fix: preserve named params when loading rule args

rule.expand_params returns (params, non_derived_params) in current snakemake; passing the tuple straight into Params() dropped both items in as unnamed positional values, so snakemake.params["<name>"] raised AttributeError. Index [0] like expand_input/expand_output already do.

Author: Hoeze

.gitignore

@@ -108,3 +108,6 @@ slurm*out
 # intellij
 .idea
 
+# devcontainer-bound conda env
+.devcontainer/devenv/
+

snakemk_util/rule_args.py

@@ -229,7 +229,7 @@ def load_rule_args(
         smk_resources = rule.expand_resources(default_wildcards, smk_input, attempt=1)
         smk_threads = smk_resources._cores
         smk_output = OutputFiles(rule.expand_output(default_wildcards)[0])
-        smk_params = Params(rule.expand_params(default_wildcards, smk_input, smk_output, None))
+        smk_params = Params(rule.expand_params(default_wildcards, smk_input, smk_output, None)[0])
         smk_log = rule.log
         smk_config = workflow.config
 

tests/data/test_named_params/Snakefile

@@ -0,0 +1,16 @@
+ds_config = {"testdir": {"assembly": "GRCh37"}}
+
+rule all:
+  input:
+    "testdir/out.txt"
+
+rule samplerule:
+  output:
+    of="{ds_dir}/out.txt"
+  input:
+  params:
+    assembly=lambda wildcards: ds_config[wildcards.ds_dir]["assembly"],
+    output_basedir="some/base",
+    nb_script="script.py",
+  shell:
+    "echo 'OK' > {output.of}"

tests/test_rule_args.py

@@ -89,6 +89,30 @@ def test_rule_args_workdir_pythonrule(workflow_dir):
     assert os.path.isdir(workflow_dir + "/testdir")
 
 
+def test_named_params(workflow_dir):
+    """Regression test: named params in a rule must be addressable by name on
+    the loaded Snakemake object. Previously the tuple returned by
+    rule.expand_params was passed to Params() without indexing [0], which
+    stripped all names and surfaced as `AttributeError: 'Params' object has
+    no attribute '<name>'` when accessing snakemake.params["<name>"].
+    """
+    workflow_dir = copy_data(workflow_dir, "test_named_params")
+
+    snakefile_path = workflow_dir + "/Snakefile"
+
+    snakemake = load_rule_args(
+        snakefile=snakefile_path,
+        rule_name="samplerule",
+        default_wildcards={"ds_dir": "testdir"},
+    )
+
+    assert list(snakemake.params.keys()) == ["assembly", "output_basedir", "nb_script"]
+    assert snakemake.params["assembly"] == "GRCh37"
+    assert snakemake.params.assembly == "GRCh37"
+    assert snakemake.params["output_basedir"] == "some/base"
+    assert snakemake.params["nb_script"] == "script.py"
+
+
 def test_output_args(workflow_dir):
     workflow_dir = copy_data(workflow_dir, "test_output_args")