Merge branch 'develop' into coerce_longitude_9_jan

.github/workflows/build.yml

@@ -19,12 +19,17 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.8
-      - name: Install Forest dependencies
+      - name: Install Forest dependencies for Linux
         # required by librosa
         if: ${{ startsWith(matrix.os, 'ubuntu') }}
         run: |
           sudo apt-get update
           sudo apt-get install -y ffmpeg libsndfile1
+      - name: Install Forest dependencies for Windows
+        # required by librosa
+        if: ${{ startsWith(matrix.os, 'windows') }}
+        uses: FedericoCarboni/setup-ffmpeg@v2
+        id: setup-ffmpeg
       - name: Install Forest
         run: pip install -e .
       - name: Install dev dependencies

.gitignore

@@ -1,8 +1,9 @@
 __pycache__/
 .DS_Store
 
-# IntelliJ project files
+# IntelliJ, VsCode project files
 .idea
+.vscode
 
 # for installing Forest in editable mode when developing
 /forest.egg-info/
@@ -18,3 +19,6 @@ __pycache__/
 
 #sphinx build
 docs/_build/
+
+# any python environment files
+.python-version

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
+    MINUTE = 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(
@@ -179,6 +179,10 @@ def collapse_data(
     # Filter out rows where the GPS accuracy is beyond
     # the provided accuracy_limit
     data = data[data.accuracy < accuracy_limit]
+    if data.shape[0] == 0:
+        raise ValueError(
+            f"No GPS record with accuracy less than {accuracy_limit}."
+        )
 
     # Get the start and end timestamps in seconds
     t_start = sorted(np.array(data.timestamp))[0] / 1000
@@ -1008,7 +1012,8 @@ def infer_mobmat(mobmat: np.ndarray, interval: float, r: float) -> np.ndarray:
         (mobmat, np.ones(n_rows).reshape(n_rows, 1))
     )
     # Append new pauses to the trajectory matrix
-    mobmat = np.vstack((mobmat, new_pauses_array))
+    if new_pauses_array.shape[0] > 0:
+        mobmat = np.vstack((mobmat, new_pauses_array))
     # Sort the matrix by start time
     mobmat = mobmat[mobmat[:, 3].argsort()].astype(float)
 

forest/jasmine/mobmat2traj.py

@@ -3,7 +3,6 @@
 """
 import logging
 import math
-import sys
 from typing import Optional, Tuple
 
 import numpy as np
@@ -13,8 +12,8 @@
 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)]
@@ -278,7 +277,7 @@ def indicate_flight(
     # Calculate k1 using the specified method
     k1 = calculate_k1(method, current_t, current_x, current_y, bv_subset, pars)
     if k1 is None:
-        sys.exit("Invalid method for calculate_k1.")
+        raise ValueError("Invalid method for calculate_k1.")
 
     # Select flight and pause indicators from the bv_subset
     flight_k = k1[bv_subset[:, 0] == 1]
@@ -662,8 +661,8 @@ def forward_impute(
             method, start_t, start_x, start_y,
             flight_table, pars
         )
-        if weight is None:
-            sys.exit("Invalid method for calculate_k1.")
+        if weight is None or len(weight) == 0:
+            raise ValueError("Invalid method for calculate_k1.")
 
         normalize_w = (weight + 1e-5) / float(sum(weight + 1e-5))
         flight_index = np.random.choice(flight_table.shape[0], p=normalize_w)
@@ -743,7 +742,7 @@ def forward_impute(
                 pause_table, pars
             )
             if weight is None:
-                sys.exit("Invalid method for calculate_k1.")
+                raise ValueError("Invalid method for calculate_k1.")
 
             normalize_w = (weight + 1e-5) / float(sum(weight + 1e-5))
             pause_index = np.random.choice(pause_table.shape[0], p=normalize_w)
@@ -832,7 +831,7 @@ def backward_impute(
             flight_table, pars
         )
         if weight is None:
-            sys.exit("Invalid method for calculate_k1.")
+            raise ValueError("Invalid method for calculate_k1.")
 
         normalize_w = (weight + 1e-5) / float(sum(weight + 1e-5))
         flight_index = np.random.choice(flight_table.shape[0], p=normalize_w)
@@ -907,8 +906,8 @@ def backward_impute(
                 method, end_t, end_x, end_y,
                 pause_table, pars
             )
-            if weight is None:
-                sys.exit("Invalid method for calculate_k1.")
+            if weight is None or len(weight) == 0:
+                raise ValueError("Invalid method for calculate_k1.")
 
             normalize_w = (weight + 1e-5) / float(sum(weight + 1e-5))
             pause_index = np.random.choice(pause_table.shape[0], p=normalize_w)
@@ -972,6 +971,11 @@ def impute_gps(
     # for observed flights, observed pauses, and missing intervals
     flight_table, pause_table, mis_table = create_tables(mob_mat, bv_subset)
 
+    if len(flight_table) == 0:
+        raise ValueError("No flight observed in the data.")
+    if len(pause_table) == 0:
+        raise ValueError("No pause observed in the data.")
+
     # initialize the imputed trajectory table
     imp_table = np.zeros((1, 7))
 

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

@@ -654,7 +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
@@ -664,7 +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
@@ -674,7 +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
@@ -684,7 +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