fixes

snakemake/caching/hash.py

@@ -11,6 +11,7 @@
 from snakemake import script
 from snakemake import wrapper
 from snakemake.exceptions import WorkflowError
+from snakemake.settings import DeploymentMethod
 
 # ATTENTION: increase version number whenever the hashing algorithm below changes!
 __version__ = "0.1"
@@ -114,9 +115,13 @@ def _get_provenance_hash(self, job: Job, cache_mode: str):
 
         # Hash used containers or conda environments.
         if cache_mode != "omit-software":
-            if workflow.deployment_settings.use_conda and job.conda_env:
+            if (
+                DeploymentMethod.CONDA in workflow.deployment_settings.deployment_method
+                and job.conda_env
+            ):
                 if (
-                    workflow.deployment_settings.use_singularity
+                    DeploymentMethod.APPTAINER
+                    in workflow.deployment_settings.deployment_method
                     and job.conda_env.container_img_url
                 ):
                     h.update(job.conda_env.container_img_url.encode())

snakemake/cli.py

@@ -111,8 +111,7 @@ def parse_set_resource_scope(args):
     if args is not None:
         try:
             return ResourceScopes(
-                parse_key_value_arg(entry, errmsg=err_msg)
-                for entry in args
+                parse_key_value_arg(entry, errmsg=err_msg) for entry in args
             )
         except ResourceScopesException as err:
             invalid_resources = ", ".join(

snakemake/settings.py

@@ -298,6 +298,10 @@ class ResourceSettings(SettingsBase):
     overwrite_resources: Mapping[str, Mapping[str, int]] = immutables.Map()
     default_resources: Optional[DefaultResources] = None
 
+    def __post_init__(self):
+        if self.default_resources is None:
+            self.default_resources = DefaultResources(mode="bare")
+
 
 @dataclass
 class ConfigSettings(SettingsBase):

snakemake/workflow.py

@@ -723,11 +723,11 @@ def printrulegraph(self):
     def printfilegraph(self):
         self._prepare_dag(
             forceall=self.dag_settings.forceall,
-            ignore_incomplete=self.execution_settings.ignore_incomplete,
+            ignore_incomplete=True,
             lock_warn_only=True,
         )
         self._build_dag()
-        self.dag.filegraph_dot()
+        print(self.dag.filegraph_dot())
 
     def printd3dag(self):
         self._prepare_dag(

tests/common.py

@@ -170,6 +170,10 @@ def run(
     max_threads=None,
     overwrite_groups=dict(),
     configfiles=list(),
+    overwrite_resources=dict(),
+    batch=None,
+    envvars=list(),
+    cache=None,
 ):
     """
     Test the Snakefile in the path.
@@ -251,7 +255,9 @@ def run(
         if cluster is not None:
             executor = "cluster-generic"
             plugin = ExecutorPluginRegistry().get_plugin(executor)
-            executor_settings = plugin.executor_settings_class(submit_cmd=cluster, status_cmd=cluster_status)
+            executor_settings = plugin.executor_settings_class(
+                submit_cmd=cluster, status_cmd=cluster_status
+            )
             nodes = 3
 
         success = True
@@ -273,6 +279,7 @@ def run(
                         if overwrite_resource_scopes is not None
                         else dict()
                     ),
+                    overwrite_resources=overwrite_resources,
                     resources=resources,
                     default_resources=default_resources,
                     max_threads=max_threads,
@@ -298,6 +305,7 @@ def run(
                     until=until,
                     omit_from=omit_from,
                     forcerun=forcerun,
+                    batch=batch,
                 ),
                 deployment_settings=settings.DeploymentSettings(
                     conda_frontend=conda_frontend,
@@ -319,10 +327,12 @@ def run(
                         cleanup_scripts=cleanup_scripts,
                         shadow_prefix=shadow_prefix,
                         retries=retries,
+                        cache=cache,
                     ),
                     remote_execution_settings=settings.RemoteExecutionSettings(
                         container_image=container_image,
                         seconds_between_status_checks=0,
+                        envvars=envvars,
                     ),
                     scheduling_settings=settings.SchedulingSettings(
                         ilp_solver=scheduler_ilp_solver,