Apply suggestions from code review

Co-authored-by: Michael R. Crusoe <[email protected]>

Author: rupertnash

.coveragerc

@@ -1,6 +1,7 @@
 [run]
 branch = True
 source = cwltool
+omit = cwltool/run_job.py
 
 [report]
 exclude_lines =

README.rst

@@ -317,11 +317,11 @@ This file may be specified as either XML or YAML and very simply describes vario
 plugins to enable to "resolve" ``SoftwareRequirement`` dependencies.
 
 Using these hints will allow cwltool to modify the environment in
-which your tool runs, for example by loading one or more environment
-modules. The enviroment is constructed as normal (i.e. standard CWL
+which your tool runs, for example by loading one or more Environment
+Modules. The environment is constructed as normal (i.e. standard CWL
 runtime enviroment, ``EnvVarRequirement``, ``--preserve-environment``
-are applied), then this is modified. This currently means that you
-cannot override variables set in this way.
+are applied), then the environment may modified by the selected tool resolver.  This currently means that you
+cannot override any environment variables set by the selected tool resolver.
 
 To discuss some of these plugins and how to configure them, first consider the
 following ``hint`` definition for an example CWL tool.

tests/test_dependencies.py

@@ -44,6 +44,7 @@ def test_bioconda() -> None:
 @pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")
 @pytest.mark.skipif(not which("modulecmd"), reason="modulecmd not installed")
 def test_modules(monkeypatch: pytest.MonkeyPatch) -> None:
+    """Do a basic smoke test using environment modules to satisfy a SoftwareRequirement."""
     wflow = get_data("tests/random_lines.cwl")
     job = get_data("tests/random_lines_job.json")
     monkeypatch.setenv(
@@ -65,6 +66,11 @@ def test_modules(monkeypatch: pytest.MonkeyPatch) -> None:
 @pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")
 @pytest.mark.skipif(not which("modulecmd"), reason="modulecmd not installed")
 def test_modules_environment(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
+    """
+    Check that the environment variables set by a module are being propagated correctly.
+
+    Do so by  by running `env` as the tool and parsing its output.
+    """
     monkeypatch.setenv(
         "MODULEPATH", os.path.join(os.getcwd(), "tests/test_deps_env/modulefiles")
     )