fix: rule inheritance within modules (did previously lead to key erro…

…rs) (#1292)

* fix: rule inheritance within modules (did previously lead to key errors)

* skip on windows

snakemake/modules.py

@@ -13,18 +13,24 @@
 from snakemake.common import Rules, Scatter, Gather
 
 
-def get_name_modifier_func(rules=None, name_modifier=None):
+def get_name_modifier_func(rules=None, name_modifier=None, parent_modifier=None):
     if name_modifier is None:
         return None
     else:
+        if parent_modifier is None:
+            parent_modifier_func = lambda rulename: rulename
+        else:
+            parent_modifier_func = parent_modifier.modify_rulename
         if "*" in name_modifier:
-            return lambda rulename: name_modifier.replace("*", rulename)
+            return lambda rulename: parent_modifier_func(
+                name_modifier.replace("*", rulename)
+            )
         elif name_modifier is not None:
             if len(rules) > 1:
                 raise SyntaxError(
                     "Multiple rules in 'use rule' statement but name modification ('as' statement) does not contain a wildcard '*'."
                 )
-            return lambda rulename: name_modifier
+            return lambda rulename: parent_modifier_func(name_modifier)
 
 
 class ModuleInfo:

snakemake/workflow.py

@@ -1819,11 +1819,13 @@ def decorate(maybe_ruleinfo):
                     raise WorkflowError(
                         "'use rule' statement from rule in the same module must declare a single rule but multiple rules are declared."
                     )
-                orig_rule = self._rules[rules[0]]
+                orig_rule = self._rules[self.modifier.modify_rulename(rules[0])]
                 ruleinfo = maybe_ruleinfo if not callable(maybe_ruleinfo) else None
                 with WorkflowModifier(
                     self,
-                    rulename_modifier=get_name_modifier_func(rules, name_modifier),
+                    rulename_modifier=get_name_modifier_func(
+                        rules, name_modifier, parent_modifier=self.modifier
+                    ),
                     ruleinfo_overwrite=ruleinfo,
                 ):
                     self.rule(

tests/test_modules_ruledeps_inheritance/Snakefile

@@ -0,0 +1,25 @@
+rule all:
+    input:
+        "test2.txt",
+        "test3.txt",
+        "test4.txt",
+
+
+module somemodule:
+    snakefile:
+        "module/Snakefile"
+    config:
+        config
+
+
+use rule * from somemodule as somemodule_*
+
+
+module someothermodule:
+    snakefile:
+        "module2/Snakefile"
+    config:
+        config
+
+
+use rule * from someothermodule as someothermodule_*

tests/test_modules_ruledeps_inheritance/expected-results/test2.txt

@@ -0,0 +1 @@
+test

tests/test_modules_ruledeps_inheritance/module/Snakefile

@@ -0,0 +1,20 @@
+rule a:
+    output:
+        "test.txt"
+    shell:
+        "echo test > {output}"
+
+
+rule b:
+    input:
+        rules.a.output[0]
+    output:
+        "test2.txt"
+    shell:
+        "cp {input} {output}"
+
+
+
+use rule b as c with:
+    output:
+        "test4.txt"

tests/test_modules_ruledeps_inheritance/module2/Snakefile

@@ -0,0 +1,5 @@
+rule a:
+    output:
+        "test3.txt"
+    shell:
+        "echo foo > {output}"

tests/tests.py

@@ -1377,3 +1377,8 @@ def test_ancient_dag():
 @skip_on_windows
 def test_checkpoint_allowed_rules():
     run(dpath("test_checkpoint_allowed_rules"), targets=["c"], cluster="./qsub")
+
+
+@skip_on_windows
+def test_modules_ruledeps_inheritance():
+    run(dpath("test_modules_ruledeps_inheritance"))