include tests

setup.py

@@ -99,12 +99,9 @@ def run_setup():
         install_requires=install_requires,
         extras_require=extras_require,
         package_dir={'': 'src'},
-        packages=find_packages(where='src',
-                               # Note that we intentionally include the top-level `test` package for
-                               # functionality like the @experimental and @integrative decorators:
-                               exclude=['*.test.*']),
+        packages=find_packages(where='src'),
         package_data={
-            '': ['*.yml', '*.yaml', 'cloud-config'],
+            '': ['*.yml', '*.yaml', 'cloud-config', '*.cwl'],
         },
         # Unfortunately, the names of the entry points are hard-coded elsewhere in the code base so
         # you can't just change them here. Luckily, most of them are pretty unique strings, and thus

src/toil/lib/misc.py

@@ -129,6 +129,9 @@ def call_command(cmd: List[str], *args: str, input: Optional[str] = None, timeou
     :returns: Command standard output, decoded as utf-8.
     """
 
+    # NOTE: Interface MUST be kept in sync with call_sacct and call_scontrol in
+    # test_slurm.py, which monkey-patch this!
+
     # using non-C locales can cause GridEngine commands, maybe other to
     # generate errors
     if useCLocale:

src/toil/test/batchSystems/test_slurm.py

@@ -8,8 +8,10 @@
 from toil.lib.misc import CalledProcessErrorStderr
 from toil.test import ToilTest
 
+# TODO: Come up with a better way to mock the commands then monkey-patching the
+# command-calling functions.
 
-def call_sacct(args) -> str:
+def call_sacct(args, **_) -> str:
     """
     The arguments passed to `call_command` when executing `sacct` are:
     ['sacct', '-n', '-j', '<comma-separated list of job-ids>', '--format',
@@ -41,7 +43,7 @@ def call_sacct(args) -> str:
     return stdout
 
 
-def call_scontrol(args) -> str:
+def call_scontrol(args, **_) -> str:
     """
     The arguments passed to `call_command` when executing `scontrol` are:
     ['scontrol', 'show', 'job'] or ['scontrol', 'show', 'job', '<job-id>']