Prepare snow depth observations for JEDI-based Land DA. (#1609)

This PR:
- adds a job to prepare IMS snow depth observations as a task in the workflow.  This task depends on the `prep.sh` job to bring IMS data.  To test this type of data `DMPDIR` in `config.base` needed to be pointed to `"/scratch1/NCEPDEV/global/Jiarui.Dong/JEDI/GlobalWorkflow/para_gfs/glopara_dump"`
- `land_analysis.py` introduces a method `prepare_IMS` for this type of data.
- Updates are necessary in the `GDASApp` repo.  See companion PR NOAA-EMC/GDASApp#472

This job only runs at the `18z` cycle in the workflow.  This is controlled in the XML and not in the script.
Consequently, updates are in the `workflow/` scripts to make this happen.

Other updates included:
- Adds a method (and associated test) to provide a datetime in the form of Julian day of the year.  The method is `to_julian` in `timetools.py`
- `executable.py` was updated to accept a `list` of arguments (in addition to `str`).

**Note:**
- `calcfIMS.exe` is a serial executable and yet requires to be run with `srun`.  I recommend compiling this executable without MPI. @jiaruidong2017 @CoryMartin-NOAA 
- There are several deprecation warnings from the python IODA converter that will need to be addressed.  I recommend creating an issue to be resolved later. @jiaruidong2017 @CoryMartin-NOAA 

Part of Land DA work for snow depth assimilation, for which there is no issue open.

ush/python/pygw/src/pygw/executable.py

@@ -2,7 +2,7 @@
 import shlex
 import subprocess
 import sys
-from typing import Any, Optional
+from typing import Any, Optional, Union, List
 
 __all__ = ["Executable", "which", "CommandNotFoundError"]
 
@@ -47,15 +47,18 @@ def __init__(self, name: str):
         if not self.exe:
             raise ProcessError(f"Cannot construct executable for '{name}'")
 
-    def add_default_arg(self, arg: str) -> None:
+    def add_default_arg(self, arg: Union[str, List]) -> None:
         """
         Add a default argument to the command.
         Parameters
         ----------
         arg : str
               argument to the executable
         """
-        self.exe.append(arg)
+        if isinstance(arg, list):
+            self.exe.extend(arg)
+        else:
+            self.exe.append(arg)
 
     def add_default_env(self, key: str, value: Any) -> None:
         """

ush/python/pygw/src/pygw/jinja.py

@@ -6,7 +6,7 @@
 from pathlib import Path
 from typing import Dict
 
-from .timetools import strftime, to_YMDH, to_YMD, to_fv3time, to_isotime
+from .timetools import strftime, to_YMDH, to_YMD, to_fv3time, to_isotime, to_julian
 
 __all__ = ['Jinja']
 
@@ -114,6 +114,7 @@ def get_set_env(self, loader: jinja2.BaseLoader) -> jinja2.Environment:
         env.filters["to_fv3time"] = lambda dt: to_fv3time(dt) if not isinstance(dt, SilentUndefined) else dt
         env.filters["to_YMDH"] = lambda dt: to_YMDH(dt) if not isinstance(dt, SilentUndefined) else dt
         env.filters["to_YMD"] = lambda dt: to_YMD(dt) if not isinstance(dt, SilentUndefined) else dt
+        env.filters["to_julian"] = lambda dt: to_julian(dt) if not isinstance(dt, SilentUndefined) else dt
         return env
 
     @staticmethod

ush/python/pygw/src/pygw/timetools.py

@@ -3,10 +3,10 @@
 
 
 __all__ = ["to_datetime", "to_timedelta",
-           "datetime_to_YMDH", "datetime_to_YMD",
+           "datetime_to_YMDH", "datetime_to_YMD", "datetime_to_JDAY",
            "timedelta_to_HMS",
            "strftime", "strptime",
-           "to_YMDH", "to_YMD",
+           "to_YMDH", "to_YMD", "to_JDAY", "to_julian",
            "to_isotime", "to_fv3time",
            "add_to_datetime", "add_to_timedelta"]
 
@@ -151,6 +151,29 @@ def datetime_to_YMD(dt: datetime.datetime) -> str:
         raise Exception(f"Bad datetime: '{dt}'")
 
 
+def datetime_to_JDAY(dt: datetime.datetime) -> str:
+    """
+    Description
+    -----------
+    Translate a datetime object to 'YYYYDOY' format.
+
+
+    Parameters
+    ----------
+    dt : datetime.datetime
+        Datetime object to translate
+
+    Returns
+    -------
+    str: str
+        Formatted string in 'YYYYDOY' format.
+    """
+    try:
+        return dt.strftime('%Y%j')
+    except Exception:
+        raise Exception(f"Bad datetime: '{dt}'")
+
+
 def timedelta_to_HMS(td: datetime.timedelta) -> str:
     """
     Description
@@ -289,3 +312,5 @@ def add_to_timedelta(td1, td2):
 
 to_YMDH = datetime_to_YMDH
 to_YMD = datetime_to_YMD
+to_JDAY = datetime_to_JDAY
+to_julian = datetime_to_JDAY

ush/python/pygw/src/tests/test_timetools.py

@@ -45,7 +45,7 @@ def test_strftime():
 
 def test_strptime():
     assert strptime(current_date.strftime('%Y%m%d'), '%Y%m%d') == \
-           datetime.strptime(current_date.strftime('%Y%m%d'), '%Y%m%d')
+        datetime.strptime(current_date.strftime('%Y%m%d'), '%Y%m%d')
 
 
 def test_to_isotime():
@@ -56,13 +56,17 @@ def test_to_fv3time():
     assert to_fv3time(current_date) == current_date.strftime('%Y%m%d.%H%M%S')
 
 
+def test_to_julian():
+    assert to_julian(current_date) == current_date.strftime('%Y%j')
+
+
 def test_add_to_timedelta():
     assert add_to_timedelta(timedelta(days=1), timedelta(hours=3)) == \
-           timedelta(days=1, hours=3)
+        timedelta(days=1, hours=3)
     assert add_to_timedelta(timedelta(hours=5, minutes=30), timedelta(minutes=15)) == \
-           timedelta(hours=5, minutes=45)
+        timedelta(hours=5, minutes=45)
     assert add_to_timedelta(timedelta(seconds=45), timedelta(milliseconds=500)) == \
-           timedelta(seconds=45, milliseconds=500)
+        timedelta(seconds=45, milliseconds=500)
 
 
 def test_add_to_datetime():