toil 6.1.0a1__py3-none-any.whl → 8.0.0__py3-none-any.whl

toil/test/mesos/helloWorld.py

@@ -23,14 +23,15 @@ from toil.job import Job
 childMessage = "The child job is now running!"
 parentMessage = "The parent job is now running!"
 
+
 def hello_world(job):
 
     job.fileStore.log_to_leader(parentMessage)
-    with open('foo_bam.txt', 'w') as handle:
-        handle.write('\nThis is a triumph...\n')
+    with open("foo_bam.txt", "w") as handle:
+        handle.write("\nThis is a triumph...\n")
 
     # Assign FileStoreID to a given file
-    foo_bam = job.fileStore.writeGlobalFile('foo_bam.txt')
+    foo_bam = job.fileStore.writeGlobalFile("foo_bam.txt")
 
     # Spawn child
     job.addChildJobFn(hello_world_child, foo_bam, memory=100, cores=0.5, disk="3G")
@@ -43,13 +44,13 @@ def hello_world_child(job, hw):
     # NOTE: path and the udpated file are stored to /tmp
     # If we want to SAVE our changes to this tmp file, we must write it out.
     with open(path) as r:
-        with open('bar_bam.txt', 'w') as handle:
+        with open("bar_bam.txt", "w") as handle:
             for line in r.readlines():
                 handle.write(line)
 
     # Assign FileStoreID to a given file
     # can also use:  job.updateGlobalFile() given the FileStoreID instantiation.
-    job.fileStore.writeGlobalFile('bar_bam.txt')
+    job.fileStore.writeGlobalFile("bar_bam.txt")
 
 
 def main():
@@ -67,5 +68,5 @@ def main():
         toil.start(i)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

toil/test/mesos/stress.py

@@ -17,58 +17,63 @@ from configargparse import ArgumentParser
 from toil.job import Job
 
 
-def touchFile( fileStore ):
+def touchFile(fileStore):
     with fileStore.writeGlobalFileStream() as (f, id):
-        f.write( "This is a triumph" )
+        f.write("This is a triumph")
+
 
 class LongTestJob(Job):
     def __init__(self, numJobs):
-        Job.__init__(self,  memory=100000, cores=0.01)
+        Job.__init__(self, memory=100000, cores=0.01)
         self.numJobs = numJobs
 
     def run(self, fileStore):
-        for i in range(0,self.numJobs):
+        for i in range(0, self.numJobs):
             self.addChild(HelloWorldJob(i))
         self.addFollowOn(LongTestFollowOn())
 
+
 class LongTestFollowOn(Job):
 
     def __init__(self):
-        Job.__init__(self,  memory=1000000, cores=0.01)
+        Job.__init__(self, memory=1000000, cores=0.01)
 
     def run(self, fileStore):
-        touchFile( fileStore )
+        touchFile(fileStore)
 
-class HelloWorldJob(Job):
 
-    def __init__(self,i):
-        Job.__init__(self,  memory=100000, cores=0.01)
-        self.i=i
+class HelloWorldJob(Job):
 
+    def __init__(self, i):
+        Job.__init__(self, memory=100000, cores=0.01)
+        self.i = i
 
     def run(self, fileStore):
-        touchFile( fileStore )
+        touchFile(fileStore)
         self.addFollowOn(HelloWorldFollowOn(self.i))
 
+
 class HelloWorldFollowOn(Job):
 
-    def __init__(self,i):
-        Job.__init__(self,  memory=200000, cores=0.01)
+    def __init__(self, i):
+        Job.__init__(self, memory=200000, cores=0.01)
         self.i = i
 
     def run(self, fileStore):
-        touchFile( fileStore)
+        touchFile(fileStore)
+
 
 def main(numJobs):
     # Boilerplate -- startToil requires options
     parser = ArgumentParser()
     Job.Runner.addToilOptions(parser)
-    options = parser.parse_args( args=['./toilTest'] )
-    options.batchSystem="mesos"
-    options.mesos_endpoint="localhost:5050"
+    options = parser.parse_args(args=["./toilTest"])
+    options.batchSystem = "mesos"
+    options.mesos_endpoint = "localhost:5050"
     # Launch first toil Job
-    i = LongTestJob( numJobs )
-    Job.Runner.startToil(i,  options )
+    i = LongTestJob(numJobs)
+    Job.Runner.startToil(i, options)
+
 
-if __name__=="__main__":
+if __name__ == "__main__":
     main(numJobs=5)

toil/test/options/__init__.py

@@ -0,0 +1,13 @@
+# Copyright (C) 2015-2021 Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

toil/test/options/options.py

@@ -0,0 +1,42 @@
+from configargparse import ArgParser
+
+from toil.common import Toil, addOptions
+from toil.test import ToilTest
+
+
+class OptionsTest(ToilTest):
+    """
+    Class to test functionality of all Toil options
+    """
+
+    def test_default_caching_slurm(self):
+        """
+        Test to ensure that caching will be set to false when running on Slurm
+        :return:
+        """
+        parser = ArgParser()
+        addOptions(parser, jobstore_as_flag=True, wdl=False, cwl=False)
+        test_args = ["--jobstore=example-jobstore", "--batchSystem=slurm"]
+        options = parser.parse_args(test_args)
+        with Toil(options) as toil:
+            caching_value = toil.config.caching
+        self.assertEqual(caching_value, False)
+
+    def test_caching_option_priority(self):
+        """
+        Test to ensure that the --caching option takes priority over the default_caching() return value
+        :return:
+        """
+        parser = ArgParser()
+        addOptions(parser, jobstore_as_flag=True, wdl=False, cwl=False)
+        # the kubernetes batchsystem (and I think all batchsystems including singlemachine) return False
+        # for default_caching
+        test_args = [
+            "--jobstore=example-jobstore",
+            "--batchSystem=kubernetes",
+            "--caching=True",
+        ]
+        options = parser.parse_args(test_args)
+        with Toil(options) as toil:
+            caching_value = toil.config.caching
+        self.assertEqual(caching_value, True)