helpers: allow to overwrite config in mock_snakemake and allow mock_snakemake to be called from repo root

scripts/_helpers.py

@@ -295,7 +295,7 @@ def get_aggregation_strategies(aggregation_strategies):
     return bus_strategies, generator_strategies
 
 
-def mock_snakemake(rulename, **wildcards):
+def mock_snakemake(rulename, configfiles=[], **wildcards):
     """
     This function is expected to be executed from the 'scripts'-directory of '
     the snakemake project. It returns a snakemake.script.Snakemake object,
@@ -307,6 +307,8 @@ def mock_snakemake(rulename, **wildcards):
     ----------
     rulename: str
         name of the rule for which the snakemake object should be generated
+    configfiles: list, str
+        list of configfiles to be used to update the config
     **wildcards:
         keyword arguments fixing the wildcards. Only necessary if wildcards are
         needed.
@@ -319,17 +321,35 @@ def mock_snakemake(rulename, **wildcards):
     from snakemake.script import Snakemake
 
     script_dir = Path(__file__).parent.resolve()
-    assert (
-        Path.cwd().resolve() == script_dir
-    ), f"mock_snakemake has to be run from the repository scripts directory {script_dir}"
-    os.chdir(script_dir.parent)
+    root_dir = script_dir.parent
+
+    user_in_script_dir = Path.cwd().resolve() == script_dir
+    if user_in_script_dir:
+        os.chdir(root_dir)
+    elif Path.cwd().resolve() != root_dir:
+        raise RuntimeError(
+            "mock_snakemake has to be run from the repository root"
+            f" {root_dir} or scripts directory {script_dir}"
+        )
+    try:
         for p in sm.SNAKEFILE_CHOICES:
             if os.path.exists(p):
                 snakefile = p
                 break
-    kwargs = dict(rerun_triggers=[]) if parse(sm.__version__) > Version("7.7.0") else {}
-    workflow = sm.Workflow(snakefile, overwrite_configfiles=[], **kwargs)
+        kwargs = (
+            dict(rerun_triggers=[]) if parse(sm.__version__) > Version("7.7.0") else {}
+        )
+        workflow = sm.Workflow(snakefile, **kwargs)
         workflow.include(snakefile)
+
+        if isinstance(configfiles, str):
+            configfiles = [configfiles]
+        if configfiles:
+            for f in configfiles:
+                if not os.path.exists(f):
+                    raise FileNotFoundError(f"Config file {f} does not exist.")
+                workflow.configfile(f)
+
         workflow.global_resources = {}
         rule = workflow.get_rule(rulename)
         dag = sm.dag.DAG(workflow, rules=[rule])
@@ -358,6 +378,8 @@ def mock_snakemake(rulename, **wildcards):
         for path in list(snakemake.log) + list(snakemake.output):
             Path(path).parent.mkdir(parents=True, exist_ok=True)
 
+    finally:
+        if user_in_script_dir:
             os.chdir(script_dir)
     return snakemake