Add support for ingesting multi-night ImageCollections (#46)

* Add multi_night_workflow for ingesting multi-night ImageCollections

* Specify guess distances in the parsl runtime config file.

* Comibine ic_to_wu and reproject steps

* Revert local klone config changes

* Clean up redundant task from earlier version

src/kbmod_wf/multi_night_workflow.py

@@ -0,0 +1,148 @@
+import argparse
+import os
+
+import toml
+import parsl
+from parsl import python_app, File
+import parsl.executors
+
+from kbmod_wf.utilities import (
+    apply_runtime_updates,
+    get_resource_config,
+    get_executors,
+    get_configured_logger,
+)
+
+from kbmod_wf.workflow_tasks import create_manifest, kbmod_search
+
+
+@python_app(
+    cache=True,
+    executors=get_executors(["local_dev_testing", "sharded_reproject"]),
+    ignore_for_cache=["logging_file"],
+)
+def reproject_wu(inputs=(), outputs=(), runtime_config={}, logging_file=None):
+    from kbmod_wf.utilities.logger_utilities import get_configured_logger, ErrorLogger
+
+    logger = get_configured_logger("task.reproject_wu", logging_file.filepath)
+
+    from kbmod_wf.task_impls.reproject_multi_chip_multi_night_wu import reproject_wu
+    guess_dist = inputs[1] # heliocentric guess distance in AU
+    logger.info(f"Starting reproject_ic for guess distance {guess_dist}")
+    with ErrorLogger(logger):
+        reproject_wu(
+            guess_dist,
+            ic_filepath=inputs[0],
+            reprojected_wu_filepath=outputs[0].filepath,
+            runtime_config=runtime_config,
+            logger=logger,
+        )
+    logger.info("Completed reproject_ic")
+    return outputs[0]
+
+
+def workflow_runner(env=None, runtime_config={}):
+    """This function will load and configure Parsl, and run the workflow.
+
+    Parameters
+    ----------
+    env : str, optional
+        Environment string used to define which resource configuration to use,
+        by default None
+    runtime_config : dict, optional
+        Dictionary of assorted runtime configuration parameters, by default {}
+    """
+    resource_config = get_resource_config(env=env)
+    resource_config = apply_runtime_updates(resource_config, runtime_config)
+
+    app_configs = runtime_config.get("apps", {})
+
+    dfk = parsl.load(resource_config)
+    if dfk:
+        logging_file = File(os.path.join(dfk.run_dir, "kbmod.log"))
+        logger = get_configured_logger("workflow.workflow_runner", logging_file.filepath)
+
+        if runtime_config is not None:
+            logger.info(f"Using runtime configuration definition:\n{toml.dumps(runtime_config)}")
+
+        logger.info("Starting workflow")
+
+        # gather all the *.collection files that are staged for processing
+        create_manifest_config = app_configs.get("create_manifest", {})
+        manifest_file = File(
+            os.path.join(create_manifest_config.get("output_directory", os.getcwd()), "manifest.txt")
+        )
+        create_manifest_future = create_manifest(
+            inputs=[],
+            outputs=[manifest_file],
+            runtime_config=app_configs.get("create_manifest", {}),
+            logging_file=logging_file,
+        )
+
+        # reproject each WorkUnit for a range of distances
+        reproject_futures = []
+        repro_wu_filenames = []
+        runtime_config=app_configs.get("reproject_wu", {})
+        with open(create_manifest_future.result(), "r") as f:
+            for line in f:
+                collection_file = File(line.strip())
+                wu_filename = line + ".wu"
+                # Get the requested heliocentric guess distances (in AU) for reflex correction.
+                # If none are provided, default to 42.0 AU.
+                distances = runtime_config["helio_guess_dists"] if "helio_guess_dists" in runtime_config else [42.0]
+                for dist in distances:
+                    output_filename=wu_filename + f".{dist}.repro"
+                    repro_wu_filenames.append(output_filename)
+                    reproject_futures.append(
+                        reproject_wu(
+                            inputs=[collection_file, dist],
+                            outputs=[File(output_filename)],
+                            runtime_config=runtime_config,
+                            logging_file=logging_file,
+                        )
+                    )
+
+        # run kbmod search on each reprojected WorkUnit
+        search_futures = []
+        for i in range(len(reproject_futures)):
+            f = reproject_futures[i]
+            search_futures.append(
+                kbmod_search(
+                    inputs=[f],
+                    outputs=[File(repro_wu_filenames[i] + ".search.ecsv")],
+                    runtime_config=app_configs.get("kbmod_search", {}),
+                    logging_file=logging_file,
+                )
+            )
+
+        [f.result() for f in search_futures]
+
+        logger.info("Workflow complete")
+
+    parsl.clear()
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--env",
+        type=str,
+        choices=["dev", "klone"],
+        help="The environment to run the workflow in.",
+    )
+
+    parser.add_argument(
+        "--runtime-config",
+        type=str,
+        help="The complete runtime configuration filepath to use for the workflow.",
+    )
+
+    args = parser.parse_args()
+
+    # if a runtime_config file was provided and exists, load the toml as a dict.
+    runtime_config = {}
+    if args.runtime_config is not None and os.path.exists(args.runtime_config):
+        with open(args.runtime_config, "r") as toml_runtime_config:
+            runtime_config = toml.load(toml_runtime_config)
+
+    workflow_runner(env=args.env, runtime_config=runtime_config)

src/kbmod_wf/task_impls/ic_to_wu.py

@@ -9,7 +9,7 @@
 
 
 def ic_to_wu(
-    ic_filepath: str = None, wu_filepath: str = None, runtime_config: dict = {}, logger: Logger = None
+    ic_filepath: str = None, wu_filepath: str = None, save: bool = True, runtime_config: dict = {}, logger: Logger = None
 ):
     """This task will convert an ImageCollection to a WorkUnit.
 
@@ -19,18 +19,20 @@ def ic_to_wu(
         The fully resolved filepath to the input ImageCollection file, by default None
     wu_filepath : str, optional
         The fully resolved filepath for the output WorkUnit file, by default None
+    save : bool, optional
+        Flag to save the WorkUnit to disk, by default True. If False, the WorkUnit is returned.
     runtime_config : dict, optional
         Additional configuration parameters to be used at runtime, by default {}
     logger : Logger, optional
         Primary logger for the workflow, by default None
 
     Returns
     -------
-    str
-        The fully resolved filepath of the output WorkUnit file.
+    str | WorkUnit
+        The fully resolved filepath of the output WorkUnit file or the WorkUnit object itself if save=False.
     """
     ic_to_wu_converter = ICtoWUConverter(
-        ic_filepath=ic_filepath, wu_filepath=wu_filepath, runtime_config=runtime_config, logger=logger
+        ic_filepath=ic_filepath, wu_filepath=wu_filepath, save=save, runtime_config=runtime_config, logger=logger
     )
 
     return ic_to_wu_converter.create_work_unit()
@@ -41,25 +43,19 @@ def __init__(
         self,
         ic_filepath: str = None,
         wu_filepath: str = None,
+        save: bool = True,
         runtime_config: dict = {},
         logger: Logger = None,
     ):
         self.ic_filepath = ic_filepath
         self.wu_filepath = wu_filepath
+        self.save = save
         self.runtime_config = runtime_config
         self.logger = logger
 
-        self.overwrite = self.runtime_config.get("overwrite", False)
         self.search_config_filepath = self.runtime_config.get("search_config_filepath", None)
 
     def create_work_unit(self):
-        if len(glob.glob(self.wu_filepath)):
-            if self.overwrite:
-                self.logger.info(f"Overwrite was {self.overwrite}. Deleting existing {self.wu_filepath}.")
-                os.remove(self.wu_filepath)
-            else:
-                make_wu = False
-
         ic = ImageCollection.read(self.ic_filepath, format="ascii.ecsv")
         self.logger.info(f"ImageCollection read from {self.ic_filepath}, creating work unit next.")
 
@@ -76,6 +72,10 @@ def create_work_unit(self):
         elapsed = round(time.time() - last_time, 1)
         self.logger.debug(f"Required {elapsed}[s] to create WorkUnit.")
 
+        if not self.save:
+            self.logger.debug(f"Required {elapsed}[s] to create the WorkUnit.")
+            return orig_wu
+
         self.logger.info(f"Saving sharded work unit to: {self.wu_filepath}")
         last_time = time.time()
         directory_containing_shards, wu_filename = os.path.split(self.wu_filepath)