{"action":"created","comment":{"url":"https://api.github.com/repos/BD2KGenomics/toil/pulls/comments/58666209","id":58666209,"diff_hunk":"@@ -109,7 +109,7 @@ def runToil(self, rootJob, retryCount=1, badWorker=0.5, badWorkedFailInterval=0.\n         options.logLevel = \"INFO\"\n         \n         options.retryCount = retryCount\n-        #options.clean = \"never\"\n+        options.clean = \"never\"","path":"src/toil/test/src/jobServiceTest.py","position":5,"original_position":5,"commit_id":"48c0cd705711f6bcbeb3ff25903800ad390ce8fe","original_commit_id":"50f1f0fbad41b5f505fb1f5ad024ccba877eff8f","user":{"login":"hannes-ucsc","id":5143256,"avatar_url":"https://avatars.githubusercontent.com/u/5143256?v=3","gravatar_id":"","url":"https://api.github.com/users/hannes-ucsc","html_url":"https://github.com/hannes-ucsc","followers_url":"https://api.github.com/users/hannes-ucsc/followers","following_url":"https://api.github.com/users/hannes-ucsc/following{/other_user}","gists_url":"https://api.github.com/users/hannes-ucsc/gists{/gist_id}","starred_url":"https://api.github.com/users/hannes-ucsc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hannes-ucsc/subscriptions","organizations_url":"https://api.github.com/users/hannes-ucsc/orgs","repos_url":"https://api.github.com/users/hannes-ucsc/repos","events_url":"https://api.github.com/users/hannes-ucsc/events{/privacy}","received_events_url":"https://api.github.com/users/hannes-ucsc/received_events","type":"User","site_admin":false},"body":"Presumably these tests succeed on master which doesn't have this change. If that is true, then a) your changes introduced the error you quote above or b) your other changes fix a bug in Toil which was masked by this line being commented out (options.clean defaulting to 'onsucess').","created_at":"2016-04-06T08:09:19Z","updated_at":"2016-04-06T08:09:20Z","html_url":"https://github.com/BD2KGenomics/toil/pull/723#discussion_r58666209","pull_request_url":"https://api.github.com/repos/BD2KGenomics/toil/pulls/723","_links":{"self":{"href":"https://api.github.com/repos/BD2KGenomics/toil/pulls/comments/58666209"},"html":{"href":"https://github.com/BD2KGenomics/toil/pull/723#discussion_r58666209"},"pull_request":{"href":"https://api.github.com/repos/BD2KGenomics/toil/pulls/723"}}},"pull_request":{"url":"https://api.github.com/repos/BD2KGenomics/toil/pulls/723","id":64402345,"html_url":"https://github.com/BD2KGenomics/toil/pull/723","diff_url":"https://github.com/BD2KGenomics/toil/pull/723.diff","patch_url":"https://github.com/BD2KGenomics/toil/pull/723.patch","issue_url":"https://api.github.com/repos/BD2KGenomics/toil/issues/723","number":723,"state":"open","locked":false,"title":"Refactored setupToil and other methods into common.Toil class (resolves #619)","user":{"login":"JakeNarkizian","id":10471159,"avatar_url":"https://avatars.githubusercontent.com/u/10471159?v=3","gravatar_id":"","url":"https://api.github.com/users/JakeNarkizian","html_url":"https://github.com/JakeNarkizian","followers_url":"https://api.github.com/users/JakeNarkizian/followers","following_url":"https://api.github.com/users/JakeNarkizian/following{/other_user}","gists_url":"https://api.github.com/users/JakeNarkizian/gists{/gist_id}","starred_url":"https://api.github.com/users/JakeNarkizian/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JakeNarkizian/subscriptions","organizations_url":"https://api.github.com/users/JakeNarkizian/orgs","repos_url":"https://api.github.com/users/JakeNarkizian/repos","events_url":"https://api.github.com/users/JakeNarkizian/events{/privacy}","received_events_url":"https://api.github.com/users/JakeNarkizian/received_events","type":"User","site_admin":false},"body":"The Toil class is meant to be used as a context manager and has all of the functionality of setupToil. Many of the  top level methods in common that\r\nsetupToil previously used have been refactored as regular or static methods of common.Toil.\r\n\r\nHere is a list of methods that were refactored and their common.Toil counter parts:\r\n    - (loadBatchSystem, loadBatchSystemClass, createBatchSystem) >> Toil.createBatchSystem\r\n    - loadJobStore >> Toil.loadOrCreateJobStore\r\n    - serialiseEnvironment >> Toil._serialiseEnvironment\r\n    - getToilWorkflowDir >> Toil.getWorkflowDir\r\n\r\nA word on the loadBatchSystem, loadBatchSystemClass, createBatchSystem:\r\nThese methods were extremely redundant. createBatchSystem did almost nothing; loadBatchSystem simply calls createBatchSystem and there was\r\nno useful use case for the loadBatchSystemClass method, which returns a class, without instantiating said class immediately after. Thus it made sense\r\nto flatten the three batch system methods into a single createBatchSystem.\r\n\r\nSome inlined functionality in setupToil has also been refactored into Toil methods to improve readability.\r\n\r\nHere is a list of these new methods :\r\n    - Toil._setBatchSystemEnvVars\r\n    - Toil._cacheJobs\r\n\r\ncommon.Toil includes a run method which is a refactoring of the functionality of job.startToil. Note that job.startToil has been reimplemented to use Toil.run()\r\nin order to support legacy toil scripts. Toil.run must be called inside the Toil context manager. This will allow future features to easily add setup and clean up\r\nfunctionalities that will not break backwards compatibility.\r\n\r\nTake note that Toil.__exit__ now deletes the current job store instead of 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