fix: ensure that rule inheritance considers the same globals and othe…

…r settings as parent module (#1621)

* fix: ensure that workflow module globals are available for inherited rules.

* inherit from parent modifier

* add missing files

* fix GS bucket names

snakemake/modules.py

@@ -131,6 +131,7 @@ class WorkflowModifier:
     def __init__(
         self,
         workflow,
+        parent_modifier=None,
         globals=None,
         config=None,
         base_snakefile=None,
@@ -146,12 +147,29 @@ def __init__(
         replace_wrapper_tag=None,
         namespace=None,
     ):
+        if parent_modifier is not None:
+            # init with values from parent modifier
+            self.base_snakefile = parent_modifier.base_snakefile
+            self.globals = parent_modifier.globals
+            self.skip_configfile = parent_modifier.skip_configfile
+            self.rulename_modifier = parent_modifier.rulename_modifier
+            self.skip_validation = parent_modifier.skip_validation
+            self.skip_global_report_caption = parent_modifier.skip_global_report_caption
+            self.rule_whitelist = parent_modifier.rule_whitelist
+            self.ruleinfo_overwrite = parent_modifier.ruleinfo_overwrite
+            self.allow_rule_overwrite = parent_modifier.allow_rule_overwrite
+            self.path_modifier = parent_modifier.path_modifier
+            self.replace_wrapper_tag = parent_modifier.replace_wrapper_tag
+            self.namespace = parent_modifier.namespace
+        else:
+            # default settings for globals if not inheriting from parent
+            self.globals = (
+                globals if globals is not None else dict(workflow.vanilla_globals)
+            )
+
         self.workflow = workflow
         self.base_snakefile = base_snakefile
 
-        self.globals = (
-            globals if globals is not None else dict(workflow.vanilla_globals)
-        )
         if config is not None:
             self.globals["config"] = config
 

snakemake/workflow.py

@@ -1933,6 +1933,7 @@ def decorate(maybe_ruleinfo):
                 ruleinfo = maybe_ruleinfo if not callable(maybe_ruleinfo) else None
                 with WorkflowModifier(
                     self,
+                    parent_modifier=self.modifier,
                     rulename_modifier=get_name_modifier_func(
                         rules, name_modifier, parent_modifier=self.modifier
                     ),

tests/test01/Snakefile

@@ -1,3 +1,4 @@
+
 from snakemake.utils import min_version
 
 from snakemake import __version__
@@ -27,6 +28,8 @@ onerror:
     print(log)
 
 
+
+
 ruleorder: rule2 > rule4
 
 def testin(wildcards):

tests/test_google_lifesciences.py

@@ -57,9 +57,13 @@ def create_google_storage(bucket_name="snakemake-testing"):
     return client.create_bucket(bucket_name)
 
 
+def get_temp_bucket_name():
+    return "snakemake-testing-%s-bucket" % next(tempfile._get_candidate_names())
+
+
 @google_credentials
 def test_google_lifesciences():
-    bucket_name = "snakemake-testing-%s" % next(tempfile._get_candidate_names())
+    bucket_name = get_temp_bucket_name()
     create_google_storage(bucket_name)
     storage_prefix = "test_google_lifesciences"
     workdir = dpath("test_google_lifesciences")
@@ -82,7 +86,7 @@ def test_google_lifesciences():
 )
 @google_credentials
 def test_touch_remote_prefix():
-    bucket_name = "snakemake-testing-%s-bucket" % next(tempfile._get_candidate_names())
+    bucket_name = get_temp_bucket_name()
     create_google_storage(bucket_name)
     storage_prefix = "test_touch_remote_prefix"
     workdir = dpath("test_touch_remote_prefix")
@@ -101,7 +105,7 @@ def test_touch_remote_prefix():
 @google_credentials
 def test_cloud_checkpoints_issue574():
     """see Github issue #574"""
-    bucket_name = "snakemake-testing-%s" % next(tempfile._get_candidate_names())
+    bucket_name = get_temp_bucket_name()
     create_google_storage(bucket_name)
     storage_prefix = "test_cloud_checkpoints_issue574"
     workdir = dpath("test_cloud_checkpoints_issue574")
@@ -118,7 +122,7 @@ def test_cloud_checkpoints_issue574():
 
 
 def test_github_issue1396():
-    bucket_name = "snakemake-testing-%s" % next(tempfile._get_candidate_names())
+    bucket_name = get_temp_bucket_name()
     create_google_storage(bucket_name)
     storage_prefix = "test_github_issue1396"
     workdir = dpath("test_github_issue1396")
@@ -135,7 +139,7 @@ def test_github_issue1396():
 
 
 def test_github_issue1460():
-    bucket_name = "snakemake-testing-%s" % next(tempfile._get_candidate_names())
+    bucket_name = get_temp_bucket_name()
     create_google_storage(bucket_name)
     storage_prefix = "test_github_issue1460"
     prefix = "%s/%s" % (bucket_name, storage_prefix)

tests/test_rule_inheritance_globals/.snakemake/metadata/Zm9vLnR4dA==

@@ -0,0 +1 @@
+{"version": null, "code": "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", "rule": "b", "input": [], "log": [], "params": [], "shellcmd": "echo test '{}' > foo.txt", "incomplete": false, "starttime": 1651478820.4933672, "endtime": 1651478820.5000339, "job_hash": 8740185748842, "conda_env": null, "container_img_url": null}

tests/test_rule_inheritance_globals/Snakefile

@@ -0,0 +1,10 @@
+rule a:
+    output:
+        "test.out"
+    shell:
+        "echo test '{config}' > {output}"
+
+
+use rule a as b with:
+    output:
+        report("foo.txt", caption="caption.rst")

tests/test_rule_inheritance_globals/foo.txt

@@ -0,0 +1 @@
+test {}

tests/tests.py

@@ -1614,3 +1614,12 @@ def test_cleanup_metadata_fail():
 @skip_on_windows  # same on win, no need to test
 def test_github_issue1389():
     run(dpath("test_github_issue1389"), resources={"foo": 4}, shouldfail=True)
+
+
+def test_rule_inheritance_globals():
+    run(
+        dpath("test_rule_inheritance_globals"),
+        report="report.html",
+        targets=["foo.txt"],
+        check_md5=False,
+    )