Rename CmdlineTask's entry method runDataDef

Prepare Tasks for Gen3 PipelineTask conversion by:
* Renaming CmdlineTask's entry method to `runDataRef`.  The default
  CmdlineTask.TaskRunner now calls a Task's `runDataRef` method on the
  parsed command line inputs.
  `runDataRef` method can take any Gen2 Butler data products.
* Renaming CmdlineTasks previous core methods (e.g. assemble,
  characterize) to `run` when they exist.

python/lsst/ap/pipe/apPipeTaskRunner.py

@@ -81,7 +81,7 @@ def __call__(self, args):
         Parameters
         ----------
         args
-            A path to the database file, followed by arguments for Task.run().
+            A Butler data reference, followed by option arguments for Task.runDataRef().
 
         Returns
         -------
@@ -108,10 +108,10 @@ def __call__(self, args):
         result = None  # in case the task fails
         exitStatus = 0  # exit status for the shell
         if self.doRaise:
-            result = task.run(dataRef, **kwargs)
+            result = task.runDataRef(dataRef, **kwargs)
         else:
             try:
-                result = task.run(dataRef, **kwargs)
+                result = task.runDataRef(dataRef, **kwargs)
             except Exception as e:
                 # The shell exit value will be the number of dataRefs returning
                 # non-zero, so the actual value used here is lost.

python/lsst/ap/pipe/ap_pipe.py

@@ -165,7 +165,7 @@ def _copyConfig(config):
         return configClass(**contents)
 
     @pipeBase.timeMethod
-    def run(self, rawRef, templateIds=None, reuse=None):
+    def runDataRef(self, rawRef, templateIds=None, reuse=None):
         """Execute the ap_pipe pipeline on a single image.
 
         Parameters
@@ -187,8 +187,8 @@ def run(self, rawRef, templateIds=None, reuse=None):
 
             - l1Database : handle for accessing the final association database, conforming to
                 `ap_association`'s DB access API
-            - ccdProcessor : output of `config.ccdProcessor.run` (`lsst.pipe.base.Struct` or `None`).
-            - differencer : output of `config.differencer.run` (`lsst.pipe.base.Struct` or `None`).
+            - ccdProcessor : output of `config.ccdProcessor.runDataRef` (`lsst.pipe.base.Struct` or `None`).
+            - differencer : output of `config.differencer.runDataRef` (`lsst.pipe.base.Struct` or `None`).
             - associator : output of `config.associator.run` (`lsst.pipe.base.Struct` or `None`).
         """
         if reuse is None:
@@ -247,14 +247,14 @@ def runProcessCcd(self, sensorRef):
         Returns
         -------
         result : `lsst.pipe.base.Struct`
-            Output of `config.ccdProcessor.run`.
+            Output of `config.ccdProcessor.runDataRef`.
 
         Notes
         -----
         The input repository corresponding to ``sensorRef`` must already contain the refcats.
         """
         self.log.info("Running ProcessCcd...")
-        return self.ccdProcessor.run(sensorRef)
+        return self.ccdProcessor.runDataRef(sensorRef)
 
     @pipeBase.timeMethod
     def runDiffIm(self, sensorRef, templateIds=None):
@@ -275,10 +275,10 @@ def runDiffIm(self, sensorRef, templateIds=None):
         Returns
         -------
         result : `lsst.pipe.base.Struct`
-            Output of `config.differencer.run`.
+            Output of `config.differencer.runDataRef`.
         """
         self.log.info("Running ImageDifference...")
-        return self.differencer.run(sensorRef, templateIdList=templateIds)
+        return self.differencer.runDataRef(sensorRef, templateIdList=templateIds)
 
     @pipeBase.timeMethod
     def runAssociation(self, sensorRef):