From: Michael R. Crusoe <crusoe@debian.org>
Subject: Fix typos
Forwarded: https://github.com/DataBiosphere/toil/pull/5403
--- toil.orig/docs/running/hpcEnvironments.rst
+++ toil/docs/running/hpcEnvironments.rst
@@ -28,7 +28,7 @@
 
 By default, this does not include any time limit or particular Slurm partition. If your Slurm cluster requires time limits, add the ``--slurmTime`` option to set the time limit to use for jobs.
 
-If you do specify a time limit, a partition will be automatically selected that can acommodate jobs of that duration, and a partition will be automatically selected for jobs that need GPUs. To use a particular partition, use the ``--slurmPartition`` argument. If you are running GPU jobs and they need to go to a different partition, use the ``--slurmGPUPartition`` argument. For example, to :ref:`run a WDL workflow from Dockstore <runWdl>` using GPUs on Slurm, with a time limit of 4 hours per job and partitions manually specified, you would run::
+If you do specify a time limit, a partition will be automatically selected that can accommodate jobs of that duration, and a partition will be automatically selected for jobs that need GPUs. To use a particular partition, use the ``--slurmPartition`` argument. If you are running GPU jobs and they need to go to a different partition, use the ``--slurmGPUPartition`` argument. For example, to :ref:`run a WDL workflow from Dockstore <runWdl>` using GPUs on Slurm, with a time limit of 4 hours per job and partitions manually specified, you would run::
 
     $ toil-wdl-runner '#workflow/github.com/vgteam/vg_wdl/GiraffeDeepVariantFromGAF:gbz' \
       https://raw.githubusercontent.com/vgteam/vg_wdl/refs/heads/gbz/params/giraffe_and_deepvariant_gaf.json \
--- toil.orig/src/toil/common.py
+++ toil/src/toil/common.py
@@ -1275,7 +1275,7 @@
 
         Does not validate the set of possible job store types.
 
-        :raises RuntimeError: if the locator is not in the approproate syntax.
+        :raises RuntimeError: if the locator is not in the appropriate syntax.
         """
         if locator[0] in "/." or ":" not in locator:
             return "file", locator
--- toil.orig/src/toil/lib/dockstore.py
+++ toil/src/toil/lib/dockstore.py
@@ -83,7 +83,7 @@
 
     dateExecuted: str
     """
-    ISO 8601 UTC timestamp when the execution happend.
+    ISO 8601 UTC timestamp when the execution happened.
     """
 
     executionStatus: ExecutionStatus
@@ -140,7 +140,7 @@
 
     dateExecuted: str
     """
-    ISO 8601 UTC timestamp when the execution happend.
+    ISO 8601 UTC timestamp when the execution happened.
     """
 
     taskExecutions: list[RunExecution]
@@ -195,7 +195,7 @@
     :param rutime: Execution duration in seconds.
     :param jobstore_type: Kind of job store used, like "file" or "aws".
     :param batch_system: Python class name implementing the batch system used.
-    :param caching: Whether Toil filestore-level cahcing was used.
+    :param caching: Whether Toil filestore-level caching was used.
     :param toil_version: Version of Toil used (without any Git hash).
     :param python_version: Version of Python used.
     :param platform_system: Operating system type (like "Darwin" or "Linux").
--- toil.orig/src/toil/provisioners/clusterScaler.py
+++ toil/src/toil/provisioners/clusterScaler.py
@@ -1439,7 +1439,7 @@
         self.stop = False
         self.clusterName = clusterName
         self.batchSystem = batchSystem
-        self.scaleable = (
+        self.scalable = (
             isinstance(self.batchSystem, AbstractScalableBatchSystem)
             if batchSystem
             else False
@@ -1460,7 +1460,7 @@
                     return fullName
                 counter += 1
 
-        if self.statsPath and self.scaleable:
+        if self.statsPath and self.scalable:
             self.stop = True
             for thread in self.statsThreads:
                 thread.join()
@@ -1492,7 +1492,7 @@
                 time=time.time(),  # add time stamp
             )
 
-        if self.scaleable:
+        if self.scalable:
             logger.debug("Starting to gather statistics")
             stats: dict[str, list[dict[str, Any]]] = {}
             if not isinstance(self.batchSystem, AbstractScalableBatchSystem):
--- toil.orig/src/toil/batchSystems/slurm.py
+++ toil/src/toil/batchSystems/slurm.py
@@ -362,7 +362,7 @@
             :raises CalledProcessErrorStderr: if communicating with Slurm went
                 wrong.
             
-            :raises OSError: if job details are not available becasue a Slurm
+            :raises OSError: if job details are not available because a Slurm
                 command could not start.
             """
             logger.log(
@@ -402,7 +402,7 @@
                 value is a tuple containing the job's state and exit code.
             :raises CalledProcessErrorStderr: if communicating with Slurm went
                 wrong.
-            :raises OSError: if job details are not available becasue a Slurm
+            :raises OSError: if job details are not available because a Slurm
                 command could not start.
             """
 
--- toil.orig/src/toil/lib/io.py
+++ toil/src/toil/lib/io.py
@@ -91,7 +91,7 @@
     """
     Return True if a URL is a toildir: URL.
 
-    Note that this may point to either a direcotry or a leaf file.
+    Note that this may point to either a directory or a leaf file.
     """
     return is_url_with_scheme(filename, [TOIL_DIR_URI_SCHEME])
 
--- toil.orig/src/toil/lib/plugins.py
+++ toil/src/toil/lib/plugins.py
@@ -51,7 +51,7 @@
         the resulting type must extend
         :class:`toil.batchSystems.abstractBatchSystem.AbstractBatchSystem`. For
         URL access plugins, it must extend :class:`toil.lib.url.URLAccess`.
-        Note that the function used here should return the class itslef; it
+        Note that the function used here should return the class itself; it
         should not construct an instance of the class.
     """
     _registry[plugin_type][plugin_name] = plugin_being_registered
