Merge branch 'hackdna/fix-logging' into beiwe-taskrunner

docs/source/logging.md

@@ -37,13 +37,6 @@ import logging
 logger = logging.getLogger(__name__)
 ```
 
-Or like this:
-
-```
-from logging import getLogger
-logger = getLogger(__name__)
-```
-
 ## 3. How to insert log messages into definitions
 
 Basic `logging` messages:

forest/bonsai/simulate_gps_data.py

@@ -27,8 +27,8 @@
 TRAVELLING_STATUS_LIST = range(11)
 
 
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger()
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 
 class PossibleExits(Enum):

forest/constants.py

@@ -20,12 +20,13 @@
 
 class Frequency(Enum):
     """This class enumerates possible frequencies for summary data."""
-    HOURLY = 1
-    DAILY = 24
-    HOURLY_AND_DAILY = "hourly_and_daily"
-    THREE_HOURLY = 3
-    SIX_HOURLY = 6
-    TWELVE_HOURLY = 12
+    MINUTELY = 1
+    HOURLY = 60
+    THREE_HOURLY = 3 * 60
+    SIX_HOURLY = 6 * 60
+    TWELVE_HOURLY = 12 * 60
+    DAILY = 24 * 60
+    HOURLY_AND_DAILY = -1
 
 
 class OSMTags(Enum):

forest/jasmine/data2mobmat.py

@@ -15,8 +15,8 @@
 TOLERANCE = 1e-6
 
 
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger()
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 
 def cartesian(

forest/jasmine/mobmat2traj.py

@@ -13,8 +13,8 @@
 from .data2mobmat import great_circle_dist, exist_knot
 
 
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger()
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 
 # the details of the functions are in paper [Liu and Onnela (2020)]

forest/jasmine/sogp_gps.py

@@ -14,8 +14,8 @@
 import numpy as np
 
 
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger()
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 
 def calculate_k0(x1: np.ndarray, x2: np.ndarray, pars: list) -> float:

forest/jasmine/tests/test_traj2stats.py

@@ -399,6 +399,87 @@ def test_gps_summaries_log_format(
     assert np.all(dates_stats == dates_log)
 
 
+def test_gps_summaries_summary_vals(
+    coords1, sample_trajectory, sample_nearby_locations, mocker
+):
+    """Testing gps summaries summary values are correct"""
+    mocker.patch(
+        "forest.jasmine.traj2stats.get_nearby_locations",
+        return_value=sample_nearby_locations,
+    )
+    mocker.patch("forest.jasmine.traj2stats.locate_home", return_value=coords1)
+
+    parameters = Hyperparameters()
+
+    summary, _ = gps_summaries(
+        traj=sample_trajectory,
+        tz_str="Europe/London",
+        frequency=Frequency.DAILY,
+        parameters=parameters,
+    )
+
+    assert np.all(summary["obs_duration"] == 24)
+    assert summary["obs_day"].iloc[0] == 10
+    assert summary["obs_night"].iloc[0] == 14
+    assert summary["obs_day"].iloc[1] == 24
+    assert summary["obs_night"].iloc[1] == 0
+    assert np.all(summary["home_time"] == 0)
+    assert summary["dist_traveled"].iloc[0] == 0.208
+    assert summary["dist_traveled"].iloc[1] == 0
+    assert np.round(summary["max_dist_home"].iloc[0], 3) == 0.915
+    assert np.round(summary["max_dist_home"].iloc[1], 3) == 0.915
+    assert np.round(summary["radius"].iloc[0], 3) == 0.013
+    assert summary["radius"].iloc[1] == 0
+    assert np.round(summary["diameter"].iloc[0], 3) == 0.064
+    assert summary["diameter"].iloc[1] == 0
+    assert summary["num_sig_places"].iloc[0] == 2
+    assert summary["num_sig_places"].iloc[1] == 1
+    assert np.round(summary["entropy"].iloc[0], 3) == 0.468
+    assert summary["entropy"].iloc[1] == 0
+    assert round(summary["total_flight_time"].iloc[0], 3) == 1.528
+    assert summary["total_flight_time"].iloc[1] == 0
+    assert round(summary["av_flight_length"].iloc[0], 3) == 0.052
+    assert summary["av_flight_length"].iloc[1] == 0
+    assert round(summary["sd_flight_length"].iloc[0], 3) == 0.012
+    assert summary["sd_flight_length"].iloc[1] == 0
+    assert round(summary["av_flight_duration"].iloc[0], 3) == 0.382
+    assert summary["av_flight_duration"].iloc[1] == 0
+    assert round(summary["sd_flight_duration"].iloc[0], 3) == 0.132
+    assert summary["sd_flight_duration"].iloc[1] == 0
+    assert round(summary["total_pause_time"].iloc[0], 3) == 22.472
+    assert summary["total_pause_time"].iloc[1] == 24
+    assert round(summary["av_pause_duration"].iloc[0], 3) == 4.494
+    assert summary["av_pause_duration"].iloc[1] == 24
+    assert round(summary["sd_pause_duration"].iloc[0], 3) == 3.496
+    assert summary["sd_pause_duration"].iloc[1] == 0
+
+
+def test_gps_summaries_pcr(
+    coords1, sample_trajectory, sample_nearby_locations, mocker
+):
+    """Testing gps summaries pcr"""
+    mocker.patch(
+        "forest.jasmine.traj2stats.get_nearby_locations",
+        return_value=sample_nearby_locations,
+    )
+    mocker.patch("forest.jasmine.traj2stats.locate_home", return_value=coords1)
+
+    parameters = Hyperparameters()
+    parameters.pcr_bool = True
+
+    summary, _ = gps_summaries(
+        traj=sample_trajectory,
+        tz_str="Europe/London",
+        frequency=Frequency.DAILY,
+        parameters=parameters,
+    )
+
+    assert summary["physical_circadian_rhythm"].iloc[0] == 0
+    assert summary["physical_circadian_rhythm"].iloc[1] == 1
+    assert summary["physical_circadian_rhythm_stratified"].iloc[0] == 0
+    assert summary["physical_circadian_rhythm_stratified"].iloc[1] == 0
+
+
 @pytest.fixture()
 def mobmat1():
     """mobility matrix 1"""
@@ -573,7 +654,7 @@ def test_compute_window_size(sample_trajectory):
     """Testing window size is correct"""
 
     window, _ = compute_window_and_count(
-        sample_trajectory[0, 3], sample_trajectory[-1, 6], 1
+        sample_trajectory[0, 3], sample_trajectory[-1, 6], 60
     )
 
     assert window == 3600
@@ -583,7 +664,7 @@ def test_compute_window_count(sample_trajectory):
     """Testing number of windows is correct"""
 
     _, num_windows = compute_window_and_count(
-        sample_trajectory[0, 3], sample_trajectory[-1, 6], 1
+        sample_trajectory[0, 3], sample_trajectory[-1, 6], 60
     )
 
     assert num_windows == 24
@@ -593,7 +674,7 @@ def test_compute_window_size_6_hour(sample_trajectory):
     """Testing window size is correct 6 hour window"""
 
     window, _ = compute_window_and_count(
-        sample_trajectory[0, 3], sample_trajectory[-1, 6], 6
+        sample_trajectory[0, 3], sample_trajectory[-1, 6], 360
     )
 
     assert window == 3600 * 6
@@ -603,7 +684,7 @@ def test_compute_window_count_6_hour(sample_trajectory):
     """Testing number of windows is correct 6 hour window"""
 
     _, num_windows = compute_window_and_count(
-        sample_trajectory[0, 3], sample_trajectory[-1, 6], 6
+        sample_trajectory[0, 3], sample_trajectory[-1, 6], 360
     )
 
     assert num_windows == 4

forest/jasmine/traj2stats.py

@@ -32,8 +32,8 @@
 from forest.utils import get_ids
 
 
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger()
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 
 @dataclass
@@ -1125,8 +1125,8 @@ def gps_summaries(
         ValueError: Frequency is not valid
     """
 
-    if frequency == Frequency.HOURLY_AND_DAILY:
-        raise ValueError("Frequency must be 'hourly' or 'daily'")
+    if frequency in [Frequency.HOURLY_AND_DAILY, Frequency.MINUTELY]:
+        raise ValueError(f"Frequency cannot be {frequency.name.lower()}.")
 
     if frequency != Frequency.DAILY:
         parameters.split_day_night = False
@@ -1161,7 +1161,7 @@ def gps_summaries(
             traj, [3, 4, 5], tz_str, 3600*24
         )
         window, num_windows = compute_window_and_count(
-            start_stamp, end_stamp, 24, parameters.split_day_night
+            start_stamp, end_stamp, 24*60, parameters.split_day_night
         )
 
     if num_windows <= 0:
@@ -1484,23 +1484,23 @@ def get_time_range(
 
 
 def compute_window_and_count(
-    start_stamp: int, end_stamp: int, window_hours: int,
+    start_stamp: int, end_stamp: int, window_minutes: int,
     split_day_night: bool = False
 ) -> Tuple[int, int]:
     """Computes the window and number of windows based on given time stamps.
 
     Args:
         start_stamp: int, starting time stamp
         end_stamp: int, ending time stamp
-        window_hours: int, window in hours
+        window_minutes: int, window in minutes
         split_day_night: bool, True if split day and night
     Returns:
         A tuple of two integers (window, num_windows):
             window: int, window in seconds
             num_windows: int, number of windows
     """
 
-    window = window_hours * 60 * 60
+    window = window_minutes * 60
     num_windows = (end_stamp - start_stamp) // window
     if split_day_night:
         num_windows *= 2
@@ -1596,7 +1596,13 @@ def gps_stats_main(
             as pickle files for future use
         and a record csv file to show which users are processed
         and logger csv file to show warnings and bugs during the run
+    Raises:
+        ValueError: Frequency is not valid
     """
+    # no minutely analysis on GPS data
+    if frequency == Frequency.MINUTELY:
+        raise ValueError("Frequency cannot be minutely.")
+
     if parameters is None:
         parameters = Hyperparameters()