fix: fix a bug leading to duplicate conda env initializations; fix di…

…splay of jobs and output files with changes

snakemake/dag.py

@@ -282,6 +282,7 @@ def create_conda_envs(
             for job in jobs
             if job.conda_env_spec and (self.workflow.run_local or job.is_local)
         }
+
         # Then based on md5sum values
         self.conda_envs = dict()
         for (env_spec, simg_url) in env_set:

snakemake/deployment/conda.py

@@ -696,6 +696,14 @@ def is_file(self):
     def contains_wildcard(self):
         ...
 
+    @abstractmethod
+    def __hash__(self):
+        ...
+
+    @abstractmethod
+    def __eq__(self):
+        ...
+
 
 class CondaEnvFileSpec(CondaEnvSpec):
     def __init__(self, filepath: str, rule=None):
@@ -731,6 +739,12 @@ def is_file(self):
     def contains_wildcard(self):
         return contains_wildcard(self.file)
 
+    def __hash__(self):
+        return hash(self.file)
+
+    def __eq__(self, other):
+        return self.file == other.file
+
 
 class CondaEnvNameSpec(CondaEnvSpec):
     def __init__(self, name: str):
@@ -756,6 +770,12 @@ def check(self):
     def contains_wildcard(self):
         return contains_wildcard(self.name)
 
+    def __hash__(self):
+        return hash(self.name)
+
+    def __eq__(self, other):
+        return self.name == other.name
+
 
 def is_conda_env_file(spec: str):
     return spec.endswith(".yaml") or spec.endswith(".yml")

snakemake/persistence.py

@@ -323,36 +323,40 @@ def code(self, path):
         return self.metadata(path).get("code")
 
     def version_changed(self, job, file=None):
-        """Yields output files with changed versions of bool if file given."""
+        """Yields output files with changed versions or bool if file given."""
         return _bool_or_gen(self._version_changed, job, file=file)
 
     def code_changed(self, job, file=None):
-        """Yields output files with changed code of bool if file given."""
+        """Yields output files with changed code or bool if file given."""
         return _bool_or_gen(self._code_changed, job, file=file)
 
     def input_changed(self, job, file=None):
-        """Yields output files with changed input of bool if file given."""
+        """Yields output files with changed input or bool if file given."""
         return _bool_or_gen(self._input_changed, job, file=file)
 
     def params_changed(self, job, file=None):
-        """Yields output files with changed params of bool if file given."""
+        """Yields output files with changed params or bool if file given."""
         return _bool_or_gen(self._params_changed, job, file=file)
 
     def _version_changed(self, job, file=None):
         assert file is not None
-        return self.version(file) != job.rule.version
+        recorded = self.version(file)
+        return recorded is not None and recorded != job.rule.version
 
     def _code_changed(self, job, file=None):
         assert file is not None
-        return self.code(file) != self._code(job.rule)
+        recorded = self.code(file)
+        return recorded is not None and recorded != self._code(job.rule)
 
     def _input_changed(self, job, file=None):
         assert file is not None
-        return self.input(file) != self._input(job)
+        recorded = self.input(file)
+        return recorded is not None and recorded != self._input(job)
 
     def _params_changed(self, job, file=None):
         assert file is not None
-        return self.params(file) != self._params(job)
+        recorded = self.params(file)
+        return recorded is not None and recorded != self._params(job)
 
     def noop(self, *args):
         pass