Fix 2.0 bug with child class constructors

ceci/pipeline.py

@@ -185,16 +185,7 @@ def build_stage_object(self, args):
             self.stage_class = PipelineStage.get_stage(
                 self.class_name, self.module_name
             )
-        # EAC.  Ideally we would just pass the aliases into the c'tor of self.stage_class(),
-        # but that would requiring changing the signature of every sub-class, so we do this
-        # instead.  At some point we might want to migrate to doing it the better way
-        try:
-            self.stage_obj = self.stage_class(args, aliases=self.aliases)
-        except TypeError:
-            self.stage_obj = self.stage_class(args)
-            self.stage_obj._aliases.update(**self.aliases)
-            self.stage_obj._io_checked = False
-            self.stage_obj.check_io()
+        self.stage_obj = self.stage_class(args, aliases=self.aliases)
         return self.stage_obj
 
     def generate_full_command(self, inputs, outputs, config):
@@ -674,9 +665,11 @@ def build_stage(self, stage_class, **kwargs):
         `Pipeline.pipeline_files` data member, so that they are available to later stages
         """
         kwcopy = kwargs.copy()
+        aliases = kwcopy.pop("aliases", {})
+        comm = kwcopy.pop("comm", None)
         kwcopy.update(**self.pipeline_files)
-        aliases = kwcopy.pop("aliases", None)
-        stage = stage_class(kwcopy, aliases=aliases)
+
+        stage = stage_class(kwcopy, comm=comm, aliases=aliases)
         return self.add_stage(stage)
 
     def remove_stage(self, name):

ceci/stage.py

@@ -8,6 +8,7 @@
 import cProfile
 import pdb
 import datetime
+import warnings
 
 from abc import abstractmethod
 from . import errors
@@ -102,6 +103,8 @@ def __init__(self, args, comm=None, aliases=None):
         if comm is not None:
             self.setup_mpi(comm)
 
+        self.check_io()
+
 
     @classmethod
     def make_stage(cls, **kwargs):
@@ -117,13 +120,7 @@ def make_stage(cls, **kwargs):
             for output_ in cls.outputs:  # pylint: disable=no-member
                 outtag = output_[0]
                 aliases[outtag] = f"{outtag}_{name}"
-        # EAC.  Ideally we would just pass the aliases into the construction call
-        # but that would requiring changing the signature of every sub-class, so we do this
-        # instead.  At some point we might want to migrate to doing it the better way
-        stage = cls(kwcopy, comm=comm)
-        stage._aliases.update(**aliases)
-        stage._io_checked = False
-        stage.check_io()
+        stage = cls(kwcopy, comm=comm, aliases=aliases)
         return stage
 
     def get_aliases(self):
@@ -181,7 +178,6 @@ def load_configs(self, args):
             error_class = type(error)
             msg = str(error)
             raise error_class(f"Error configuring {self.instance_name}: {msg}")
-        self.check_io(args)
 
     def check_io(self, args=None):
         """

ceci/update_pipelines_for_ceci_2.py

@@ -77,15 +77,20 @@ def update_pipeline_file_group(pipeline_files):
 def scan_directory_and_update(base_dir):
     groups = collections.defaultdict(list)
     yaml = ruamel.yaml.YAML()
-    for dirpath, subdirs, filenames in os.walk(base_dir):
+    yaml.allow_duplicate_keys = True
+    for dirpath, _, filenames in os.walk(base_dir):
         # just process yaml files
         for filename in filenames:
             if not (filename.endswith(".yaml") or filename.endswith(".yml")):
                 continue
             filepath = os.path.join(dirpath, filename)
             with open(filepath) as f:
                 yaml_str = f.read()
-            info = yaml.load(yaml_str)
+            try:
+                info = yaml.load(yaml_str)
+            except:
+                print("# Could not read yaml file:", filepath)
+                continue
 
             if is_pipeline_file(info):
                 config = info["config"]

tests/test_interactive.py

@@ -137,4 +137,3 @@ def test_inter_pipe():
 
 if __name__ == "__main__":
     test_config()
-    test_interactive()

tests/test_stage.py

@@ -569,8 +569,6 @@ class LimaSerial(LimaParallel):
         assert LimaSerial.parse_command_line(["LimaSerial", "--mpi"]).mpi
 
 
-# could add more tests here for constructor, but the regression tests here and in TXPipe are
-# pretty thorough.
 
 if __name__ == "__main__":
     test_construct()