fix: fix pepfile handling in case of module usage (#1387)

* fix: fix pepfile handling in case of module usage

* skip on win

snakemake/parser.py

@@ -248,7 +248,9 @@ class Configfile(GlobalKeywordState):
 
 
 class Pepfile(GlobalKeywordState):
-    pass
+    @property
+    def keyword(self):
+        return "set_pepfile"
 
 
 class Pepschema(GlobalKeywordState):

snakemake/workflow.py

@@ -1241,40 +1241,36 @@ def workdir(self, workdir):
 
     def configfile(self, fp):
         """Update the global config with data from the given file."""
-        global config
         if not self.modifier.skip_configfile:
             if os.path.exists(fp):
                 self.configfiles.append(fp)
                 c = snakemake.io.load_configfile(fp)
-                update_config(config, c)
+                update_config(self.config, c)
                 if self.overwrite_config:
                     logger.info(
                         "Config file {} is extended by additional config specified via the command line.".format(
                             fp
                         )
                     )
-                    update_config(config, self.overwrite_config)
+                    update_config(self.config, self.overwrite_config)
             elif not self.overwrite_configfiles:
                 raise WorkflowError(
                     "Workflow defines configfile {} but it is not present or accessible.".format(
                         fp
                     )
                 )
 
-    def pepfile(self, path):
-        global pep
+    def set_pepfile(self, path):
 
         try:
             import peppy
         except ImportError:
             raise WorkflowError("For PEP support, please install peppy.")
 
         self.pepfile = path
-        pep = peppy.Project(self.pepfile)
+        self.globals["pep"] = peppy.Project(self.pepfile)
 
     def pepschema(self, schema):
-        global pep
-
         try:
             import eido
         except ImportError:
@@ -1285,7 +1281,9 @@ def pepschema(self, schema):
             schema = self.current_basedir.join(schema).get_path_or_uri()
         if self.pepfile is None:
             raise WorkflowError("Please specify a PEP with the pepfile directive.")
-        eido.validate_project(project=pep, schema=schema, exclude_case=True)
+        eido.validate_project(
+            project=self.globals["pep"], schema=schema, exclude_case=True
+        )
 
     def report(self, path):
         """Define a global report description in .rst format."""

tests/test_modules_peppy/Snakefile

@@ -0,0 +1,15 @@
+shell.executable("bash")
+
+configfile: "config/config.yaml"
+
+
+module test:
+    snakefile:
+        "module-test/Snakefile"
+    config:
+        config
+    prefix:
+        "foo"
+
+
+use rule * from test

tests/test_modules_peppy/config/config.yaml

@@ -0,0 +1,2 @@
+test: 1
+pepfile: "pep/config.yaml"

tests/test_modules_peppy/expected-results/foo/results/test.out

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

tests/test_modules_peppy/module-test/Snakefile

@@ -0,0 +1,14 @@
+configfile: "config.yaml" # does not exist, but this statement should be ignored on module import
+pepfile: config["pepfile"]
+
+def some_func():
+    return 15
+
+print(pep)
+
+rule a:
+    output:
+        "results/test.out",
+        "/tmp/foo.txt"
+    shell:
+        "echo {config[test]} > {output[0]}; touch {output[1]}"

tests/test_modules_peppy/pep/config.yaml

@@ -0,0 +1,2 @@
+pep_version: "2.0.0"
+sample_table: sample_table.csv

tests/test_modules_peppy/pep/sample_table.csv

@@ -0,0 +1,3 @@
+sample_name,protocol
+a,test
+b,test2

tests/test_peppy/workflow/Snakefile → tests/test_peppy/Snakefile

@@ -1,5 +1,7 @@
 pepfile: "pep/config.yaml"
-pepschema: "schemas/pep.yaml"
+pepfile: "pep/config.yaml" # test overwriting
+
+pepschema: "workflow/schemas/pep.yaml"
 
 rule all:
     input:

tests/tests.py

@@ -1289,6 +1289,11 @@ def test_modules_prefix():
     run(dpath("test_modules_prefix"), targets=["a"])
 
 
+@skip_on_windows
+def test_modules_peppy():
+    run(dpath("test_modules_peppy"), targets=["a"])
+
+
 def test_modules_specific():
     run(dpath("test_modules_specific"), targets=["test_a"])
 
@@ -1427,3 +1432,8 @@ def test_github_issue1384():
         )
     finally:
         shutil.rmtree(tmpdir)
+
+
+@skip_on_windows
+def test_peppy():
+    run(dpath("test_peppy"))