fix: remove deprecated and add missing arguments to internal functions

snakemake/dag.py

@@ -1782,7 +1782,7 @@ def build_ruledag(job, key=lambda job: job.rule.name):
         for job in self.targetjobs:
             build_ruledag(job)
 
-        return self._dot(dag.keys(), print_wildcards=False, print_types=False, dag=dag)
+        return self._dot(dag.keys())
 
     def rule_dot(self):
         graph = defaultdict(set)

snakemake/deployment/conda.py

@@ -701,7 +701,7 @@ def __hash__(self):
         ...
 
     @abstractmethod
-    def __eq__(self):
+    def __eq__(self, other):
         ...
 
 

snakemake/remote/__init__.py

@@ -52,8 +52,8 @@ def __copy__(self):
         copied_wrapped = copy.copy(self.__wrapped__)
         return type(self)(copied_wrapped)
 
-    def __deepcopy__(self):
-        copied_wrapped = copy.deepcopy(self.__wrapped__)
+    def __deepcopy__(self, memo):
+        copied_wrapped = copy.deepcopy(self.__wrapped__, memo)
         return type(self)(copied_wrapped)