Merge commit '5a54388667a7d22f13405bf27a396f0cb5a9f5bc' into trackval…

…idation

README.rst

@@ -76,6 +76,9 @@ Status
 .. image:: https://landscape.io/github/GeoscienceAustralia/tcrm/develop/landscape.svg?style=flat
     :target: https://landscape.io/github/GeoscienceAustralia/tcrm/v2.1
     :alt: Code Health
+
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3741493.svg
+   :target: https://doi.org/10.5281/zenodo.3741493
 
 Screenshot
 ==========

Utilities/config.py

@@ -12,6 +12,8 @@
 
 import io
 from configparser import RawConfigParser
+import os.path
+
 #from ast import literal_eval as eval
 
 def parseBool(txt):
@@ -273,6 +275,8 @@ def read(self, filename):
             return
         if self.readonce:
             return
+        if not os.path.exists(filename):
+            raise ValueError("config file does not exist: {}".format(filename))
         RawConfigParser.read(self, filename)
         self.readonce = True
 

Utilities/nctools.py

@@ -130,7 +130,7 @@ def ncGetData(ncobj, var):
     try:
         varobj = ncobj.variables[var]
     except KeyError:
-        logger.exception(f"{ncobj.filepath()} does not contain variable {name}")
+        logger.exception(f"{ncobj.filepath()} does not contain variable {var}")
         raise
 
     # Automatic conversion of masked values and unpacking

Utilities/timeseries.py

@@ -11,11 +11,11 @@
 """
 
 import logging
-import numpy as np
-
 from os.path import join as pjoin
-
 from configparser import NoOptionError
+
+import numpy as np
+
 from Utilities.config import ConfigParser
 from Utilities.files import flLoadFile
 from Utilities.maputils import find_index
@@ -31,14 +31,14 @@
 OUTPUT_NAMES = ('Station', 'Time', 'Longitude', 'Latitude',
                 'Speed', 'UU', 'VV', 'Bearing',
                 'Pressure')
-OUTPUT_TYPES = ['|U16', '|U16',  'f8', 'f8',  'f8', 'f8', 'f8', 'f8', 'f8']
+OUTPUT_TYPES = ['|U16', '|U16', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8']
 OUTPUT_FMT = ['%s', '%s', '%9.5f', '%9.5f',
               '%6.2f', '%6.2f', '%6.2f', '%6.2f',
               '%7.2f']
 
 MINMAX_NAMES = ('Station', 'Time', 'Longitude', 'Latitude',
                 'Speed', 'UU', 'VV', 'Bearing', 'Pressure')
-MINMAX_TYPES = ['|U16', '|U16',  'f8', 'f8',  'f8', 'f8', 'f8', 'f8', 'f8']
+MINMAX_TYPES = ['|U16', '|U16', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8', 'f8']
 MINMAX_FMT = ['%s', '%s', '%9.5f', '%9.5f',
               '%6.2f', '%6.2f', '%6.2f', '%6.2f',
               '%7.2f']
@@ -49,6 +49,21 @@
 """
 
 class Station(object):
+    """Station:
+
+    Description: An object to represent a location for which time series 
+                 data will be extracted
+
+    Members:
+    `id`: Unique id string for the station
+    `lon`: Longitude of the station (geographic coordinates)
+    `lat`: Latitude of the station (geographic coordinates)
+    `data`: A `DynamicRecArray` to hold the time series data
+
+    Methods:
+    `insideGrid`: Determine if the station is inside the simulation domain.
+    """
+
     def __init__(self, stationid, longitude, latitude):
 
         self.id = stationid
@@ -61,8 +76,7 @@ def __getattr__(self, key):
         """
         Get the `key` from the `data` object.
 
-        :type  key: str
-        :param key: the key to lookup in the `data` object.
+        :param str key: the key to lookup in the `data` object.
         """
         if key.startswith('__') and key.endswith('__'):
             return super(Station, self).__getattr__(key)
@@ -84,12 +98,24 @@ def insideGrid(self, gridx, gridy):
 class Timeseries(object):
     """Timeseries:
 
-    Description:
+    Description: Extract data at a set of :class:`Station`s 
 
     Parameters:
+
+    :param str configFile: Path to a TCRM configuration file
+
     Members:
+    `meta`: Boolean whether additional metadata is attached to the `Station`s
+    `outputPath`: Directory where extracted data will be stored in csv-format files
+    `minfile`: Name of the file where minima for all `Station`s will be stored. 
+               This will be the `outputPath` folder
+    `maxfile`: As above, but for maxima (e.g. maximum wind speeds)
+    `stations`: A list of `Station` objects, read from a file containing details of the stations
+    
     Methods:
+    
     Internal methods:
+    
     """
 
     def __init__(self, configFile):
@@ -107,16 +133,16 @@ def __init__(self, configFile):
 
         stnFile = config.get('Timeseries', 'LocationFile')
         self.outputPath = pjoin(config.get('Output', 'Path'),
-                                    'process', 'timeseries')
+                                'process', 'timeseries')
 
         self.maxfile = pjoin(config.get('Output', 'Path'),
-                                    'process', 'maxima.csv')
+                             'process', 'maxima.csv')
         self.minfile = pjoin(config.get('Output', 'Path'),
-                                    'process', 'minima.csv')
+                             'process', 'minima.csv')
 
 
-        log.info("Loading timeseries stations from %s"%stnFile)
-        log.debug("Timeseries data will be written into %s"%self.outputPath)
+        log.info(f"Loading timeseries stations from {stnFile}")
+        log.debug(f"Timeseries data will be written into {self.outputPath}")
         self.stations = []
         if stnFile.endswith("shp"):
             try:
@@ -145,8 +171,8 @@ def __init__(self, configFile):
             stnlat = stndata[:, 2].astype(float)
             for sid, lon, lat in zip(stnid, stnlon, stnlat):
                 self.stations.append(Station(sid, lon, lat))
-        log.info("There are {0} stations that will collect timeseries data".format(len(self.stations)))
-        
+        log.info(f"There are {len(self.stations)} stations that will collect timeseries data")
+
     def sample(self, lon, lat, spd, uu, vv, prs, gridx, gridy):
         """
         Extract values from 2-dimensional grids at the given lat/lon.
@@ -195,14 +221,14 @@ def extract(self, dt, spd, uu, vv, prs, gridx, gridy):
             if stn.insideGrid(gridx, gridy):
                 stns += 1
                 result = self.sample(stn.lon, stn.lat, spd, uu, vv, prs,
-                                      gridx, gridy)
+                                     gridx, gridy)
                 ss, ux, vy, bb, pp = result
                 stn.data.append((str(stn.id), dt, stn.lon, stn.lat, ss,
-                                ux, vy, bb, pp))
+                                 ux, vy, bb, pp))
 
             else:
                 stn.data.append((str(stn.id), dt, stn.lon, stn.lat, 0.0, 0.0,
-                                          0.0, 0.0, prs[0, 0]))
+                                 0.0, 0.0, prs[0, 0]))
         log.debug("Extracted data for {0} stations".format(stns))
 
     def shutdown(self):
@@ -212,7 +238,7 @@ def shutdown(self):
 
         header = 'Station,Time,Longitude,Latitude,Speed,UU,VV,Bearing,Pressure'
         maxheader = ('Station,Time,Longitude,Latitude,Speed,'
-                        'UU,VV,Bearing,Pressure')
+                     'UU,VV,Bearing,Pressure')
 
         max_data = DynamicRecArray(dtype={'names': MINMAX_NAMES,
                                           'formats':MINMAX_TYPES})
@@ -236,9 +262,9 @@ def shutdown(self):
 
 
         np.savetxt(self.maxfile, max_data.data, fmt=MINMAX_FMT, delimiter=',',
-                    header=maxheader, comments='')
+                   header=maxheader, comments='')
         np.savetxt(self.minfile, min_data.data, fmt=MINMAX_FMT, delimiter=',',
-                    header=maxheader, comments='')
+                   header=maxheader, comments='')
         """
         for stn in self.stations:
             if type(self.maxdata[stn.id][3]) == datetime.datetime:
@@ -272,4 +298,3 @@ def shutdown(self):
                    #  '%6.2f','%6.2f','%7.2f'] )
         """
         log.info("Station data written to file")
-

wind/windmodels.py

@@ -332,7 +332,7 @@ def secondDerivative(self):
             assert d2Vm < 0.0
         except AssertionError:
             log.critical(("Pressure deficit: {0:.2f} hPa,"
-                          " RMW: {1:%2f} km".format(dP/100., rMax/1000.)))
+                          " RMW: {1:.2f} km".format(dP/100., rMax/1000.)))
             raise
 
         return d2Vm