style: Updating syntax

OceanColor/backend/common.py

@@ -57,7 +57,7 @@ def __setitem__(self, index, value):
         raise NotImplementedError("Missing __setitem__ for this Backend")
 
 
-class FileSystem(object):
+class FileSystem:
     """Backend for OceanColorDB based on files and directories
 
     A file system backend for OceanColorDB to save the data files in
@@ -197,8 +197,7 @@ def __getitem__(self, index):
         return ds
 
     def __setitem__(self, index, ds):
-        """Saves Dataset ds identified by index
-        """
+        """Saves Dataset ds identified by index"""
         if not isinstance(ds, xr.Dataset):
             self.logger.warn("Trying to save a non xr.Dataset object")
             raise ValueError
@@ -216,7 +215,7 @@ def path(self, product_name: str):
         return p.replace(".nc", ".zarr")
 
 
-class Filename(object):
+class Filename:
     """Parse implicit information on NASA's filename
 
     NASA's data filename, and granules, follows a logical standard that can be
@@ -338,7 +337,7 @@ class InMemory(BaseStorage):
 
     __data = OrderedDict()
 
-    def __init__(self, quota: int = 5 * 1024 ** 3):
+    def __init__(self, quota: int = 5 * 1024**3):
         """Initialize an InMemory object
 
         Parameters

OceanColor/catalog.py

@@ -2,7 +2,8 @@
 
 import logging
 import os
-from typing import Any, Dict, Optional, Sequence
+from typing import Any, Dict, Optional
+from collections.abc import Sequence
 
 import numpy as np
 import pandas as pd
@@ -35,7 +36,7 @@ def ds_attrs(ds):
     return output
 
 
-class Catalog(object):
+class Catalog:
     """
 
     ToDo
@@ -49,10 +50,12 @@ class Catalog(object):
     """
 
     def __init__(self, dbfilename):
-        self.store = pd.HDFStore(dbfilename, mode="a", complevel=9, fletcher32=True)
+        self.store = pd.HDFStore(
+            dbfilename, mode="a", complevel=9, fletcher32=True
+        )
 
     def __getitem__(self, product_name):
-        record = self.store.select("catalog", "index == '{}'".format(product_name))
+        record = self.store.select("catalog", f"index == '{product_name}'")
         if record.size == 0:
             raise KeyError
 
@@ -76,7 +79,9 @@ def __setitem__(self, key, value):
         self.store.append("catalog", value, format="t", data_columns=True)
 
     def __del__(self):
-        module_logger.debug("Closing Catalog's storage: {}".format(self.store.filename))
+        module_logger.debug(
+            f"Closing Catalog's storage: {self.store.filename}"
+        )
         # self.store.flush()
         self.store.close()
 
@@ -88,18 +93,22 @@ def record(self, ds):
         assert attrs["product_name"] not in self, (
             "There is a record in the database for %s" % attrs["filename"]
         )
-        module_logger.debug("New record: {}".format(attrs))
+        module_logger.debug(f"New record: {attrs}")
         attrs = pd.DataFrame([attrs])
         attrs = attrs.set_index("product_name")
         # if ('catalog' in self.store):
         #     tmp = tmp.set_index(tmp.index + self.store.catalog.index.max() + 1)
         self.store.append(
-            "catalog", attrs, format="t", data_columns=True, min_itemsize={"values": 42}
+            "catalog",
+            attrs,
+            format="t",
+            data_columns=True,
+            min_itemsize={"values": 42},
         )
 
     def bloom_filter(
         self,
-        track: Sequence[Dict],
+        track: Sequence[dict],
         sensor: Optional[Any] = None,
         dtype: Optional[Any] = None,
         dt_tol: Optional[Any] = None,
@@ -113,12 +122,11 @@ def bloom_filter(
         cond = []
         cond.append("time_coverage_end >= %r" % (track.time.min() - dt_tol))
         cond.append("time_coverage_start <= %r" % (track.time.max() + dt_tol))
-        cond.append("geospatial_lat_max > {}".format(track.lat.min()))
-        cond.append("geospatial_lat_min > {}".format(track.lat.max()))
+        cond.append(f"geospatial_lat_max > {track.lat.min()}")
+        cond.append(f"geospatial_lat_min > {track.lat.max()}")
         cond.append(
             "(geospatial_lon_min <= {} & geospatial_lon_max >= {}) or (geospatial_lon_max < 0 & geospatial_lon_min > 0)".format(
                 track.lon.max(), track.lon.min()
             )
         )
-        for f in self.store.select("catalog", where=cond).index:
-            yield f
+        yield from self.store.select("catalog", where=cond).index

OceanColor/cli.py

@@ -10,33 +10,50 @@
 # At this point it's just a Proof of concept
 #  OceanColor InRange --username=myUser --password=myPassword 2019-05-21,15,-38
 
+
 @click.group()
 def main():
     """Console script for OceanColor."""
     pass
 
 
 @main.command(name="InRange")
-@click.option('--username', required=True,
-    help="Username on NASA's EarthData System")
-@click.option('--password', required=True,
-    help="Password on NASA's EarthData System")
-@click.option('--sensor', type=click.Choice(['aqua', 'terra']),
-        default='aqua')
-@click.option('--data-type', 'dtype', type=click.Choice(['L2', 'L3m']),
-        default='L3m')
-@click.option('--time-tolerance', 'dt_tol', type=click.INT , default=12,
-              help='Time difference [hours] tolerance to matchup')
-@click.option('--distance-tolerance', 'dL_tol', type=float, default=10e3,
-              help='Distance difference [m] tolerance to matchup')
-@click.argument('track', required=True)
+@click.option(
+    "--username", required=True, help="Username on NASA's EarthData System"
+)
+@click.option(
+    "--password", required=True, help="Password on NASA's EarthData System"
+)
+@click.option("--sensor", type=click.Choice(["aqua", "terra"]), default="aqua")
+@click.option(
+    "--data-type", "dtype", type=click.Choice(["L2", "L3m"]), default="L3m"
+)
+@click.option(
+    "--time-tolerance",
+    "dt_tol",
+    type=click.INT,
+    default=12,
+    help="Time difference [hours] tolerance to matchup",
+)
+@click.option(
+    "--distance-tolerance",
+    "dL_tol",
+    type=float,
+    default=10e3,
+    help="Distance difference [m] tolerance to matchup",
+)
+@click.argument("track", required=True)
 def cli_inrange(username, password, sensor, dtype, dt_tol, dL_tol, track):
-    time, lat, lon = track.split(',')
-    track = pd.DataFrame({"time": [np.datetime64(time)],
-                          "lat": [float(lat)],
-                          "lon": [float(lon)]})
+    time, lat, lon = track.split(",")
+    track = pd.DataFrame(
+        {
+            "time": [np.datetime64(time)],
+            "lat": [float(lat)],
+            "lon": [float(lon)],
+        }
+    )
 
-    dt_tol = np.timedelta64(dt_tol, 'h')
+    dt_tol = np.timedelta64(dt_tol, "h")
     matchup = InRange(username, password, npes=3)
     matchup.search(track, sensor, dtype, dt_tol, dL_tol)
     for m in matchup:

OceanColor/cmr.py

@@ -99,7 +99,7 @@ def granules_search(
     granules = api.downloadable().get()
     print([g["producer_granule_id"] for g in granules])
     for granule in api.get():
-        yield granule['producer_granule_id']
+        yield granule["producer_granule_id"]
 
 
 def search_criteria(**kwargs):

OceanColor/gsfc.py

@@ -4,7 +4,8 @@
 
 import json
 import logging
-from typing import Any, Dict, Optional, Sequence
+from typing import Any, Dict, Optional
+from collections.abc import Sequence
 import urllib
 
 import aiohttp
@@ -76,7 +77,9 @@ def oceandata_file_search(
     if (edate - sdate) > block:
         for start in np.arange(sdate, edate, block):
             end = start + block - np.timedelta64(1, "D")
-            filenames = oceandata_file_search(sensor, dtype, start, end, search)
+            filenames = oceandata_file_search(
+                sensor, dtype, start, end, search
+            )
             yield from filenames
         return
 
@@ -178,7 +181,7 @@ def search_criteria(**kwargs):
 
 
 def bloom_filter(
-    track: Sequence[Dict],
+    track: Sequence[dict],
     sensor: [Sequence[str], str],
     dtype: str,
     dt_tol: Optional[Any] = None,
@@ -214,8 +217,7 @@ def bloom_filter(
 
     search = search_criteria(sensor=sensor, dtype=dtype)
     filenames = oceandata_file_search(sensor, dtype, sdate, edate, search)
-    for f in filenames:
-        yield f
+    yield from filenames
 
 
 def read_remote_file(filename, username, password):
@@ -227,7 +229,9 @@ def read_remote_file(filename, username, password):
     url_base = "https://oceandata.sci.gsfc.nasa.gov/ob/getfile/"
     url = requests.compat.urljoin(url_base, filename)
 
-    fs = fsspec.filesystem('https', client_kwargs={'auth': aiohttp.BasicAuth(username, password)})
+    fs = fsspec.filesystem(
+        "https", client_kwargs={"auth": aiohttp.BasicAuth(username, password)}
+    )
     f = fs.open(url)
     content = f.read()
     return content