Allow missing/empty cycle time files in timeseries (JCSDA-internal#211)

## Description

- Added support for missing/empty cycle time files when running in
timeseries mode
- Adding requirements that work on discover milan nodes

## Demonstration
Comparing two time series of different lengths:

![time_series_omb](https://github.com/user-attachments/assets/0b91a062-28a3-4bb2-ae0d-6aa8d919abfe)


Timeseries with a missing cycle time:

![time_series_omb](https://github.com/user-attachments/assets/d97dd883-7f62-410d-a8f7-31e30edc4eb5)

requirements.txt

@@ -1,18 +1,13 @@
-setuptools>=59.4.0
-pyyaml>=6.0
-pycodestyle>=2.8.0
-netCDF4>=1.5.3
-matplotlib>=3.9.0
-cartopy>=0.21.1
-scipy>=1.9.3
-xarray>=2022.3.0
-pandas>=1.4.0
-numpy>=2.0.0
-
-# Not explicitly part of eva but dependcies of eva dependencies already in spack-stack
-# versions need to be set to avoid other versions being picked
-pyproj==3.1.0
-importlib-metadata==4.8.2
+setuptools
+pyyaml
+pycodestyle
+netCDF4
+matplotlib
+cartopy
+scipy
+xarray
+pandas
+numpy
 
 # Additional packages
 git+https://github.com/NOAA-EMC/emcpy.git@f7b863d9508b921a78d7ff0e53de0b95e9a176f7#egg=emcpy

requirements_gmao.txt

@@ -0,0 +1,26 @@
+setuptools>=59.4.0
+pyyaml>=6.0
+pycodestyle>=2.8.0
+netCDF4
+matplotlib
+cartopy>=0.21.1
+scipy>=1.9.3
+xarray>=2022.3.0
+pandas>=1.4.0
+numpy==1.22.3
+
+# Not explicitly part of eva but dependcies of eva dependencies already in spack-stack
+# versions need to be set to avoid other versions being picked
+pyproj
+importlib-metadata==4.8.2
+contourpy==1.0.7
+
+# Additional packages
+git+https://github.com/NOAA-EMC/emcpy.git@f7b863d9508b921a78d7ff0e53de0b95e9a176f7#egg=emcpy
+scikit-learn
+seaborn
+hvplot
+nbconvert
+bokeh
+geopandas
+geoviews

requirements_sles15.txt

@@ -0,0 +1,28 @@
+setuptools>=59.4.0
+pyyaml>=6.0
+pycodestyle>=2.8.0
+netCDF4
+matplotlib
+cartopy>=0.21.1
+scipy>=1.9.3
+xarray>=2022.3.0
+pandas>=1.4.0
+numpy==1.22.3
+attrs==21.4.0
+
+# Not explicitly part of eva but dependcies of eva dependencies already in spack-stack
+# versions need to be set to avoid other versions being picked
+pyproj
+importlib_metadata==7.1.0
+contourpy==1.0.7
+msgpack>=1.0.0
+
+# Additional packages
+git+https://github.com/NOAA-EMC/emcpy.git@f7b863d9508b921a78d7ff0e53de0b95e9a176f7#egg=emcpy
+scikit-learn
+seaborn
+hvplot
+nbconvert
+bokeh
+geopandas
+geoviews

src/eva/eva_driver.py

@@ -13,19 +13,22 @@
 import argparse
 import os
 from collections import defaultdict
+import xarray as xr
+import numpy as np
 
 from eva.utilities.config import get
 from eva.utilities.logger import Logger
 from eva.utilities.timing import Timing
 from eva.data.data_driver import data_driver
+from eva.time_series.time_series import add_empty_to_timeseries
 from eva.time_series.time_series import collapse_collection_to_time_series
+from eva.time_series.time_series_utils import create_empty_data, get_filename, check_file
 from eva.transforms.transform_driver import transform_driver
 from eva.plotting.batch.base.plot_tools.figure_driver import figure_driver
 from eva.data.data_collections import DataCollections
 from eva.utilities.duration import iso_duration_to_timedelta
 from eva.utilities.utils import load_yaml_file
 
-
 # --------------------------------------------------------------------------------------------------
 
 
@@ -160,14 +163,29 @@ def read_transform_time_series(logger, timing, eva_dict, data_collections):
                 if name == time_series_config['collection']:
                     transform_dict['transforms'].append(transform)
 
-        # Assert that datasets_config is the same length as dates
-        logger.assert_abort(len(datasets_config) == len(dates), 'When running in time ' +
-                            'series mode the number of datasets must be the same as the ' +
-                            'number of dates.')
+        # Check if first file is empty. If it is, abort.
+        empty_dataset_config = datasets_config[0]
+        filename = get_filename(empty_dataset_config, logger)
+        check_file(filename, logger)
 
         # Loop over datasets reading each one in turn, internally appending the data_collections
         for ind, dataset_config in enumerate(datasets_config):
 
+            # Pull out information to check for missing date
+            date = dates[ind]
+
+            # Check if file exists, if not add empty and continue
+            filename = get_filename(dataset_config, logger)
+            if not os.path.isfile(filename):
+                add_empty_to_timeseries(logger, date, ind, timing, time_series_config,
+                                        empty_dataset_config, data_collections)
+                continue
+            # Check if file exists but is size zero, add empty and continue
+            elif os.stat(filename).st_size == 0:
+                add_empty_to_timeseries(logger, date, ind, timing, time_series_config,
+                                        empty_dataset_config, data_collections)
+                continue
+
             # Create a temporary collection for this time step
             data_collections_tmp = DataCollections()
 
@@ -185,7 +203,6 @@ def read_transform_time_series(logger, timing, eva_dict, data_collections):
                 timing.stop('TransformDriverExecute')
 
             # Collapse data into time series
-            date = dates[ind]
             collapse_collection_to_time_series(logger, ind, date, time_series_config,
                                                data_collections, data_collections_tmp)
 

src/eva/tests/config/testIodaObsSpaceAmsuaN19_TimeSeries.yaml

@@ -10,6 +10,15 @@ datasets:
       - name: ObsValue
         variables: &variables [brightnessTemperature]
       - name: hofx
+  #Empty
+  - name: experiment
+    type: IodaObsSpace
+    filenames:
+      - ${data_input_path}/ioda_obs_space.amsua_n19.hofx.2020-12-14T000000Z.nc4
+    channels: *channels
+    groups:
+      - name: ObsValue
+      - name: hofx
   - name: experiment
     type: IodaObsSpace
     filenames:
@@ -31,7 +40,7 @@ transforms:
 time_series:
 
   - begin_date: '2020-12-14T21:00:00'
-    final_date: '2020-12-15T03:00:00'
+    final_date: '2020-12-15T09:00:00'
     interval: 'PT6H'
 
     collection: experiment

src/eva/tests/config/testJediVariationalBiasCorrectionAmsuaN19.yaml

@@ -11,10 +11,16 @@ datasets:
     bias_file: ${data_input_path}/gsi.x0048v2.bc.amsua_n19.2021-12-11T21:00:00Z.satbias
     lapse_file: ${data_input_path}/gsi.x0048v2.bc.amsua_n19.2021-12-11T21:00:00Z.tlapse
 
+  # Empty
+  - name: experiment
+    type: JediVariationalBiasCorrection
+    bias_file: ${data_input_path}/gsi.x0048v2.bc.amsua_n19.2021-12-12T03:00:00Z.satbias
+    lapse_file: ${data_input_path}/gsi.x0048v2.bc.amsua_n19.2021-12-12T03:00:00Z.tlapse
+
 time_series:
 
-  - begin_date: '2020-12-15T00:00:00'
-    final_date: '2020-12-15T06:00:00'
+  - begin_date: '2021-12-11T15:00:00'
+    final_date: '2021-12-12T03:00:00'
     interval: 'PT6H'
 
     collection: experiment

src/eva/time_series/time_series.py

@@ -12,7 +12,8 @@
 
 import numpy as np
 import xarray as xr
-
+from eva.data.data_collections import DataCollections
+from eva.time_series.time_series_utils import create_empty_data
 
 # --------------------------------------------------------------------------------------------------
 
@@ -23,6 +24,17 @@
 }
 
 
+# --------------------------------------------------------------------------------------------------
+
+def add_empty_to_timeseries(logger, date, ind, timing, time_series_config,
+                            dataset_config, data_collections):
+
+    ''' Add empty collection to timeseries for missing date  '''
+    empty_data_collection = create_empty_data(time_series_config, dataset_config, timing, logger)
+    collapse_collection_to_time_series(logger, ind, date, time_series_config, data_collections,
+                                       empty_data_collection)
+
+
 # --------------------------------------------------------------------------------------------------
 
 

src/eva/time_series/time_series_utils.py

@@ -0,0 +1,43 @@
+import os
+import numpy as np
+import xarray as xr
+from eva.data.data_driver import data_driver
+from eva.data.data_collections import DataCollections
+
+
+filename_retrieval = {
+    "IodaObsSpace": lambda dataset_config: dataset_config["filenames"][0],
+    "JediVariationalBiasCorrection": lambda dataset_config: dataset_config["bias_file"],
+}
+
+
+def get_filename(dataset_config, logger):
+    """ Retrieve filename using given type  """
+
+    dataset_type = dataset_config["type"]
+    logger.assert_abort(dataset_type in filename_retrieval,
+                        f'Unknown dataset_type {dataset_type}')
+    filename = filename_retrieval[dataset_type](dataset_config)
+    return filename
+
+
+def check_file(filename, logger):
+    """ Check if first file exists and is nonzero  """
+
+    if not os.path.isfile(filename):
+        logger.abort('First file provided to timeseries must exist.')
+    elif os.stat(filename).st_size == 0:
+        logger.abort('First file provided to timeseries must be nonzero.')
+
+
+def create_empty_data(timeseries_config, dataset_config, timing, logger):
+    """ Creating an empty data collection to use for missing cycle times  """
+
+    dc_tmp = DataCollections()
+    collection = timeseries_config["collection"]
+    data_driver(dataset_config, dc_tmp, timing, logger)
+    dataset = dc_tmp.get_data_collection(collection)
+    empty_data = xr.full_like(dataset, np.nan)
+    dc = DataCollections()
+    dc.create_or_add_to_collection(collection, empty_data)
+    return dc

src/eva/utilities/utils.py

@@ -6,7 +6,6 @@
 
 # --------------------------------------------------------------------------------------------------
 
-
 import re
 import string
 import yaml