toil 6.1.0__py3-none-any.whl → 7.0.0__py3-none-any.whl

toil/worker.py

@@ -26,7 +26,7 @@ import sys
 import time
 import traceback
 from contextlib import contextmanager
-from typing import Any, Callable, Iterator, List, Optional
+from typing import Any, Callable, Iterator, List, Set, Optional
 
 from configargparse import ArgParser
 
@@ -36,13 +36,12 @@ from toil.cwl.utils import (CWL_UNSUPPORTED_REQUIREMENT_EXCEPTION,
                             CWL_UNSUPPORTED_REQUIREMENT_EXIT_CODE)
 from toil.deferred import DeferredFunctionManager
 from toil.fileStores.abstractFileStore import AbstractFileStore
-from toil.job import CheckpointJobDescription, Job, JobDescription
+from toil.job import CheckpointJobDescription, Job, JobDescription, DebugStoppingPointReached
 from toil.jobStores.abstractJobStore import AbstractJobStore
 from toil.lib.expando import MagicExpando
 from toil.lib.io import make_public_dir
-from toil.lib.resources import (get_total_cpu_time,
-                                get_total_cpu_time_and_memory_usage)
-from toil.statsAndLogging import configure_root_logger, set_log_level
+from toil.lib.resources import ResourceMonitor
+from toil.statsAndLogging import configure_root_logger, set_log_level, install_log_color
 
 logger = logging.getLogger(__name__)
 
@@ -53,24 +52,24 @@ class StatsDict(MagicExpando):
     jobs: List[MagicExpando]
 
 
-def nextChainable(predecessor: JobDescription, jobStore: AbstractJobStore, config: Config) -> Optional[JobDescription]:
+def nextChainable(predecessor: JobDescription, job_store: AbstractJobStore, config: Config) -> Optional[JobDescription]:
     """
     Returns the next chainable job's JobDescription after the given predecessor
     JobDescription, if one exists, or None if the chain must terminate.
 
     :param predecessor: The job to chain from
-    :param jobStore: The JobStore to fetch JobDescriptions from.
+    :param job_store: The JobStore to fetch JobDescriptions from.
     :param config: The configuration for the current run.
     """
     #If no more jobs to run or services not finished, quit
-    if predecessor.nextSuccessors() is None or len(predecessor.services) > 0 or (isinstance(predecessor, CheckpointJobDescription) and predecessor.checkpoint != None):
+    if predecessor.nextSuccessors() is None or len(predecessor.services) > 0 or (isinstance(predecessor, CheckpointJobDescription) and predecessor.checkpoint is not None):
         logger.debug("Stopping running chain of jobs: no successors: %s, services: %s, checkpoint: %s",
-                     predecessor.nextSuccessors() is None, len(predecessor.services), (isinstance(predecessor, CheckpointJobDescription) and predecessor.checkpoint != None))
+                     predecessor.nextSuccessors() is None, len(predecessor.services), (isinstance(predecessor, CheckpointJobDescription) and predecessor.checkpoint is not None))
         return None
 
 
     #Get the next set of jobs to run
-    jobs = list(predecessor.nextSuccessors())
+    jobs = list(predecessor.nextSuccessors() or set())
     if len(jobs) == 0:
         # If there are no jobs, we might just not have any children.
         logger.debug("Stopping running chain of jobs because job has no ready children or follow-ons")
@@ -89,7 +88,7 @@ def nextChainable(predecessor: JobDescription, jobStore: AbstractJobStore, confi
     logger.debug("%s would chain to ID %s", predecessor, successorID)
 
     # Load the successor JobDescription
-    successor = jobStore.load_job(successorID)
+    successor = job_store.load_job(successorID)
 
     #We check the requirements of the successor to see if we can run it
     #within the current worker
@@ -118,17 +117,38 @@ def nextChainable(predecessor: JobDescription, jobStore: AbstractJobStore, confi
         logger.debug("Next job is checkpoint, so finishing")
         return None
 
+    if not config.run_local_jobs_on_workers and predecessor.local and not successor.local:
+        # This job might be running on the leader, but the next job may not.
+        #
+        # TODO: Optimize by detecting whether we actually are on the leader,
+        # somehow.
+        logger.debug("Next job is not allowed to run on the leader, so finishing")
+        return None
+
     # Made it through! This job is chainable.
     return successor
 
-def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobStoreID: str, redirectOutputToLogFile: bool = True) -> int:
+def workerScript(
+    job_store: AbstractJobStore,
+    config: Config,
+    job_name: str,
+    job_store_id: str,
+    redirect_output_to_log_file: bool = True,
+    local_worker_temp_dir: Optional[str] = None,
+    debug_flags: Optional[Set[str]] = None
+) -> int:
     """
     Worker process script, runs a job.
 
-    :param jobStore: The JobStore to fetch JobDescriptions from.
+    :param job_store: The JobStore to fetch JobDescriptions from.
     :param config: The configuration for the current run.
-    :param jobName: The "job name" (a user friendly name) of the job to be run
-    :param jobStoreID: The job store ID of the job to be run
+    :param job_name: The "job name" (a user friendly name) of the job to be run
+    :param job_store_id: The job store ID of the job to be run
+    :param redirect_output_to_log_file: If False, log directly to the console
+        instead of capturing job output.
+    :param local_worker_temp_dir: The directory for the worker to work in. May
+        be recursively removed after the job runs.
+    :param debug_flags: Flags to set on each job before running it.
 
     :return int: 1 if a job failed, or 0 if all jobs succeeded
     """
@@ -136,6 +156,11 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
     configure_root_logger()
     set_log_level(config.logLevel)
 
+    if config.colored_logs:
+        install_log_color()
+
+    logger.debug("Worker started for job %s...", job_name)
+
     ##########################################
     #Create the worker killer, if requested
     ##########################################
@@ -182,7 +207,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
     ##########################################
 
     #First load the environment for the job.
-    with jobStore.read_shared_file_stream("environment.pickle") as fileHandle:
+    with job_store.read_shared_file_stream("environment.pickle") as fileHandle:
         environment = safeUnpickleFromStream(fileHandle)
     env_reject = {
         "TMPDIR",
@@ -228,8 +253,10 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
     toilWorkflowDir = Toil.getLocalWorkflowDir(config.workflowID, config.workDir)
     # Dir to put lock files in, ideally not on NFS.
     toil_coordination_dir = Toil.get_local_workflow_coordination_dir(config.workflowID, config.workDir, config.coordination_dir)
-    localWorkerTempDir = make_public_dir(in_directory=toilWorkflowDir)
-    os.chmod(localWorkerTempDir, 0o755)
+    if local_worker_temp_dir is None:
+        # Invent a temp directory to work in
+        local_worker_temp_dir = make_public_dir(toilWorkflowDir)
+    os.chmod(local_worker_temp_dir, 0o755)
 
     ##########################################
     #Setup the logging
@@ -245,12 +272,12 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
     #file descriptor 1, and standard error is file descriptor 2.
 
     # Do we even want to redirect output? Let the config make us not do it.
-    redirectOutputToLogFile = redirectOutputToLogFile and not config.disableWorkerOutputCapture
+    redirect_output_to_log_file = redirect_output_to_log_file and not config.disableWorkerOutputCapture
 
     #What file do we want to point FDs 1 and 2 to?
-    tempWorkerLogPath = os.path.join(localWorkerTempDir, "worker_log.txt")
+    tempWorkerLogPath = os.path.join(local_worker_temp_dir, "worker_log.txt")
 
-    if redirectOutputToLogFile:
+    if redirect_output_to_log_file:
         # Announce that we are redirecting logging, and where it will now go.
         # This is only important if we are trying to manually trace a faulty worker invocation.
         logger.debug("Redirecting logging to %s", tempWorkerLogPath)
@@ -313,17 +340,17 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
         # Load the JobDescription
         ##########################################
 
-        jobDesc = jobStore.load_job(jobStoreID)
+        jobDesc = job_store.load_job(job_store_id)
         logger.debug("Parsed job description")
 
         ##########################################
         # Cleanup from any earlier invocation of the job
         ##########################################
 
-        if jobDesc.command is None:
+        if not jobDesc.has_body():
             logger.debug("Job description has no body to run.")
             # Cleanup jobs already finished
-            jobDesc.clear_nonexistent_dependents(jobStore)
+            jobDesc.clear_nonexistent_dependents(job_store)
             logger.debug("Cleaned up any references to completed successor jobs")
 
         # This cleans the old log file which may
@@ -331,8 +358,8 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
         oldLogFile = jobDesc.logJobStoreFileID
         if oldLogFile is not None:
             jobDesc.logJobStoreFileID = None
-            jobStore.update_job(jobDesc)  # Update first, before deleting any files
-            jobStore.delete_file(oldLogFile)
+            job_store.update_job(jobDesc)  # Update first, before deleting any files
+            job_store.delete_file(oldLogFile)
 
         ##########################################
         # If a checkpoint exists, restart from the checkpoint
@@ -350,13 +377,13 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
                 if jobDesc.remainingTryCount < 0:
                     raise RuntimeError("The try count of the job cannot be negative.")
                 jobDesc.remainingTryCount = max(0, jobDesc.remainingTryCount - 1)
-                jobDesc.restartCheckpoint(jobStore)
+                jobDesc.restartCheckpoint(job_store)
             # Otherwise, the job and successors are done, and we can cleanup stuff we couldn't clean
             # because of the job being a checkpoint
             else:
                 logger.debug("The checkpoint jobs seems to have completed okay, removing any checkpoint files to delete.")
                 #Delete any remnant files
-                list(map(jobStore.delete_file, list(filter(jobStore.file_exists, jobDesc.checkpointFilesToDelete))))
+                list(map(job_store.delete_file, list(filter(job_store.file_exists, jobDesc.checkpointFilesToDelete))))
 
         ##########################################
         #Setup the stats, if requested
@@ -365,7 +392,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
         if config.stats:
             # Remember the cores from the first job, which is how many we have reserved for us.
             statsDict.workers.requested_cores = jobDesc.cores
-            startClock = get_total_cpu_time()
+            startClock = ResourceMonitor.get_total_cpu_time()
 
         startTime = time.time()
         while True:
@@ -375,20 +402,22 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
             logger.info("Working on job %s", jobDesc)
 
-            if jobDesc.command is not None:
-                if not jobDesc.command.startswith("_toil "):
-                    raise RuntimeError("Job command must start with '_toil' before being converted to an executable command.")
-                logger.debug("Got a command to run: %s" % jobDesc.command)
+            if jobDesc.has_body():
                 # Load the job. It will use the same JobDescription we have been using.
-                job = Job.loadJob(jobStore, jobDesc)
+                job = Job.loadJob(job_store, jobDesc)
                 if isinstance(jobDesc, CheckpointJobDescription):
-                    # If it is a checkpoint job, save the command
-                    jobDesc.checkpoint = jobDesc.command
+                    # If it is a checkpoint job, set the checkpoint
+                    jobDesc.set_checkpoint()
 
                 logger.info("Loaded body %s from description %s", job, jobDesc)
 
+                if debug_flags:
+                    for flag in debug_flags:
+                        logger.debug("Turning on debug flag %s on job", flag)
+                        job.set_debug_flag(flag)
+
                 # Create a fileStore object for the job
-                fileStore = AbstractFileStore.createFileStore(jobStore, jobDesc, localWorkerTempDir, blockFn,
+                fileStore = AbstractFileStore.createFileStore(job_store, jobDesc, local_worker_temp_dir, blockFn,
                                                               caching=config.caching)
                 with job._executor(stats=statsDict if config.stats else None,
                                    fileStore=fileStore):
@@ -406,11 +435,11 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
                             # wants across multiple Toil versions. We also
                             # still pass a jobGraph argument to placate old
                             # versions of Cactus.
-                            job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
+                            job._runner(jobGraph=None, jobStore=job_store, fileStore=fileStore, defer=defer)
 
                             # When the executor for the job finishes it will
-                            # kick off a commit with the command link to the
-                            # job body cut.
+                            # kick off a commit with the link to the job body
+                            # cut.
 
                 # Accumulate messages from this job & any subsequent chained jobs
                 statsDict.workers.logs_to_leader += fileStore.logging_messages
@@ -419,9 +448,9 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
                 logger.info("Completed body for %s", jobDesc)
 
             else:
-                #The command may be none, in which case
-                #the JobDescription is either a shell ready to be deleted or has
-                #been scheduled after a failure to cleanup
+                # The body may not be attached, in which case the
+                # JobDescription is either a shell ready to be deleted or has
+                # been scheduled after a failure to cleanup
                 logger.debug("No user job to run, so finishing")
                 break
 
@@ -431,7 +460,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
             ##########################################
             #Establish if we can run another job within the worker
             ##########################################
-            successor = nextChainable(jobDesc, jobStore, config)
+            successor = nextChainable(jobDesc, job_store, config)
             if successor is None or config.disableChaining:
                 # Can't chain any more jobs. We are going to stop.
 
@@ -470,7 +499,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
             # Build a fileStore to update the job and commit the replacement.
             # TODO: can we have a commit operation without an entire FileStore???
-            fileStore = AbstractFileStore.createFileStore(jobStore, jobDesc, localWorkerTempDir, blockFn,
+            fileStore = AbstractFileStore.createFileStore(job_store, jobDesc, local_worker_temp_dir, blockFn,
                                                           caching=config.caching)
 
             # Update blockFn to wait for that commit operation.
@@ -485,7 +514,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
         #Finish up the stats
         ##########################################
         if config.stats:
-            totalCPUTime, totalMemoryUsage = get_total_cpu_time_and_memory_usage()
+            totalCPUTime, totalMemoryUsage = ResourceMonitor.get_total_cpu_time_and_memory_usage()
             statsDict.workers.time = str(time.time() - startTime)
             statsDict.workers.clock = str(totalCPUTime - startClock)
             statsDict.workers.memory = str(totalMemoryUsage)
@@ -501,16 +530,20 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
 
         # log the worker log path here so that if the file is truncated the path can still be found
-        if redirectOutputToLogFile:
-            logger.info("Worker log can be found at %s. Set --cleanWorkDir to retain this log", localWorkerTempDir)
+        if redirect_output_to_log_file:
+            logger.info("Worker log can be found at %s. Set --cleanWorkDir to retain this log", local_worker_temp_dir)
 
         logger.info("Finished running the chain of jobs on this node, we ran for a total of %f seconds", time.time() - startTime)
 
     ##########################################
     #Trapping where worker goes wrong
     ##########################################
+    except DebugStoppingPointReached:
+        # Job wants the worker to stop for debugging
+        raise
     except BaseException as e: #Case that something goes wrong in worker, or we are asked to stop
-        traceback.print_exc()
+        if not isinstance(e, SystemExit):
+            logger.critical("Worker crashed with traceback:\n%s", traceback.format_exc())
         logger.error("Exiting the worker because of a failed job on host %s", socket.gethostname())
         if isinstance(e, CWL_UNSUPPORTED_REQUIREMENT_EXCEPTION):
             # We need to inform the leader that this is a CWL workflow problem
@@ -551,7 +584,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
 
         # Clobber any garbage state we have for this job from failing with
         # whatever good state is still stored in the JobStore
-        jobDesc = jobStore.load_job(jobStoreID)
+        jobDesc = job_store.load_job(job_store_id)
         # Remember that we failed
         jobAttemptFailed = True
 
@@ -563,7 +596,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
     # Flush at the Python level
     sys.stdout.flush()
     sys.stderr.flush()
-    if redirectOutputToLogFile:
+    if redirect_output_to_log_file:
         # Flush at the OS level
         os.fsync(1)
         os.fsync(2)
@@ -590,11 +623,11 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
     # relative to the end (since Python won't decode Unicode backward, or even
     # interpret seek offsets in characters for us). TODO: We may get invalid or
     # just different Unicode by breaking up a character at the boundary!
-    if jobAttemptFailed and redirectOutputToLogFile:
-        jobDesc.logJobStoreFileID = logJobStoreFileID = jobStore.getEmptyFileStoreID(
+    if jobAttemptFailed and redirect_output_to_log_file:
+        jobDesc.logJobStoreFileID = logJobStoreFileID = job_store.getEmptyFileStoreID(
             jobDesc.jobStoreID, cleanup=True
         )
-        with jobStore.update_file_stream(logJobStoreFileID) as w:
+        with job_store.update_file_stream(logJobStoreFileID) as w:
             with open(tempWorkerLogPath, 'rb') as f:
                 if os.path.getsize(tempWorkerLogPath) > logFileByteReportLimit !=0:
                     if logFileByteReportLimit > 0:
@@ -604,10 +637,10 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
                 # Dump the possibly-invalid-Unicode bytes into the log file
                 w.write(f.read()) # TODO load file using a buffer
         # Commit log file reference back to JobStore
-        jobStore.update_job(jobDesc)
+        job_store.update_job(jobDesc)
 
     elif ((debugging or (config.writeLogsFromAllJobs and not jobDesc.local))
-          and redirectOutputToLogFile):  # write log messages
+          and redirect_output_to_log_file):  # write log messages
         with open(tempWorkerLogPath, 'rb') as logFile:
             if os.path.getsize(tempWorkerLogPath) > logFileByteReportLimit != 0:
                 if logFileByteReportLimit > 0:
@@ -624,7 +657,7 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
         # We have stats/logging to report back.
         # We report even if the job attempt failed.
         # TODO: Will that upset analysis of the stats?
-        jobStore.write_logs(json.dumps(statsDict, ensure_ascii=True))
+        job_store.write_logs(json.dumps(statsDict, ensure_ascii=True))
 
     # Remove the temp dir
     cleanUp = config.cleanWorkDir
@@ -642,14 +675,14 @@ def workerScript(jobStore: AbstractJobStore, config: Config, jobName: str, jobSt
                 os.chmod(os.path.dirname(path),  stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR)
             except PermissionError as e:
                 logger.error('Could not set permissions on %s to allow cleanup of %s: %s', os.path.dirname(path), path, e)
-        shutil.rmtree(localWorkerTempDir, onerror=make_parent_writable)
+        shutil.rmtree(local_worker_temp_dir, onerror=make_parent_writable)
 
     # This must happen after the log file is done with, else there is no place to put the log
     if (not jobAttemptFailed) and jobDesc.is_subtree_done():
         for merged_in in jobDesc.get_chain():
             # We can now safely get rid of the JobDescription, and all jobs it chained up
-            jobStore.delete_job(merged_in.job_store_id)
-        
+            job_store.delete_job(merged_in.job_store_id)
+
 
     if jobAttemptFailed:
         return failure_exit_code
@@ -719,25 +752,19 @@ def in_contexts(contexts: List[str]) -> Iterator[None]:
 def main(argv: Optional[List[str]] = None) -> None:
     if argv is None:
         argv = sys.argv
-
     # Parse our command line
     options = parse_args(argv)
 
-    # Parse input args
-    jobName = argv[1]
-    jobStoreLocator = argv[2]
-    jobStoreID = argv[3]
-
     ##########################################
     #Load the jobStore/config file
     ##########################################
 
-    jobStore = Toil.resumeJobStore(options.jobStoreLocator)
-    config = jobStore.config
+    job_store = Toil.resumeJobStore(options.jobStoreLocator)
+    config = job_store.config
 
     with in_contexts(options.context):
         # Call the worker
-        exit_code = workerScript(jobStore, config, options.jobName, options.jobStoreID)
+        exit_code = workerScript(job_store, config, options.jobName, options.jobStoreID)
 
     # Exit with its return value
     sys.exit(exit_code)

{toil-6.1.0.dist-info → toil-7.0.0.dist-info}/LICENSE

@@ -202,3 +202,28 @@
    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.
+
+All code in this repository excluding src/toil/statsAndLogging.py::install_log_color is under the Apache License as outlined directly above.
+Some code in src/toil/statsAndLogging.py::install_log_color is under the MiniWDL MIT License as outlined directly below.
+
+MIT License
+
+Copyright (c) 2018 Chan Zuckerberg Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{toil-6.1.0.dist-info → toil-7.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: toil
-Version: 6.1.0
+Version: 7.0.0
 Summary: Pipeline management software for clusters.
 Home-page: https://github.com/DataBiosphere/toil
 Author: Benedict Paten and the Toil community
@@ -29,30 +29,32 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: System :: Distributed Computing
 Classifier: Topic :: Utilities
 Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: dill <0.4,>=0.3.2
-Requires-Dist: requests <3,>=2
+Requires-Dist: requests <=2.31.0
 Requires-Dist: docker <8,>=6.1.0
 Requires-Dist: urllib3 <3,>=1.26.0
 Requires-Dist: python-dateutil
 Requires-Dist: psutil <6,>=3.0.1
 Requires-Dist: PyPubSub <5,>=4.0.3
 Requires-Dist: addict <2.5,>=2.2.1
-Requires-Dist: pytz >=2012
 Requires-Dist: enlighten <2,>=1.5.2
 Requires-Dist: configargparse <2,>=1.7
 Requires-Dist: ruamel.yaml >=0.15
 Requires-Dist: pyyaml <7,>=6
 Requires-Dist: typing-extensions <5,>=4.6.2
+Requires-Dist: coloredlogs <16,>=15
 Provides-Extra: all
-Requires-Dist: boto <3,>=2.48.0 ; extra == 'all'
-Requires-Dist: boto3-stubs[boto3,iam,s3,sdb,sts] <2,>=1.28.3.post2 ; extra == 'all'
+Requires-Dist: boto3-stubs[autoscaling,boto3,ec2,iam,s3,sdb,sts] <2,>=1.28.3.post2 ; extra == 'all'
 Requires-Dist: mypy-boto3-iam <2,>=1.28.3.post2 ; extra == 'all'
-Requires-Dist: moto <5,>=4.1.11 ; extra == 'all'
-Requires-Dist: cwltool ==3.1.20240112164112 ; extra == 'all'
+Requires-Dist: mypy-boto3-s3 <2,>=1.28.3.post2 ; extra == 'all'
+Requires-Dist: moto <6,>=5.0.3 ; extra == 'all'
+Requires-Dist: ec2-metadata <3 ; extra == 'all'
+Requires-Dist: cwltool ==3.1.20240508115724 ; extra == 'all'
 Requires-Dist: schema-salad <9,>=8.4.20230128170514 ; extra == 'all'
-Requires-Dist: galaxy-tool-util <23 ; extra == 'all'
-Requires-Dist: galaxy-util <23 ; extra == 'all'
+Requires-Dist: galaxy-tool-util <25 ; extra == 'all'
+Requires-Dist: galaxy-util <25 ; extra == 'all'
 Requires-Dist: ruamel.yaml <=0.19,>=0.15 ; extra == 'all'
 Requires-Dist: ruamel.yaml.clib >=0.2.6 ; extra == 'all'
 Requires-Dist: networkx !=2.8.1,<4 ; extra == 'all'
@@ -66,28 +68,29 @@ Requires-Dist: kubernetes-stubs ==v22.6.0post1 ; extra == 'all'
 Requires-Dist: types-urllib3 ; extra == 'all'
 Requires-Dist: types-PyYAML ; extra == 'all'
 Requires-Dist: idna >=2 ; extra == 'all'
-Requires-Dist: miniwdl ==1.11.1 ; extra == 'all'
+Requires-Dist: miniwdl ==1.12.0 ; extra == 'all'
 Requires-Dist: wdlparse ==0.1.0 ; extra == 'all'
 Requires-Dist: connexion[swagger-ui] <3,>=2.10.0 ; extra == 'all'
 Requires-Dist: flask <3,>=2.0 ; extra == 'all'
 Requires-Dist: werkzeug <3,>=2.0 ; extra == 'all'
-Requires-Dist: flask-cors ==4.0.0 ; extra == 'all'
-Requires-Dist: gunicorn ==21.2.0 ; extra == 'all'
+Requires-Dist: flask-cors ==4.0.1 ; extra == 'all'
+Requires-Dist: gunicorn ==22.0.0 ; extra == 'all'
 Requires-Dist: celery <6,>=5.1.0 ; extra == 'all'
 Requires-Dist: wes-service <5,>=4.0.0 ; extra == 'all'
 Requires-Dist: ruamel.yaml <0.19,>=0.15 ; extra == 'all'
 Requires-Dist: pymesos <0.4,>=0.3.15 ; (python_version < "3.11") and extra == 'all'
 Requires-Dist: graphlib-backport ==1.0 ; (python_version < "3.9") and extra == 'all'
 Provides-Extra: aws
-Requires-Dist: boto <3,>=2.48.0 ; extra == 'aws'
-Requires-Dist: boto3-stubs[boto3,iam,s3,sdb,sts] <2,>=1.28.3.post2 ; extra == 'aws'
+Requires-Dist: boto3-stubs[autoscaling,boto3,ec2,iam,s3,sdb,sts] <2,>=1.28.3.post2 ; extra == 'aws'
 Requires-Dist: mypy-boto3-iam <2,>=1.28.3.post2 ; extra == 'aws'
-Requires-Dist: moto <5,>=4.1.11 ; extra == 'aws'
+Requires-Dist: mypy-boto3-s3 <2,>=1.28.3.post2 ; extra == 'aws'
+Requires-Dist: moto <6,>=5.0.3 ; extra == 'aws'
+Requires-Dist: ec2-metadata <3 ; extra == 'aws'
 Provides-Extra: cwl
-Requires-Dist: cwltool ==3.1.20240112164112 ; extra == 'cwl'
+Requires-Dist: cwltool ==3.1.20240508115724 ; extra == 'cwl'
 Requires-Dist: schema-salad <9,>=8.4.20230128170514 ; extra == 'cwl'
-Requires-Dist: galaxy-tool-util <23 ; extra == 'cwl'
-Requires-Dist: galaxy-util <23 ; extra == 'cwl'
+Requires-Dist: galaxy-tool-util <25 ; extra == 'cwl'
+Requires-Dist: galaxy-util <25 ; extra == 'cwl'
 Requires-Dist: ruamel.yaml <=0.19,>=0.15 ; extra == 'cwl'
 Requires-Dist: ruamel.yaml.clib >=0.2.6 ; extra == 'cwl'
 Requires-Dist: networkx !=2.8.1,<4 ; extra == 'cwl'
@@ -112,13 +115,44 @@ Provides-Extra: server
 Requires-Dist: connexion[swagger-ui] <3,>=2.10.0 ; extra == 'server'
 Requires-Dist: flask <3,>=2.0 ; extra == 'server'
 Requires-Dist: werkzeug <3,>=2.0 ; extra == 'server'
-Requires-Dist: flask-cors ==4.0.0 ; extra == 'server'
-Requires-Dist: gunicorn ==21.2.0 ; extra == 'server'
+Requires-Dist: flask-cors ==4.0.1 ; extra == 'server'
+Requires-Dist: gunicorn ==22.0.0 ; extra == 'server'
 Requires-Dist: celery <6,>=5.1.0 ; extra == 'server'
 Requires-Dist: wes-service <5,>=4.0.0 ; extra == 'server'
 Requires-Dist: ruamel.yaml <0.19,>=0.15 ; extra == 'server'
 Provides-Extra: wdl
-Requires-Dist: miniwdl ==1.11.1 ; extra == 'wdl'
+Requires-Dist: miniwdl ==1.12.0 ; extra == 'wdl'
 Requires-Dist: wdlparse ==0.1.0 ; extra == 'wdl'
 Requires-Dist: graphlib-backport ==1.0 ; (python_version < "3.9") and extra == 'wdl'
 
+.. image:: https://badges.gitter.im/bd2k-genomics-toil/Lobby.svg
+   :alt: Join the chat at https://gitter.im/bd2k-genomics-toil/Lobby
+   :target: https://gitter.im/bd2k-genomics-toil/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
+
+Toil is a scalable, efficient, cross-platform (Linux & macOS) pipeline management system,
+written entirely in Python, and designed around the principles of functional
+programming. It supports running workflows written in either Common Workflow Language (`CWL`_) 1.0-1.2 or 
+Workflow Description Language (`WDL`_) 1.0-1.1, as well as having its own rich Python API for writing workflows against. 
+It supports running workflows locally on your system (e.g. a laptop), on an HPC cluster, or in the cloud. 
+
+* Check the `website`_ for a description of Toil and its features.
+* Full documentation for the latest stable release can be found at
+  `Read the Docs`_.
+* Please subscribe to low-volume `announce`_ mailing list so we keep you informed
+* Google Groups discussion `forum`_
+* See our occasional `blog`_ for tutorials. 
+* Use `biostars`_ channel for discussion.
+
+.. _website: http://toil.ucsc-cgl.org/
+.. _Read the Docs: https://toil.readthedocs.io/en/latest
+.. _announce: https://groups.google.com/forum/#!forum/toil-announce
+.. _forum: https://groups.google.com/forum/#!forum/toil-community
+.. _blog: https://toilpipelines.wordpress.com/
+.. _biostars: https://www.biostars.org/t/toil/
+.. _CWL: https://www.commonwl.org/
+.. _WDL: https://openwdl.org/
+
+Notes:
+
+* Toil moved from https://github.com/BD2KGenomics/toil to https://github.com/DataBiosphere/toil on July 5th, 2018.
+* Toil dropped Python 2.7 support on February 13, 2020 (the last working py2.7 version is 3.24.0).