move delete_work config option from task_runtime to file_io

WDL/runtime/config_templates/default.cfg

@@ -43,8 +43,21 @@ copy_input_files = false
 # Each succeeded run directory has an "output_links/" folder containing (by default) a symbolic
 # link to each output file in its original working location. If output_hardlinks is true, then
 # output_links/ is populated with hardlinks instead of symlinks. Beware the potential confusion
-# arising from files with multiple hardlinks! See also [task_runtime] delete_work, below.
+# arising from files with multiple hardlinks! See also delete_work, below.
 output_hardlinks = false
+# Delete task working directory upon completion. The task container's working directory is a
+# bind-mounted host directory, so files written into it are left behind after the container is torn
+# down. If tasks write large non-output files into their working directory (instead of $TMPDIR as
+# they should), then it can be useful to delete them automatically.
+# Values:
+#   false   = never delete (default)
+#   success = delete working directories of succeeded tasks
+#   failure =            "                  failed tasks
+#   always  =            "                  both succeeded and failed tasks
+# The "success" and "always" settings require output_hardlinks, above, to be true; otherwise,
+# output files would be deleted too. Input/output JSON, logs, and stdout/stderr are always retained
+# in the task run directory (above the container working directory).
+delete_work = false
 
 
 [task_runtime]
@@ -66,19 +79,6 @@ defaults = {
 # Run the command script as the invoking user's uid:gid instead of usually running as root. More
 # secure, but interferes with commands that assume root access e.g. apt-get. --as-me
 as_user = false
-# Delete task working directory upon completion. The task container's working directory is a
-# bind-mounted host directory, so files written into it are left behind after the container is torn
-# down. If tasks write large non-output files into their working directory (instead of $TMPDIR as
-# they should), then it can be useful to delete them automatically.
-# Values:
-#   false   = never delete (default)
-#   success = delete working directories of succeeded tasks
-#   failure =            "                  failed tasks
-#   always  =            "                  both succeeded and failed tasks
-# The "success" and "always" settings require [file_io] output_hardlinks, above, to be true;
-# otherwise, output files would be deleted too. Input/output JSON, logs, and stdout/stderr are
-# always retained in the task run directory (above the container working directory).
-delete_work = false
 
 
 [download_cache]

WDL/runtime/task.py

@@ -1141,7 +1141,7 @@ def _try_task(
                 logger,
                 interruptions + retries - 1,
                 delete_work=(
-                    cfg["task_runtime"]["delete_work"].strip().lower() in ["always", "failure"]
+                    cfg["file_io"]["delete_work"].strip().lower() in ["always", "failure"]
                 ),
             )
 
@@ -1280,11 +1280,11 @@ def map_files(v: Value.Base, dn: str) -> Value.Base:
 
 
 def _delete_work(cfg: config.Loader, logger: logging.Logger, run_dir: str, success: bool) -> None:
-    opt = cfg["task_runtime"]["delete_work"].strip().lower()
+    opt = cfg["file_io"]["delete_work"].strip().lower()
     if opt == "always" or (success and opt == "success") or (not success and opt == "failure"):
         if success and not cfg["file_io"].get_bool("output_hardlinks"):
             logger.warning(
-                "ignoring configuration [task_runtime] delete_work because it requires [file_io] output_hardlinks = true"
+                "ignoring configuration [file_io] delete_work because it requires also output_hardlinks = true"
             )
             return
         for dn in ["write_", "work", "failed_tries"]:

tests/test_4taskrun.py

@@ -971,15 +971,15 @@ def test_delete_work(self):
             outfile.write("Ben\n")
         inputs = {"files": [os.path.join(self._dir, "alyssa.txt"), os.path.join(self._dir, "ben.txt")]}
         cfg = WDL.runtime.config.Loader(logging.getLogger(self.id()), [])
-        cfg.override({"file_io": {"output_hardlinks": True}, "task_runtime": {"delete_work": "success"}})
+        cfg.override({"file_io": {"output_hardlinks": True, "delete_work": "success"}})
         output = self._test_task(txt, inputs, cfg=cfg)
         self.assertFalse(os.path.isdir(os.path.join(self._rundir, "work")))
         self.assertFalse(os.path.isdir(os.path.join(self._rundir, "write_")))
         for fn in output["outfiles"]:
             self.assertTrue(os.path.isfile(fn) and not os.path.islink(fn))
 
         cfg = WDL.runtime.config.Loader(logging.getLogger(self.id()), [])
-        cfg.override({"file_io": {"output_hardlinks": False}, "task_runtime": {"delete_work": "success"}})
+        cfg.override({"file_io": {"output_hardlinks": False, "delete_work": "success"}})
         output = self._test_task(txt, inputs, cfg=cfg)
         self.assertTrue(os.path.isfile(os.path.join(self._rundir, "work", "foo.txt")))
 

tests/test_6workflowrun.py

@@ -1011,7 +1011,7 @@ def test_retry(self):
         self.assertGreaterEqual(outputs["finish_time"], outputs["start_time"] + 20)
         self.assertTrue(os.path.isfile(os.path.join(self._rundir, "call-finish", "failed_tries", "0", "work", "iwuzhere")))
         cfg = WDL.runtime.config.Loader(logging.getLogger(self.id()), [])
-        cfg.override({"task_runtime": {"delete_work": "failure", "_mock_interruptions": 2}})
+        cfg.override({"file_io": {"delete_work": "failure"}, "task_runtime": {"_mock_interruptions": 2}})
         outputs = self._test_workflow(txt, cfg=cfg)
         self.assertGreaterEqual(outputs["finish_time"], outputs["start_time"] + 20)
         self.assertFalse(os.path.isdir(os.path.join(self._rundir, "call-finish", "failed_tries")))