Merge pull request #8 from schism-dev/feature/extend_atmos

Completed 6-hourly forecasts with NWM+GFS

.github/workflows/test.yml

@@ -7,9 +7,9 @@ jobs:
     name: Python ${{ matrix.python-version }}
     runs-on: ubuntu-latest
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
-        python-version: [ 3.6, 3.7, 3.8 ]
+        python-version: [ 3.7, 3.8 ]
 
     steps:
       - name: Checkout repository

.gitignore

@@ -5,3 +5,10 @@ dist/
 __pycache__
 *_env
 .ipynb_checkpoints
+forecast
+.vscode
+*.swp
+*.nc
+hgrid.*
+fgrid.*
+vgrid.*

examples/example_1/example_1_tide-gfs.py

@@ -10,7 +10,13 @@
 from pyschism.forcing.atmosphere.nws.nws2 import NWS2
 from pyschism.forcing.atmosphere.gfs import GlobalForecastSystem as GFS
 
+#logging.basicConfig(filename='test.log',
+#                    level=logging.INFO, 
+#                    format='%(asctime)s:%(levelnames'
+#                   )
 
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 SIMPLE_SLURM_DRIVER = """#!/bin/bash --login
 #SBATCH -D .
@@ -41,26 +47,25 @@
 
 PARENT = pathlib.Path(__file__).parent
 
-logging.basicConfig(level=logging.INFO)
-
-_logger = logging.getLogger(__name__)
 
 if __name__ == '__main__':
     # open gr3 file
-    _logger.info('Reading hgrid file...')
+    logger.info('Reading hgrid file...')
     _tic = time()
     hgrid = Hgrid.open(PARENT / 'hgrid.gr3',crs='EPSG:4326')
-    _logger.info(f'Reading hgrind file took {time()-_tic}.')
+    logger.info(f'Reading hgrind file took {time()-_tic}.')
 
     vgrid = Vgrid()
     fgrid = Fgrid.open(PARENT / 'drag.gr3',crs='EPSG:4326')
 
     # setup model domain
     domain = ModelDomain(hgrid, vgrid, fgrid)
+    logger.info('Model domain setup finished')
 
     # set tidal boundary conditions
     elevbc = Tides()
     elevbc.use_all()  # activate all forcing constituents
+    logger.info('Tidal boundary setup finished')
 
     # connect the boundary condition to the domain
     domain.add_boundary_condition(elevbc)

pyschism/__main__.py

@@ -1,10 +1,17 @@
 #! /usr/bin/env python
 import argparse
+from datetime import datetime
+import logging
+
+from pytz import timezone
 
 from pyschism.cmd.forecast.forecast import ForecastCli, add_forecast
 from pyschism.cmd.bctides import BctidesCli, add_bctides
 
 
+# logging.getLogger().setLevel(logging.NOTSET)
+
+
 def parse_args():
     parser = argparse.ArgumentParser()
     subparsers = parser.add_subparsers(dest='mode')
@@ -20,6 +27,19 @@ def parse_args():
 def main():
     args = parse_args()
 
+    logging.basicConfig(
+        level={
+            'warning': logging.WARNING,
+            'info': logging.INFO,
+            'debug': logging.DEBUG,
+        }[args.log_level],
+        format='[%(asctime)s] %(name)s %(levelname)s: %(message)s',
+        force=True,
+    )
+
+    logging.Formatter.converter = lambda *args: datetime.now(
+        tz=timezone('UTC')).timetuple()
+
     if args.mode == 'forecast':
         ForecastCli(args)
 

pyschism/cmd/forecast/forecast.py

@@ -52,8 +52,6 @@ def add_forecast_init(actions):
         help="Number of days used for model initialization. "
         "Defaults to 15 days spinup.",
         type=float, default=15.)
-    init.add_argument("--forecast-interval", type=float, default=24)
-    init.add_argument("--timezone", default='UTC')
     init.add_argument(
         "--skip-run", action="store_true",
         help="Skips running the model.")
@@ -102,7 +100,9 @@ def add_forecast(subparsers):
         help="Allow overwrite of output directory.")
     forecast.add_argument(
         "--log-level",
-        choices=[name.lower() for name in logging._nameToLevel])
+        choices=['info', 'warning', 'debug'],
+        default='info'
+    )
     actions = forecast.add_subparsers(dest="action")
     add_forecast_init(actions)
     add_forecast_update(actions)
@@ -173,6 +173,8 @@ def _add_tidal_constituents(parser):
     tides = parser.add_argument_group('tides')
     options = tides.add_mutually_exclusive_group()
     options.required = True
+    options.add_argument("--tidal-database", choices=['tpxo', 'hamtide'],
+                         default='hamtide')
     options.add_argument("--all-constituents", action="store_true")
     options.add_argument("--major-constituents", action="store_true")
     options.add_argument(

pyschism/cmd/forecast/init.py

@@ -1,7 +1,7 @@
 from argparse import Namespace
-from datetime import datetime, timedelta
+from datetime import datetime, timedelta, timezone
 import json
-# import logging
+import logging
 import os
 import pathlib
 import shutil
@@ -54,22 +54,6 @@ def __get__(self, obj, val):
         return coldstart_directory
 
 
-class TargetDatetime:
-
-    def __get__(self, obj, val):
-        target_datetime = obj.__dict__.get('target_datetime')
-        if target_datetime is None:
-            utcnow = pytz.timezone('UTC').localize(datetime.utcnow())
-            # localnow = utcnow.astimezone(pytz.timezone(obj.args.timezone))
-            nowcast_cycle = int(obj.forecast_interval * np.floor(
-                utcnow.hour/obj.forecast_interval))  # % 24
-            target_datetime = datetime(
-                utcnow.year, utcnow.month, utcnow.day, nowcast_cycle,
-                tzinfo=pytz.timezone(obj.args.timezone))
-            obj.__dict__['target_datetime'] = target_datetime
-        return target_datetime
-
-
 class ColdstartDomain:
 
     def __get__(self, obj, val):
@@ -111,18 +95,6 @@ def __get__(self, obj, val):
         return coldstart
 
 
-class ForecastInterval:
-
-    def __get__(self, obj, val):
-        forecast_interval = obj.__dict__.get('forecast_interval')
-        if forecast_interval is None:
-            if obj.args.forecast_interval != 24:
-                raise NotImplementedError(
-                    'Forecast interval only at 24 hours for now.')
-            obj.__dict__['forecast_interval'] = obj.args.forecast_interval
-        return obj.__dict__['forecast_interval']
-
-
 class HgridPath:
 
     def __get__(self, obj, val):
@@ -197,7 +169,10 @@ def __get__(self, obj, val):
                     and not obj.args.constituents:
                 return
             else:
-                tides = Tides(velocity=obj.args.bnd_vel)
+                tides = Tides(
+                    database=obj.args.tidal_database,
+                    velocity=obj.args.bnd_vel
+                )
                 if obj.args.all_constituents:
                     tides.use_all()
                 if obj.args.major_constituents:
@@ -245,10 +220,8 @@ class ForecastInit:
     project_directory = ProjectDirectory()
     config_file = ConfigFile()
     coldstart_directory = ColdstartDirectory()
-    target_datetime = TargetDatetime()
     coldstart_domain = ColdstartDomain()
     coldstart_driver = ColdstartDriver()
-    forecast_interval = ForecastInterval()
     static_files_directory = StaticFilesDirectory()
     hgrid_path = HgridPath()
     vgrid_path = VgridPath()
@@ -267,7 +240,7 @@ def __init__(self, args: Namespace):
         self._write_config_file()
         self._symlink_files(self.coldstart_directory,
                             self.coldstart_domain.ics)
-        # self.logger.info('Writting coldstart files to disk...')
+        self.logger.info('Writting coldstart files to disk...')
         self.coldstart_driver.write(
             self.coldstart_directory,
             hgrid=False,
@@ -279,11 +252,11 @@ def __init__(self, args: Namespace):
 
         if self.args.skip_run is False:
             # release memory before launching SCHISM.
-            # self.logger.info('Releasing memory before calling SCHISM...')
+            self.logger.info('Releasing memory before calling SCHISM...')
             for item in list(self.__dict__.keys()):
                 if not item.startswith('_'):
                     del self.__dict__[item]
-            # self.logger.info('Calling SCHISM using make.')
+            self.logger.info('Calling SCHISM using make.')
             subprocess.check_call(
                 ["make", "run"],
                 cwd=self.coldstart_directory
@@ -304,14 +277,14 @@ def _write_config_file(self):
                 'been initialized previously. Please use\npyschism '
                 'forecast --overwrite init [...]\nto allow overwrite of '
                 'previous initialization options.')
-        # self.logger.info(
-            # f"Writting configuration file to path {self.config_file}")
+        self.logger.info(
+            f"Writting configuration file to path {self.config_file}")
         with open(self.config_file, 'w') as fp:
             json.dump(self.args.__dict__, fp, indent=4)
 
     def _symlink_files(self, target_directory, ics):
-        # self.logger.info(
-            # f"Establishing symlinks to target_directory: {target_directory}")
+        self.logger.info(
+            f"Establishing symlinks to target_directory: {target_directory}")
         hgrid_lnk = target_directory / 'hgrid.gr3'
         vgrid_lnk = target_directory / 'vgrid.in'
         fgrid_lnk = target_directory / f'{self.fgrid_path.name}'
@@ -345,13 +318,20 @@ def _symlink_hgridll(self, target_directory):
         os.symlink(os.path.relpath(
             self.hgrid_path, target_directory), hgridll_lnk)
 
-    # @property
-    # def logger(self):
-    #     try:
-    #         return self._logger
-    #     except AttributeError:
-    #         self._logger = get_logger(
-    #             console_level=logging._nameToLevel[self.args.log_level.upper()]
-    #             )
-    #         self._logger.propagate = 0
-    #         return self._logger
+    @property
+    def target_datetime(self):
+        if not hasattr(self, '_target_datetime'):
+            now_utc = datetime.now(timezone.utc)
+            nearest_cycle = int(6 * np.floor(now_utc.hour/6))
+            self._target_datetime = datetime(
+                now_utc.year, now_utc.month, now_utc.day, nearest_cycle,
+                tzinfo=timezone.utc)
+            self.logger.info(
+                f'Target datetime is: {str(self._target_datetime)}.')
+        return self._target_datetime
+
+    @property
+    def logger(self):
+        if not hasattr(self, '_logger'):
+            self._logger = logging.getLogger(f"{self.__class__.__name__}")
+        return self._logger

pyschism/dates.py

@@ -0,0 +1,33 @@
+from datetime import datetime
+
+import numpy as np
+import pytz
+
+
+def pivot_time(input_datetime=None):
+    """
+    "pivot time" is defined as the nearest floor t00z for any given datetime.
+    If this function is called without arguments, it will return the pivot time
+    for the current datetime in UTC.
+    """
+    input_datetime = nearest_cycle_date() if input_datetime is None else \
+        localize_datetime(input_datetime).astimezone(pytz.utc)
+    return localize_datetime(
+        datetime(input_datetime.year, input_datetime.month, input_datetime.day)
+        )
+
+
+def nearest_cycle_date(input_datetime=None, period=6):
+    if input_datetime is None:
+        input_datetime = localize_datetime(datetime.utcnow())
+    current_cycle = int(period * np.floor(input_datetime.hour / period))
+    return pytz.timezone('UTC').localize(
+        datetime(input_datetime.year, input_datetime.month,
+                 input_datetime.day, current_cycle))
+
+
+def localize_datetime(d):
+    # datetime is naïve iff:
+    if d.tzinfo is None or d.tzinfo.utcoffset(d) is None:
+        return pytz.timezone('UTC').localize(d)
+    return d