pep8 requirements

FusRoman · Apr 7, 2023 · 335ed75 · 335ed75
1 parent f66aa4d
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Showing 14 changed files with 174 additions and 106 deletions.
diff --git a/.flake8 b/.flake8
@@ -13,4 +13,5 @@ per-file-ignores =
     ../Fink_GRB/fink_grb/online/ztf_join_gcn.py:W503,E402
     ../Fink_GRB/fink_grb/offline/spark_offline.py:W503,W605
     ../Fink_GRB/fink_grb/utils/fun_utils.py:F811
-    ../Fink_GRB/fink_grb/distribution/distribution.py:W503
+    ../Fink_GRB/fink_grb/distribution/distribution.py:W503
+    ../Fink_GRB/fink_grb/observatory/__init__.py:E402
diff --git a/fink_grb/conftest.py b/fink_grb/conftest.py
@@ -20,66 +20,112 @@ def init_test(doctest_namespace):
 @pytest.fixture(autouse=True)
 def init_fermi(doctest_namespace):
 
-    doctest_namespace["fermi_gbm_voevent_path"] = 'fink_grb/test/test_data/VODB/fermi/voevent_number=193.xml'
-    doctest_namespace["fermi_lat_voevent_path"] = 'fink_grb/test/test_data/VODB/fermi/voevent_number=2842.xml'
+    doctest_namespace[
+        "fermi_gbm_voevent_path"
+    ] = "fink_grb/test/test_data/VODB/fermi/voevent_number=193.xml"
+    doctest_namespace[
+        "fermi_lat_voevent_path"
+    ] = "fink_grb/test/test_data/VODB/fermi/voevent_number=2842.xml"
+
+    fermi_gbm = voevent_to_class(
+        load_voevent_from_path(doctest_namespace["fermi_gbm_voevent_path"])
+    )
+    fermi_lat = voevent_to_class(
+        load_voevent_from_path(doctest_namespace["fermi_lat_voevent_path"])
+    )
 
-    fermi_gbm = voevent_to_class(load_voevent_from_path(doctest_namespace["fermi_gbm_voevent_path"]))
-    fermi_lat = voevent_to_class(load_voevent_from_path(doctest_namespace["fermi_lat_voevent_path"]))
-
-
     doctest_namespace["fermi_gbm"] = fermi_gbm
     doctest_namespace["fermi_lat"] = fermi_lat
 
+
 @pytest.fixture(autouse=True)
 def init_swift(doctest_namespace):
 
-    doctest_namespace["swift_bat_voevent_path"] = 'fink_grb/test/test_data/VODB/swift/voevent_number=392.xml'
-    doctest_namespace["swift_xrt_voevent_path"] = 'fink_grb/test/test_data/VODB/swift/voevent_number=4554.xml'
-    doctest_namespace["swift_uvot_voevent_path"] = 'fink_grb/test/test_data/VODB/swift/voevent_number=8582.xml'
-
-    swift_bat = voevent_to_class(load_voevent_from_path(doctest_namespace["swift_bat_voevent_path"]))
-    swift_xrt = voevent_to_class(load_voevent_from_path(doctest_namespace["swift_xrt_voevent_path"]))
-    swift_uvot = voevent_to_class(load_voevent_from_path(doctest_namespace["swift_uvot_voevent_path"]))
+    doctest_namespace[
+        "swift_bat_voevent_path"
+    ] = "fink_grb/test/test_data/VODB/swift/voevent_number=392.xml"
+    doctest_namespace[
+        "swift_xrt_voevent_path"
+    ] = "fink_grb/test/test_data/VODB/swift/voevent_number=4554.xml"
+    doctest_namespace[
+        "swift_uvot_voevent_path"
+    ] = "fink_grb/test/test_data/VODB/swift/voevent_number=8582.xml"
+
+    swift_bat = voevent_to_class(
+        load_voevent_from_path(doctest_namespace["swift_bat_voevent_path"])
+    )
+    swift_xrt = voevent_to_class(
+        load_voevent_from_path(doctest_namespace["swift_xrt_voevent_path"])
+    )
+    swift_uvot = voevent_to_class(
+        load_voevent_from_path(doctest_namespace["swift_uvot_voevent_path"])
+    )
 
     doctest_namespace["swift_bat"] = swift_bat
     doctest_namespace["swift_xrt"] = swift_xrt
     doctest_namespace["swift_uvot"] = swift_uvot
 
+
 @pytest.fixture(autouse=True)
 def init_integral(doctest_namespace):
 
-    doctest_namespace["integral_weak_voevent_path"] = 'fink_grb/test/test_data/VODB/integral/voevent_number=737.xml'
-    doctest_namespace["integral_wakeup_voevent_path"] = 'fink_grb/test/test_data/VODB/integral/voevent_number=18790.xml'
-    doctest_namespace["integral_refined_voevent_path"] = 'fink_grb/test/test_data/VODB/integral/voevent_number=18791.xml'
-
-    integral_weak = voevent_to_class(load_voevent_from_path(doctest_namespace["integral_weak_voevent_path"]))
-    integral_wakeup = voevent_to_class(load_voevent_from_path(doctest_namespace["integral_wakeup_voevent_path"]))
-    integral_refined = voevent_to_class(load_voevent_from_path(doctest_namespace["integral_refined_voevent_path"]))
+    doctest_namespace[
+        "integral_weak_voevent_path"
+    ] = "fink_grb/test/test_data/VODB/integral/voevent_number=737.xml"
+    doctest_namespace[
+        "integral_wakeup_voevent_path"
+    ] = "fink_grb/test/test_data/VODB/integral/voevent_number=18790.xml"
+    doctest_namespace[
+        "integral_refined_voevent_path"
+    ] = "fink_grb/test/test_data/VODB/integral/voevent_number=18791.xml"
+
+    integral_weak = voevent_to_class(
+        load_voevent_from_path(doctest_namespace["integral_weak_voevent_path"])
+    )
+    integral_wakeup = voevent_to_class(
+        load_voevent_from_path(doctest_namespace["integral_wakeup_voevent_path"])
+    )
+    integral_refined = voevent_to_class(
+        load_voevent_from_path(doctest_namespace["integral_refined_voevent_path"])
+    )
 
     doctest_namespace["integral_weak"] = integral_weak
     doctest_namespace["integral_wakeup"] = integral_wakeup
     doctest_namespace["integral_refined"] = integral_refined
 
+
 @pytest.fixture(autouse=True)
 def init_icecube(doctest_namespace):
 
-    doctest_namespace["icecube_cascade_voevent_path"] = 'fink_grb/test/test_data/VODB/icecube/voevent_number=825.xml'
-    doctest_namespace["icecube_bronze_voevent_path"] = 'fink_grb/test/test_data/VODB/icecube/voevent_number=3028.xml'
-    doctest_namespace["icecube_gold_voevent_path"] = 'fink_grb/test/test_data/VODB/icecube/voevent_number=45412.xml'
-
-    icecube_cascade = voevent_to_class(load_voevent_from_path(doctest_namespace["icecube_cascade_voevent_path"]))
-    icecube_bronze = voevent_to_class(load_voevent_from_path(doctest_namespace["icecube_bronze_voevent_path"]))
-    icecube_gold = voevent_to_class(load_voevent_from_path(doctest_namespace["icecube_gold_voevent_path"]))
+    doctest_namespace[
+        "icecube_cascade_voevent_path"
+    ] = "fink_grb/test/test_data/VODB/icecube/voevent_number=825.xml"
+    doctest_namespace[
+        "icecube_bronze_voevent_path"
+    ] = "fink_grb/test/test_data/VODB/icecube/voevent_number=3028.xml"
+    doctest_namespace[
+        "icecube_gold_voevent_path"
+    ] = "fink_grb/test/test_data/VODB/icecube/voevent_number=45412.xml"
+
+    icecube_cascade = voevent_to_class(
+        load_voevent_from_path(doctest_namespace["icecube_cascade_voevent_path"])
+    )
+    icecube_bronze = voevent_to_class(
+        load_voevent_from_path(doctest_namespace["icecube_bronze_voevent_path"])
+    )
+    icecube_gold = voevent_to_class(
+        load_voevent_from_path(doctest_namespace["icecube_gold_voevent_path"])
+    )
 
     doctest_namespace["icecube_cascade"] = icecube_cascade
     doctest_namespace["icecube_bronze"] = icecube_bronze
     doctest_namespace["icecube_gold"] = icecube_gold
 
+
 @pytest.fixture(autouse=True, scope="session")
 def init_spark(doctest_namespace):
 
     from astropy.time import Time
-    import os
 
     online_output_tempdir = tempfile.TemporaryDirectory()
     doctest_namespace["online_output_tempdir"] = online_output_tempdir
@@ -88,13 +134,14 @@ def init_spark(doctest_namespace):
 
     grb_data = "fink_grb/test/test_data/gcn_test/raw/year=2019/month=09/day=03"
     join_data = "fink_grb/test/test_data/join_raw_datatest.parquet"
-    alert_data = "fink_grb/test/test_data/ztf_test/online/science/year=2019/month=09/day=03/"
+    alert_data = (
+        "fink_grb/test/test_data/ztf_test/online/science/year=2019/month=09/day=03/"
+    )
 
     doctest_namespace["grb_data"] = grb_data
     doctest_namespace["join_data"] = join_data
     doctest_namespace["alert_data"] = alert_data
 
-
     ztf_datatest = "fink_grb/test/test_data/ztf_test/online"
     gcn_datatest = "fink_grb/test/test_data/gcn_test"
     join_data_test = "fink_grb/test/test_data/grb_join_output.parquet"
@@ -113,7 +160,11 @@ def init_spark(doctest_namespace):
     import tabulate
 
     maxtimeout = 10
-    myconfig = {"username": "rlm", "bootstrap.servers": "localhost:9092", "group_id": "rlm_fink"}
+    myconfig = {
+        "username": "rlm",
+        "bootstrap.servers": "localhost:9092",
+        "group_id": "rlm_fink",
+    }
     topics = ["fink_grb_bronze"]
 
     headers = [
@@ -167,5 +218,6 @@ def init_spark(doctest_namespace):
     doctest_namespace["spark"] = spark
 
     import numpy as np
+
     if np.__version__ >= "1.14.0":
         np.set_printoptions(legacy="1.13")
diff --git a/fink_grb/gcn_stream/gcn_reader.py b/fink_grb/gcn_stream/gcn_reader.py
@@ -3,7 +3,7 @@
 from lxml.objectify import ObjectifiedElement
 
 
-def load_voevent_from_path(file_path: str, verbose:bool = False) -> ObjectifiedElement:
+def load_voevent_from_path(file_path: str, verbose: bool = False) -> ObjectifiedElement:
     """
     Load a voevent from a file object.
     Raise an exception if the voevent cannot be parse.
@@ -29,17 +29,21 @@ def load_voevent_from_path(file_path: str, verbose:bool = False) -> ObjectifiedE
     'ivo://nasa.gsfc.gcn/Fermi#GBM_Fin_Pos2022-07-29T10:17:31.51_680782656_0-655'
     """
     try:
-        with open(file_path, 'rb') as f:
+        with open(file_path, "rb") as f:
             return vp.load(f)
     except Exception as e:  # pragma: no cover
         if verbose:
             print(
-                "failed to load the voevent:\n\tlocation={}\n\tcause={}".format(file_path, e)
+                "failed to load the voevent:\n\tlocation={}\n\tcause={}".format(
+                    file_path, e
+                )
             )
         raise e
 
 
-def load_voevent_from_file(file: io.BufferedReader, verbose:bool = False) -> ObjectifiedElement:
+def load_voevent_from_file(
+    file: io.BufferedReader, verbose: bool = False
+) -> ObjectifiedElement:
     """
     Load a voevent from a file object.
     Raise an exception if the voevent cannot be parse.

diff --git a/fink_grb/gcn_stream/gcn_stream.py b/fink_grb/gcn_stream/gcn_stream.py
@@ -13,6 +13,7 @@
 from fink_grb.utils.fun_utils import return_verbose_level, get_hdfs_connector
 from fink_grb.observatory import voevent_to_class, TOPICS
 
+
 def signal_handler(signal, frame):  # pragma: no cover
     """
     The signal handler function for the gcn stream.
@@ -51,7 +52,7 @@ def load_and_parse_gcn(gcn, gcn_rawdatapath, logger, logs=False, gcn_fs=None):
 
     Examples
     --------
-    
+
     >>> f = open('fink_grb/test/test_data/voevent_number=9897.xml').read().encode("UTF-8")
     >>> logger = init_logging()
     >>> with tempfile.TemporaryDirectory() as tmp_dir_gcn:
@@ -125,28 +126,25 @@ def start_gcn_stream(arguments):
 
     try:
         consumer_config = {
-            'group.id': 'fink_mm',
-            'auto.offset.reset': 'earliest',
-            'enable.auto.commit': False
+            "group.id": "fink_mm",
+            "auto.offset.reset": "earliest",
+            "enable.auto.commit": False,
         }
-        
+
         consumer = Consumer(
             config=consumer_config,
-            client_id=config["CLIENT"]["id"], 
-            client_secret=config["CLIENT"]["secret"]
+            client_id=config["CLIENT"]["id"],
+            client_secret=config["CLIENT"]["secret"],
         )
 
         if arguments["--test"]:
-            consumer_config = {
-                'group.id': '',
-                'auto.offset.reset': 'earliest'
-            }
+            consumer_config = {"group.id": "", "auto.offset.reset": "earliest"}
 
             consumer = Consumer(
                 config=consumer_config,
-                client_id=config["CLIENT"]["id"], 
+                client_id=config["CLIENT"]["id"],
                 client_secret=config["CLIENT"]["secret"],
-                domain='test.gcn.nasa.gov'
+                domain="test.gcn.nasa.gov",
             )
     except Exception as e:
         logger.error("Config entry not found \n\t {}".format(e))
@@ -191,7 +189,7 @@ def start_gcn_stream(arguments):
 
     while True:
         message = consumer.consume(timeout=2)
-        
+
         if len(message) != 0:
             for gcn in message:
                 if logs:

diff --git a/fink_grb/observatory/Fermi/Fermi.py b/fink_grb/observatory/Fermi/Fermi.py
@@ -1,4 +1,3 @@
-import json
 import voeventparse as vp
 import os.path as path
 
@@ -7,6 +6,7 @@
 from fink_grb.observatory import OBSERVATORY_PATH
 from fink_grb.observatory.observatory import Observatory, BadInstrument
 
+
 class Fermi(Observatory):
     """
     Fermi instrument
@@ -47,8 +47,8 @@ def get_trigger_id(self):
     def err_to_arcminute(self):
         """
         Return the error box of the voevent in arcminute
-        
-        Example 
+
+        Example
         -------
         >>> fermi_gbm.err_to_arcminute()
         680.4
@@ -57,7 +57,7 @@ def err_to_arcminute(self):
         """
         instrument = self.detect_instruments()
         coords = vp.get_event_position(self.voevent)
-        err = 1/60 if coords.err == 0.0 else coords.err
+        err = 1 / 60 if coords.err == 0.0 else coords.err
 
         if instrument == "GBM":
             return err * 60
@@ -66,7 +66,8 @@ def err_to_arcminute(self):
         else:
             raise BadInstrument("{} is not a Fermi instrument".format(instrument))
 
+
 if __name__ == "__main__":
 
     fermi = Fermi()
-    print(fermi)
+    print(fermi)
diff --git a/fink_grb/observatory/IceCube/IceCube.py b/fink_grb/observatory/IceCube/IceCube.py
@@ -28,7 +28,9 @@ def __init__(self, voevent):
         >>> type(obs)
         <class 'IceCube.IceCube'>
         """
-        super().__init__(path.join(OBSERVATORY_PATH, "IceCube", "icecube.json"), voevent)
+        super().__init__(
+            path.join(OBSERVATORY_PATH, "IceCube", "icecube.json"), voevent
+        )
 
     def get_trigger_id(self):
         """
@@ -53,8 +55,8 @@ def detect_instruments(self):
     def err_to_arcminute(self):
         """
         Return the error box of the voevent in arcminute
-        
-        Example 
+
+        Example
         -------
         >>> icecube_cascade.err_to_arcminute()
         773.778
@@ -147,4 +149,4 @@ def voevent_to_df(self):
         df["month"] = df["triggerTimeUTC"].dt.strftime("%m")
         df["day"] = df["triggerTimeUTC"].dt.strftime("%d")
 
-        return df
+        return df
diff --git a/fink_grb/observatory/Integral/Integral.py b/fink_grb/observatory/Integral/Integral.py
@@ -1,4 +1,3 @@
-import json
 import voeventparse as vp
 import os.path as path
 
@@ -26,7 +25,9 @@ def __init__(self, voevent):
         >>> type(obs)
         <class 'Integral.Integral'>
         """
-        super().__init__(path.join(OBSERVATORY_PATH, "Integral", "integral.json"), voevent)
+        super().__init__(
+            path.join(OBSERVATORY_PATH, "Integral", "integral.json"), voevent
+        )
 
     def get_trigger_id(self):
         """
@@ -48,8 +49,8 @@ def get_trigger_id(self):
     def err_to_arcminute(self):
         """
         Return the error box of the voevent in arcminute
-        
-        Example 
+
+        Example
         -------
         >>> integral_weak.err_to_arcminute()
         0.0656
@@ -64,4 +65,4 @@ def err_to_arcminute(self):
         if instrument == "Weak" or instrument == "Wakeup" or instrument == "Refined":
             return coords.err
         else:
-            raise BadInstrument("{} is not a IceCube events".format(instrument))
+            raise BadInstrument("{} is not a IceCube events".format(instrument))