diff --git a/docs/source/installing.rst b/docs/source/installing.rst index 8097825af..fbbb35f92 100644 --- a/docs/source/installing.rst +++ b/docs/source/installing.rst @@ -34,7 +34,7 @@ Once installed run:: usage: maestro [-h] [-l LOGPATH] [-d DEBUG_LVL] [-c] {cancel,run,status} ... - The Maestro Workflow Conductor for specifiying, launching, and managing general workflows. + The Maestro Workflow Conductor for specifying, launching, and managing general workflows. positional arguments: {cancel,run,status} diff --git a/maestrowf/abstracts/__init__.py b/maestrowf/abstracts/__init__.py index 0f6d0c861..c920262ff 100644 --- a/maestrowf/abstracts/__init__.py +++ b/maestrowf/abstracts/__init__.py @@ -31,7 +31,7 @@ The core abstract APIs that define various class behaviors. This module contains all of the abstract classes and APIs for defining objects. -Abstracts include abstract data stuctures (like a graph), APIs for concepts +Abstracts include abstract data structures (like a graph), APIs for concepts such as queueing adapters and environment APIs, as well as fundamental data structures. """ diff --git a/maestrowf/abstracts/abstractclassmethod.py b/maestrowf/abstracts/abstractclassmethod.py index d7fb2cd9c..389702813 100644 --- a/maestrowf/abstracts/abstractclassmethod.py +++ b/maestrowf/abstracts/abstractclassmethod.py @@ -32,7 +32,7 @@ class abstractclassmethod(classmethod): """Python 2.7 does not include built in @abstractclassmethod so we create - our own class that extends @classmethod and then attachs a + our own class that extends @classmethod and then attaches a __isabstractmethod variable to the callable function. See ref: https://stackoverflow.com/a/11218474""" diff --git a/maestrowf/abstracts/envobject.py b/maestrowf/abstracts/envobject.py index aa629d18f..172b2ffde 100644 --- a/maestrowf/abstracts/envobject.py +++ b/maestrowf/abstracts/envobject.py @@ -43,7 +43,7 @@ class EnvObject: The EnvObject is meant to be used to represent entities in the larger environment that affect the execution of a study (and therefore jobs). - This abstact base class should be used to represent things such as data + This abstract base class should be used to represent things such as data dependencies, code dependencies, variables, aliases, etc. The only method we require is _verify, to allow users to verify that they've provided the minimal information for the object to be valid. @@ -112,8 +112,8 @@ def apply(self, data): Apply the Source to some string data. Subclasses of Source should use this method in order to apply an - environment alterating change. The 'data' parameter should be a string - representing a command to apply Source to or a list of other comands + environment altering change. The 'data' parameter should be a string + representing a command to apply Source to or a list of other commands that Source should be included with. :param data: A string representing a command or set of other sources. @@ -139,7 +139,7 @@ class Dependency(Substitution): * External APIs that a workflow needs to pull data from The goal of this base class is to make it so that this package is able to - pull exernal dependencies in a consistent manner. + pull external dependencies in a consistent manner. """ @abstractmethod diff --git a/maestrowf/abstracts/interfaces/schedulerscriptadapter.py b/maestrowf/abstracts/interfaces/schedulerscriptadapter.py index 8c633d707..9406a3d56 100644 --- a/maestrowf/abstracts/interfaces/schedulerscriptadapter.py +++ b/maestrowf/abstracts/interfaces/schedulerscriptadapter.py @@ -75,7 +75,7 @@ def __init__(self, **kwargs): # NOTE: The _batch member should be used to store persistent batching # parameters. The entries in this dictionary are meant to capture the # the base settings for submission to a batch. This member variables - # should never be used publicallly outside of an instance. + # should never be used publicly outside of an instance. # Call super to set self._exec super(SchedulerScriptAdapter, self).__init__(**kwargs) @@ -105,7 +105,7 @@ def get_header(self, step): @abstractmethod def get_parallelize_command(self, procs, nodes, **kwargs): """ - Generate the parallelization segement of the command line. + Generate the parallelization segment of the command line. :param procs: Number of processors to allocate to the parallel call. :param nodes: Number of nodes to allocate to the parallel call @@ -117,7 +117,7 @@ def get_parallelize_command(self, procs, nodes, **kwargs): def _substitute_parallel_command(self, step_cmd, **kwargs): """ - Substitute parallelized segements into a specified command. + Substitute parallelized segments into a specified command. :param step_cmd: Command string to parallelize. :param nodes: Total number of requested nodes. diff --git a/maestrowf/conductor.py b/maestrowf/conductor.py index cbd56f393..eb03dabff 100644 --- a/maestrowf/conductor.py +++ b/maestrowf/conductor.py @@ -347,7 +347,7 @@ def monitor_study(self): LOGGER.info("Checking DAG status at %s", str(datetime.now())) # Execute steps that are ready - # Recieves StudyStatus enum + # Receives StudyStatus enum completion_status = dag.execute_ready_steps() # Re-pickle the ExecutionGraph. dag.pickle(pkl_path) diff --git a/maestrowf/datastructures/core/parameters.py b/maestrowf/datastructures/core/parameters.py index 4f48a29b2..76c6ec527 100644 --- a/maestrowf/datastructures/core/parameters.py +++ b/maestrowf/datastructures/core/parameters.py @@ -176,7 +176,7 @@ class ParameterGenerator: defined and will generate each combination one by one. The end user should NEVER SEE AN INVALID COMBINATION. Because this class generates the combinations as specified by the parameters added (eventually with types - or enforced inheritence), and eventually constraints, it opens up being + or enforced inheritance), and eventually constraints, it opens up being able to quietly change how this class generates its combinations. Easily convert studies to other types of studies. Because the API doesn't diff --git a/maestrowf/datastructures/core/study.py b/maestrowf/datastructures/core/study.py index d6843a037..51aa51d4b 100644 --- a/maestrowf/datastructures/core/study.py +++ b/maestrowf/datastructures/core/study.py @@ -135,7 +135,7 @@ def __eq__(self, other): : returns: True if other is equal to self, False otherwise. """ if isinstance(other, self.__class__): - # This works because the classes are currently intefaces over + # This works because the classes are currently interfaces over # internals that are all based on Python builtin classes. # NOTE: This method will need to be reworked if something more # complex is done with the class. @@ -798,7 +798,7 @@ def _stage_linear(self, dag): used_spaces = re.findall(WSREGEX, cmd) for match in used_spaces: # In this case we don't need to look for any parameters, or - # combination depdendent ("funnel") steps. It's a simple sub. + # combination dependent ("funnel") steps. It's a simple sub. LOGGER.info("Workspace found -- %s", match) workspace_var = "$({}.workspace)".format(match) ws = self.workspaces[match] diff --git a/maestrowf/datastructures/dag.py b/maestrowf/datastructures/dag.py index 3ca7f221e..1b6bf5497 100644 --- a/maestrowf/datastructures/dag.py +++ b/maestrowf/datastructures/dag.py @@ -27,7 +27,7 @@ # SOFTWARE. ############################################################################### -"""Module that contains the implemenation of a Directed-Acyclic Graph.""" +"""Module that contains the implementation of a Directed-Acyclic Graph.""" from collections import deque, OrderedDict import logging diff --git a/maestrowf/datastructures/environment/gitdependency.py b/maestrowf/datastructures/environment/gitdependency.py index e453434ed..ff0021feb 100644 --- a/maestrowf/datastructures/environment/gitdependency.py +++ b/maestrowf/datastructures/environment/gitdependency.py @@ -58,7 +58,7 @@ def __init__(self, name, value, path, token='$', **kwargs): Currently, the GitDependency class only supports three optional parameters: branch, hash, and tag. Each operate as their name specifies according to how they would be used in git. The class will acquire the - specfic repository in accordance with a specified optional (example: + specific repository in accordance with a specified optional (example: if a tag is specfied, the class will clone then checkout the tag). The only caveat to the optionals is that only one may be used at a time. diff --git a/maestrowf/interfaces/script/__init__.py b/maestrowf/interfaces/script/__init__.py index 72c50d197..9d56acb19 100644 --- a/maestrowf/interfaces/script/__init__.py +++ b/maestrowf/interfaces/script/__init__.py @@ -58,7 +58,7 @@ def job_identifier(self): """ Property for the job identifier for the record. - :returns: A string representing the job identifer assigned by the + :returns: A string representing the job identifier assigned by the scheduler. """ return self._info.get("jobid", None) diff --git a/maestrowf/interfaces/script/slurmscriptadapter.py b/maestrowf/interfaces/script/slurmscriptadapter.py index b23f2da82..21ebf0462 100644 --- a/maestrowf/interfaces/script/slurmscriptadapter.py +++ b/maestrowf/interfaces/script/slurmscriptadapter.py @@ -186,7 +186,7 @@ def get_parallelize_command(self, procs, nodes=None, **kwargs): for key in supported: value = kwargs.get(key) if key not in self._cmd_flags: - LOGGER.warning("'%s' is not supported -- ommitted.", key) + LOGGER.warning("'%s' is not supported -- omitted.", key) continue if value: args += [ diff --git a/maestrowf/maestro.py b/maestrowf/maestro.py index b272052a1..666c0dbef 100644 --- a/maestrowf/maestro.py +++ b/maestrowf/maestro.py @@ -331,7 +331,7 @@ def setup_argparser(): """Set up the program's argument parser.""" parser = ArgumentParser( prog="maestro", - description="The Maestro Workflow Conductor for specifiying, launching" + description="The Maestro Workflow Conductor for specifying, launching" ", and managing general workflows.", formatter_class=RawTextHelpFormatter) subparsers = parser.add_subparsers(dest='subparser') @@ -439,7 +439,7 @@ def main(): This function uses command line arguments to locate the study description. It makes use of the maestrowf core data structures as a high level class - inerface. + interface. """ # Set up the necessary base data structures to begin study set up. parser = setup_argparser() diff --git a/samples/documentation/lulesh_sample1_unix_commented.yaml b/samples/documentation/lulesh_sample1_unix_commented.yaml index 83132010c..a92d01678 100644 --- a/samples/documentation/lulesh_sample1_unix_commented.yaml +++ b/samples/documentation/lulesh_sample1_unix_commented.yaml @@ -84,7 +84,7 @@ env: # Study Block (Required) #################################### # The study block is where the steps in the workflow are defined. This section -# of the specfication represents the unexpanded set of tasks that the study +# of the specification represents the unexpanded set of tasks that the study # is composed of. #################################### study: @@ -214,7 +214,7 @@ study: # There are three keys per parameter: # 1. A list of values that the parameter takes. # 2. A label that represents a "pretty printed" version of the parameter. The -# parameter values is specfied by the '%%' moniker (for example, for SIZE -- +# parameter values is specified by the '%%' moniker (for example, for SIZE -- # when SIZE is equal to 10, the label will be 'SIZE.10'). To access the label # for SIZE, for example, the token '$(SIZE.label)' is used. # Labels can take one of two forms: A single string with the '%%' marker or diff --git a/samples/parameterization/lulesh_itertools_pgen.py b/samples/parameterization/lulesh_itertools_pgen.py index a7eaa1170..7e4366b76 100644 --- a/samples/parameterization/lulesh_itertools_pgen.py +++ b/samples/parameterization/lulesh_itertools_pgen.py @@ -7,7 +7,7 @@ def get_custom_generator(env, **kwargs): Create a custom populated ParameterGenerator. This function recreates the exact same parameter set as the sample LULESH specifications. The difference here is that itertools is employed to - programatically generate the samples instead of manually writing out + programmatically generate the samples instead of manually writing out all of the combinations. :params env: A StudyEnvironment object containing custom information. :params kwargs: A dictionary of keyword arguments this function uses. diff --git a/tests/interfaces/test_script_adapter.py b/tests/interfaces/test_script_adapter.py index ccaa073c0..259a18782 100644 --- a/tests/interfaces/test_script_adapter.py +++ b/tests/interfaces/test_script_adapter.py @@ -50,7 +50,7 @@ def test_factory(): def test_get_valid_adapters(): """ Test to verify that the keys in the internal factory is the same set as - the resutls from get_valid_adapters() + the results from get_valid_adapters() """ saf = ScriptAdapterFactory assert(saf.factories.keys() == ScriptAdapterFactory.get_valid_adapters())