fix: in rules from imported modules, exclude modified paths from module prefixing

snakemake/rules.py

@@ -118,7 +118,10 @@ def __init__(self, *args, lineno=None, snakefile=None, restart_times=0):
             self.is_checkpoint = False
             self.restart_times = 0
             self.basedir = None
-            self.path_modifer = None
+            self.input_modifier = None
+            self.output_modifier = None
+            self.log_modifier = None
+            self.benchmark_modifier = None
             self.ruleinfo = None
         elif len(args) == 1:
             other = args[0]
@@ -168,7 +171,10 @@ def __init__(self, *args, lineno=None, snakefile=None, restart_times=0):
             self.is_checkpoint = other.is_checkpoint
             self.restart_times = other.restart_times
             self.basedir = other.basedir
-            self.path_modifier = other.path_modifier
+            self.input_modifier = other.input_modifier
+            self.output_modifier = other.output_modifier
+            self.log_modifier = other.log_modifier
+            self.benchmark_modifier = other.benchmark_modifier
             self.ruleinfo = other.ruleinfo
 
     def dynamic_branch(self, wildcards, input=True):
@@ -348,7 +354,9 @@ def benchmark(self, benchmark):
         if isinstance(benchmark, Path):
             benchmark = str(benchmark)
         if not callable(benchmark):
-            benchmark = self.apply_path_modifier(benchmark, property="benchmark")
+            benchmark = self.apply_path_modifier(
+                benchmark, self.benchmark_modifier, property="benchmark"
+            )
             benchmark = self._update_item_wildcard_constraints(benchmark)
 
         self._benchmark = IOFile(benchmark, rule=self)
@@ -471,9 +479,9 @@ def check_output_duplicates(self):
                 )
             seen[value] = name or idx
 
-    def apply_path_modifier(self, item, property=None):
-        assert self.path_modifier is not None
-        apply = partial(self.path_modifier.modify, property=property)
+    def apply_path_modifier(self, item, path_modifier, property=None):
+        assert path_modifier is not None
+        apply = partial(path_modifier.modify, property=property)
 
         assert not callable(item)
         if isinstance(item, dict):
@@ -528,9 +536,14 @@ def _set_inoutput_item(self, item, output=False, name=None):
             if isinstance(item, _IOFile) and item.rule and item in item.rule.output:
                 rule_dependency = item.rule
 
-            item = self.apply_path_modifier(
-                item, property="output" if output else "input"
-            )
+            if output:
+                path_modifier = self.output_modifier
+                property = "output"
+            else:
+                path_modifier = self.input_modifier
+                property = "input"
+
+            item = self.apply_path_modifier(item, path_modifier, property=property)
 
             # Check to see that all flags are valid
             # Note that "remote", "dynamic", and "expand" are valid for both inputs and outputs.
@@ -685,7 +698,7 @@ def _set_log_item(self, item, name=None):
             item = str(item)
         if isinstance(item, str) or callable(item):
             if not callable(item):
-                item = self.apply_path_modifier(item, property="log")
+                item = self.apply_path_modifier(item, self.log_modifier, property="log")
                 item = self._update_item_wildcard_constraints(item)
 
             self.log.append(IOFile(item, rule=self) if isinstance(item, str) else item)
@@ -769,7 +782,7 @@ def _apply_wildcards(
         mapping=None,
         no_flattening=False,
         aux_params=None,
-        apply_path_modifier=True,
+        path_modifier=None,
         property=None,
         incomplete_checkpoint_func=lambda e: None,
         allow_unpack=True,
@@ -835,8 +848,10 @@ def _apply_wildcards(
                             "Function did not return str or list of str.", rule=self
                         )
 
-                    if from_callable and apply_path_modifier and not incomplete:
-                        item_ = self.apply_path_modifier(item_, property=property)
+                    if from_callable and path_modifier is not None and not incomplete:
+                        item_ = self.apply_path_modifier(
+                            item_, path_modifier, property=property
+                        )
 
                     concrete = concretize(item_, wildcards, _is_callable)
                     newitems.append(concrete)
@@ -882,6 +897,7 @@ def handle_incomplete_checkpoint(exception):
                 concretize=concretize_iofile,
                 mapping=mapping,
                 incomplete_checkpoint_func=handle_incomplete_checkpoint,
+                path_modifier=self.input_modifier,
                 property="input",
                 groupid=groupid,
             )
@@ -944,7 +960,6 @@ def handle_incomplete_checkpoint(exception):
                 omit_callable=omit_callable,
                 allow_unpack=False,
                 no_flattening=True,
-                apply_path_modifier=False,
                 property="params",
                 aux_params={
                     "input": input._plainstrings(),
@@ -993,7 +1008,12 @@ def concretize_logfile(f, wildcards, is_from_callable):
 
         try:
             self._apply_wildcards(
-                log, self.log, wildcards, concretize=concretize_logfile, property="log"
+                log,
+                self.log,
+                wildcards,
+                concretize=concretize_logfile,
+                path_modifier=self.log_modifier,
+                property="log",
             )
         except WildcardError as e:
             raise WildcardError(

snakemake/workflow.py

@@ -1249,7 +1249,7 @@ def func(*args, **wildcards):
             return expand(
                 *args,
                 scatteritem=map("{{}}-of-{}".format(n).format, range(1, n + 1)),
-                **wildcards
+                **wildcards,
             )
 
         for key in content:
@@ -1369,18 +1369,21 @@ def decorate(ruleinfo):
             if ruleinfo.wildcard_constraints:
                 rule.set_wildcard_constraints(
                     *ruleinfo.wildcard_constraints[0],
-                    **ruleinfo.wildcard_constraints[1]
+                    **ruleinfo.wildcard_constraints[1],
                 )
             if ruleinfo.name:
                 rule.name = ruleinfo.name
                 del self._rules[name]
                 self._rules[ruleinfo.name] = rule
                 name = rule.name
-            rule.path_modifier = ruleinfo.path_modifier
             if ruleinfo.input:
-                rule.set_input(*ruleinfo.input[0], **ruleinfo.input[1])
+                pos_files, keyword_files, modifier = ruleinfo.input
+                rule.input_modifier = modifier
+                rule.set_input(*pos_files, **keyword_files)
             if ruleinfo.output:
-                rule.set_output(*ruleinfo.output[0], **ruleinfo.output[1])
+                pos_files, keyword_files, modifier = ruleinfo.output
+                rule.output_modifier = modifier
+                rule.set_output(*pos_files, **keyword_files)
             if ruleinfo.params:
                 rule.set_params(*ruleinfo.params[0], **ruleinfo.params[1])
             # handle default resources
@@ -1418,9 +1421,9 @@ def decorate(ruleinfo):
                 if ruleinfo.shadow_depth is True:
                     rule.shadow_depth = "full"
                     logger.warning(
-                        "Shadow is set to True in rule {} (equivalent to 'full'). It's encouraged to use the more explicit options 'minimal|copy-minimal|shallow|full' instead.".format(
-                            rule
-                        )
+                        f"Shadow is set to True in rule {rule} (equivalent to 'full'). "
+                        "It's encouraged to use the more explicit options "
+                        "'minimal|copy-minimal|shallow|full' instead."
                     )
                 else:
                     rule.shadow_depth = ruleinfo.shadow_depth
@@ -1455,11 +1458,15 @@ def decorate(ruleinfo):
             if ruleinfo.version:
                 rule.version = ruleinfo.version
             if ruleinfo.log:
-                rule.set_log(*ruleinfo.log[0], **ruleinfo.log[1])
+                pos_files, keyword_files, modifier = ruleinfo.log
+                rule.log_modifier = modifier
+                rule.set_log(*pos_files, **keyword_files)
             if ruleinfo.message:
                 rule.message = ruleinfo.message
             if ruleinfo.benchmark:
-                rule.benchmark = ruleinfo.benchmark
+                benchmark, modifier = ruleinfo.benchmark
+                rule.benchmark_modifier = modifier
+                rule.benchmark = benchmark
             if not self.run_local:
                 group = self.overwrite_groups.get(name) or ruleinfo.group
                 if group is not None:
@@ -1627,14 +1634,14 @@ def decorate(ruleinfo):
 
     def input(self, *paths, **kwpaths):
         def decorate(ruleinfo):
-            ruleinfo.input = (paths, kwpaths)
+            ruleinfo.input = (paths, kwpaths, self.modifier.path_modifier)
             return ruleinfo
 
         return decorate
 
     def output(self, *paths, **kwpaths):
         def decorate(ruleinfo):
-            ruleinfo.output = (paths, kwpaths)
+            ruleinfo.output = (paths, kwpaths, self.modifier.path_modifier)
             return ruleinfo
 
         return decorate
@@ -1679,7 +1686,7 @@ def decorate(ruleinfo):
 
     def benchmark(self, benchmark):
         def decorate(ruleinfo):
-            ruleinfo.benchmark = benchmark
+            ruleinfo.benchmark = (benchmark, self.modifier.path_modifier)
             return ruleinfo
 
         return decorate
@@ -1770,7 +1777,7 @@ def decorate(ruleinfo):
 
     def log(self, *logs, **kwlogs):
         def decorate(ruleinfo):
-            ruleinfo.log = (logs, kwlogs)
+            ruleinfo.log = (logs, kwlogs, self.modifier.path_modifier)
             return ruleinfo
 
         return decorate

tests/test_module_no_prefixing_modified_paths/Snakefile

@@ -0,0 +1,27 @@
+module module1:
+    snakefile: "module1/Snakefile"
+    config: config
+
+
+use rule * from module1 as module1_*
+
+
+# provide a prefix for all paths in module2
+module module2:
+    snakefile: "module2/Snakefile"
+    config: config
+    prefix: "module2"
+
+
+use rule * from module2 as module2_*
+
+# overwrite the input to remove the module2 prefix specified above
+use rule c from module2 as module2_c with:
+    input:
+        "test.txt"
+
+
+rule joint_all:
+    input:
+        "module2/test_final.txt",
+    default_target: True

tests/test_module_no_prefixing_modified_paths/expected-results/module2/test_final.txt

@@ -0,0 +1,2 @@
+test_a
+test_c

tests/test_module_no_prefixing_modified_paths/module1/Snakefile

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

tests/test_module_no_prefixing_modified_paths/module2/Snakefile

@@ -0,0 +1,17 @@
+rule b:
+    output:
+        "test.txt"
+    shell:
+        "echo test_b > {output}"
+
+
+rule c:
+    input:
+        "test.txt"
+    output:
+        "test_final.txt"
+    shell:
+        """
+        cp {input} {output};
+        echo test_c >> {output}
+        """

tests/tests.py

@@ -1390,6 +1390,14 @@ def test_module_complex2():
     run(dpath("test_module_complex2"), dryrun=True)
 
 
+@skip_on_windows
+def test_module_no_prefixing_modified_paths():
+    run(
+        dpath("test_module_no_prefixing_modified_paths"),
+        targets=["module2/test_final.txt"],
+    )
+
+
 def test_module_with_script():
     run(dpath("test_module_with_script"))