add missing docstrings

Author: mr-c

cwltool/command_line_tool.py

@@ -480,6 +480,7 @@ def make_path_mapper(
         return PathMapper(reffiles, runtimeContext.basedir, stagedir, separateDirs)
 
     def updatePathmap(self, outdir: str, pathmap: PathMapper, fn: CWLObjectType) -> None:
+        """Update a PathMapper with a CWL File or Directory object."""
         if not isinstance(fn, MutableMapping):
             raise WorkflowException("Expected File or Directory object, was %s" % type(fn))
         basename = cast(str, fn["basename"])

cwltool/context.py

@@ -54,6 +54,7 @@ def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
 
 
 def make_tool_notimpl(toolpath_object: CommentedMap, loadingContext: "LoadingContext") -> "Process":
+    """Fake implementation of the make tool function."""
     raise NotImplementedError()
 
 

cwltool/main.py

@@ -668,6 +668,7 @@ def __init__(self) -> None:
         super().__init__("[%(asctime)sZ] %(message)s")
 
     def formatTime(self, record: logging.LogRecord, datefmt: Optional[str] = None) -> str:
+        """Override the default formatTime to include the timezone."""
         formatted_time = time.strftime("%Y-%m-%dT%H:%M:%S", time.gmtime(float(record.created)))
         with_msecs = f"{formatted_time},{record.msecs:03f}"
         return with_msecs

cwltool/pathmapper.py

@@ -234,6 +234,7 @@ def reversemap(
         return None
 
     def update(self, key: str, resolved: str, target: str, ctype: str, stage: bool) -> MapperEnt:
+        """Update an existine entry."""
         m = MapperEnt(resolved, target, ctype, stage)
         self._pathmap[key] = m
         return m

cwltool/process.py

@@ -470,6 +470,7 @@ def avroize_type(
 
 
 def get_overrides(overrides: MutableSequence[CWLObjectType], toolid: str) -> CWLObjectType:
+    """Combine overrides for the target tool ID."""
     req: CWLObjectType = {}
     if not isinstance(overrides, MutableSequence):
         raise ValidationException("Expected overrides to be a list, but was %s" % type(overrides))
@@ -534,6 +535,8 @@ def eval_resource(
 
 @mypyc_attr(allow_interpreted_subclasses=True)
 class Process(HasReqsHints, metaclass=abc.ABCMeta):
+    """Abstract CWL Process."""
+
     def __init__(self, toolpath_object: CommentedMap, loadingContext: LoadingContext) -> None:
         """Build a Process object from the provided dictionary."""
         super().__init__()
@@ -1029,6 +1032,7 @@ def checkRequirements(
                             )
 
     def validate_hints(self, avsc_names: Names, hints: List[CWLObjectType], strict: bool) -> None:
+        """Process the hints field."""
         if self.doc_loader is None:
             return
         debug = _logger.isEnabledFor(logging.DEBUG)

cwltool/procgenerator.py

@@ -24,6 +24,7 @@ def __init__(self, procgenerator: "ProcessGenerator") -> None:
         self.processStatus = None  # type: Optional[str]
 
     def receive_output(self, jobout: Optional[CWLObjectType], processStatus: str) -> None:
+        """Process the results."""
         self.jobout = jobout
         self.processStatus = processStatus
 

cwltool/provenance.py

@@ -333,6 +333,7 @@ def _initialize_bagit(self) -> None:
             bag_it_file.write("Tag-File-Character-Encoding: %s\n" % ENCODING)
 
     def open_log_file_for_activity(self, uuid_uri: str) -> Union[TextIOWrapper, WritableBagFile]:
+        """Begin the per-activity log."""
         self.self_check()
         # Ensure valid UUID for safe filenames
         activity_uuid = uuid.UUID(uuid_uri)
@@ -578,6 +579,7 @@ def guess_mediatype(
         return aggregates
 
     def add_uri(self, uri: str, timestamp: Optional[datetime.datetime] = None) -> Aggregate:
+        """Create and store an aggreate for the given URI."""
         self.self_check()
         aggr = {"uri": uri}  # type: Aggregate
         aggr["createdOn"], aggr["createdBy"] = self._self_made(timestamp=timestamp)

cwltool/singularity.py

@@ -298,6 +298,7 @@ def get_from_requirements(
 
     @staticmethod
     def append_volume(runtime: List[str], source: str, target: str, writable: bool = False) -> None:
+        """Add binding arguments to the runtime list."""
         runtime.append("--bind")
         # Mounts are writable by default, so 'rw' is optional and not
         # supported (due to a bug) in some 3.6 series releases.

cwltool/utils.py

@@ -297,6 +297,7 @@ def mark(d: Dict[str, str]) -> None:
 
 
 def get_listing(fs_access: "StdFsAccess", rec: CWLObjectType, recursive: bool = True) -> None:
+    """Expand, recursively, any 'listing' fields in a Directory."""
     if rec.get("class") != "Directory":
         finddirs: List[CWLObjectType] = []
         visit_class(rec, ("Directory",), finddirs.append)
@@ -502,6 +503,7 @@ def __init__(self) -> None:
         self.hints: List[CWLObjectType] = []
 
     def get_requirement(self, feature: str) -> Tuple[Optional[CWLObjectType], Optional[bool]]:
+        """Retrieve the named feature from the requirements field, or the hints field."""
         for item in reversed(self.requirements):
             if item["class"] == feature:
                 return (item, True)

cwltool/validate_js.py

@@ -203,6 +203,7 @@ def dump_jshint_error() -> None:
 
 
 def print_js_hint_messages(js_hint_messages: List[str], source_line: Optional[SourceLine]) -> None:
+    """Log the message from JSHint, using the line number."""
     if source_line is not None:
         for js_hint_message in js_hint_messages:
             _logger.warning(source_line.makeError(js_hint_message))