fix: proper interpretation of standard resources given as strings (e.…

…g. runtime as '5m'). Avoid the need to set additional quotes around size or timespan resources. Improved error messages for resource handling. (#2716)

### Description

Eventually, human-readable resource parsing for runtimes from
workflow-profiles ought to be enabled.

### QC

* [ x] The PR contains a test case for the changes, or the changes are
already covered by an existing test case.
* [ ] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).

---------

Co-authored-by: Johannes Koester <johannes.koester@uni-due.de>

snakemake/cli.py

@@ -1683,17 +1683,24 @@ def parse_args(argv):
         if args.profile:
             profiles.append(args.profile)
         if workflow_profile:
-            workflow_profile_stmt = f" and workflow specific profile {workflow_profile}"
+            workflow_profile_stmt = f" {'and ' if profiles else ''}workflow specific profile {workflow_profile}"
             profiles.append(workflow_profile)
         else:
             workflow_profile_stmt = ""
 
-        print(
-            f"Using profile{'s' if len(profiles) > 1 else ''} "
-            f"{' and '.join(map(str, profiles))}{workflow_profile_stmt} for setting default command line arguments.",
-            file=sys.stderr,
+        fmt_profiles = profiles if not workflow_profile else profiles[:-1]
+        profile_stmt = (
+            f"Using profile{'s' if len(profiles) > 1 else ''} {' and '.join(map(str, fmt_profiles))}"
+            if fmt_profiles
+            else "Using"
         )
 
+        if profiles:
+            print(
+                f"{profile_stmt}{workflow_profile_stmt} for setting default command line arguments.",
+                file=sys.stderr,
+            )
+
         parser = get_argument_parser(profiles=profiles)
         args = parser.parse_args(argv)
 

snakemake/resources.py

@@ -12,6 +12,7 @@
     is_file_not_found_error,
 )
 from snakemake.common.tbdstring import TBDString
+from snakemake.logging import logger
 
 
 @dataclass
@@ -537,6 +538,8 @@ def generic_callable(val, threads_arg, **kwargs):
         except NameError:
             return val
         except Exception as e:
+            if is_humanfriendly_resource(val):
+                return val
             if not is_file_not_found_error(e, kwargs["input"]):
                 # Missing input files are handled by the caller
                 raise WorkflowError(
@@ -545,7 +548,10 @@ def generic_callable(val, threads_arg, **kwargs):
                     "    String arguments may need additional "
                     "quoting. E.g.: --default-resources "
                     "\"tmpdir='/home/user/tmp'\" or "
-                    "--set-resources \"compute1:slurm_extra='--nice=100'\".",
+                    "--set-resources \"somerule:someresource='--nice=100'\". "
+                    "This also holds for setting resources inside of a profile, where "
+                    "you might have to enclose them in single and double quotes, "
+                    "i.e. someresource: \"'--nice=100'\".",
                     e,
                 )
             raise e
@@ -639,8 +645,28 @@ def infer_resources(name, value, resources: dict):
         and not isinstance(value, TBDString)
     ):
         try:
-            resources["runtime"] = max(int(round(parse_timespan(value) / 60)), 1)
+            parsed = max(int(round(parse_timespan(value) / 60)), 1)
         except InvalidTimespan:
             raise WorkflowError(
                 f"Cannot parse runtime value into minutes for setting runtime resource: {value}"
             )
+        logger.debug(f"Inferred runtime value of {parsed} minutes from {value}")
+        resources["runtime"] = parsed
+
+
+def is_humanfriendly_resource(value):
+    from humanfriendly import parse_size, parse_timespan, InvalidTimespan, InvalidSize
+
+    try:
+        parse_size(value)
+        return True
+    except InvalidSize:
+        pass
+
+    try:
+        parse_timespan(value)
+        return True
+    except InvalidTimespan:
+        pass
+
+    return False

snakemake/rules.py

@@ -992,21 +992,23 @@ def apply(name, res, threads=None):
 
                 if value is not None:
                     resources[name] = value
-                    # Infer standard resources from eventual human readable forms.
-                    infer_resources(name, value, resources)
 
-                    # infer additional resources
-                    for mb_item, mib_item in (
-                        ("mem_mb", "mem_mib"),
-                        ("disk_mb", "disk_mib"),
-                    ):
-                        if (
-                            name == mb_item
-                            and mib_item not in self.resources.keys()
-                            and isinstance(value, int)
+                    if not isinstance(value, TBDString):
+                        # Infer standard resources from eventual human readable forms.
+                        infer_resources(name, value, resources)
+
+                        # infer additional resources
+                        for mb_item, mib_item in (
+                            ("mem_mb", "mem_mib"),
+                            ("disk_mb", "disk_mib"),
                         ):
-                            # infer mem_mib (memory in Mebibytes) as additional resource
-                            resources[mib_item] = mb_to_mib(value)
+                            if (
+                                name == mb_item
+                                and mib_item not in self.resources.keys()
+                                and isinstance(value, int)
+                            ):
+                                # infer mem_mib (memory in Mebibytes) as additional resource
+                                resources[mib_item] = mb_to_mib(value)
 
         resources = Resources(fromdict=resources)
         return resources

tests/test_runtime_conversion_from_workflow_profile/workflow/Snakefile

@@ -0,0 +1,12 @@
+rule a:
+     output: "a.out"
+     #resources:
+     #   runtime="5m"
+     shell: """
+          if [ {resources.runtime} -eq 5 ]; then
+             touch {output}
+          else
+             echo "Runtime is not 300 seconds"
+             exit 1
+          fi
+          """

tests/test_runtime_conversion_from_workflow_profile/workflow/profiles/default/config.yaml

@@ -0,0 +1,3 @@
+set-resources:
+    a:
+        runtime: 5m

tests/tests.py

@@ -1918,6 +1918,16 @@ def test_no_workflow_profile():
     )
 
 
+@skip_on_windows  # not platform dependent
+def test_runtime_conversion_from_workflow_profile():
+    test_path = dpath("test_runtime_conversion_from_workflow_profile")
+    run(
+        test_path,
+        snakefile="workflow/Snakefile",
+        shellcmd=f"snakemake -c1",
+    )
+
+
 @skip_on_windows
 def test_localrule():
     run(dpath("test_localrule"), targets=["1.txt", "2.txt"])