From 0c2c321266e94f6ca487084d2dd7e50b91f6ffde Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Tue, 30 Jul 2024 13:02:15 -0400
Subject: [PATCH 01/14] Adding logger, and test for get_logger

---
 src/wristpy/core/config.py | 21 +++++++++++++++++++++
 tests/unit/test_logger.py  | 22 ++++++++++++++++++++++
 2 files changed, 43 insertions(+)
 create mode 100644 tests/unit/test_logger.py

diff --git a/src/wristpy/core/config.py b/src/wristpy/core/config.py
index 2aa8df8b..45d3d01d 100644
--- a/src/wristpy/core/config.py
+++ b/src/wristpy/core/config.py
@@ -1,5 +1,7 @@
 """Configuration module for wristpy."""
 
+import logging
+
 import pydantic_settings
 
 
@@ -9,3 +11,22 @@ class Settings(pydantic_settings.BaseSettings):
     LIGHT_THRESHOLD: float = 0.03
     MODERATE_THRESHOLD: float = 0.1
     VIGOROUS_THRESHOLD: float = 0.3
+
+    LOGGING_VERBOSITY: int = 20
+
+
+def get_logger() -> logging.Logger:
+    """Gets the wristpy logger."""
+    if logging.getLogger("wristpy").hasHandlers():
+        return logging.getLogger("wristpy")
+    logger = logging.getLogger("wristpy")
+    logger.setLevel(Settings().LOGGING_VERBOSITY)
+
+    formatter = logging.Formatter(
+        "%(asctime)s - %(name)s - %(levelname)s - %(filename)s:%(lineno)s - %(funcName)s - %(message)s",  # noqa: E501
+    )
+
+    handler = logging.StreamHandler()
+    handler.setFormatter(formatter)
+    logger.addHandler(handler)
+    return logger
diff --git a/tests/unit/test_logger.py b/tests/unit/test_logger.py
new file mode 100644
index 00000000..43455bd8
--- /dev/null
+++ b/tests/unit/test_logger.py
@@ -0,0 +1,22 @@
+"""Test logging in config.py."""
+
+import pytest
+
+from wristpy.core import config
+
+logger = config.get_logger()
+
+
+def test_get_logger(caplog: pytest.LogCaptureFixture) -> None:
+    """Test the wristpy logger with level set to 20 (info)."""
+    caplog.set_level(config.Settings().LOGGING_VERBOSITY)
+    logger = config.get_logger()
+
+    logger.debug("Debug message here.")
+    logger.info("Info message here.")
+    logger.warning("Warning message here")
+
+    assert logger.getEffectiveLevel() == 20
+    assert "Debug message here" not in caplog.text
+    assert "Info message here" in caplog.text
+    assert "Warning message here" in caplog.text

From bf31e19e3ce35b842ef01b1f89c7fb6f4a450e80 Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Tue, 30 Jul 2024 13:04:15 -0400
Subject: [PATCH 02/14] typos

---
 tests/unit/test_logger.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/unit/test_logger.py b/tests/unit/test_logger.py
index 43455bd8..637ece7f 100644
--- a/tests/unit/test_logger.py
+++ b/tests/unit/test_logger.py
@@ -14,9 +14,9 @@ def test_get_logger(caplog: pytest.LogCaptureFixture) -> None:
 
     logger.debug("Debug message here.")
     logger.info("Info message here.")
-    logger.warning("Warning message here")
+    logger.warning("Warning message here.")
 
     assert logger.getEffectiveLevel() == 20
     assert "Debug message here" not in caplog.text
-    assert "Info message here" in caplog.text
-    assert "Warning message here" in caplog.text
+    assert "Info message here." in caplog.text
+    assert "Warning message here." in caplog.text

From cf7f7213d33c644746a7dc4451bedd1529bce444 Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Tue, 30 Jul 2024 14:03:48 -0400
Subject: [PATCH 03/14] duplicate line.

---
 tests/unit/test_logger.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/unit/test_logger.py b/tests/unit/test_logger.py
index 637ece7f..908de3a4 100644
--- a/tests/unit/test_logger.py
+++ b/tests/unit/test_logger.py
@@ -4,8 +4,6 @@
 
 from wristpy.core import config
 
-logger = config.get_logger()
-
 
 def test_get_logger(caplog: pytest.LogCaptureFixture) -> None:
     """Test the wristpy logger with level set to 20 (info)."""

From 5a0820d64bd08dc1d4806d66178e208012a79b8b Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Tue, 30 Jul 2024 14:05:09 -0400
Subject: [PATCH 04/14] var name change

---
 src/wristpy/core/config.py | 4 ++--
 tests/unit/test_logger.py  | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/wristpy/core/config.py b/src/wristpy/core/config.py
index 45d3d01d..abf26e16 100644
--- a/src/wristpy/core/config.py
+++ b/src/wristpy/core/config.py
@@ -12,7 +12,7 @@ class Settings(pydantic_settings.BaseSettings):
     MODERATE_THRESHOLD: float = 0.1
     VIGOROUS_THRESHOLD: float = 0.3
 
-    LOGGING_VERBOSITY: int = 20
+    LOGGING_LEVEL: int = 20
 
 
 def get_logger() -> logging.Logger:
@@ -20,7 +20,7 @@ def get_logger() -> logging.Logger:
     if logging.getLogger("wristpy").hasHandlers():
         return logging.getLogger("wristpy")
     logger = logging.getLogger("wristpy")
-    logger.setLevel(Settings().LOGGING_VERBOSITY)
+    logger.setLevel(Settings().LOGGING_LEVEL)
 
     formatter = logging.Formatter(
         "%(asctime)s - %(name)s - %(levelname)s - %(filename)s:%(lineno)s - %(funcName)s - %(message)s",  # noqa: E501
diff --git a/tests/unit/test_logger.py b/tests/unit/test_logger.py
index 908de3a4..f5c17f4e 100644
--- a/tests/unit/test_logger.py
+++ b/tests/unit/test_logger.py
@@ -7,7 +7,7 @@
 
 def test_get_logger(caplog: pytest.LogCaptureFixture) -> None:
     """Test the wristpy logger with level set to 20 (info)."""
-    caplog.set_level(config.Settings().LOGGING_VERBOSITY)
+    caplog.set_level(config.Settings().LOGGING_LEVEL)
     logger = config.get_logger()
 
     logger.debug("Debug message here.")

From b8d3c73c64ee3d7bbc236905c75826cdb74c66c3 Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Tue, 30 Jul 2024 15:29:50 -0400
Subject: [PATCH 05/14] work around for .hasHandlers() issue.

---
 src/wristpy/core/config.py | 6 +++---
 tests/unit/test_logger.py  | 1 -
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/wristpy/core/config.py b/src/wristpy/core/config.py
index abf26e16..40b19787 100644
--- a/src/wristpy/core/config.py
+++ b/src/wristpy/core/config.py
@@ -17,11 +17,11 @@ class Settings(pydantic_settings.BaseSettings):
 
 def get_logger() -> logging.Logger:
     """Gets the wristpy logger."""
-    if logging.getLogger("wristpy").hasHandlers():
-        return logging.getLogger("wristpy")
     logger = logging.getLogger("wristpy")
-    logger.setLevel(Settings().LOGGING_LEVEL)
+    if logger.handlers:
+        return logger
 
+    logger.setLevel(Settings().LOGGING_LEVEL)
     formatter = logging.Formatter(
         "%(asctime)s - %(name)s - %(levelname)s - %(filename)s:%(lineno)s - %(funcName)s - %(message)s",  # noqa: E501
     )
diff --git a/tests/unit/test_logger.py b/tests/unit/test_logger.py
index f5c17f4e..454abe54 100644
--- a/tests/unit/test_logger.py
+++ b/tests/unit/test_logger.py
@@ -7,7 +7,6 @@
 
 def test_get_logger(caplog: pytest.LogCaptureFixture) -> None:
     """Test the wristpy logger with level set to 20 (info)."""
-    caplog.set_level(config.Settings().LOGGING_LEVEL)
     logger = config.get_logger()
 
     logger.debug("Debug message here.")

From 6e2e9a90625291c1069e09cf2fe0e3dacdd10ae9 Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Thu, 1 Aug 2024 11:52:17 -0400
Subject: [PATCH 06/14] Added second test to hit first return statement.

---
 tests/unit/test_logger.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/tests/unit/test_logger.py b/tests/unit/test_logger.py
index 454abe54..a0790a5d 100644
--- a/tests/unit/test_logger.py
+++ b/tests/unit/test_logger.py
@@ -17,3 +17,13 @@ def test_get_logger(caplog: pytest.LogCaptureFixture) -> None:
     assert "Debug message here" not in caplog.text
     assert "Info message here." in caplog.text
     assert "Warning message here." in caplog.text
+
+
+def test_get_logger_second_call() -> None:
+    """Test get logger when a handler already exists."""
+    logger = config.get_logger()
+    second_logger = config.get_logger()
+
+    assert len(logger.handlers) == len(second_logger.handlers) == 1
+    assert logger.handlers[0] is second_logger.handlers[0]
+    assert logger is second_logger

From 4eba6c86709c0bceffaf1174125f0e8904eae29f Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Wed, 28 Aug 2024 10:16:56 -0400
Subject: [PATCH 07/14] added log to calibraiton.

---
 src/wristpy/processing/calibration.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/wristpy/processing/calibration.py b/src/wristpy/processing/calibration.py
index d6424ba2..13054799 100644
--- a/src/wristpy/processing/calibration.py
+++ b/src/wristpy/processing/calibration.py
@@ -11,7 +11,9 @@
 from sklearn import linear_model
 from sklearn import metrics as sklearn_metrics
 
-from wristpy.core import computations, models
+from wristpy.core import computations, config, models
+
+logger = config.get_logger()
 
 
 class SphereCriteriaError(Exception):
@@ -409,7 +411,8 @@ def _closest_point_fit(self, no_motion_data: np.ndarray) -> LinearTransformation
             weights = np.minimum(
                 1 / np.linalg.norm(current - closest_point, axis=1), 100
             )
-
+            logger.debug(f"scale: {scale}, offset: {offset}")
+            logger.debug(f"residual: {residual}")
             if abs(residual - previous_residual) < self.error_tolerance:
                 break
 

From 3715187b635851bc376b4f9f402e1e346864569c Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Wed, 28 Aug 2024 16:30:03 -0400
Subject: [PATCH 08/14] Adding logs

---
 src/wristpy/processing/analytics.py   |  3 +++
 src/wristpy/processing/calibration.py | 28 ++++++++++++++++++++++-----
 src/wristpy/processing/metrics.py     |  9 ++++++++-
 3 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/src/wristpy/processing/analytics.py b/src/wristpy/processing/analytics.py
index 2ffe97c5..7443f19c 100644
--- a/src/wristpy/processing/analytics.py
+++ b/src/wristpy/processing/analytics.py
@@ -15,6 +15,8 @@
 MODERATE_THRESHOLD = settings.MODERATE_THRESHOLD
 VIGOROUS_THRESHOLD = settings.VIGOROUS_THRESHOLD
 
+logger = config.get_logger()
+
 
 @dataclass
 class SleepWindow:
@@ -83,6 +85,7 @@ def run_sleep_detection(self) -> List[SleepWindow]:
             A list of SleepWindow instances, each instance contains a sleep onset/wakeup
             time pair.
         """
+        logger.debug("Beginning sleep detection.")
         spt_window = self._spt_window(self.anglez)
         sib_periods = self._calculate_sib_periods(self.anglez)
         spt_window_periods = self._find_periods(spt_window)
diff --git a/src/wristpy/processing/calibration.py b/src/wristpy/processing/calibration.py
index 13054799..4a3402a5 100644
--- a/src/wristpy/processing/calibration.py
+++ b/src/wristpy/processing/calibration.py
@@ -16,25 +16,38 @@
 logger = config.get_logger()
 
 
-class SphereCriteriaError(Exception):
+class LoggedException(Exception):
+    """Base class that automatically logs messages."""
+
+    def __init__(self, message: str) -> None:
+        """Initialize a new instance of the LoggedException class.
+
+        Args:
+            message: The message to display.
+        """
+        logger.exception(message)
+        super().__init__(message)
+
+
+class SphereCriteriaError(LoggedException):
     """Data did not meet the sphere criteria."""
 
     pass
 
 
-class CalibrationError(Exception):
+class CalibrationError(LoggedException):
     """Was not able to lower calibration below error threshold."""
 
     pass
 
 
-class NoMotionError(Exception):
+class NoMotionError(LoggedException):
     """No epochs with zero movement could be found in the data."""
 
     pass
 
 
-class ZeroScaleError(Exception):
+class ZeroScaleError(LoggedException):
     """Scale value went to zero."""
 
     pass
@@ -203,6 +216,7 @@ def _chunked_calibration(
             CalibrationError: If all possible chunks have been used and the calibration
                 process fails to get below the `min_calibration_error` threshold.
         """
+        logger.debug("running chunked calibration.")
         for chunk in self._get_chunk(acceleration):
             try:
                 return self._calibrate(chunk)
@@ -224,6 +238,7 @@ def _get_chunk(
             everytime the generator function is called.
 
         """
+        logger.debug("Getting chunk.")
         sampling_rate = Calibration._get_sampling_rate(timestamps=acceleration.time)
         min_samples = int(self.min_calibration_hours * 3600 * sampling_rate)
         chunk_size = int(12 * 3600 * sampling_rate)
@@ -273,6 +288,7 @@ def _calibrate(self, acceleration: models.Measurement) -> LinearTransformation:
             and temperature: an evaluation on four continents. J Appl Physiol (1985)
             2014 Oct 1;117(7):738-44. doi: 10.1152/japplphysiol.00421.2014.
         """
+        logger.debug("attempting calibration...")
         no_motion_data = self._extract_no_motion(acceleration=acceleration)
         linear_transformation = self._closest_point_fit(no_motion_data=no_motion_data)
 
@@ -295,7 +311,7 @@ def _calibrate(self, acceleration: models.Measurement) -> LinearTransformation:
                 f"Initial Error: {cal_error_initial}, Final Error: {cal_error_end},"
                 f"Error threshold: {self.min_calibration_error}"
             )
-
+        logger.debug("Calibration successful, returning scale and offset values.")
         return linear_transformation
 
     def _extract_no_motion(self, acceleration: models.Measurement) -> np.ndarray:
@@ -326,6 +342,7 @@ def _extract_no_motion(self, acceleration: models.Measurement) -> np.ndarray:
             and temperature: an evaluation on four continents. J Appl Physiol (1985)
             2014 Oct 1;117(7):738-44. doi: 10.1152/japplphysiol.00421.2014.
         """
+        logger.debug("extracting no motion.")
         moving_sd = computations.moving_std(acceleration, 10)
         moving_mean = computations.moving_mean(acceleration, 10)
         no_motion_check = np.all(
@@ -373,6 +390,7 @@ def _closest_point_fit(self, no_motion_data: np.ndarray) -> LinearTransformation
             and temperature: an evaluation on four continents. J Appl Physiol (1985)
             2014 Oct 1;117(7):738-44. doi: 10.1152/japplphysiol.00421.2014.
         """
+        logger.debug("Beginning closest point fit.")
         sphere_criteria_check = np.all(
             (no_motion_data.min(axis=0) < -self.min_acceleration)
             & (no_motion_data.max(axis=0) > self.min_acceleration)
diff --git a/src/wristpy/processing/metrics.py b/src/wristpy/processing/metrics.py
index 8628b2dd..962f929a 100644
--- a/src/wristpy/processing/metrics.py
+++ b/src/wristpy/processing/metrics.py
@@ -3,7 +3,9 @@
 import numpy as np
 import polars as pl
 
-from wristpy.core import models
+from wristpy.core import config, models
+
+logger = config.get_logger()
 
 
 def euclidean_norm_minus_one(acceleration: models.Measurement) -> models.Measurement:
@@ -93,6 +95,7 @@ def detect_nonwear(
     Returns:
         A new Measurment instance with the non-wear flag and corresponding timestamps.
     """
+    logger.debug("Detecting non-wear data.")
     acceleration_grouped_by_short_window = _group_acceleration_data_by_time(
         acceleration, short_epoch_length
     )
@@ -109,6 +112,10 @@ def detect_nonwear(
     )
     non_wear_flag = np.where(nonwear_value_array_cleaned >= 2, 1, 0)
 
+    logger.debug(
+        f"Returning non-wear array of length {len(non_wear_flag)},",
+        f"time stamps of length {len(acceleration_grouped_by_short_window["time"])}",
+    )
     return models.Measurement(
         measurements=non_wear_flag, time=acceleration_grouped_by_short_window["time"]
     )

From 8b1b13e91a2c6ea3e8614aae44a2254211e52f8c Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Wed, 28 Aug 2024 17:25:09 -0400
Subject: [PATCH 09/14] logs for sleep

---
 src/wristpy/processing/analytics.py | 13 ++++++++++---
 src/wristpy/processing/metrics.py   |  4 ----
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/wristpy/processing/analytics.py b/src/wristpy/processing/analytics.py
index 34d8248d..2724b37c 100644
--- a/src/wristpy/processing/analytics.py
+++ b/src/wristpy/processing/analytics.py
@@ -93,7 +93,9 @@ def run_sleep_detection(self) -> List[SleepWindow]:
         sleep_onset_wakeup = self._find_onset_wakeup_times(
             spt_window_periods, sib_window_periods
         )
-
+        logger.debug(
+            f"Sleep detection complete. Windows detected: {len(sleep_onset_wakeup)}"
+        )
         return sleep_onset_wakeup
 
     def _spt_window(
@@ -123,6 +125,7 @@ def _spt_window(
               using an accelerometer without sleep diary. Sci Rep 8, 12975 (2018).
               https://doi.org/10.1038/s41598-018-31266-z
         """
+        logger.debug(f"Finding spt windows, Threshold: {threshold}")
         long_epoch_median = 300
         long_block = 360
         short_block_gap = 720
@@ -142,7 +145,7 @@ def _spt_window(
         sleep_idx_array_filled = self._fill_false_blocks(
             sleep_candidates, short_block_gap
         )
-
+        logger.debug("Found SPT windows")
         return models.Measurement(
             measurements=sleep_idx_array_filled, time=anglez_median_long_epoch.time
         )
@@ -314,6 +317,7 @@ def _find_periods(
         a period. For isolated ones the function returns the same start
         and end time. The list is sorted by time.
     """
+    logger.debug("Finding periods.")
     edge_detection = np.convolve([1, 3, 1], window_measurement.measurements, "same")
     single_one = np.nonzero(edge_detection == 3)[0]
 
@@ -403,8 +407,11 @@ def compute_physical_activty_categories(
     Raises:
         ValueError: If the threshold values are not in ascending order.
     """
+    logger.debug(f"Computing physical activity levels, thresholds: {thresholds}")
     if list(thresholds) != sorted(thresholds):
-        raise ValueError("Thresholds must be in ascending order.")
+        message = "Thresholds must be in ascending order."
+        logger.error("ValueError, thresholds must be in ascending order.")
+        raise ValueError(message)
 
     activity_levels = (
         (
diff --git a/src/wristpy/processing/metrics.py b/src/wristpy/processing/metrics.py
index 962f929a..be44459d 100644
--- a/src/wristpy/processing/metrics.py
+++ b/src/wristpy/processing/metrics.py
@@ -112,10 +112,6 @@ def detect_nonwear(
     )
     non_wear_flag = np.where(nonwear_value_array_cleaned >= 2, 1, 0)
 
-    logger.debug(
-        f"Returning non-wear array of length {len(non_wear_flag)},",
-        f"time stamps of length {len(acceleration_grouped_by_short_window["time"])}",
-    )
     return models.Measurement(
         measurements=non_wear_flag, time=acceleration_grouped_by_short_window["time"]
     )

From a6cb3a89ea5e6b2d17069cfbb8e5e0c483a9b1ae Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Thu, 29 Aug 2024 11:20:32 -0400
Subject: [PATCH 10/14] more logs for calibration and analytics

---
 src/wristpy/processing/analytics.py   | 15 +++++++++++----
 src/wristpy/processing/calibration.py | 14 ++++++++++----
 2 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/src/wristpy/processing/analytics.py b/src/wristpy/processing/analytics.py
index 2724b37c..a59e341d 100644
--- a/src/wristpy/processing/analytics.py
+++ b/src/wristpy/processing/analytics.py
@@ -145,7 +145,6 @@ def _spt_window(
         sleep_idx_array_filled = self._fill_false_blocks(
             sleep_candidates, short_block_gap
         )
-        logger.debug("Found SPT windows")
         return models.Measurement(
             measurements=sleep_idx_array_filled, time=anglez_median_long_epoch.time
         )
@@ -172,6 +171,7 @@ def _calculate_sib_periods(
             Duration Using a Wrist-Worn Accelerometer. PLoS One 10, e0142533 (2015).
             https://doi.org/10.1371/journal.pone.0142533
         """
+        logger.debug(f"Calculating SIB period threshold: {threshold_degrees} degrees")
         anglez_abs_diff = self._compute_abs_diff_mean_anglez(anglez_data)
 
         anglez_pl_df = pl.DataFrame(
@@ -220,6 +220,11 @@ def _find_onset_wakeup_times(
             If there is no overlap between spt_windows and sib_periods,
             the onset and wakeup lists will be empty.
         """
+        logger.debug(
+            "Searching for SIB periods within SPT windows."
+            f"SPT periods: {len(spt_periods)},"
+            f"SIB periods: {len(sib_periods)}"
+        )
         sleep_windows = []
         for sleep_guide in spt_periods:
             min_onset = None
@@ -235,7 +240,7 @@ def _find_onset_wakeup_times(
                         max_wakeup = inactivity_bout[1]
             if min_onset is not None and max_wakeup is not None:
                 sleep_windows.append(SleepWindow(onset=min_onset, wakeup=max_wakeup))
-
+        logger.debug(f"{sleep_windows} sleep windows found.")
         return sleep_windows
 
     def _fill_false_blocks(
@@ -317,7 +322,7 @@ def _find_periods(
         a period. For isolated ones the function returns the same start
         and end time. The list is sorted by time.
     """
-    logger.debug("Finding periods.")
+    logger.debug("Finding periods in window measurement.")
     edge_detection = np.convolve([1, 3, 1], window_measurement.measurements, "same")
     single_one = np.nonzero(edge_detection == 3)[0]
 
@@ -335,6 +340,7 @@ def _find_periods(
     all_periods = single_periods + block_periods
     all_periods.sort()
 
+    logger.debug(f"Found {len(all_periods)} periods.")
     return all_periods
 
 
@@ -356,6 +362,7 @@ def remove_nonwear_from_sleep(
     Returns:
         A List of the filtered sleep windows.
     """
+    logger.debug(f"Finding non-wear periods within {len(sleep_windows)} sleep windows.")
     nonwear_periods = _find_periods(non_wear_array)
 
     filtered_sleep_windows = []
@@ -376,6 +383,7 @@ def remove_nonwear_from_sleep(
             ):
                 filtered_sleep_windows.append(sleep_window)
 
+    logger.debug(f"Non-wear removed. {len(sleep_windows)} sleep windows remain.")
     return filtered_sleep_windows
 
 
@@ -426,5 +434,4 @@ def compute_physical_activty_categories(
         * 2
         + (enmo_epoch1.measurements > thresholds[2]) * 3
     )
-
     return models.Measurement(measurements=activity_levels, time=enmo_epoch1.time)
diff --git a/src/wristpy/processing/calibration.py b/src/wristpy/processing/calibration.py
index 4a3402a5..0576ac7e 100644
--- a/src/wristpy/processing/calibration.py
+++ b/src/wristpy/processing/calibration.py
@@ -170,6 +170,7 @@ def run(self, acceleration: models.Measurement) -> models.Measurement:
             CalibrationError: If the calibration process fails to get below the
                 `min_calibration_error` threshold.
         """
+        logger.debug("Starting calibration.")
         data_range = cast(datetime, acceleration.time.max()) - cast(
             datetime, acceleration.time.min()
         )
@@ -288,7 +289,7 @@ def _calibrate(self, acceleration: models.Measurement) -> LinearTransformation:
             and temperature: an evaluation on four continents. J Appl Physiol (1985)
             2014 Oct 1;117(7):738-44. doi: 10.1152/japplphysiol.00421.2014.
         """
-        logger.debug("attempting calibration...")
+        logger.debug("attempting to calibrate...")
         no_motion_data = self._extract_no_motion(acceleration=acceleration)
         linear_transformation = self._closest_point_fit(no_motion_data=no_motion_data)
 
@@ -311,7 +312,11 @@ def _calibrate(self, acceleration: models.Measurement) -> LinearTransformation:
                 f"Initial Error: {cal_error_initial}, Final Error: {cal_error_end},"
                 f"Error threshold: {self.min_calibration_error}"
             )
-        logger.debug("Calibration successful, returning scale and offset values.")
+        logger.debug(
+            "Calibration successful.",
+            f"scale: {linear_transformation.scale}.",
+            f"Offset: {linear_transformation.offset}.",
+        )
         return linear_transformation
 
     def _extract_no_motion(self, acceleration: models.Measurement) -> np.ndarray:
@@ -429,9 +434,10 @@ def _closest_point_fit(self, no_motion_data: np.ndarray) -> LinearTransformation
             weights = np.minimum(
                 1 / np.linalg.norm(current - closest_point, axis=1), 100
             )
-            logger.debug(f"scale: {scale}, offset: {offset}")
-            logger.debug(f"residual: {residual}")
+
+            logger.debug(f"scale: {scale}, offset: {offset}, residual: {residual}")
             if abs(residual - previous_residual) < self.error_tolerance:
+                logger.debug("Change in residual below error tolerance, ending loop.}")
                 break
 
             previous_residual = residual

From a18667aa185109fe690e35bd5eca5401007de8d4 Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Tue, 3 Sep 2024 08:54:05 -0400
Subject: [PATCH 11/14] Fixing capitalizations, changed f-strings to arg
 formatting.

---
 src/wristpy/processing/analytics.py   | 27 ++++++++++++++-------------
 src/wristpy/processing/calibration.py | 18 +++++++++---------
 2 files changed, 23 insertions(+), 22 deletions(-)

diff --git a/src/wristpy/processing/analytics.py b/src/wristpy/processing/analytics.py
index a59e341d..aff8bc6a 100644
--- a/src/wristpy/processing/analytics.py
+++ b/src/wristpy/processing/analytics.py
@@ -94,7 +94,7 @@ def run_sleep_detection(self) -> List[SleepWindow]:
             spt_window_periods, sib_window_periods
         )
         logger.debug(
-            f"Sleep detection complete. Windows detected: {len(sleep_onset_wakeup)}"
+            "Sleep detection complete. Windows detected: %s", len(sleep_onset_wakeup)
         )
         return sleep_onset_wakeup
 
@@ -125,7 +125,7 @@ def _spt_window(
               using an accelerometer without sleep diary. Sci Rep 8, 12975 (2018).
               https://doi.org/10.1038/s41598-018-31266-z
         """
-        logger.debug(f"Finding spt windows, Threshold: {threshold}")
+        logger.debug("Finding spt windows, Threshold: %s", threshold)
         long_epoch_median = 300
         long_block = 360
         short_block_gap = 720
@@ -171,7 +171,7 @@ def _calculate_sib_periods(
             Duration Using a Wrist-Worn Accelerometer. PLoS One 10, e0142533 (2015).
             https://doi.org/10.1371/journal.pone.0142533
         """
-        logger.debug(f"Calculating SIB period threshold: {threshold_degrees} degrees")
+        logger.debug("Calculating SIB period threshold: %s degrees", threshold_degrees)
         anglez_abs_diff = self._compute_abs_diff_mean_anglez(anglez_data)
 
         anglez_pl_df = pl.DataFrame(
@@ -221,9 +221,9 @@ def _find_onset_wakeup_times(
             the onset and wakeup lists will be empty.
         """
         logger.debug(
-            "Searching for SIB periods within SPT windows."
-            f"SPT periods: {len(spt_periods)},"
-            f"SIB periods: {len(sib_periods)}"
+            "Finding SIB periods within SPT windows. SPT periods:%s, SIB periods: %s",
+            spt_periods,
+            sib_periods,
         )
         sleep_windows = []
         for sleep_guide in spt_periods:
@@ -240,7 +240,7 @@ def _find_onset_wakeup_times(
                         max_wakeup = inactivity_bout[1]
             if min_onset is not None and max_wakeup is not None:
                 sleep_windows.append(SleepWindow(onset=min_onset, wakeup=max_wakeup))
-        logger.debug(f"{sleep_windows} sleep windows found.")
+        logger.debug("Sleep windows found: %s", len(sleep_windows))
         return sleep_windows
 
     def _fill_false_blocks(
@@ -340,7 +340,7 @@ def _find_periods(
     all_periods = single_periods + block_periods
     all_periods.sort()
 
-    logger.debug(f"Found {len(all_periods)} periods.")
+    logger.debug("Found %s periods.", len(all_periods))
     return all_periods
 
 
@@ -362,7 +362,9 @@ def remove_nonwear_from_sleep(
     Returns:
         A List of the filtered sleep windows.
     """
-    logger.debug(f"Finding non-wear periods within {len(sleep_windows)} sleep windows.")
+    logger.debug(
+        "Finding non-wear periods within %s sleep windows.", len(sleep_windows)
+    )
     nonwear_periods = _find_periods(non_wear_array)
 
     filtered_sleep_windows = []
@@ -383,7 +385,7 @@ def remove_nonwear_from_sleep(
             ):
                 filtered_sleep_windows.append(sleep_window)
 
-    logger.debug(f"Non-wear removed. {len(sleep_windows)} sleep windows remain.")
+    logger.debug("Non-wear removed. %s sleep windows remain.", len(sleep_windows))
     return filtered_sleep_windows
 
 
@@ -415,11 +417,10 @@ def compute_physical_activty_categories(
     Raises:
         ValueError: If the threshold values are not in ascending order.
     """
-    logger.debug(f"Computing physical activity levels, thresholds: {thresholds}")
+    logger.debug("Computing physical activity levels, thresholds: %s", thresholds)
     if list(thresholds) != sorted(thresholds):
-        message = "Thresholds must be in ascending order."
         logger.error("ValueError, thresholds must be in ascending order.")
-        raise ValueError(message)
+        raise ValueError("Thresholds must be in ascending order.")
 
     activity_levels = (
         (
diff --git a/src/wristpy/processing/calibration.py b/src/wristpy/processing/calibration.py
index 0576ac7e..a6ef0f56 100644
--- a/src/wristpy/processing/calibration.py
+++ b/src/wristpy/processing/calibration.py
@@ -217,7 +217,7 @@ def _chunked_calibration(
             CalibrationError: If all possible chunks have been used and the calibration
                 process fails to get below the `min_calibration_error` threshold.
         """
-        logger.debug("running chunked calibration.")
+        logger.debug("Running chunked calibration.")
         for chunk in self._get_chunk(acceleration):
             try:
                 return self._calibrate(chunk)
@@ -289,7 +289,7 @@ def _calibrate(self, acceleration: models.Measurement) -> LinearTransformation:
             and temperature: an evaluation on four continents. J Appl Physiol (1985)
             2014 Oct 1;117(7):738-44. doi: 10.1152/japplphysiol.00421.2014.
         """
-        logger.debug("attempting to calibrate...")
+        logger.debug("Attempting to calibrate...")
         no_motion_data = self._extract_no_motion(acceleration=acceleration)
         linear_transformation = self._closest_point_fit(no_motion_data=no_motion_data)
 
@@ -308,14 +308,14 @@ def _calibrate(self, acceleration: models.Measurement) -> LinearTransformation:
             cal_error_end >= self.min_calibration_error
         ):
             raise CalibrationError(
-                "Calibration error could not be sufficiently minimized."
-                f"Initial Error: {cal_error_initial}, Final Error: {cal_error_end},"
+                "Calibration error could not be sufficiently minimized. "
+                f"Initial Error: {cal_error_initial}, Final Error: {cal_error_end}, "
                 f"Error threshold: {self.min_calibration_error}"
             )
         logger.debug(
-            "Calibration successful.",
-            f"scale: {linear_transformation.scale}.",
-            f"Offset: {linear_transformation.offset}.",
+            "Calibration successful. Scale: %s, Offset: %s",
+            linear_transformation.scale,
+            linear_transformation.offset,
         )
         return linear_transformation
 
@@ -347,7 +347,7 @@ def _extract_no_motion(self, acceleration: models.Measurement) -> np.ndarray:
             and temperature: an evaluation on four continents. J Appl Physiol (1985)
             2014 Oct 1;117(7):738-44. doi: 10.1152/japplphysiol.00421.2014.
         """
-        logger.debug("extracting no motion.")
+        logger.debug("Extracting no motion.")
         moving_sd = computations.moving_std(acceleration, 10)
         moving_mean = computations.moving_mean(acceleration, 10)
         no_motion_check = np.all(
@@ -435,7 +435,7 @@ def _closest_point_fit(self, no_motion_data: np.ndarray) -> LinearTransformation
                 1 / np.linalg.norm(current - closest_point, axis=1), 100
             )
 
-            logger.debug(f"scale: {scale}, offset: {offset}, residual: {residual}")
+            logger.debug("Scale: %s, Offset: %s, Residual: %s", scale, offset, residual)
             if abs(residual - previous_residual) < self.error_tolerance:
                 logger.debug("Change in residual below error tolerance, ending loop.}")
                 break

From 32fbb554672d33f2b222320f754598c184de35c3 Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Tue, 3 Sep 2024 09:01:55 -0400
Subject: [PATCH 12/14] typo

---
 src/wristpy/core/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/wristpy/core/config.py b/src/wristpy/core/config.py
index 40b19787..f338d5f3 100644
--- a/src/wristpy/core/config.py
+++ b/src/wristpy/core/config.py
@@ -12,7 +12,7 @@ class Settings(pydantic_settings.BaseSettings):
     MODERATE_THRESHOLD: float = 0.1
     VIGOROUS_THRESHOLD: float = 0.3
 
-    LOGGING_LEVEL: int = 20
+    LOGGING_LEVEL = logging.INFO
 
 
 def get_logger() -> logging.Logger:

From a8d069bc62f64ed35da74f3978e19cc0ff3abb8c Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Tue, 3 Sep 2024 09:08:38 -0400
Subject: [PATCH 13/14] type annotation

---
 src/wristpy/core/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/wristpy/core/config.py b/src/wristpy/core/config.py
index f338d5f3..aa6a19c7 100644
--- a/src/wristpy/core/config.py
+++ b/src/wristpy/core/config.py
@@ -12,7 +12,7 @@ class Settings(pydantic_settings.BaseSettings):
     MODERATE_THRESHOLD: float = 0.1
     VIGOROUS_THRESHOLD: float = 0.3
 
-    LOGGING_LEVEL = logging.INFO
+    LOGGING_LEVEL: int = logging.INFO
 
 
 def get_logger() -> logging.Logger:

From f3e6c10b3d3439e2bc089f7c1ce3b7f2ef6f45de Mon Sep 17 00:00:00 2001
From: frey-perez <160774979+frey-perez@users.noreply.github.com>
Date: Tue, 3 Sep 2024 10:42:02 -0400
Subject: [PATCH 14/14] doc string edit.

---
 src/wristpy/processing/analytics.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/wristpy/processing/analytics.py b/src/wristpy/processing/analytics.py
index aff8bc6a..90858d21 100644
--- a/src/wristpy/processing/analytics.py
+++ b/src/wristpy/processing/analytics.py
@@ -363,7 +363,8 @@ def remove_nonwear_from_sleep(
         A List of the filtered sleep windows.
     """
     logger.debug(
-        "Finding non-wear periods within %s sleep windows.", len(sleep_windows)
+        "Finding non-wear periods that overlap with any of the %s sleep windows.",
+        len(sleep_windows),
     )
     nonwear_periods = _find_periods(non_wear_array)