
+
 def goodChild(job):
     """
     Does nothing.

toil/test/src/retainTempDirTest.py

@@ -14,8 +14,8 @@
 import os
 import shutil
 
-from toil.job import Job
 from toil.exceptions import FailedJobsException
+from toil.job import Job
 from toil.test import ToilTest
 
 

toil/test/src/systemTest.py

@@ -1,9 +1,9 @@
 import errno
 import multiprocessing
 import os
-import tempfile
 from functools import partial
 
+from toil.lib.io import mkdtemp
 from toil.lib.threading import cpu_count
 from toil.test import ToilTest
 
@@ -37,7 +37,7 @@ class SystemTest(ToilTest):
 
 
 def _testAtomicityOfNonEmptyDirectoryRenamesTask(parent, child, _):
-    tmpChildDir = tempfile.mkdtemp(dir=parent, prefix='child', suffix='.tmp')
+    tmpChildDir = mkdtemp(dir=parent, prefix='child', suffix='.tmp')
     grandChild = os.path.join(tmpChildDir, 'grandChild')
     open(grandChild, 'w').close()
     grandChildId = os.stat(grandChild).st_ino

toil/test/src/toilContextManagerTest.py

@@ -61,10 +61,10 @@ class ToilContextManagerTest(ToilTest):
 
 class HelloWorld(Job):
     def __init__(self):
-        Job.__init__(self, memory=100000, cores=2, disk='1M')
+        Job.__init__(self, memory=100000, disk='1M')
 
     def run(self, fileStore):
-        fileID = self.addChildJobFn(childFn, cores=1, memory='1M', disk='1M').rv()
+        fileID = self.addChildJobFn(childFn, memory='1M', disk='1M').rv()
         return self.addFollowOn(FollowOn(fileID)).rv()
 
 

toil/test/src/userDefinedJobArgTypeTest.py

@@ -59,7 +59,7 @@ class UserDefinedJobArgTypeTest(ToilTest):
 
 class JobClass(Job):
     def __init__(self, level, foo):
-        Job.__init__(self, memory=100000, cores=2, disk="300M")
+        Job.__init__(self, memory=100000, cores=1, disk="300M")
         self.level = level
         self.foo = foo