fix: various bug fixes for resource parsing (#2711)

### Description

<!--Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] 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).

snakemake/cli.py

@@ -35,6 +35,7 @@
 from snakemake.io import flag
 from snakemake.resources import (
     DefaultResources,
+    ParsedResource,
     ResourceScopes,
     eval_resource_expression,
     parse_resources,
@@ -96,7 +97,9 @@ def parse_set_resources(args):
                 value = eval_resource_expression(orig_value)
             if isinstance(value, int) and value < 0:
                 raise ValueError(errmsg)
-            assignments[rule][resource] = flag(value, "orig_arg", orig_value)
+            assignments[rule][resource] = ParsedResource(
+                value=value, orig_arg=orig_value
+            )
     return assignments
 
 

snakemake/resources.py

@@ -1,8 +1,10 @@
 from collections import UserDict, defaultdict
+from dataclasses import dataclass
 import itertools as it
 import operator as op
 import re
 import tempfile
+from typing import Any
 
 from snakemake.exceptions import (
     ResourceScopesException,
@@ -12,6 +14,12 @@
 from snakemake.common.tbdstring import TBDString
 
 
+@dataclass
+class ParsedResource:
+    orig_arg: str
+    value: Any
+
+
 class DefaultResources:
     defaults = {
         "mem_mb": "min(max(2*input.size_mb, 1000), 8000)",
@@ -536,7 +544,8 @@ def generic_callable(val, threads_arg, **kwargs):
                     f"'{val}'.\n"
                     "    String arguments may need additional "
                     "quoting. E.g.: --default-resources "
-                    "\"tmpdir='/home/user/tmp'\".",
+                    "\"tmpdir='/home/user/tmp'\" or "
+                    "--set-resources \"compute1:slurm_extra='--nice=100'\".",
                     e,
                 )
             raise e

snakemake/settings.py

@@ -20,7 +20,7 @@
 
 from snakemake.common import dict_to_key_value_args, get_container_image
 from snakemake.common.configfile import load_configfile
-from snakemake.resources import DefaultResources
+from snakemake.resources import DefaultResources, ParsedResource
 from snakemake.utils import update_config
 from snakemake.exceptions import WorkflowError
 

snakemake/spawn_jobs.py

@@ -4,6 +4,7 @@
 import sys
 from typing import Mapping, TypeVar, TYPE_CHECKING, Any
 from snakemake_interface_executor_plugins.utils import format_cli_arg, join_cli_args
+from snakemake.resources import ParsedResource
 from snakemake_interface_storage_plugins.registry import StoragePluginRegistry
 
 from snakemake import common
@@ -73,19 +74,23 @@ def get_storage_provider_args(self):
         for plugin, field, field_settings in self._get_storage_provider_setting_items():
             if not field.metadata.get("env_var", False):
                 cli_arg = plugin.get_cli_arg(field.name)
+                if isinstance(field_settings[0], bool) and field.default is not True:
+                    # so far no tagged settings for flags with default value False
+                    assert len(field_settings) == 1
+                    field_settings = field_settings[0]
                 yield format_cli_arg(cli_arg, field_settings)
 
     def get_storage_provider_envvars(self):
         return {
             plugin.get_envvar(field.name): " ".join(map(str, field_settings))
             for plugin, field, field_settings in self._get_storage_provider_setting_items()
-            if "env_var" in field.metadata
+            if field.metadata.get("env_var")
         }
 
     def get_set_resources_args(self):
         def get_orig_arg(value):
-            if is_flagged(value, "orig_arg"):
-                return get_flag_value(value, "orig_arg")
+            if isinstance(value, ParsedResource):
+                return value.orig_arg
             else:
                 return value
 

snakemake/workflow.py

@@ -109,7 +109,7 @@
 )
 from snakemake.utils import simplify_path
 from snakemake.checkpoints import Checkpoints
-from snakemake.resources import ResourceScopes
+from snakemake.resources import ParsedResource, ResourceScopes
 from snakemake.caching.local import OutputFileCache as LocalOutputFileCache
 from snakemake.caching.storage import OutputFileCache as StorageOutputFileCache
 from snakemake.modules import ModuleInfo, WorkflowModifier, get_name_modifier_func
@@ -1628,7 +1628,19 @@ def decorate(ruleinfo):
                     )
                 rule.resources.update(resources)
             if name in self.resource_settings.overwrite_resources:
-                rule.resources.update(self.resource_settings.overwrite_resources[name])
+
+                def get_value(value):
+                    if isinstance(value, ParsedResource):
+                        return value.value
+                    else:
+                        return value
+
+                rule.resources.update(
+                    (resource, get_value(value))
+                    for resource, value in self.resource_settings.overwrite_resources[
+                        name
+                    ].items()
+                )
 
             if ruleinfo.priority:
                 if not isinstance(ruleinfo.priority, int) and not isinstance(

tests/tests.py

@@ -2002,3 +2002,19 @@ def test_queue_input_forceall():
 @skip_on_windows  # OS independent
 def test_issue2685():
     run(dpath("test_issue2685"))
+
+
+@skip_on_windows
+def test_set_resources_complex():
+    run(
+        dpath("test05"),
+        shellcmd="snakemake -c1 --set-resources \"compute1:slurm_extra='--nice=10'\"",
+    )
+
+
+@skip_on_windows
+def test_set_resources_human_readable():
+    run(
+        dpath("test05"),
+        shellcmd="snakemake -c1 --set-resources \"compute1:runtime='50h'\"",
+    )