add some missing docstrings

Author: mr-c

cwltool/main.py

@@ -729,6 +729,8 @@ def setup_loadingContext(
 def make_template(
     tool: Process,
 ) -> None:
+    """Make a template CWL input object for the give Process."""
+
     def my_represent_none(
         self: Any, data: Any
     ) -> Any:  # pylint: disable=unused-argument
@@ -750,7 +752,7 @@ def choose_target(
     tool: Process,
     loadingContext: LoadingContext,
 ) -> Optional[Process]:
-
+    """Walk the given Workflow and find the process that matches args.target."""
     if loadingContext.loader is None:
         raise Exception("loadingContext.loader cannot be None")
 
@@ -783,6 +785,7 @@ def choose_target(
 def check_working_directories(
     runtimeContext: RuntimeContext,
 ) -> Optional[int]:
+    """Make any needed working directories."""
     for dirprefix in ("tmpdir_prefix", "tmp_outdir_prefix", "cachedir"):
         if (
             getattr(runtimeContext, dirprefix)

cwltool/mpi.py

@@ -1,3 +1,4 @@
+"""Experimental support for MPI."""
 import inspect
 import os
 import re

cwltool/pathmapper.py

@@ -219,6 +219,7 @@ def reversemap(
         self,
         target: str,
     ) -> Optional[Tuple[str, str]]:
+        """Find the (source, resolved_path) for the given target, if any."""
         for k, v in self._pathmap.items():
             if v[1] == target:
                 return (k, v[0])

cwltool/provenance.py

@@ -130,6 +130,7 @@ def __init__(self, research_object: "ResearchObject", rel_path: str) -> None:
         super(WritableBagFile, self).__init__(path, mode="w")
 
     def write(self, b: Any) -> int:
+        """Write some content to the Bag."""
         real_b = b if isinstance(b, (bytes, mmap, array)) else b.encode("utf-8")
         total = 0
         length = len(real_b)

cwltool/workflow_job.py

@@ -119,6 +119,11 @@ def setTotal(
         total: int,
         steps: List[Optional[JobsGeneratorType]],
     ) -> None:
+        """
+        Set the total number of expected outputs along with the steps.
+
+        This is necessary to finish the setup.
+        """
         self.total = total
         self.steps = steps
         if self.completed == self.total:

tests/test_mpi.py

@@ -1,3 +1,4 @@
+"""Tests of the experimental MPI extension."""
 import json
 import os.path
 import sys

tests/util.py

@@ -67,9 +67,10 @@ def get_data(filename: str) -> str:
 )
 
 needs_singularity_3_or_newer = pytest.mark.skipif(
-     (not bool(distutils.spawn.find_executable("singularity"))) or (not is_version_3_or_newer()),
-     reason="Requires that version 3.x of singularity executable version is on the system path.",
- )
+    (not bool(distutils.spawn.find_executable("singularity")))
+    or (not is_version_3_or_newer()),
+    reason="Requires that version 3.x of singularity executable version is on the system path.",
+)
 
 
 windows_needs_docker = pytest.mark.skipif(