Add single-variable time series file generation function from ADF

README.md

@@ -4,15 +4,9 @@ Python Framework for Generating Diagnostics from CESM
 
 ## Project Vision
 
-CUPiD is a collaborative effort that unifies all CESM component diagnostics and provides
+CUPiD is a “one stop shop” that enables and integrates timeseries file generation, data standardization, diagnostics, and metrics from all CESM components.
 
-- Python code that
-  1. runs in an easy-to-generate conda environment, and
-  1. can be launched via CIME workflow or independently
-- Diagnostics for single/multiple runs and single/multiple components
-- Ability to call post-processing tools that other groups are working on
-- An API that makes it easy to include outside code
-- Ongoing support and software maintenance
+This collaborative effort aims to simplify the user experience of running diagnostics by calling post-processing tools directly from CUPiD, running all component diagnostics from the same tool as either part of the CIME workflow or independently, and sharing python code and a standard conda environment across components.
 
 ## Installing
 
@@ -94,4 +88,7 @@ if not serial:
   client = Client(cluster)
 
 client
-```
+```
+
+### Timeseries File Generation
+CUPiD also has the capability to generate single variable timeseries files from history files for all components. To run timeseries, edit the `config.yml` file's timeseries section to fit your preferences, and then run `cupid-run config.yml -ts`.

cupid/run.py

@@ -2,42 +2,82 @@
 
 import click
 import os
-import sys
 from glob import glob
 import papermill as pm
 import intake
 import cupid.util
+import cupid.timeseries
 from dask.distributed import Client
 import dask
 import time
 import ploomber
+import yaml
+
+CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
+
 
-CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help'])
 @click.command(context_settings=CONTEXT_SETTINGS)
 @click.option("--serial", "-s", is_flag=True, help="Do not use LocalCluster objects")
-@click.option("--time-series", "-ts", is_flag=True,
-              help="Run time series generation scripts prior to diagnostics")
+@click.option(
+    "--time-series",
+    "-ts",
+    is_flag=True,
+    help="Run time series generation scripts prior to diagnostics",
+)
 @click.argument("config_path")
 def run(config_path, serial=False, time_series=False):
     """
     Main engine to set up running all the notebooks.
     """
 
-    # Abort if run with --time-series (until feature is added)
-    if time_series:
-        sys.tracebacklimit = 0
-        raise NotImplementedError("--time-series option not implemented yet")
-
     # Get control structure
     control = cupid.util.get_control_dict(config_path)
     cupid.util.setup_book(config_path)
 
+   #####################################################################
+    # Managing global parameters
+
+    global_params = dict()
+
+    if "global_params" in control:
+        global_params = control["global_params"]
+    ####################################################################
+
+    if time_series:
+        timeseries_params = control["timeseries"]
+
+        # general timeseries arguments for all components
+        num_procs = timeseries_params["num_procs"]
+
+
+
+        for component in ['atm', 'ocn', 'lnd', 'ice', 'glc']:
+            cupid.timeseries.create_time_series(
+            component,
+            timeseries_params[f"{component}_vars"],
+            timeseries_params[f"derive_vars_{component}"],
+            [timeseries_params["case_name"]],  # could also grab from compute_notebooks section of config file
+            timeseries_params[f"{component}_hist_str"],
+            [global_params["CESM_output_dir"] + "/" + timeseries_params["case_name"] + f"/{component}/hist/"],  # could also grab from compute_notebooks section of config file
+            [global_params["CESM_output_dir"]+'/'+timeseries_params['case_name']+f'/{component}/proc/tseries/'],
+            # Note that timeseries output will eventually go in /glade/derecho/scratch/${USER}/archive/${CASE}/${component}/proc/tseries/
+            timeseries_params["ts_done"],
+            timeseries_params["overwrite_ts"],
+            timeseries_params[f"{component}_start_years"],  # could get from yaml file in adf_quick_run.parameter_groups.none.config_fil_str, or for other notebooks config files, eg ocean_surface.parameter_gropus.none.mom6_tools_config.start_date
+            timeseries_params[f"{component}_end_years"],  # could get from yaml file in adf_quick_run.parameter_groups.none.config_fil_str, or for other notebooks config files, eg ocean_surface.parameter_gropus.none.mom6_tools_config.end_date
+            timeseries_params[f"{component}_level"],
+            num_procs,
+            serial,
+        )
+
     # Grab paths
 
-    run_dir = os.path.realpath(os.path.expanduser(control['data_sources']['run_dir']))
-    output_dir = run_dir + "/computed_notebooks/" + control['data_sources']['sname']
-    temp_data_path = run_dir + "/temp_data" 
-    nb_path_root = os.path.realpath(os.path.expanduser(control['data_sources']['nb_path_root']))
+    run_dir = os.path.realpath(os.path.expanduser(control["data_sources"]["run_dir"]))
+    output_dir = run_dir + "/computed_notebooks/" + control["data_sources"]["sname"]
+    temp_data_path = run_dir + "/temp_data"
+    nb_path_root = os.path.realpath(
+        os.path.expanduser(control["data_sources"]["nb_path_root"])
+    )
 
     #####################################################################
     # Managing catalog-related stuff
@@ -46,67 +86,71 @@ def run(config_path, serial=False, time_series=False):
 
     cat_path = None
 
-    if 'path_to_cat_json' in control['data_sources']:
+    if "path_to_cat_json" in control["data_sources"]:
         use_catalog = True
-        full_cat_path = os.path.realpath(os.path.expanduser(control['data_sources']['path_to_cat_json']))
+        full_cat_path = os.path.realpath(
+            os.path.expanduser(control["data_sources"]["path_to_cat_json"])
+        )
         full_cat = intake.open_esm_datastore(full_cat_path)
 
-    # Doing initial subsetting on full catalog, e.g. to only use certain cases
+        # Doing initial subsetting on full catalog, e.g. to only use certain cases
 
-        if 'subset' in control['data_sources']:
-            first_subset_kwargs = control['data_sources']['subset']
+        if "subset" in control["data_sources"]:
+            first_subset_kwargs = control["data_sources"]["subset"]
             cat_subset = full_cat.search(**first_subset_kwargs)
             # This pulls out the name of the catalog from the path
-            cat_subset_name = full_cat_path.split("/")[-1].split('.')[0] + "_subset"
-            cat_subset.serialize(directory=temp_data_path, name=cat_subset_name, catalog_type="file")
+            cat_subset_name = full_cat_path.split("/")[-1].split(".")[0] + "_subset"
+            cat_subset.serialize(
+                directory=temp_data_path, name=cat_subset_name, catalog_type="file"
+            )
             cat_path = temp_data_path + "/" + cat_subset_name + ".json"
         else:
             cat_path = full_cat_path
 
-
-    #####################################################################
-    # Managing global parameters
-
-    global_params = dict()
-
-    if 'global_params' in control:
-        global_params = control['global_params']
-
-
     #####################################################################
     # Ploomber - making a DAG
 
     dag = ploomber.DAG(executor=ploomber.executors.Serial())
 
-
     #####################################################################
     # Organizing notebooks - holdover from manually managing dependencies before
 
     all_nbs = dict()
 
-    for nb, info in control['compute_notebooks'].items():
+    for nb, info in control["compute_notebooks"].items():
 
         all_nbs[nb] = info
 
     # Setting up notebook tasks
 
     for nb, info in all_nbs.items():
 
-        global_params['serial'] = serial
+        global_params["serial"] = serial
         if "dependency" in info:
-            cupid.util.create_ploomber_nb_task(nb, info, cat_path, nb_path_root, output_dir, global_params, dag, dependency = info["dependency"])
+            cupid.util.create_ploomber_nb_task(
+                nb,
+                info,
+                cat_path,
+                nb_path_root,
+                output_dir,
+                global_params,
+                dag,
+                dependency=info["dependency"],
+            )
 
         else:
-            cupid.util.create_ploomber_nb_task(nb, info, cat_path, nb_path_root, output_dir, global_params, dag)
+            cupid.util.create_ploomber_nb_task(
+                nb, info, cat_path, nb_path_root, output_dir, global_params, dag
+            )
 
     #####################################################################
     # Organizing scripts
 
-    if 'compute_scripts' in control:
+    if "compute_scripts" in control:
 
         all_scripts = dict()
 
-        for script, info in control['compute_scripts'].items():
+        for script, info in control["compute_scripts"].items():
 
             all_scripts[script] = info
 
@@ -115,14 +159,23 @@ def run(config_path, serial=False, time_series=False):
         for script, info in all_scripts.items():
 
             if "dependency" in info:
-                cupid.util.create_ploomber_script_task(script, info, cat_path, nb_path_root, global_params, dag, dependency = info["dependency"])
+                cupid.util.create_ploomber_script_task(
+                    script,
+                    info,
+                    cat_path,
+                    nb_path_root,
+                    global_params,
+                    dag,
+                    dependency=info["dependency"],
+                )
 
             else:
-                cupid.util.create_ploomber_script_task(script, info, cat_path, nb_path_root, global_params, dag)
+                cupid.util.create_ploomber_script_task(
+                    script, info, cat_path, nb_path_root, global_params, dag
+                )
 
     # Run the full DAG
 
     dag.build()
 
     return None
-