fix walltime conversion issue

add test for walltime conversion

merlin/examples/workflows/slurm/slurm_test.yaml

@@ -4,6 +4,7 @@ description:
 
 batch:
   type: slurm
+  walltime: 10:00:00
 
 env:
   variables:

merlin/spec/merlinspec.json

@@ -280,7 +280,12 @@
       "launch_args": {"type": "string", "minLength": 1},
       "worker_launch": {"type": "string", "minLength": 1},
       "nodes": {"type": "integer", "minimum": 1},
-      "walltime": {"type": "string", "pattern": "^(?:(?:([0-9][0-9]|2[0-3]):)?([0-5][0-9]):)?([0-5][0-9])$"}
+      "walltime": {
+        "anyOf": [
+          {"type": "string", "pattern": "^(?:(?:([0-9][0-9]|2[0-3]):)?([0-5][0-9]):)?([0-5][0-9])$"},
+          {"type": "integer"}
+        ]
+      }
     }
   }
 }

merlin/spec/specification.py

@@ -38,12 +38,14 @@
 import os
 import shlex
 from copy import deepcopy
+from datetime import timedelta
 from io import StringIO
 
 import yaml
 from maestrowf.specification import YAMLSpecification
 
 from merlin.spec import all_keys, defaults
+from merlin.utils import repr_timedelta
 
 
 LOG = logging.getLogger(__name__)
@@ -179,6 +181,18 @@ def load_spec_from_string(cls, string, needs_IO=True, needs_verification=False):
             spec.verify()
             LOG.debug("Merlin spec verified.")
 
+        # Convert the walltime value back to HMS if PyYAML messed with it
+        for _, section in spec.yaml_sections.items():
+            # Section is a list for the study block
+            if isinstance(section, list):
+                for step in section:
+                    if "walltime" in step and isinstance(step["walltime"], int):
+                        step["walltime"] = repr_timedelta(timedelta(seconds=step["walltime"]))
+            # Section is a dict for all other blocks
+            if isinstance(section, dict):
+                if "walltime" in section and isinstance(section["walltime"], int):
+                    section["walltime"] = repr_timedelta(timedelta(seconds=section["walltime"]))
+
         return spec
 
     @classmethod
@@ -315,7 +329,7 @@ def verify_batch_block(self, schema):
             try:
                 err_msg = "Walltime must be of the form SS, MM:SS, or HH:MM:SS."
                 walltime = self.batch["walltime"]
-                if len(walltime) > 2:
+                if isinstance(walltime, str) and len(walltime) > 2:
                     # Walltime must have : if it's not of the form SS
                     if ":" not in walltime:
                         raise ValueError(err_msg)

tests/integration/test_definitions.py

@@ -228,9 +228,11 @@ def define_tests():  # pylint: disable=R0914,R0915
             "conditions": [HasReturnCode(), HasRegex(celery_slurm_regex)],
             "run type": "local",
         },
+        # TODO if we ever implement a way to modify yaml files for testing, use that for testing walltime here
         "run-workers echo slurm_test": {
             "cmds": f"{workers} {slurm} --echo",
-            "conditions": [HasReturnCode(), HasRegex(celery_slurm_regex)],
+            # Making sure walltime isn't set to an integer w/ last two conditions here
+            "conditions": [HasReturnCode(), HasRegex(celery_slurm_regex), HasRegex(r"36000", negate=True), HasRegex(r"10:00:00")],
             "run type": "local",
         },
         "run-workers echo lsf_test": {