update formatting and docstrings

Author: mr-c

cwltool/command_line_tool.py

@@ -345,6 +345,7 @@ def check_valid_locations(fs_access: StdFsAccess, ob: CWLObjectType) -> None:
 
 class ParameterOutputWorkflowException(WorkflowException):
     def __init__(self, msg: str, port: CWLObjectType, **kwargs: Any) -> None:
+        """Exception for when there was an error collecting output for a parameter."""
         super(ParameterOutputWorkflowException, self).__init__(
             "Error collecting output for parameter '%s':\n%s"
             % (shortname(cast(str, port["id"])), msg),

cwltool/docker.py

@@ -100,6 +100,7 @@ def __init__(
         hints: List[CWLObjectType],
         name: str,
     ) -> None:
+        """Initialize a command line builder using the Docker software container engine."""
         super(DockerCommandLineJob, self).__init__(
             builder, joborder, make_path_mapper, requirements, hints, name
         )

cwltool/executors.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-""" Single and multi-threaded executors."""
+"""Single and multi-threaded executors."""
 import datetime
 import logging
 import os
@@ -443,7 +443,7 @@ def run_jobs(
 
 
 class NoopJobExecutor(JobExecutor):
-    """ Do nothing executor, for testing purposes only. """
+    """Do nothing executor, for testing purposes only."""
 
     def run_jobs(
         self,

cwltool/job.py

@@ -292,7 +292,11 @@ def _execute(
         # execution.
         if self.mpi_procs:
             menv = runtimeContext.mpi_config
-            mpi_runtime = [menv.runner, menv.nproc_flag, str(self.mpi_procs)] + menv.extra_flags
+            mpi_runtime = [
+                menv.runner,
+                menv.nproc_flag,
+                str(self.mpi_procs),
+            ] + menv.extra_flags
             runtime = mpi_runtime + runtime
             menv.pass_through_env_vars(env)
             menv.set_env_vars(env)
@@ -927,11 +931,15 @@ def _job_popen(
         if stdin_path is not None:
             stdin = open(stdin_path, "rb")
 
-        stdout = default_stdout if default_stdout is not None else sys.stderr  # type: Union[IO[bytes], TextIO]
+        stdout = (
+            default_stdout if default_stdout is not None else sys.stderr
+        )  # type: Union[IO[bytes], TextIO]
         if stdout_path is not None:
             stdout = open(stdout_path, "wb")
 
-        stderr = default_stderr if default_stderr is not None else sys.stderr  # type: Union[IO[bytes], TextIO]
+        stderr = (
+            default_stderr if default_stderr is not None else sys.stderr
+        )  # type: Union[IO[bytes], TextIO]
         if stderr_path is not None:
             stderr = open(stderr_path, "wb")
 
@@ -976,13 +984,13 @@ def terminate():  # type: () -> None
         if tm is not None:
             tm.cancel()
 
-        if isinstance(stdin, IOBase) and hasattr(stdin, 'close'):
+        if isinstance(stdin, IOBase) and hasattr(stdin, "close"):
             stdin.close()
 
-        if stdout is not sys.stderr and hasattr(stdout, 'close'):
+        if stdout is not sys.stderr and hasattr(stdout, "close"):
             stdout.close()
 
-        if stderr is not sys.stderr and hasattr(stderr, 'close'):
+        if stderr is not sys.stderr and hasattr(stderr, "close"):
             stderr.close()
 
         return rcode

cwltool/main.py

@@ -101,6 +101,7 @@
 from .workflow import Workflow
 from .mpi import MpiConfig
 
+
 def _terminate_processes() -> None:
     """Kill all spawned processes.
 
@@ -653,6 +654,7 @@ class ProvLogFormatter(logging.Formatter):
     """Enforce ISO8601 with both T and Z."""
 
     def __init__(self) -> None:
+        """Use the default formatter with our custom formatstring."""
         super(ProvLogFormatter, self).__init__("[%(asctime)sZ] %(message)s")
 
     def formatTime(

cwltool/mpi.py

@@ -9,6 +9,7 @@
 
 MPIRequirementName = "http://commonwl.org/cwltool#MPIRequirement"
 
+
 class MpiConfig:
     def __init__(
         self,
@@ -20,8 +21,10 @@ def __init__(
         env_pass_regex: List[str] = [],
         env_set: Mapping[str, str] = {},
     ) -> None:
-        """Initialize from the argument mapping with the following defaults:
+        """
+        Initialize from the argument mapping.
 
+        Defaults are:
         runner: "mpirun"
         nproc_flag: "-n"
         default_nproc: 1
@@ -30,7 +33,8 @@ def __init__(
         env_pass_regex: []
         env_set: {}
 
-        Any unknown keys will result in an exception."""
+        Any unknown keys will result in an exception.
+        """
         self.runner = runner
         self.nproc_flag = nproc_flag
         self.default_nproc = int(default_nproc)
@@ -56,9 +60,7 @@ def load(cls: Type[MpiConfigT], config_file_name: str) -> MpiConfigT:
             raise ValueError("Unknown key(s) in MPI configuration: {}".format(unknown))
 
     def pass_through_env_vars(self, env: MutableMapping[str, str]) -> None:
-        """Here we take the configured list of environment variables and
-        simply pass them through to the executed process.
-        """
+        """Take the configured list of environment variables and pass them to the executed process."""
         for var in self.env_pass:
             if var in os.environ:
                 env[var] = os.environ[var]
@@ -70,6 +72,5 @@ def pass_through_env_vars(self, env: MutableMapping[str, str]) -> None:
                     env[k] = os.environ[k]
 
     def set_env_vars(self, env: MutableMapping[str, str]) -> None:
-        """Here we set some variables to the value configured.
-        """
+        """Set some variables to the value configured."""
         env.update(self.env_set)

cwltool/pathmapper.py

@@ -229,4 +229,5 @@ def __contains__(self, key: str) -> bool:
         return key in self._pathmap
 
     def __iter__(self) -> Iterator[MapperEnt]:
+        """Get iterator for the maps."""
         return self._pathmap.values().__iter__()

cwltool/process.py

@@ -1,3 +1,4 @@
+"""Classes and methods relevant for all CWL Proccess types."""
 import abc
 import copy
 import functools
@@ -266,7 +267,6 @@ def stage_files(
     fix_conflicts: bool = False,
 ) -> None:
     """Link or copy files to their targets. Create them as needed."""
-
     targets = {}  # type: Dict[str, MapperEnt]
     for key, entry in pathmapper.items():
         if "File" not in entry.type:
@@ -864,9 +864,10 @@ def inc(d):  # type: (List[int]) -> None
                     runtime_context.stagedir or tempfile.mkdtemp()
                 )
 
-        cwl_version = cast(str, self.metadata.get(
-            "http://commonwl.org/cwltool#original_cwlVersion", None
-        ))
+        cwl_version = cast(
+            str,
+            self.metadata.get("http://commonwl.org/cwltool#original_cwlVersion", None),
+        )
         builder = Builder(
             job,
             files,

cwltool/procgenerator.py

@@ -28,6 +28,7 @@
 
 class ProcessGeneratorJob(object):
     def __init__(self, procgenerator: "ProcessGenerator") -> None:
+        """Create a ProccessGenerator Job."""
         self.procgenerator = procgenerator
         self.jobout = None  # type: Optional[CWLObjectType]
         self.processStatus = None  # type: Optional[str]
@@ -79,6 +80,7 @@ class ProcessGenerator(Process):
     def __init__(
         self, toolpath_object: CommentedMap, loadingContext: LoadingContext,
     ) -> None:
+        """Create a ProcessGenerator from the given dictionary and context."""
         super(ProcessGenerator, self).__init__(toolpath_object, loadingContext)
         self.loadingContext = loadingContext  # type: LoadingContext
         try:

cwltool/singularity.py

@@ -95,6 +95,7 @@ def __init__(
         hints: List[CWLObjectType],
         name: str,
     ) -> None:
+        """Builder for invoking the Singularty software container engine."""
         super(SingularityCommandLineJob, self).__init__(
             builder, joborder, make_path_mapper, requirements, hints, name
         )