From 4f7d88cb62449c38da0cb96c9a8106f8614cf552 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Tue, 16 May 2023 12:21:03 +0200
Subject: [PATCH 01/17] docs: modify rtd configuration

Refs: ST-2, ST-122
---
 readthedocs.yml => .readthedocs.yaml | 11 ++++++++++-
 docs/source/conf.py                  |  2 +-
 pyproject.toml                       |  2 +-
 3 files changed, 12 insertions(+), 3 deletions(-)
 rename readthedocs.yml => .readthedocs.yaml (60%)

diff --git a/readthedocs.yml b/.readthedocs.yaml
similarity index 60%
rename from readthedocs.yml
rename to .readthedocs.yaml
index 5ec698c..9c3a5ef 100644
--- a/readthedocs.yml
+++ b/.readthedocs.yaml
@@ -3,13 +3,22 @@ version: 2
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "3.11"
+    python: "3.8"
 
 # Build from the docs/ directory with Sphinx
 sphinx:
+  builder: html
   configuration: docs/source/conf.py
 
 # Explicitly set the version of Python and its requirements
 python:
   install:
     - requirements: dev-requirements.txt
+    - method: pip
+      path: src/scintillometry
+      extra_requirements:
+        - dev
+
+submodules:
+  include: all
+  recursive: true
diff --git a/docs/source/conf.py b/docs/source/conf.py
index d36b443..2b35451 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -49,7 +49,7 @@ def setup(app):
 project = "Scintillometry"
 copyright = f"2019-{date.today().year}, Scintillometry Contributors"
 author = "Scintillometry Contributors"
-release = "1.0.0"
+release = "1.0.2"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
diff --git a/pyproject.toml b/pyproject.toml
index fd435ec..76a4ea8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "scintillometry"
-version = "1.0.0"
+version = "1.0.2"
 authors = [
   { name="Scintillometry Contributors", email="" },
 ]

From c32a030df520a1c82d4154870ad4c18bde9dfd70 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Tue, 16 May 2023 12:25:29 +0200
Subject: [PATCH 02/17] docs: fix rtd configuration

Corrects package installation path.

Refs: ST-2, ST-122
---
 .readthedocs.yaml   | 3 +--
 docs/source/conf.py | 2 +-
 pyproject.toml      | 2 +-
 3 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 9c3a5ef..59ef9f6 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -15,10 +15,9 @@ python:
   install:
     - requirements: dev-requirements.txt
     - method: pip
-      path: src/scintillometry
+      path: .
       extra_requirements:
         - dev
-
 submodules:
   include: all
   recursive: true
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 2b35451..ec6105d 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -49,7 +49,7 @@ def setup(app):
 project = "Scintillometry"
 copyright = f"2019-{date.today().year}, Scintillometry Contributors"
 author = "Scintillometry Contributors"
-release = "1.0.2"
+release = "1.0.3"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
diff --git a/pyproject.toml b/pyproject.toml
index 76a4ea8..16219f1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "scintillometry"
-version = "1.0.2"
+version = "1.0.3"
 authors = [
   { name="Scintillometry Contributors", email="" },
 ]

From 5bc2beba488b68409a0af52533e1dabe99dd7763 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Tue, 16 May 2023 14:14:19 +0200
Subject: [PATCH 03/17] fix: main interface references incorrect arguments

Refs: ST-26, ST-123
---
 docs/source/conf.py                        | 7 ++++---
 pyproject.toml                             | 2 +-
 src/scintillometry/main.py                 | 4 ++--
 src/scintillometry/wrangler/data_parser.py | 2 +-
 4 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index ec6105d..7fabb0b 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -1,4 +1,4 @@
-"""Copyright 2023 Scintillometry-Tools Contributors.
+"""Copyright 2023 Scintillometry Contributors.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -16,7 +16,8 @@
 
 Configuration file for the Sphinx documentation builder.
 
-For the full list of built-in configuration values, see the documentation:
+For the full list of built-in configuration values, see the
+documentation:
 https://www.sphinx-doc.org/en/master/usage/configuration.html
 """
 
@@ -49,7 +50,7 @@ def setup(app):
 project = "Scintillometry"
 copyright = f"2019-{date.today().year}, Scintillometry Contributors"
 author = "Scintillometry Contributors"
-release = "1.0.3"
+release = "1.0.4"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
diff --git a/pyproject.toml b/pyproject.toml
index 16219f1..b55a2c0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "scintillometry"
-version = "1.0.3"
+version = "1.0.4"
 authors = [
   { name="Scintillometry Contributors", email="" },
 ]
diff --git a/src/scintillometry/main.py b/src/scintillometry/main.py
index b2cf757..2ae1058 100644
--- a/src/scintillometry/main.py
+++ b/src/scintillometry/main.py
@@ -301,13 +301,13 @@ def perform_data_parsing(**kwargs):
     data_parser = DataParser.WranglerParsing()
 
     # Parse BLS, weather, and topographical data
-    datasets = data_parser.stitch.wrangle_data(
+    datasets = data_parser.wrangle_data(
         bls_path=kwargs["input"],
         transect_path=kwargs["transect_path"],
         calibrate=kwargs["calibration"],
         station_id=kwargs["station_id"],
         tzone=kwargs["timezone"],
-        source="zamg",
+        weather_source="zamg",
     )
 
     # Parse vertical measurements
diff --git a/src/scintillometry/wrangler/data_parser.py b/src/scintillometry/wrangler/data_parser.py
index c729c64..6dccdf3 100644
--- a/src/scintillometry/wrangler/data_parser.py
+++ b/src/scintillometry/wrangler/data_parser.py
@@ -1009,7 +1009,7 @@ def wrangle_data(
         weather_data = self.weather.parse_weather(
             timestamp=bls_time,
             source=weather_source,
-            klima_id=station_id,
+            station_id=station_id,
             data_dir=weather_dir,
             timezone=tzone,
         )

From 083a52e0c97c3d71b1643489a12ada8cf99becc6 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Tue, 23 May 2023 17:10:50 +0200
Subject: [PATCH 04/17] feat(metrics): perform regression on datasets

Adds method to MetricsFlux to perform regression on labelled data.

Refs: ST-7, ST-106
---
 docs/source/conf.py                        |  3 +-
 pyproject.toml                             |  2 +-
 src/scintillometry/metrics/calculations.py | 38 +++++++++++++++++++-
 tests/test_metrics_calculations.py         | 40 ++++++++++++++++++++++
 4 files changed, 80 insertions(+), 3 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 7fabb0b..d142dce 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -50,7 +50,7 @@ def setup(app):
 project = "Scintillometry"
 copyright = f"2019-{date.today().year}, Scintillometry Contributors"
 author = "Scintillometry Contributors"
-release = "1.0.4"
+release = "1.0.5"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -124,6 +124,7 @@ def setup(app):
 .. |Psi_m| replace:: :math:`\\Psi_{{m}}`
 .. |Q_0| replace:: :math:`Q_{{0}}`
 .. |r| replace:: :math:`r`
+.. |R^2| replace:: math:`R^{{2}}`
 .. |R_dry| replace:: :math:`R_{{dry}}`
 .. |R_v| replace:: :math:`R_{{v}}`
 .. |rho| replace:: :math:`\\rho`
diff --git a/pyproject.toml b/pyproject.toml
index b55a2c0..17aba01 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "scintillometry"
-version = "1.0.4"
+version = "1.0.5"
 authors = [
   { name="Scintillometry Contributors", email="" },
 ]
diff --git a/src/scintillometry/metrics/calculations.py b/src/scintillometry/metrics/calculations.py
index 4ff9ea3..34009fd 100755
--- a/src/scintillometry/metrics/calculations.py
+++ b/src/scintillometry/metrics/calculations.py
@@ -19,11 +19,12 @@
 
 import kneed
 import pandas as pd
+from sklearn.linear_model import LinearRegression
 
-from scintillometry.backend.iterations import IterationMost
 from scintillometry.backend.constants import AtmosConstants
 from scintillometry.backend.constructions import ProfileConstructor
 from scintillometry.backend.derivations import DeriveScintillometer
+from scintillometry.backend.iterations import IterationMost
 from scintillometry.backend.transects import TransectParameters
 from scintillometry.visuals.plotting import FigurePlotter
 
@@ -216,6 +217,41 @@ def match_time_at_threshold(self, series, threshold, lessthan=True, min_time=Non
 
         return match_time
 
+    def get_regression(self, x_data, y_data, intercept=True):
+        """Performs regression on labelled data.
+
+        Args:
+            x_data (pd.Series): Labelled explanatory data.
+            y_data (pd.Series): Labelled response data.
+            intercept (bool): If True, calculate intercept (e.g. data is
+            not centred). Default True.
+
+        Returns:
+            dict: Contains the fitted estimator for regression data, the
+            coefficient of determination |R^2|, and predicted values for
+            a fitted regression line.
+        """
+
+        scatter_frame = pd.merge(
+            x_data, y_data, left_index=True, right_index=True, sort=True
+        )
+        scatter_frame = scatter_frame.dropna(axis=0)
+        x_fit_data = scatter_frame.iloc[:, 0].values.reshape(-1, 1)
+        y_fit_data = scatter_frame.iloc[:, 1].values.reshape(-1, 1)
+
+        linear_regressor = LinearRegression(fit_intercept=intercept)
+        estimator = linear_regressor.fit(x_fit_data, y_fit_data)
+        score = estimator.score(x_fit_data, y_fit_data)
+        predictions = linear_regressor.predict(x_fit_data)
+
+        regression = {
+            "fit": estimator,
+            "score": score,
+            "regression_line": predictions,
+        }
+
+        return regression
+
     def get_elbow_point(self, series, min_index=None, max_index=None):
         """Calculate elbow point using Kneedle algorithm.
 
diff --git a/tests/test_metrics_calculations.py b/tests/test_metrics_calculations.py
index 1a0559d..23e10aa 100644
--- a/tests/test_metrics_calculations.py
+++ b/tests/test_metrics_calculations.py
@@ -54,6 +54,7 @@ def test_foobar(self, foo_mock, bar_mock):
 import pandas as pd
 import pandas.api.types as ptypes
 import pytest
+import sklearn
 
 import scintillometry.backend.constants
 import scintillometry.backend.constructions
@@ -300,6 +301,45 @@ def test_match_time_at_threshold(
         else:
             assert compare_time is None
 
+    @pytest.mark.dependency(name="TestMetricsFlux::test_get_regression")
+    @pytest.mark.parametrize("arg_intercept", [True, False])
+    @pytest.mark.parametrize("arg_mismatch_index", [True, False])
+    def test_get_regression(
+        self, conftest_boilerplate, arg_intercept, arg_mismatch_index
+    ):
+        """Perform regression on labelled data."""
+
+        rng = np.random.default_rng()
+        test_index = np.arange(0, 1000, 10)
+        test_data = rng.random(size=len(test_index))
+
+        test_x = pd.Series(name="obukhov", data=test_data, index=test_index)
+        test_y = pd.Series(name="other_obukhov", data=test_data + 0.5, index=test_index)
+        if arg_mismatch_index:
+            test_y = test_y[:-5]
+            conftest_boilerplate.index_not_equal(test_x.index, test_y.index)
+
+        assert isinstance(test_x, pd.Series)
+        assert test_x.shape == (100,)
+        test_keys = ["fit", "score", "regression_line"]
+
+        compare_regression = self.test_metrics.get_regression(
+            x_data=test_x, y_data=test_y, intercept=arg_intercept
+        )
+        assert isinstance(compare_regression, dict)
+        assert all(key in compare_regression for key in test_keys)
+        assert isinstance(
+            compare_regression["fit"], sklearn.linear_model.LinearRegression
+        )
+        if not arg_intercept:
+            assert not compare_regression["fit"].fit_intercept
+        else:
+            assert compare_regression["fit"].fit_intercept
+        assert isinstance(compare_regression["score"], float)
+        assert isinstance(compare_regression["regression_line"], np.ndarray)
+        assert not (np.isnan(compare_regression["regression_line"])).any()
+        assert len(test_y.index) == len(compare_regression["regression_line"])
+
     @pytest.mark.dependency(name="TestMetricsFlux::test_get_elbow_point")
     @pytest.mark.parametrize("arg_min_index", [None, 0, 50])
     @pytest.mark.parametrize("arg_max_index", [None, 180, 190])

From 743b8a15b9b2304571c811a0b2ab200109685582 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Tue, 23 May 2023 17:16:06 +0200
Subject: [PATCH 05/17] tests(metrics): generate datetime index for series

Refs: ST-3, ST-7, ST-106
---
 tests/test_metrics_calculations.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_metrics_calculations.py b/tests/test_metrics_calculations.py
index 23e10aa..1d6ef40 100644
--- a/tests/test_metrics_calculations.py
+++ b/tests/test_metrics_calculations.py
@@ -310,7 +310,7 @@ def test_get_regression(
         """Perform regression on labelled data."""
 
         rng = np.random.default_rng()
-        test_index = np.arange(0, 1000, 10)
+        test_index = pd.date_range(start=self.test_timestamp, periods=100, freq="T")
         test_data = rng.random(size=len(test_index))
 
         test_x = pd.Series(name="obukhov", data=test_data, index=test_index)
@@ -318,7 +318,7 @@ def test_get_regression(
         if arg_mismatch_index:
             test_y = test_y[:-5]
             conftest_boilerplate.index_not_equal(test_x.index, test_y.index)
-
+            assert test_y.shape == (95,)
         assert isinstance(test_x, pd.Series)
         assert test_x.shape == (100,)
         test_keys = ["fit", "score", "regression_line"]

From 6bd371bcb3ac345b63a5bae1b3c8e18b1d9e1619 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Tue, 23 May 2023 18:21:27 +0200
Subject: [PATCH 06/17] feat(visuals): plot scatter with optional regression
 line

Creates scatter plot with optional regression line and optional
annotation for the coefficient of determination.

Refs: ST-3, ST-8, ST-106
---
 src/scintillometry/visuals/plotting.py | 72 ++++++++++++++++++++++++--
 tests/test_visuals_plotting.py         | 62 ++++++++++++++++++++++
 2 files changed, 130 insertions(+), 4 deletions(-)

diff --git a/src/scintillometry/visuals/plotting.py b/src/scintillometry/visuals/plotting.py
index 9b26d9e..bc7e417 100644
--- a/src/scintillometry/visuals/plotting.py
+++ b/src/scintillometry/visuals/plotting.py
@@ -24,6 +24,7 @@
 import matplotlib
 import matplotlib.pyplot as plt
 import numpy as np
+import pandas as pd
 
 
 class FigureFormat:
@@ -91,8 +92,8 @@ def get_site_name(self, site_name, dataframe=None):
 
         Args:
             site_name (str): Location of data collection.
-            dataframe (pd.DataFrame): Any collected dataset. Default
-                None.
+            dataframe (pd.DataFrame or pd.Series): Any collected
+                dataset. Default None.
 
         Returns:
             str: Location of data collection. Returns empty string if no
@@ -193,7 +194,8 @@ def get_date_and_timezone(self, data):
         """Return first time index and timezone.
 
         Args:
-            data (pd.DataFrame): TZ-aware dataframe with DatetimeIndex.
+            data (pd.DataFrame or pd.Series): TZ-aware dataframe with
+                DatetimeIndex.
 
         Returns:
             dict[str, datetime.tzinfo]: Date formatted as
@@ -227,7 +229,7 @@ def title_plot(self, title, timestamp, location=""):
         if not isinstance(timestamp, str):
             timestamp = timestamp.strftime("%d %B %Y")
 
-        title_string = "".join((f"{title}{location},\n{timestamp}"))
+        title_string = f"{title}{location},\n{timestamp}"
         plt.title(title_string, fontweight="bold")
         plt.legend(loc="upper left")
 
@@ -654,6 +656,68 @@ def plot_innflux(self, iter_data, innflux_data, name="obukhov", site=""):
 
         return figure, axes
 
+    def plot_scatter(
+        self, x_data, y_data, name, sources, score=None, regression_line=None, site=""
+    ):
+        """Plots scatter between two datasets with a regression line.
+
+        Args:
+            x_data (pd.Series): Labelled explanatory data.
+            y_data (pd.Series): Labelled response data.
+            name (str): Name of variable.
+            sources (list[str, str]): Names of data sources formatted
+                as: [<Explanatory Source>, <Response Source>].
+            score (float): Coefficient of determination |R^2|.
+                Default None.
+            regression_line (np.ndarray): Values for regression line.
+                Default None.
+            site (str): Location of data collection. Default empty
+                string.
+
+        Returns:
+            tuple[plt.Figure, plt.Axes]: Regression plot of explanatory
+            and response data, with fitted regression line and
+            regression score.
+        """
+
+        figure = plt.figure(figsize=(8, 8))
+        date = self.get_date_and_timezone(data=x_data)["date"]
+        scatter_frame = pd.merge(
+            x_data, y_data, left_index=True, right_index=True, sort=True
+        )
+
+        scatter_frame = scatter_frame.dropna(axis=0)  # drop mismatched index
+        x_fit_data = scatter_frame.iloc[:, 0].values.reshape(-1, 1)
+        y_fit_data = scatter_frame.iloc[:, 1].values.reshape(-1, 1)
+        plt.scatter(x_fit_data, y_fit_data, marker=".", color="gray")
+
+        if regression_line is not None:
+            plt.plot(
+                x_fit_data, regression_line, color="black", label="Line of Best Fit"
+            )
+
+        axes = plt.gca()
+        if score is not None:
+            plt.text(
+                0.05,
+                0.9,
+                f"R$^{2}$= {score:.5f}",
+                horizontalalignment="left",
+                verticalalignment="bottom",
+                transform=axes.transAxes,
+            )
+        variable_name = self.label_selector(name)
+        sources_string = f"{sources[0].title()} and {sources[1].title()}"
+        title_string = f"{variable_name[0]} Regression Between\n{sources_string}"
+        site_label = self.get_site_name(site_name=site, dataframe=x_data)
+        self.title_plot(title=title_string, timestamp=date, location=site_label)
+        x_label = self.merge_label_with_unit(label=variable_name)
+        y_label = self.merge_label_with_unit(label=variable_name)
+        plt.xlabel(f"{sources[0].title()} {x_label}")
+        plt.ylabel(f"{sources[1].title()} {y_label}")
+
+        return figure, axes
+
     def plot_vertical_profile(
         self, vertical_data, time_idx, name, site="", y_lim=None, **kwargs
     ):
diff --git a/tests/test_visuals_plotting.py b/tests/test_visuals_plotting.py
index 6616ad4..d1039c5 100644
--- a/tests/test_visuals_plotting.py
+++ b/tests/test_visuals_plotting.py
@@ -683,6 +683,68 @@ def test_plot_innflux(
 
         plt.close("all")
 
+    @pytest.mark.dependency(name="TestVisualsPlotting::test_plot_scatter")
+    @pytest.mark.parametrize("arg_site", ["", "Test Location", None])
+    @pytest.mark.parametrize("arg_score", [None, 0.561734521])
+    @pytest.mark.parametrize("arg_regression", [True, False])
+    def test_plot_scatter(
+        self, conftest_boilerplate, arg_score, arg_site, arg_regression
+    ):
+        """Plot scatter between two datasets with regression line."""
+
+        test_name = "obukhov"
+        rng = np.random.default_rng()
+        test_index = pd.date_range(start=self.test_timestamp, periods=100, freq="T")
+        test_data = rng.random(size=len(test_index))
+        test_x = pd.Series(name=test_name, data=test_data, index=test_index)
+        test_y = pd.Series(name=test_name, data=test_data + 0.5, index=test_index)
+        for series in [test_x, test_y]:
+            assert isinstance(series, pd.Series)
+            assert series.shape == (100,)
+            assert not (series.isnull()).any()
+        if arg_site:
+            test_site = f" at {arg_site},"
+        else:
+            test_site = ","
+        test_title = (
+            "Obukhov Length Regression Between",
+            f"Baseline and Comparison{test_site}",
+            f"{self.test_date}",
+        )
+        if not arg_regression:
+            test_line = None
+        else:
+            test_line = np.arange(0, 1000, 10)
+
+        compare_fig, compare_ax = self.test_plotting.plot_scatter(
+            x_data=test_x,
+            y_data=test_y,
+            name=test_name,
+            sources=["Baseline", "Comparison"],
+            site=arg_site,
+            score=arg_score,
+            regression_line=test_line,
+        )
+        compare_params = {
+            "plot": (compare_fig, compare_ax),
+            "x_label": "Baseline Obukhov Length, [m]",
+            "y_label": "Comparison Obukhov Length, [m]",
+            "title": "\n".join(test_title),
+        }
+        conftest_boilerplate.check_plot(plot_params=compare_params)
+
+        if arg_regression:
+            _, labels = compare_params["plot"][1].get_legend_handles_labels()
+            assert "Line of Best Fit" in labels
+
+        if arg_score is not None:
+            assert (
+                compare_params["plot"][1].texts[0].get_text()
+                == f"R$^{2}$= {arg_score:.5f}"
+            )
+
+        plt.close("all")
+
     @pytest.mark.dependency(
         name="TestVisualsPlotting::test_plot_vertical_profile",
         depends=["TestVisualsFormatting::test_plot_constant_lines"],

From c5b47467a5464b695407b8defffec38d66f527f8 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Wed, 24 May 2023 15:55:56 +0200
Subject: [PATCH 07/17] refactor!: plots from metrics calculations are paired
 into lists

Matplotlib plots generated by methods in metrics_calculations are now
structured as list[tuple[plt.Figure, plt.Axes]] instead of stacked
into a single tuple.

Refs: ST-3, ST-7, ST-8, ST-124, ST-126
---
 src/scintillometry/metrics/calculations.py |  79 ++++++++--------
 src/scintillometry/visuals/plotting.py     |  44 +++++----
 tests/conftest.py                          |  17 +++-
 tests/test_metrics_calculations.py         | 105 ++++++++++++---------
 tests/test_visuals_plotting.py             |  20 ++--
 5 files changed, 150 insertions(+), 115 deletions(-)

diff --git a/src/scintillometry/metrics/calculations.py b/src/scintillometry/metrics/calculations.py
index 34009fd..3225a92 100755
--- a/src/scintillometry/metrics/calculations.py
+++ b/src/scintillometry/metrics/calculations.py
@@ -397,11 +397,11 @@ def plot_lapse_rates(
                 string.
 
         Returns:
-            tuple[plt.Figure, plt.Axes, plt.Figure, plt.Axes]: Vertical
-            profiles of lapse rates on a single axis, and vertical
-            profiles of parcel temperatures on a single axis. If a
-            boundary layer height is provided, vertical lines denoting
-            its height are added to the figures.
+            list[tuple[plt.Figure, plt.Axes]]: Vertical profiles of
+            lapse rates on a single axis, and vertical profiles of
+            parcel temperatures on a single axis. If a boundary layer
+            height is provided, vertical lines denoting its height are
+            added to the figures.
         """
 
         lapse_rates = {
@@ -448,7 +448,7 @@ def plot_lapse_rates(
             suffix=f"{round_time.strftime('%H%M')}_parcel_temperatures",
         )
 
-        return fig_lapse, axes_lapse, fig_parcel, axes_parcel
+        return [(fig_lapse, axes_lapse), (fig_parcel, axes_parcel)]
 
     def get_switch_time_vertical(self, data, method="static", ri_crit=0.25):
         """Gets local time of switch between stability conditions.
@@ -617,10 +617,10 @@ def plot_switch_time_stability(self, data, local_time, location="", bl_height=No
             bl_height (int): Boundary layer height. Default None.
 
         Returns:
-            tuple[plt.Figure, plt.Axes]: Vertical profile of potential
-            temperature. If the gradient potential temperature is also
-            provided, the two vertical profiles are placed side-by-side
-            in separate subplots.
+            list[tuple[plt.Figure, plt.Axes]]: Vertical profile of
+            potential temperature. If the gradient potential temperature
+            is also provided, the two vertical profiles are placed
+            side-by-side in separate subplots.
         """
 
         round_time = self.get_nearest_time_index(
@@ -670,7 +670,7 @@ def plot_switch_time_stability(self, data, local_time, location="", bl_height=No
                 suffix=f"{mil_time}_gradient_potential_temperature_2km",
             )
 
-        return fig, ax
+        return [(fig, ax)]
 
     def calculate_switch_time(
         self, datasets, method="sun", switch_time=None, location=""
@@ -739,9 +739,9 @@ def iterate_fluxes(
         Trades speed from vectorisation for more accurate convergence.
 
         Args:
-            z_parameters (dict[float, float]): Tuples of effective and
-                mean path height |z_eff| and |z_mean| [m], with
-                stability conditions as keys.
+            z_parameters (dict[str, tuple[float, float]): Tuples of
+                effective and mean path height |z_eff| and |z_mean| [m],
+                with stability conditions as keys.
             datasets (dict): Contains parsed, tz-aware dataframes, with
                 at least |CT2|, wind speed, air density, and
                 temperature.
@@ -809,8 +809,9 @@ def plot_derived_metrics(self, derived_data, time_id, regime=None, location=""):
             string.
 
         Returns:
-            tuple[plt.Figure, plt.Axes]: Time series comparing sensible
-            heat fluxes under free convection to on-board software.
+            list[tuple[plt.Figure, plt.Axes]]: Time series comparing
+            sensible heat fluxes under free convection to on-board
+            software.
         """
 
         fig_convection, ax_convection = self.plotting.plot_convection(
@@ -819,25 +820,24 @@ def plot_derived_metrics(self, derived_data, time_id, regime=None, location=""):
         self.plotting.save_figure(
             figure=fig_convection, timestamp=time_id, suffix="free_convection"
         )
+        derived_plots = [(fig_convection, ax_convection)]
 
-        return fig_convection, ax_convection
+        return derived_plots
 
     def plot_iterated_metrics(self, iterated_data, time_stamp, site_location=""):
         """Plot and save time series and comparison of iterated fluxes.
 
         Args:
-            user_args (argparse.Namespace): Namespace of user arguments.
-            derived_data (pd.DataFrame): Interpolated tz-aware dataframe
-                with columns for sensible heat fluxes calculated with
-                MOST and for free convection.
-            time_id (pd.Timestamp): Start time of scintillometer data
+            iterated_data (pd.DataFrame): TZ-aware dataframe with
+                columns for heat fluxes and MOST parameters.
+            time_stamp (pd.Timestamp): Start time of scintillometer data
                 collection.
             site_location (str): Name of scintillometer location.
 
         Returns:
-            tuple[plt.Figure, plt.Axes, plt.Figure, plt.Axes]: Time
-            series of sensible heat flux calculated through MOST, and a
-            comparison to sensible heat flux under free convection.
+            list[tuple[plt.Figure, plt.Axes]]: Time series of sensible
+            heat flux calculated through MOST, and a comparison to
+            sensible heat flux under free convection.
         """
 
         plots = self.plotting.plot_iterated_fluxes(
@@ -872,7 +872,7 @@ def calculate_standard_metrics(
         - Calculates effective path heights for all stability
           conditions.
         - Derives |CT2| and sensible heat flux for free convection.
-        - Estimates the time where stability conditions change.
+        - Estimates the time when stability conditions change.
         - Calculates sensible heat flux using MOST.
         - Plots time series comparing sensible heat flux for free
           convection |H_free| to on-board software, time series of
@@ -965,7 +965,7 @@ def calculate_standard_metrics(
         return data
 
     def compare_innflux(self, own_data, innflux_data, location=""):
-        """Compares SHF and Obukhov lengths to InnFLUX measurements.
+        """Compares SHF and Obukhov lengths to innFLUX measurements.
 
         This wrapper function:
 
@@ -977,7 +977,6 @@ def compare_innflux(self, own_data, innflux_data, location=""):
         with an argparse.Namespace object.
 
         Args:
-            arguments (argparse.Namespace): User arguments.
             own_data (pd.DataFrame): Labelled data for SHF and Obukhov
                 length.
             innflux_data (pd.DataFrame): Eddy covariance data from
@@ -986,9 +985,9 @@ def compare_innflux(self, own_data, innflux_data, location=""):
                 string.
 
         Returns:
-            tuple[plt.Figure, plt.Axes, plt.Figure, plt.Axes]: Time
-            series comparing Obukhov length and sensible heat flux to
-            innFlux measurements.
+            list[tuple[plt.Figure, plt.Axes]]: Time series comparing
+            Obukhov length and sensible heat flux to innFLUX
+            measurements.
         """
 
         data_timestamp = own_data.index[0]
@@ -1011,7 +1010,9 @@ def compare_innflux(self, own_data, innflux_data, location=""):
             figure=fig_shf, timestamp=data_timestamp, suffix="innflux_shf"
         )
 
-        return fig_obukhov, ax_obukhov, fig_shf, ax_shf
+        plots = [(fig_obukhov, ax_obukhov), (fig_shf, ax_shf)]
+
+        return plots
 
     def compare_eddy(self, own_data, ext_data, source="innflux", location=""):
         """Compares data to an external source of eddy covariance data.
@@ -1024,17 +1025,19 @@ def compare_eddy(self, own_data, ext_data, source="innflux", location=""):
         with an argparse.Namespace object.
 
         Args:
-            arguments (argparse.Namespace): User arguments.
             own_data (pd.DataFrame): Labelled data.
             ext_data (pd.DataFrame): Eddy covariance data from an
                 external source.
+            source (str): Data source of vertical measurements.
+                Currently supports processed innFLUX data.
+                Default "innflux".
             location (str): Location of data collection. Default empty
                 string.
 
         Returns:
-            tuple[plt.Figure, plt.Axes, plt.Figure, plt.Axes]: Time
-            series comparing Obukhov length and sensible heat flux to
-            innFlux measurements.
+            list[tuple[plt.Figure, plt.Axes]]: Time series comparing
+            Obukhov length and sensible heat flux to innFLUX
+            measurements.
 
         Raises:
             NotImplementedError: <source> measurements are not
@@ -1043,7 +1046,7 @@ def compare_eddy(self, own_data, ext_data, source="innflux", location=""):
         """
 
         if source.lower() == "innflux":
-            fig_obukhov, ax_obukhov, fig_shf, ax_shf = self.compare_innflux(
+            eddy_plots = self.compare_innflux(
                 own_data=own_data, innflux_data=ext_data, location=location
             )
         else:
@@ -1052,4 +1055,4 @@ def compare_eddy(self, own_data, ext_data, source="innflux", location=""):
             )
             raise NotImplementedError(error_msg)
 
-        return fig_obukhov, ax_obukhov, fig_shf, ax_shf
+        return eddy_plots
diff --git a/src/scintillometry/visuals/plotting.py b/src/scintillometry/visuals/plotting.py
index bc7e417..e051adc 100644
--- a/src/scintillometry/visuals/plotting.py
+++ b/src/scintillometry/visuals/plotting.py
@@ -594,7 +594,8 @@ def plot_iterated_fluxes(self, iteration_data, time_id, location=""):
                 string.
 
         Returns:
-            tuple[plt.Figure, plt.Figure]: Time series and comparison.
+            list[tuple[plt.Figure, plt.Axes]]: Time series and
+            comparison.
         """
 
         fig_shf, ax_shf = self.plot_generic(iteration_data, "shf", site=location)
@@ -611,7 +612,7 @@ def plot_iterated_fluxes(self, iteration_data, time_id, location=""):
         fig_comp = plt.gcf()
         self.save_figure(figure=fig_comp, timestamp=time_id, suffix="shf_comp")
 
-        return fig_shf, ax_shf, fig_comp, ax_comp
+        return [(fig_shf, ax_shf), (fig_comp, ax_comp)]
 
     def plot_innflux(self, iter_data, innflux_data, name="obukhov", site=""):
         """Plots comparison between scintillometer and InnFLUX data.
@@ -724,13 +725,14 @@ def plot_vertical_profile(
         """Plots vertical profile of variable.
 
         Args:
-            vertical_data (dict[pd.DataFrame]): Contains time series of
-                vertical profiles.
+            vertical_data (dict[str, pd.DataFrame]): Contains time
+                series of vertical measurements.
             time_idx (pd.Timestamp): The local time for which to plot a
                 vertical profile.
             name (str): Name of dependent variable, must be key in
                 <vertical_data>.
-            site (str): Location of data collection. Default empty string.
+            site (str): Location of data collection. Default empty
+                string.
             y_lim (float): Y-axis limit. Default None.
 
         Keyword Args:
@@ -782,8 +784,8 @@ def plot_vertical_profile(
             location = ",\n"
         else:
             location = f"\nat {site_label}, "
-        time_idx = time_idx.strftime("%H:%M")
-        time_label = f"{time_data['date']} {time_idx} {time_data['tzone']}"
+        time_string = time_idx.strftime("%H:%M")
+        time_label = f"{time_data['date']} {time_string} {time_data['tzone']}"
         title_string = f"{title}{location}{time_label}"
         plt.title(title_string, fontweight="bold")
         axes = plt.gca()
@@ -813,16 +815,13 @@ def plot_vertical_comparison(self, dataset, time_index, keys, site="", **kwargs)
             profiles.
         """
 
-        key_number = len(keys)
+        key_length = len(keys)
         figure, axes = plt.subplots(
-            nrows=1, ncols=key_number, sharey=False, figsize=(4 * key_number, 8)
+            nrows=1, ncols=key_length, sharey=False, figsize=(4 * key_length, 8)
         )
         subplot_labels = []
-        for i in range(key_number):
+        for i in range(key_length):
             vertical_profile = dataset[keys[i]].loc[[time_index]]
-            time_data = self.get_date_and_timezone(
-                data=dataset[keys[i]].loc[[time_index]]
-            )
             axes[i].plot(
                 vertical_profile.values[0],
                 vertical_profile.columns,
@@ -837,7 +836,6 @@ def plot_vertical_comparison(self, dataset, time_index, keys, site="", **kwargs)
 
             if kwargs:
                 self.parse_formatting_kwargs(axis=axes[i], **kwargs)
-
         axes[0].set_ylabel("Height [m]")
 
         title_name = self.merge_multiple_labels(labels=subplot_labels)
@@ -847,8 +845,9 @@ def plot_vertical_comparison(self, dataset, time_index, keys, site="", **kwargs)
             location = ",\n"
         else:
             location = f"\nat {site_label}, "
-        time_index = time_index.strftime("%H:%M")
-        time_label = f"{time_data['date']} {time_index} {time_data['tzone']}"
+        time_data = self.get_date_and_timezone(data=dataset[keys[-1]].loc[[time_index]])
+        time_string = time_index.strftime("%H:%M")
+        time_label = f"{time_data['date']} {time_string} {time_data['tzone']}"
         title_string = f"{title}{location}{time_label}"
         figure.suptitle(title_string, fontweight="bold")
 
@@ -879,15 +878,12 @@ def plot_merged_profiles(self, dataset, time_index, site="", y_lim=None, **kwarg
         """
 
         keys = list(dataset)
-        key_number = len(keys)
+        key_length = len(keys)
         figure = plt.figure(figsize=(8, 8))
         subplot_labels = []
         xlims = []
-        for i in range(key_number):
+        for i in range(key_length):
             vertical_profile = dataset[keys[i]].loc[[time_index]]
-            time_data = self.get_date_and_timezone(
-                data=dataset[keys[i]].loc[[time_index]]
-            )
             line_label = self.label_selector(dependent=keys[i])
             plt.plot(
                 vertical_profile.values[0],
@@ -903,6 +899,7 @@ def plot_merged_profiles(self, dataset, time_index, site="", y_lim=None, **kwarg
                 if xlim_max > 1:
                     xlim_min = math.floor(min(vertical_profile[heights].values[0]))
                     xlims.append(xlim_min)
+        line_label = self.label_selector(dependent=keys[-1])
         x_label = self.merge_label_with_unit(label=line_label)
         plt.xlabel(x_label)
         plt.ylabel("Height [m]")
@@ -920,8 +917,9 @@ def plot_merged_profiles(self, dataset, time_index, site="", y_lim=None, **kwarg
             location = ",\n"
         else:
             location = f"\nat {site_label}, "
-        time_index = time_index.strftime("%H:%M")
-        time_label = f"{time_data['date']} {time_index} {time_data['tzone']}"
+        time_data = self.get_date_and_timezone(data=dataset[keys[-1]].loc[[time_index]])
+        time_string = time_index.strftime("%H:%M")
+        time_label = f"{time_data['date']} {time_string} {time_data['tzone']}"
         title_name = self.merge_multiple_labels(labels=subplot_labels)
         title = f"Vertical Profiles of {title_name}"
         title_string = f"{title}{location}{time_label}"
diff --git a/tests/conftest.py b/tests/conftest.py
index 1c4708c..b7467ce 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -227,7 +227,7 @@ def test_check_timezone(self):
         self.check_timezone(dataframe=test_frame, tzone=arg_timezone)
 
     def index_not_equal(self, index_01: pd.Index, index_02: pd.Index):
-        """Check that two indices are not equal."""
+        """Check if two indices are not equal."""
 
         with pytest.raises(AssertionError, match="Index are different"):
             assert pd.testing.assert_index_equal(
@@ -338,6 +338,21 @@ def conftest_mock_save_figure():
     mock_exists.return_value = None
 
 
+# Mock random data
+@pytest.fixture(name="conftest_generate_series", scope="function", autouse=False)
+def fixture_conftest_generate_series() -> tuple[np.ndarray, pd.Timestamp]:
+    """Generates Series with random data and DatetimeIndex"""
+
+    rng = np.random.default_rng()
+    test_timestamp = pd.Timestamp("03 June 2020 05:20", tz="CET")
+    test_index = pd.date_range(start=test_timestamp, periods=100, freq="T")
+    assert ptypes.is_datetime64_any_dtype(test_index)
+    test_data = rng.random(size=len(test_index))
+    assert isinstance(test_data, np.ndarray)
+
+    yield test_data, test_index
+
+
 # Mock scintillometer data
 @pytest.fixture(name="conftest_mnd_lines", scope="function", autouse=False)
 def fixture_conftest_mock_mnd_lines():
diff --git a/tests/test_metrics_calculations.py b/tests/test_metrics_calculations.py
index 1d6ef40..8b37236 100644
--- a/tests/test_metrics_calculations.py
+++ b/tests/test_metrics_calculations.py
@@ -332,9 +332,9 @@ def test_get_regression(
             compare_regression["fit"], sklearn.linear_model.LinearRegression
         )
         if not arg_intercept:
-            assert not compare_regression["fit"].fit_intercept
-        else:
             assert compare_regression["fit"].fit_intercept
+        else:
+            assert not compare_regression["fit"].fit_intercept
         assert isinstance(compare_regression["score"], float)
         assert isinstance(compare_regression["regression_line"], np.ndarray)
         assert not (np.isnan(compare_regression["regression_line"])).any()
@@ -653,19 +653,12 @@ def test_plot_switch_time_stability(
         )
         assert isinstance(test_time, pd.Timestamp)
         test_vertical = test_dataset["vertical"]
-        if arg_location:
+        if arg_location is not None:
             test_location = f"\nat {arg_location}, "
         else:
             test_location = ",\n"
         test_labels = ["Potential Temperature, [K]"]
-        if not arg_gradient:
-            test_vertical.pop("grad_potential_temperature", None)
-            assert "grad_potential_temperature" not in test_vertical
-            test_title = (
-                f"Vertical Profile of Potential Temperature{test_location}",
-                f"{self.test_date} 05:20 CET",
-            )
-        else:
+        if arg_gradient:
             assert "grad_potential_temperature" in test_vertical
             test_title = (
                 "Vertical Profiles of Potential Temperature ",
@@ -673,23 +666,33 @@ def test_plot_switch_time_stability(
                 f"{self.test_date} 05:20 CET",
             )
             test_labels.append(r"Gradient of Potential Temperature, [K$\cdot$m$^{-1}$]")
+        else:
+            test_vertical.pop("grad_potential_temperature", None)
+            assert "grad_potential_temperature" not in test_vertical
+            test_title = (
+                f"Vertical Profile of Potential Temperature{test_location}",
+                f"{self.test_date} 05:20 CET",
+            )
 
-        compare_fig, compare_ax = self.test_metrics.plot_switch_time_stability(
+        compare_plots = self.test_metrics.plot_switch_time_stability(
             data=test_vertical, local_time=test_time, location=arg_location
         )
-        assert isinstance(compare_fig, plt.Figure)
-
-        if not arg_gradient:
-            assert isinstance(compare_ax, plt.Axes)
-            assert compare_ax.get_title() == "".join(test_title)
-            assert compare_ax.yaxis.get_label_text() == "Height [m]"
-        else:
-            assert isinstance(compare_ax, np.ndarray)
-            assert all(isinstance(ax, plt.Axes) for ax in compare_ax)
-            assert compare_fig.texts[0].get_text() == "".join(test_title)
-            assert compare_ax[0].yaxis.get_label_text() == "Height [m]"
-            for i in range(len(compare_ax)):
-                assert compare_ax[i].xaxis.get_label_text() == test_labels[i]
+        assert isinstance(compare_plots, list)
+        for compare_tuple in compare_plots:
+            assert isinstance(compare_tuple, tuple)
+            assert isinstance(compare_tuple[0], plt.Figure)
+            compare_ax = compare_tuple[1]
+            if arg_gradient:
+                assert isinstance(compare_ax, np.ndarray)
+                assert all(isinstance(ax, plt.Axes) for ax in compare_ax)
+                assert compare_tuple[0].texts[0].get_text() == "".join(test_title)
+                assert compare_ax[0].yaxis.get_label_text() == "Height [m]"
+                for i in range(len(compare_ax)):
+                    assert compare_ax[i].xaxis.get_label_text() == test_labels[i]
+            else:
+                assert isinstance(compare_ax, plt.Axes)
+                assert compare_ax.get_title() == "".join(test_title)
+                assert compare_ax.yaxis.get_label_text() == "Height [m]"
 
         plt.close("all")
 
@@ -717,32 +720,34 @@ def test_plot_lapse_rates(
         test_dataset = self.test_metrics.append_vertical_variables(data=test_dataset)
         for key in ["grad_potential_temperature", "environmental_lapse_rate"]:
             assert key in test_dataset["vertical"]
-        if arg_location:
+        if arg_location is not None:
             test_location = f"\nat {arg_location}, "
         else:
             test_location = ",\n"
         test_title = f"{test_location}{self.test_date} 05:10 CET"
 
-        fig_lapse, ax_lapse, fig_parcel, ax_parcel = self.test_metrics.plot_lapse_rates(
+        compare_plots = self.test_metrics.plot_lapse_rates(
             vertical_data=test_dataset["vertical"],
             dry_adiabat=self.test_metrics.constants.dalr,
             local_time=self.test_timestamp,
             location=arg_location,
             bl_height=arg_height,
         )
+        assert isinstance(compare_plots, list)
+        assert all(isinstance(compare_tuple, tuple) for compare_tuple in compare_plots)
 
         compare_params = {
             "lapse": {
                 "title": "Temperature Lapse Rates",
                 "x_label": r"Lapse Rate, [Km$^{-1}$]",
                 "y_label": "Height [m]",
-                "plot": (fig_lapse, ax_lapse),
+                "plot": (compare_plots[0]),
             },
             "parcel": {
                 "title": "Vertical Profiles of Parcel Temperature",
                 "x_label": "Temperature, [K]",
                 "y_label": "Height [m]",
-                "plot": (fig_parcel, ax_parcel),
+                "plot": (compare_plots[1]),
             },
         }
 
@@ -848,7 +853,7 @@ def test_plot_derived_metrics(
         _ = conftest_mock_save_figure
 
         test_frame = conftest_mock_derived_dataframe
-        if arg_regime:
+        if arg_regime is not None:
             test_conditions = f"{arg_regime.capitalize()} Conditions"
         else:
             test_conditions = "No Height Dependency"
@@ -857,14 +862,17 @@ def test_plot_derived_metrics(
             f"for Free Convection ({test_conditions}),\n{self.test_date}",
         )
 
-        compare_fig, compare_ax = self.test_metrics.plot_derived_metrics(
+        compare_plots = self.test_metrics.plot_derived_metrics(
             derived_data=test_frame,
             time_id=test_frame.index[0],
             regime=arg_regime,
             location="",
         )
+        assert isinstance(compare_plots, list)
+        assert all(isinstance(compare_tuple, tuple) for compare_tuple in compare_plots)
+
         compare_params = {
-            "plot": (compare_fig, compare_ax),
+            "plot": (compare_plots[0]),
             "x_label": "Time, CET",
             "y_label": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
             "title": " ".join(test_title),
@@ -891,33 +899,35 @@ def test_plot_iterated_metrics(
         if arg_location:
             test_frame.attrs["name"] = arg_location
             assert "name" in test_frame.attrs
-        if arg_location:
+        if arg_location is not None:
             test_location = f" at {arg_location}"
         else:
             test_location = ""
         test_title = f"{test_location},\n{self.test_date}"
 
-        plot_pairs = self.test_metrics.plot_iterated_metrics(
+        compare_plots = self.test_metrics.plot_iterated_metrics(
             iterated_data=test_frame,
             time_stamp=test_stamp,
             site_location=arg_location,
         )
+        assert isinstance(compare_plots, list)
+        assert all(isinstance(compare_tuple, tuple) for compare_tuple in compare_plots)
 
-        compare_plots = {
+        compare_params = {
             "iteration": {
-                "plot": (plot_pairs[0], plot_pairs[1]),
+                "plot": (compare_plots[0]),
                 "title": "Sensible Heat Flux",
                 "x_label": "Time, CET",
                 "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
             },
             "comparison": {
-                "plot": (plot_pairs[2], plot_pairs[3]),
+                "plot": (compare_plots[1]),
                 "title": "Sensible Heat Flux from Free Convection and Iteration",
                 "x_label": "Time, CET",
                 "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
             },
         }
-        for params in compare_plots.values():
+        for params in compare_params.values():
             conftest_boilerplate.check_plot(plot_params=params, title=test_title)
 
         plt.close("all")
@@ -1121,30 +1131,31 @@ def test_compare_innflux(
 
         _ = conftest_mock_save_figure
 
-        if arg_location:
+        if arg_location is not None:
             test_location = f" at {arg_location}"
         else:
             test_location = ""
         test_title = f"{test_location},\n{self.test_date}"
 
-        fig_obukhov, ax_obukhov, fig_shf, ax_shf = self.test_workflow.compare_innflux(
+        compare_plots = self.test_workflow.compare_innflux(
             innflux_data=conftest_mock_innflux_dataframe_tz,
             own_data=conftest_mock_iterated_dataframe,
             location=arg_location,
         )
-
+        assert isinstance(compare_plots, list)
+        assert all(isinstance(compare_tuple, tuple) for compare_tuple in compare_plots)
         compare_params = {
             "obukhov": {
                 "title": "Obukhov Length from Scintillometer and innFLUX",
                 "y_label": "Obukhov Length, [m]",
                 "x_label": "Time, CET",
-                "plot": (fig_obukhov, ax_obukhov),
+                "plot": (compare_plots[0]),
             },
             "shf": {
                 "title": "Sensible Heat Flux from Scintillometer and innFLUX",
                 "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
                 "x_label": "Time, CET",
-                "plot": (fig_shf, ax_shf),
+                "plot": (compare_plots[1]),
             },
         }
 
@@ -1196,25 +1207,27 @@ def test_compare_eddy(
         test_location = "Test Location"
         test_title = f" at {test_location},\n{self.test_date}"
 
-        fig_obukhov, ax_obukhov, fig_shf, ax_shf = self.test_workflow.compare_eddy(
+        compare_plots = self.test_workflow.compare_eddy(
             own_data=conftest_mock_iterated_dataframe,
             ext_data=conftest_mock_innflux_dataframe_tz,
             source="innflux",
             location="Test Location",
         )
+        assert isinstance(compare_plots, list)
+        assert all(isinstance(compare_tuple, tuple) for compare_tuple in compare_plots)
 
         compare_params = {
             "obukhov": {
                 "title": "Obukhov Length from Scintillometer and innFLUX",
                 "y_label": "Obukhov Length, [m]",
                 "x_label": "Time, CET",
-                "plot": (fig_obukhov, ax_obukhov),
+                "plot": (compare_plots[0]),
             },
             "shf": {
                 "title": "Sensible Heat Flux from Scintillometer and innFLUX",
                 "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
                 "x_label": "Time, CET",
-                "plot": (fig_shf, ax_shf),
+                "plot": (compare_plots[1]),
             },
         }
         for params in compare_params.values():
diff --git a/tests/test_visuals_plotting.py b/tests/test_visuals_plotting.py
index d1039c5..0cd193a 100644
--- a/tests/test_visuals_plotting.py
+++ b/tests/test_visuals_plotting.py
@@ -596,24 +596,26 @@ def test_plot_iterated_fluxes(
         test_title = f"{test_location},\n{self.test_date}"
         timestamp = test_data.index[0]
 
-        plots = self.test_plotting.plot_iterated_fluxes(
+        compare_plots = self.test_plotting.plot_iterated_fluxes(
             iteration_data=test_data,
             time_id=timestamp,
             location=arg_location,
         )
+        assert isinstance(compare_plots, list)
+        assert all(isinstance(compare_tuple, tuple) for compare_tuple in compare_plots)
 
         compare_plots = {
             "shf": {
                 "title": "Sensible Heat Flux",
                 "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
                 "xlabel": "Time, CET",
-                "plot": (plots[0], plots[1]),
+                "plot": (compare_plots[0]),
             },
             "comparison": {
                 "title": "Sensible Heat Flux from Free Convection and Iteration",
                 "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
                 "xlabel": "Time, CET",
-                "plot": (plots[2], plots[3]),
+                "plot": (compare_plots[1]),
             },
         }
 
@@ -688,14 +690,18 @@ def test_plot_innflux(
     @pytest.mark.parametrize("arg_score", [None, 0.561734521])
     @pytest.mark.parametrize("arg_regression", [True, False])
     def test_plot_scatter(
-        self, conftest_boilerplate, arg_score, arg_site, arg_regression
+        self,
+        conftest_boilerplate,
+        conftest_generate_series,
+        arg_score,
+        arg_site,
+        arg_regression,
     ):
         """Plot scatter between two datasets with regression line."""
 
         test_name = "obukhov"
-        rng = np.random.default_rng()
-        test_index = pd.date_range(start=self.test_timestamp, periods=100, freq="T")
-        test_data = rng.random(size=len(test_index))
+        test_data, test_index = conftest_generate_series
+
         test_x = pd.Series(name=test_name, data=test_data, index=test_index)
         test_y = pd.Series(name=test_name, data=test_data + 0.5, index=test_index)
         for series in [test_x, test_y]:

From 1989f644a71e65700176d1f1f0570408961e8b53 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Wed, 24 May 2023 16:54:53 +0200
Subject: [PATCH 08/17] feat(metrics): calculate, plot, save regression between
 data

Adds ability to plot and save regression between calculated fluxes and
innFLUX data.

Fixes some incorrect test conditions which led to tests being skipped.

Refs: ST-3, ST-7, ST-8, ST-106, ST-107
---
 src/scintillometry/metrics/calculations.py | 45 ++++++++++++--
 src/scintillometry/visuals/plotting.py     |  6 +-
 tests/test_metrics_calculations.py         | 71 ++++++++++++++--------
 tests/test_visuals_plotting.py             |  4 +-
 4 files changed, 92 insertions(+), 34 deletions(-)

diff --git a/src/scintillometry/metrics/calculations.py b/src/scintillometry/metrics/calculations.py
index 3225a92..5f34c69 100755
--- a/src/scintillometry/metrics/calculations.py
+++ b/src/scintillometry/metrics/calculations.py
@@ -991,26 +991,61 @@ def compare_innflux(self, own_data, innflux_data, location=""):
         """
 
         data_timestamp = own_data.index[0]
-        fig_obukhov, ax_obukhov = self.plotting.plot_innflux(
+        obukhov_plot = self.plotting.plot_innflux(
             iter_data=own_data,
             innflux_data=innflux_data,
             name="obukhov",
             site=location,
         )
         self.plotting.save_figure(
-            figure=fig_obukhov, timestamp=data_timestamp, suffix="innflux_obukhov"
+            figure=obukhov_plot[0], timestamp=data_timestamp, suffix="innflux_obukhov"
         )
-        fig_shf, ax_shf = self.plotting.plot_innflux(
+        obukhov_regression = self.get_regression(
+            x_data=own_data["obukhov"], y_data=innflux_data["obukhov"], intercept=True
+        )
+        obukhov_regression_plot = self.plotting.plot_scatter(
+            x_data=own_data,
+            y_data=innflux_data,
+            sources=["MOST Iteration", "innFLUX"],
+            name="obukhov",
+            score=obukhov_regression["score"],
+            regression_line=obukhov_regression["regression_line"],
+            site=location,
+        )
+        self.plotting.save_figure(
+            figure=obukhov_regression_plot[0],
+            timestamp=data_timestamp,
+            suffix="innflux_obukhov_regression",
+        )
+
+        shf_plot = self.plotting.plot_innflux(
             iter_data=own_data,
             innflux_data=innflux_data,
             name="shf",
             site=location,
         )
         self.plotting.save_figure(
-            figure=fig_shf, timestamp=data_timestamp, suffix="innflux_shf"
+            figure=shf_plot[0], timestamp=data_timestamp, suffix="innflux_shf"
+        )
+        shf_regression = self.get_regression(
+            x_data=own_data["obukhov"], y_data=innflux_data["obukhov"], intercept=True
+        )
+        shf_regression_plot = self.plotting.plot_scatter(
+            x_data=own_data,
+            y_data=innflux_data,
+            sources=["MOST Iteration", "innFLUX"],
+            name="shf",
+            score=shf_regression["score"],
+            regression_line=shf_regression["regression_line"],
+            site=location,
+        )
+        self.plotting.save_figure(
+            figure=shf_regression_plot[0],
+            timestamp=data_timestamp,
+            suffix="innflux_shf_regression",
         )
 
-        plots = [(fig_obukhov, ax_obukhov), (fig_shf, ax_shf)]
+        plots = [obukhov_plot, shf_plot, obukhov_regression_plot, shf_regression_plot]
 
         return plots
 
diff --git a/src/scintillometry/visuals/plotting.py b/src/scintillometry/visuals/plotting.py
index e051adc..9c99210 100644
--- a/src/scintillometry/visuals/plotting.py
+++ b/src/scintillometry/visuals/plotting.py
@@ -708,14 +708,14 @@ def plot_scatter(
                 transform=axes.transAxes,
             )
         variable_name = self.label_selector(name)
-        sources_string = f"{sources[0].title()} and {sources[1].title()}"
+        sources_string = f"{sources[0]} and {sources[1]}"
         title_string = f"{variable_name[0]} Regression Between\n{sources_string}"
         site_label = self.get_site_name(site_name=site, dataframe=x_data)
         self.title_plot(title=title_string, timestamp=date, location=site_label)
         x_label = self.merge_label_with_unit(label=variable_name)
         y_label = self.merge_label_with_unit(label=variable_name)
-        plt.xlabel(f"{sources[0].title()} {x_label}")
-        plt.ylabel(f"{sources[1].title()} {y_label}")
+        plt.xlabel(f"{x_label} ({sources[0]})")
+        plt.ylabel(f"{y_label} ({sources[1]})")
 
         return figure, axes
 
diff --git a/tests/test_metrics_calculations.py b/tests/test_metrics_calculations.py
index 8b37236..07e471c 100644
--- a/tests/test_metrics_calculations.py
+++ b/tests/test_metrics_calculations.py
@@ -280,10 +280,10 @@ def test_match_time_at_threshold(
         test_weather = conftest_mock_weather_dataframe_tz.copy(deep=True)
         if arg_empty:
             test_weather["global_irradiance"] = 20
-        if not arg_timestamp:
-            test_timestamp = None
-        else:
+        if arg_timestamp:
             test_timestamp = self.test_timestamp
+        else:
+            test_timestamp = None
 
         compare_time = self.test_metrics.match_time_at_threshold(
             series=test_weather["global_irradiance"],
@@ -331,7 +331,7 @@ def test_get_regression(
         assert isinstance(
             compare_regression["fit"], sklearn.linear_model.LinearRegression
         )
-        if not arg_intercept:
+        if arg_intercept:
             assert compare_regression["fit"].fit_intercept
         else:
             assert not compare_regression["fit"].fit_intercept
@@ -653,7 +653,7 @@ def test_plot_switch_time_stability(
         )
         assert isinstance(test_time, pd.Timestamp)
         test_vertical = test_dataset["vertical"]
-        if arg_location is not None:
+        if arg_location:
             test_location = f"\nat {arg_location}, "
         else:
             test_location = ",\n"
@@ -720,7 +720,7 @@ def test_plot_lapse_rates(
         test_dataset = self.test_metrics.append_vertical_variables(data=test_dataset)
         for key in ["grad_potential_temperature", "environmental_lapse_rate"]:
             assert key in test_dataset["vertical"]
-        if arg_location is not None:
+        if arg_location:
             test_location = f"\nat {arg_location}, "
         else:
             test_location = ",\n"
@@ -899,7 +899,7 @@ def test_plot_iterated_metrics(
         if arg_location:
             test_frame.attrs["name"] = arg_location
             assert "name" in test_frame.attrs
-        if arg_location is not None:
+        if arg_location:
             test_location = f" at {arg_location}"
         else:
             test_location = ""
@@ -918,13 +918,13 @@ def test_plot_iterated_metrics(
                 "plot": (compare_plots[0]),
                 "title": "Sensible Heat Flux",
                 "x_label": "Time, CET",
-                "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
+                "y_label": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
             },
             "comparison": {
                 "plot": (compare_plots[1]),
                 "title": "Sensible Heat Flux from Free Convection and Iteration",
                 "x_label": "Time, CET",
-                "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
+                "y_label": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
             },
         }
         for params in compare_params.values():
@@ -1122,24 +1122,32 @@ def test_calculate_standard_metrics_no_vertical(
     def test_compare_innflux(
         self,
         conftest_mock_save_figure,
-        conftest_mock_innflux_dataframe_tz,
-        conftest_mock_iterated_dataframe,
         conftest_boilerplate,
+        conftest_generate_series,
         arg_location,
     ):
-        """Compares input data to InnFLUX data."""
+        """Compares input data to innFLUX data."""
 
         _ = conftest_mock_save_figure
 
-        if arg_location is not None:
+        test_data, test_index = conftest_generate_series
+        test_obukhov = pd.Series(data=test_data, index=test_index)
+        test_shf = pd.Series(data=test_data, index=test_index)
+        test_base_dataframe = pd.DataFrame(
+            data={"obukhov": test_obukhov, "shf": test_shf},
+        )
+        test_ext_dataframe = test_base_dataframe.add(0.5)
+
+        if arg_location:
             test_location = f" at {arg_location}"
         else:
             test_location = ""
         test_title = f"{test_location},\n{self.test_date}"
+        test_regression_string = "Regression Between\nMOST Iteration and innFLUX"
 
         compare_plots = self.test_workflow.compare_innflux(
-            innflux_data=conftest_mock_innflux_dataframe_tz,
-            own_data=conftest_mock_iterated_dataframe,
+            own_data=test_base_dataframe,
+            innflux_data=test_ext_dataframe,
             location=arg_location,
         )
         assert isinstance(compare_plots, list)
@@ -1153,10 +1161,22 @@ def test_compare_innflux(
             },
             "shf": {
                 "title": "Sensible Heat Flux from Scintillometer and innFLUX",
-                "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
+                "y_label": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
                 "x_label": "Time, CET",
                 "plot": (compare_plots[1]),
             },
+            "obukhov_regression": {
+                "title": f"Obukhov Length {test_regression_string}",
+                "y_label": "Obukhov Length, [m] (innFLUX)",
+                "x_label": "Obukhov Length, [m] (MOST Iteration)",
+                "plot": (compare_plots[2]),
+            },
+            "shf_regression": {
+                "title": f"Sensible Heat Flux {test_regression_string}",
+                "y_label": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$] (innFLUX)",
+                "x_label": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$] (MOST Iteration)",
+                "plot": (compare_plots[3]),
+            },
         }
 
         for params in compare_params.values():
@@ -1194,22 +1214,25 @@ def test_compare_eddy_error(
         ],
     )
     def test_compare_eddy(
-        self,
-        conftest_mock_save_figure,
-        conftest_mock_innflux_dataframe_tz,
-        conftest_mock_iterated_dataframe,
-        conftest_boilerplate,
+        self, conftest_mock_save_figure, conftest_generate_series, conftest_boilerplate
     ):
         """Compares input data to external eddy covariance data."""
 
         _ = conftest_mock_save_figure
 
+        test_data, test_index = conftest_generate_series
+        test_obukhov = pd.Series(data=test_data, index=test_index)
+        test_shf = pd.Series(data=test_data, index=test_index)
+        test_base_dataframe = pd.DataFrame(
+            data={"obukhov": test_obukhov, "shf": test_shf},
+        )
+        test_ext_dataframe = test_base_dataframe.add(0.5)
         test_location = "Test Location"
         test_title = f" at {test_location},\n{self.test_date}"
 
         compare_plots = self.test_workflow.compare_eddy(
-            own_data=conftest_mock_iterated_dataframe,
-            ext_data=conftest_mock_innflux_dataframe_tz,
+            own_data=test_base_dataframe,
+            ext_data=test_ext_dataframe,
             source="innflux",
             location="Test Location",
         )
@@ -1225,7 +1248,7 @@ def test_compare_eddy(
             },
             "shf": {
                 "title": "Sensible Heat Flux from Scintillometer and innFLUX",
-                "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
+                "y_label": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
                 "x_label": "Time, CET",
                 "plot": (compare_plots[1]),
             },
diff --git a/tests/test_visuals_plotting.py b/tests/test_visuals_plotting.py
index 0cd193a..15533a7 100644
--- a/tests/test_visuals_plotting.py
+++ b/tests/test_visuals_plotting.py
@@ -733,8 +733,8 @@ def test_plot_scatter(
         )
         compare_params = {
             "plot": (compare_fig, compare_ax),
-            "x_label": "Baseline Obukhov Length, [m]",
-            "y_label": "Comparison Obukhov Length, [m]",
+            "x_label": "Obukhov Length, [m] (Baseline)",
+            "y_label": "Obukhov Length, [m] (Comparison)",
             "title": "\n".join(test_title),
         }
         conftest_boilerplate.check_plot(plot_params=compare_params)

From d638315d93eff1b19442dcb335bab8681226426b Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Wed, 24 May 2023 17:06:08 +0200
Subject: [PATCH 09/17] refactor: minor docstring and logic fixes

Begins:
    - ST-126: Deprecate FigurePlotter.plot_iterated_fluxes in favour of
      plot_iterated_metrics

Refs: ST-3, ST-7, ST-8
---
 src/scintillometry/metrics/calculations.py | 20 ++++++++---------
 src/scintillometry/visuals/plotting.py     |  8 +++----
 tests/test_metrics_calculations.py         | 12 +++++------
 tests/test_visuals_plotting.py             | 25 +++++++++++-----------
 4 files changed, 32 insertions(+), 33 deletions(-)

diff --git a/src/scintillometry/metrics/calculations.py b/src/scintillometry/metrics/calculations.py
index 5f34c69..e150917 100755
--- a/src/scintillometry/metrics/calculations.py
+++ b/src/scintillometry/metrics/calculations.py
@@ -56,8 +56,9 @@ def get_path_height_parameters(self, transect, regime=None):
             regime (str): Target stability condition. Default None.
 
         Returns:
-            dict[float, float]: Tuples of effective and mean path height
-            |z_eff| and |z_mean| [m], with stability conditions as keys.
+            dict[str, tuple[np.floating, np.floating]]: Tuples of
+            effective and mean path height |z_eff| and |z_mean| [m],
+            with stability conditions as keys.
         """
 
         z_params = self.transect.get_all_path_heights(path_transect=transect)
@@ -106,7 +107,6 @@ def construct_flux_dataframe(
         <interpolated_data>.
 
         Args:
-            user_args (argparse.Namespace): Namespace of user arguments.
             interpolated_data (pd.DataFrame): Dataframe containing
                 parsed and localised weather and scintillometer data
                 with matching temporal resolution.
@@ -176,7 +176,7 @@ def append_vertical_variables(self, data):
             "vertical" is updated with vertical data for water vapour
             pressure, air pressure, mixing ratio, virtual temperature,
             mean sea-level pressure, and potential temperature.
-            Otherwise the dictionary is returned unmodified.
+            Otherwise, the dictionary is returned unmodified.
         """
 
         if "vertical" in data:
@@ -283,10 +283,10 @@ def get_elbow_point(self, series, min_index=None, max_index=None):
             ]
         if series[indices[-1]] < series[indices[0]]:
             curve_direction = "decreasing"
-            online_param = "true"
+            online_param = True
         else:
             curve_direction = "increasing"
-            online_param = "true"
+            online_param = True
         knee = kneed.KneeLocator(
             series[indices],
             indices,
@@ -1004,8 +1004,8 @@ def compare_innflux(self, own_data, innflux_data, location=""):
             x_data=own_data["obukhov"], y_data=innflux_data["obukhov"], intercept=True
         )
         obukhov_regression_plot = self.plotting.plot_scatter(
-            x_data=own_data,
-            y_data=innflux_data,
+            x_data=own_data["obukhov"],
+            y_data=innflux_data["obukhov"],
             sources=["MOST Iteration", "innFLUX"],
             name="obukhov",
             score=obukhov_regression["score"],
@@ -1031,8 +1031,8 @@ def compare_innflux(self, own_data, innflux_data, location=""):
             x_data=own_data["obukhov"], y_data=innflux_data["obukhov"], intercept=True
         )
         shf_regression_plot = self.plotting.plot_scatter(
-            x_data=own_data,
-            y_data=innflux_data,
+            x_data=own_data["shf"],
+            y_data=innflux_data["shf"],
             sources=["MOST Iteration", "innFLUX"],
             name="shf",
             score=shf_regression["score"],
diff --git a/src/scintillometry/visuals/plotting.py b/src/scintillometry/visuals/plotting.py
index 9c99210..899bbce 100644
--- a/src/scintillometry/visuals/plotting.py
+++ b/src/scintillometry/visuals/plotting.py
@@ -264,7 +264,7 @@ def merge_multiple_labels(self, labels):
             labels (list[str]): Labels, which may contain duplicates.
 
         Returns:
-            str: A formatted, puncutated string with no duplicates.
+            str: A formatted, punctuated string with no duplicates.
         """
 
         unique_text = list(dict.fromkeys(labels))
@@ -286,9 +286,9 @@ def set_xy_labels(self, ax, timezone, name):
             name (str): Name or abbreviation of dependent variable.
 
         Returns:
-            plt.Axes: Plot axes with labels for local time on the x axis
-            and for the dependent variable with units on the y axis.
-            Ticks on the x axis are formatted at hourly intervals.
+            plt.Axes: Plot axes with labels for local time on the x-axis
+            and for the dependent variable with units on the y-axis.
+            Ticks on the x-axis are formatted at hourly intervals.
         """
 
         x_label = f"Time, {timezone.zone}"
diff --git a/tests/test_metrics_calculations.py b/tests/test_metrics_calculations.py
index 07e471c..468ed2c 100644
--- a/tests/test_metrics_calculations.py
+++ b/tests/test_metrics_calculations.py
@@ -107,7 +107,7 @@ def test_get_path_height_parameters(
         assert compare_metrics["None"][0] > compare_metrics["None"][1]
 
         compare_print = capsys.readouterr()
-        if not arg_regime:
+        if arg_regime is None:
             assert "Selected no height dependency:" in compare_print.out
         else:
             assert str(arg_regime) in compare_print.out
@@ -172,7 +172,7 @@ def test_construct_flux_dataframe(self, conftest_mock_merged_dataframe, arg_kwar
         """Compute sensible heat flux for free convection."""
 
         test_frame = conftest_mock_merged_dataframe[["CT2", "H_convection"]]
-        if arg_kwargs:
+        if isinstance(arg_kwargs, tuple):
             test_kwargs = {
                 "beam_wavelength": arg_kwargs[0],
                 "beam_error": arg_kwargs[1],
@@ -271,7 +271,7 @@ def test_append_vertical_variables(
     @pytest.mark.dependency(name="TestMetricsFlux::test_match_time_at_threshold")
     @pytest.mark.parametrize("arg_lessthan", [True, False])
     @pytest.mark.parametrize("arg_empty", [True, False])
-    @pytest.mark.parametrize("arg_timestamp", [True, None])
+    @pytest.mark.parametrize("arg_timestamp", [True, False])
     def test_match_time_at_threshold(
         self, conftest_mock_weather_dataframe_tz, arg_lessthan, arg_empty, arg_timestamp
     ):
@@ -373,7 +373,7 @@ def test_get_elbow_point(self, arg_min_index, arg_max_index, arg_curve):
             test_indices,
             S=1.5,
             curve="convex",
-            online="true",
+            online=True,
             direction=test_direction,
             interp_method="interp1d",
         )
@@ -806,8 +806,8 @@ def test_calculate_switch_time(
         test_dataset = {
             "weather": conftest_mock_weather_dataframe_tz.copy(deep=True),
             "timestamp": self.test_timestamp.replace(hour=5, minute=10),
+            "vertical": conftest_mock_hatpro_dataset.copy(),
         }
-        test_dataset["vertical"] = conftest_mock_hatpro_dataset.copy()
         test_dataset = self.test_metrics.append_vertical_variables(data=test_dataset)
 
         if not arg_potential:
@@ -974,7 +974,7 @@ def test_iterate_fluxes(
         for key in compare_keys:
             assert not (compare_metrics[key].isnull()).any()
             assert key in compare_metrics.keys()
-            assert all(isinstance(x, (mpmath.mpf)) for x in compare_metrics[key])
+            assert all(isinstance(x, mpmath.mpf) for x in compare_metrics[key])
         plt.close("all")
 
 
diff --git a/tests/test_visuals_plotting.py b/tests/test_visuals_plotting.py
index 15533a7..e4268ac 100644
--- a/tests/test_visuals_plotting.py
+++ b/tests/test_visuals_plotting.py
@@ -64,10 +64,11 @@ def assert_constant_lines(
     @pytest.mark.dependency(name="TestVisualsBoilerplate::test_assert_constant_lines")
     @pytest.mark.parametrize("arg_vlines", [{"v_a": 1}, {"v_a": 1, "v_b": 2.1}, None])
     @pytest.mark.parametrize("arg_hlines", [{"h_a": 1}, {"h_a": 1, "h_b": 2.1}, None])
-    def test_assert_constant_lines(self, arg_hlines, arg_vlines):
-        rng = np.random.default_rng()
-        test_index = np.arange(0, 200, 10)
-        test_data = rng.random(size=len(test_index))
+    def test_assert_constant_lines(
+        self, conftest_generate_series, arg_hlines, arg_vlines
+    ):
+        """Validate test for constant lines existing on axis."""
+        test_data, test_index = conftest_generate_series
         test_series = pd.Series(data=test_data, index=test_index)
 
         plt.figure(figsize=(10, 10))
@@ -128,13 +129,11 @@ def test_initialise_formatting(self, arg_offset):
 
     @pytest.mark.dependency(name="TestVisualsFormatting::test_parse_formatting_kwargs")
     @pytest.mark.parametrize("arg_fig", [True, False])
-    def test_parse_formatting_kwargs(self, arg_fig):
+    def test_parse_formatting_kwargs(self, arg_fig, conftest_generate_series):
         """Parse kwargs when formatting."""
 
         if arg_fig:
-            rng = np.random.default_rng()
-            test_index = np.arange(0, 200, 10)
-            test_data = rng.random(size=len(test_index))
+            test_data, test_index = conftest_generate_series
             test_series = pd.Series(data=test_data, index=test_index)
             plt.figure(figsize=(10, 10))
             plt.plot(test_index, test_series)
@@ -333,12 +332,12 @@ def test_set_xy_labels(self, arg_name):
     )
     @pytest.mark.parametrize("arg_vlines", [{"va": None}, {"va": 1, "vb": 2.1}, None])
     @pytest.mark.parametrize("arg_hlines", [{"ha": None}, {"ha": 1, "hb": 2.1}, None])
-    def test_plot_constant_lines(self, arg_hlines, arg_vlines):
+    def test_plot_constant_lines(
+        self, conftest_generate_series, arg_hlines, arg_vlines
+    ):
         """Plot horizontal and vertical lines."""
 
-        rng = np.random.default_rng()
-        test_index = np.arange(0, 200, 10)
-        test_data = rng.random(size=len(test_index))
+        test_data, test_index = conftest_generate_series
         test_series = pd.Series(data=test_data, index=test_index)
 
         plt.figure(figsize=(10, 10))
@@ -368,7 +367,7 @@ class TestVisualsPlotting(TestVisualsBoilerplate):
     test_date = "03 June 2020"
     test_timestamp = pd.Timestamp(f"{test_date} 05:20", tz="CET")
 
-    def test_visualsplotting_attributes(self):
+    def test_visuals_plotting_attributes(self):
         assert isinstance(self.test_timestamp, pd.Timestamp)
         assert self.test_timestamp.strftime("%Y-%m-%d %H:%M") == "2020-06-03 05:20"
         assert self.test_timestamp.tz.zone == "CET"

From ae5b2ff677bae286784713cf2a419c2ee9e7b26f Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Thu, 25 May 2023 13:55:07 +0200
Subject: [PATCH 10/17] refactor: begin deprecating
 FigurePlotter.plot_iterated_fluxes

Begins deprecation of FigurePlotter.plot_iterated_fluxes in favour
of MetricsFlux.plot_iterated_metrics.

The former method is redundant.

Refs: ST-7, ST-8, ST-126
---
 src/scintillometry/metrics/calculations.py | 35 ++++++++++++++++------
 src/scintillometry/visuals/plotting.py     |  9 ++++++
 2 files changed, 35 insertions(+), 9 deletions(-)

diff --git a/src/scintillometry/metrics/calculations.py b/src/scintillometry/metrics/calculations.py
index e150917..e5d735f 100755
--- a/src/scintillometry/metrics/calculations.py
+++ b/src/scintillometry/metrics/calculations.py
@@ -825,14 +825,19 @@ def plot_derived_metrics(self, derived_data, time_id, regime=None, location=""):
         return derived_plots
 
     def plot_iterated_metrics(self, iterated_data, time_stamp, site_location=""):
-        """Plot and save time series and comparison of iterated fluxes.
+        """Plots and saves iterated SHF, comparison to free convection.
+
+        .. todo::
+            ST-126: Deprecate FigurePlotter.plot_iterated_fluxes in
+                favour of plot_iterated_metrics.
 
         Args:
-            iterated_data (pd.DataFrame): TZ-aware dataframe with
-                columns for heat fluxes and MOST parameters.
-            time_stamp (pd.Timestamp): Start time of scintillometer data
-                collection.
-            site_location (str): Name of scintillometer location.
+            iteration_data (pd.DataFrame): TZ-aware with columns for
+                sensible heat fluxes calculated for free convection
+                |H_free|, and by MOST |H|.
+            time_id (pd.Timestamp): Local time of data collection.
+            site_location (str): Location of data collection. Default empty
+                string.
 
         Returns:
             list[tuple[plt.Figure, plt.Axes]]: Time series of sensible
@@ -840,11 +845,23 @@ def plot_iterated_metrics(self, iterated_data, time_stamp, site_location=""):
             sensible heat flux under free convection.
         """
 
-        plots = self.plotting.plot_iterated_fluxes(
-            iteration_data=iterated_data, time_id=time_stamp, location=site_location
+        shf_plot = self.plotting.plot_generic(iterated_data, "shf", site=site_location)
+        self.plotting.save_figure(
+            figure=shf_plot[0], timestamp=time_stamp, suffix="shf"
         )
 
-        return plots
+        comparison_plot = self.plotting.plot_comparison(
+            df_01=iterated_data,
+            df_02=iterated_data,
+            keys=["H_free", "shf"],
+            labels=["Free Convection", "Iteration"],
+            site=site_location,
+        )
+        self.plotting.save_figure(
+            figure=comparison_plot[0], timestamp=time_stamp, suffix="shf_comp"
+        )
+
+        return [shf_plot, comparison_plot]
 
 
 class MetricsWorkflow(MetricsFlux, MetricsTopography):
diff --git a/src/scintillometry/visuals/plotting.py b/src/scintillometry/visuals/plotting.py
index 899bbce..68f5ccf 100644
--- a/src/scintillometry/visuals/plotting.py
+++ b/src/scintillometry/visuals/plotting.py
@@ -585,6 +585,15 @@ def plot_comparison(self, df_01, df_02, keys, labels, site=""):
     def plot_iterated_fluxes(self, iteration_data, time_id, location=""):
         """Plots and saves iterated SHF, comparison to free convection.
 
+        .. note:: Pending deprecation in a future patch release. Use
+            :func:`MetricsFlux.plot_iterated_metrics()
+            <scintillometry.metrics.calculations.MetricsFlux.plot_iterated_metrics>`
+            instead.
+
+        .. todo::
+            ST-126: Deprecate FigurePlotter.plot_iterated_fluxes in
+                favour of plot_iterated_metrics.
+
         Args:
             iteration_data (pd.DataFrame): TZ-aware with sensible heat
                 fluxes calculated for free convection |H_free|, and

From 7ac8ee32aab87f97ba490549a22ac169d32c1b49 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Thu, 25 May 2023 14:04:18 +0200
Subject: [PATCH 11/17] fix(tests): fix incorrect type hinting in conftest

Refs: ST-3
---
 tests/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index b7467ce..9fedd24 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -340,7 +340,7 @@ def conftest_mock_save_figure():
 
 # Mock random data
 @pytest.fixture(name="conftest_generate_series", scope="function", autouse=False)
-def fixture_conftest_generate_series() -> tuple[np.ndarray, pd.Timestamp]:
+def fixture_conftest_generate_series():
     """Generates Series with random data and DatetimeIndex"""
 
     rng = np.random.default_rng()

From a2a4f222675223b89328950ceefdd1d80c9a6be0 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Thu, 25 May 2023 14:08:13 +0200
Subject: [PATCH 12/17] fix: add scikit-learn to project requirements

Refs: ST-1
---
 dev-requirements.txt | 1 +
 pyproject.toml       | 1 +
 requirements.txt     | 1 +
 3 files changed, 3 insertions(+)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index 1872c7b..cf5e94a 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -3,6 +3,7 @@ tqdm>4.8
 scipy>=1.10
 mpmath>=1.2.1
 numpy
+scikit-learn
 matplotlib
 kneed
 pytest>=7.0
diff --git a/pyproject.toml b/pyproject.toml
index 17aba01..164da57 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,6 +31,7 @@ dependencies = [
   "scipy >= 1.10",
   "mpmath >= 1.2.1",
   "numpy",
+  "scikit-learn
   "matplotlib",
   "kneed",
 ]
diff --git a/requirements.txt b/requirements.txt
index 88f6eb2..c450156 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,5 +3,6 @@ tqdm>4.8
 scipy>=1.10
 mpmath>=1.2.1
 numpy
+scikit-learn
 matplotlib
 kneed

From 856bcd9a885f3135338a47bf15ccd4e3f1eac2bc Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Thu, 25 May 2023 14:10:28 +0200
Subject: [PATCH 13/17] fix: fix broken syntax in pyproject.toml

Refs: ST-1
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 164da57..7ff6d7a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,7 +31,7 @@ dependencies = [
   "scipy >= 1.10",
   "mpmath >= 1.2.1",
   "numpy",
-  "scikit-learn
+  "scikit-learn",
   "matplotlib",
   "kneed",
 ]

From f07b6c65ca36776477bc9b7db04804d8784d9e9c Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Thu, 25 May 2023 14:48:55 +0200
Subject: [PATCH 14/17] merge: merge branch feat-ST127-refactor-project with
 develop (#8)

* refactor: minor docstring fixes

Refs: ST-2, ST-127

* refactor: update README

Refs: ST-2, ST-127

* refactor: minor efficiency fixes

Refs: ST-2, ST-5, ST-7, ST-127

* refactor: minor updates to test logic

Refs: ST-3, ST-127

* refactor: improve code legibility in main

Refs: ST-26, ST-127

* fix: remove unsupported type hinting

Refs: ST-3, ST-127

Refs: ST-1, ST-127
---
 README.md                                   |  6 ++---
 src/scintillometry/backend/constants.py     | 12 ++++------
 src/scintillometry/backend/constructions.py |  6 ++---
 src/scintillometry/backend/iterations.py    |  2 ++
 src/scintillometry/backend/transects.py     | 10 ++++----
 src/scintillometry/main.py                  | 18 +++++++-------
 src/scintillometry/metrics/calculations.py  |  7 +++---
 src/scintillometry/wrangler/data_parser.py  | 26 ++++++++-------------
 tests/test_backend_iterations.py            | 10 ++++----
 tests/test_backend_transects.py             |  2 +-
 tests/test_visuals_plotting.py              |  8 +++----
 tests/test_wrangler_data_parser.py          |  4 ++--
 12 files changed, 52 insertions(+), 59 deletions(-)

diff --git a/README.md b/README.md
index b0dca28..f1d1d8d 100644
--- a/README.md
+++ b/README.md
@@ -16,11 +16,11 @@ limitations under the License. -->
 
 [![Pytest and Flake8](https://github.com/gampnico/scintillometry/actions/workflows/python-app.yml/badge.svg?branch=main)](https://github.com/gampnico/scintillometry/actions/workflows/python-app.yml)
 
-Analyse data & 2D flux footprints from Scintec's BLS scintillometers.
+Development branch: [![Pytest and Linting](https://github.com/gampnico/scintillometry/actions/workflows/python-app.yml/badge.svg?branch=develop)](https://github.com/gampnico/scintillometry/actions/workflows/python-app.yml)
 
-This repository is a complete rewrite of gampnico/ss19-feldkurs. If you have any existing forks or local clones, **please delete them**. The legacy code no longer works. No user features will be lost, but rewriting may take some time. Contributions are always welcome.
+Analyse data & 2D flux footprints from Scintec's BLS scintillometers.
 
-This package started life as part of a field course. If you spot any missing citations or licenses please [open an issue](https://github.com/gampnico/scintillometry/issues).
+This project started life as part of a field course. If you spot any missing citations or licences please [open an issue](https://github.com/gampnico/scintillometry/issues).
 
 Comprehensive documentation is available [via ReadTheDocs](https://scintillometry.readthedocs.io/en/latest/).
 
diff --git a/src/scintillometry/backend/constants.py b/src/scintillometry/backend/constants.py
index 0a58757..91c5eaa 100644
--- a/src/scintillometry/backend/constants.py
+++ b/src/scintillometry/backend/constants.py
@@ -34,10 +34,6 @@ class AtmosConstants(object):
             BLS type.
         lamda (float): BLS wavelength, |lamda| [nm].
         lamda_error (float): BLS wavelength error, [nm].
-        m1_opt (float): Needed for |A_T| and |A_q|, from Owens (1967).
-            [#owens1967]_
-        m2_opt (float): Needed for |A_T| and |A_q|, from Owens (1967).
-            [#owens1967]_
 
         at_opt (float): |A_T| coefficient for 880 nm & typical
             atmospheric conditions, from Ward et al. (2013).
@@ -60,7 +56,7 @@ class AtmosConstants(object):
             20°C [|Jkg^-1|].
         r_dry (float): Specific gas constant for dry air,
             |R_dry| [|JK^-1| |kg^-1|].
-        r_vapour (float): Specific gas contstant for water vapour,
+        r_vapour (float): Specific gas constant for water vapour,
             |R_v| [|JK^-1| |kg^-1|].
         ratio_rmm (float): Ratio of molecular masses of water vapour and
             dry air i.e. ratio of gas constants |epsilon|.
@@ -149,7 +145,7 @@ def convert_pressure(self, pressure, base=True):
             pressure (Union[pd.DataFrame, pd.Series]): Pressure
                 measurements |P| in pascals [Pa], hectopascals [hPa], or
                 bars [bar].
-            base (bool): If True, converts to pascals [Pa]. Otherwise
+            base (bool): If True, converts to pascals [Pa]. Otherwise,
                 converts to hectopascals [hPa]. Default True.
 
         Returns:
@@ -186,12 +182,12 @@ def convert_temperature(self, temperature, base=True):
         - T [°C] < 130 °C
 
         This method should therefore only be used on pre-processed data
-        as a *convenience*. By default converts to kelvins.
+        as a *convenience*. By default, converts to kelvins.
 
         Args:
             temperature (Union[pd.DataFrame, pd.Series]): Temperature
                 measurements |T| in kelvins [K] or Celsius [°C].
-            base (bool): If True, converts to kelvins [K]. Otherwise
+            base (bool): If True, converts to kelvins [K]. Otherwise,
                 converts to Celsius [°C]. Default True.
 
         Returns:
diff --git a/src/scintillometry/backend/constructions.py b/src/scintillometry/backend/constructions.py
index d7f87ec..644037f 100644
--- a/src/scintillometry/backend/constructions.py
+++ b/src/scintillometry/backend/constructions.py
@@ -190,7 +190,7 @@ def get_mixing_ratio(self, wv_pressure, d_pressure):
 
         # (wv_pressure * self.r_dry) / (d_pressure * self.r_vapour)
         m_ratio = (wv_pressure.multiply(self.constants.r_dry)).divide(
-            (d_pressure).multiply(self.constants.r_vapour)
+            d_pressure.multiply(self.constants.r_vapour)
         )
 
         return m_ratio
@@ -236,7 +236,7 @@ def get_reduced_pressure(self, station_pressure, virtual_temperature, elevation)
             elevation (float): Station elevation, |z_stn| [m].
 
         Returns:
-            pd.DataDrame: Derived vertical measurements for mean
+            pd.DataFrame: Derived vertical measurements for mean
             sea-level pressure, |P_MSL| [Pa].
         """
 
@@ -495,7 +495,7 @@ def get_gradient(self, data, method="backward"):
         :math:`\\partial T/\\partial z` for heights |z| with time
         index t.
 
-        By default the gradient is calculated using a 1-D
+        By default, the gradient is calculated using a 1-D
         centred-differencing scheme for non-uniform meshes, since
         vertical measurements are rarely made at uniform intervals.
 
diff --git a/src/scintillometry/backend/iterations.py b/src/scintillometry/backend/iterations.py
index c7be7fa..89079b3 100644
--- a/src/scintillometry/backend/iterations.py
+++ b/src/scintillometry/backend/iterations.py
@@ -329,6 +329,8 @@ def most_iteration(self, dataframe, zm_bls, stable_flag, most_coeffs):
             stable_flag (bool): Stability conditions. If true, assumes
                 stable conditions, otherwise assumes unstable
                 conditions.
+            most_coeffs (list): MOST coefficients for unstable and
+                stable conditions.
 
         Returns:
             pd.DataFrame: Dataframe with additional columns for Obukhov
diff --git a/src/scintillometry/backend/transects.py b/src/scintillometry/backend/transects.py
index e9a1d71..5bd4059 100644
--- a/src/scintillometry/backend/transects.py
+++ b/src/scintillometry/backend/transects.py
@@ -85,7 +85,7 @@ def get_b_value(self, stability_name):
 
         Returns:
             float: Constant "b" accounting for height dependence of
-                |Cn2|. Values of "b" are from Hartogenesis et al.
+                |Cn2|. Values of "b" are from Hartogensis et al.
                 (2003) [#hartogensis2003]_, and Kleissl et al.
                 (2008) [#kleissl2008]_.
 
@@ -94,7 +94,7 @@ def get_b_value(self, stability_name):
                 stability condition.
         """
 
-        # Hartogenesis et al. (2003), Kleissl et al. (2008).
+        # Hartogensis et al. (2003), Kleissl et al. (2008).
         stability_dict = {"stable": -2 / 3, "unstable": -4 / 3}
 
         if not stability_name:
@@ -168,9 +168,9 @@ def get_all_path_heights(self, path_transect):
             path_transect (pd.DataFrame): Parsed path transect data.
 
         Returns:
-            dict[tuple[np.floating, np.floating]]: Effective and mean
-            path heights of transect |z_eff| and |z_mean| [m], with each
-            stability condition as key.
+            dict[str, tuple[np.floating, np.floating]]: Effective and
+            mean path heights of transect |z_eff| and |z_mean| [m], with
+            each stability condition as key.
         """
 
         path_heights_dict = {}
diff --git a/src/scintillometry/main.py b/src/scintillometry/main.py
index 2ae1058..391a2e6 100644
--- a/src/scintillometry/main.py
+++ b/src/scintillometry/main.py
@@ -55,8 +55,8 @@
 
 import argparse
 
-import scintillometry.metrics.calculations as MetricsCalculations
-import scintillometry.wrangler.data_parser as DataParser
+import scintillometry.metrics.calculations as calculations
+import scintillometry.wrangler.data_parser as data_parser
 
 
 def user_argumentation():
@@ -298,10 +298,10 @@ def perform_data_parsing(**kwargs):
         measurements, weather observations, and topography.
     """
 
-    data_parser = DataParser.WranglerParsing()
+    parser = data_parser.WranglerParsing()
 
     # Parse BLS, weather, and topographical data
-    datasets = data_parser.wrangle_data(
+    datasets = parser.wrangle_data(
         bls_path=kwargs["input"],
         transect_path=kwargs["transect_path"],
         calibrate=kwargs["calibration"],
@@ -312,7 +312,7 @@ def perform_data_parsing(**kwargs):
 
     # Parse vertical measurements
     if kwargs["profile_prefix"]:
-        datasets["vertical"] = data_parser.vertical.parse_vertical(
+        datasets["vertical"] = parser.vertical.parse_vertical(
             file_path=kwargs["profile_prefix"],
             source="hatpro",
             levels=None,
@@ -360,11 +360,11 @@ def perform_analysis(datasets, **kwargs):
         covariance data.
     """
 
-    metrics_class = MetricsCalculations.MetricsWorkflow()
-    data_parser = DataParser.WranglerParsing()
+    metrics_class = calculations.MetricsWorkflow()
+    parser = data_parser.WranglerParsing()
     metrics_data = metrics_class.calculate_standard_metrics(data=datasets, **kwargs)
     if kwargs["eddy_path"]:
-        eddy_frame = data_parser.eddy.parse_eddy_covariance(
+        eddy_frame = parser.eddy.parse_eddy_covariance(
             file_path=kwargs["eddy_path"], tzone=kwargs["timezone"], source="innflux"
         )
         metrics_data["eddy"] = eddy_frame
@@ -382,7 +382,7 @@ def main():
     """Parses command line arguments and executes analysis.
 
     Converts command line arguments into kwargs. Imports and parses
-    scintillomter, weather, and transect data. If the appropriate
+    scintillometer, weather, and transect data. If the appropriate
     arguments are specified:
 
         - Parses vertical measurements
diff --git a/src/scintillometry/metrics/calculations.py b/src/scintillometry/metrics/calculations.py
index e5d735f..4b044d1 100755
--- a/src/scintillometry/metrics/calculations.py
+++ b/src/scintillometry/metrics/calculations.py
@@ -829,13 +829,14 @@ def plot_iterated_metrics(self, iterated_data, time_stamp, site_location=""):
 
         .. todo::
             ST-126: Deprecate FigurePlotter.plot_iterated_fluxes in
-                favour of plot_iterated_metrics.
+                favour of plot_iterated_metrics. `site_location` should
+                be deprecated in favour of `location`.
 
         Args:
-            iteration_data (pd.DataFrame): TZ-aware with columns for
+            iterated_data (pd.DataFrame): TZ-aware with columns for
                 sensible heat fluxes calculated for free convection
                 |H_free|, and by MOST |H|.
-            time_id (pd.Timestamp): Local time of data collection.
+            time_stamp (pd.Timestamp): Local time of data collection.
             site_location (str): Location of data collection. Default empty
                 string.
 
diff --git a/src/scintillometry/wrangler/data_parser.py b/src/scintillometry/wrangler/data_parser.py
index 6dccdf3..7e1807b 100644
--- a/src/scintillometry/wrangler/data_parser.py
+++ b/src/scintillometry/wrangler/data_parser.py
@@ -93,7 +93,7 @@ def parse_iso_date(self, x, date=True):
         Args:
             x (str): Timestamp containing ISO-8601 duration and date,
                 i.e. "<ISO-8601 duration>/<ISO-8601 date>".
-            date (bool): If True, returns date. Otherwise returns
+            date (bool): If True, returns date. Otherwise, returns
                 duration. Default True.
 
         Returns:
@@ -163,10 +163,9 @@ def parse_mnd_lines(self, line_list):
             line_list (list): Lines read from .mnd file in FORMAT-1.
 
         Returns:
-            dict[list, list, str, list]: Contains a list of lines of
-            parsed BLS data, an ordered list of variable names, the file
-            timestamp, and any additional header parameters in the file
-            header.
+            dict: Contains a list of lines of parsed BLS data, an
+            ordered list of variable names, the file timestamp, and any
+            additional header parameters in the file header.
 
         Raises:
             Warning: The input file does not follow FORMAT-1.
@@ -251,7 +250,8 @@ def parse_scintillometer(self, file_path, timezone="CET", calibration=None):
         """Parses .mnd files into dataframes.
 
         Args:
-            filename (str): Path to a raw .mnd data file using FORMAT-1.
+            file_path (str): Path to a raw .mnd data file using
+                FORMAT-1.
             timezone (str): Local timezone during the scintillometer's
                 operation. Default "CET".
             calibration (list): Contains the incorrect and correct path
@@ -680,11 +680,7 @@ def parse_eddy_covariance(self, file_path, source="innflux", tzone=None):
         """
 
         if source.lower() == "innflux":
-            eddy_data = self.parse_innflux(
-                file_name=file_path,
-                timezone=tzone,
-                headers=None,
-            )
+            eddy_data = self.parse_innflux(file_name=file_path, timezone=tzone)
         else:
             error_msg = (
                 f"{source.title()} measurements are not supported. Use 'innflux'."
@@ -806,8 +802,8 @@ def parse_hatpro(
                 Default 612.0.
 
         Returns:
-            dict[pd.DataFrame, pd.DataFrame]: Vertical measurements from
-            HATPRO for temperature |T| [K], and absolute humidity
+            dict[str, pd.DataFrame]: Vertical measurements from HATPRO
+            for temperature |T| [K], and absolute humidity
             |rho_v| [|gm^-3|].
         """
 
@@ -828,9 +824,7 @@ def parse_hatpro(
             station_elevation=elevation,
         )
 
-        data = {}
-        data["humidity"] = humidity_data
-        data["temperature"] = temperature_data
+        data = {"humidity": humidity_data, "temperature": temperature_data}
 
         return data
 
diff --git a/tests/test_backend_iterations.py b/tests/test_backend_iterations.py
index e2e4526..2889f38 100644
--- a/tests/test_backend_iterations.py
+++ b/tests/test_backend_iterations.py
@@ -136,7 +136,7 @@ def test_get_most_coefficients(self):
 
     @pytest.mark.dependency(name="TestBackendIterationMost::test_similarity_function")
     @pytest.mark.parametrize("arg_obukhov", [(-100, False), (0, True), (100, True)])
-    def test_similarity_function(self, arg_obukhov):
+    def test_similarity_function(self, arg_obukhov: tuple):
         """Compute similarity function."""
 
         test_f_ct2 = self.test_class.similarity_function(
@@ -148,7 +148,7 @@ def test_similarity_function(self, arg_obukhov):
 
     @pytest.mark.dependency(name="TestBackendIterationMost::test_calc_theta_star")
     @pytest.mark.parametrize("arg_params", [(1.9e-04, 5.6, True), (2e-03, 3.6, False)])
-    def test_calc_theta_star(self, arg_params):
+    def test_calc_theta_star(self, arg_params: tuple):
         """Calculate temperature scale."""
 
         test_theta = self.test_class.calc_theta_star(
@@ -182,7 +182,7 @@ def test_calc_obukhov_length(self, arg_theta):
         """Calculate Obukhov length."""
 
         compare_lob = self.test_class.calc_obukhov_length(
-            temp=295, u_star=0.2, theta_star=mpmath.mpmathify(arg_theta)
+            temp=np.float64(295.0), u_star=0.2, theta_star=mpmath.mpmathify(arg_theta)
         )
         assert isinstance(compare_lob, mpmath.mpf)
         assert (compare_lob < 0) == (arg_theta < 0)  # obukhov and theta have same sign
@@ -224,7 +224,7 @@ def test_check_signs(self, arg_shf, arg_obukhov):
         scope="class",
     )
     @pytest.mark.parametrize("arg_stable", [(200, True), (-100, False)])
-    def test_most_iteration(self, conftest_mock_merged_dataframe, arg_stable):
+    def test_most_iteration(self, conftest_mock_merged_dataframe, arg_stable: tuple):
         """Iterate single row of dataframe using MOST."""
 
         test_data = conftest_mock_merged_dataframe.iloc[0].copy(deep=True)
@@ -310,7 +310,7 @@ def test_most_method(self, capsys, conftest_mock_merged_dataframe, arg_stable):
         for key in compare_keys:
             assert not (compare_most[key].isnull()).any()
             assert key in compare_most.keys()
-            assert all(isinstance(x, (mpmath.mpf)) for x in compare_most[key])
+            assert all(isinstance(x, mpmath.mpf) for x in compare_most[key])
 
         # signs match stability
         assert (compare_most["obukhov"] > 0).all() == arg_stable[1]
diff --git a/tests/test_backend_transects.py b/tests/test_backend_transects.py
index 6c28610..93cddf3 100644
--- a/tests/test_backend_transects.py
+++ b/tests/test_backend_transects.py
@@ -204,7 +204,7 @@ def test_print_path_heights(self, capsys, arg_stability):
         test_capture = capsys.readouterr()
 
         self.test_transect_parameters.print_path_heights(
-            z_eff=34, z_mean=31.245, stability=arg_stability
+            z_eff=np.float64(34), z_mean=np.float64(31.245), stability=arg_stability
         )
         compare_capture = capsys.readouterr()
 
diff --git a/tests/test_visuals_plotting.py b/tests/test_visuals_plotting.py
index e4268ac..7fd3f4c 100644
--- a/tests/test_visuals_plotting.py
+++ b/tests/test_visuals_plotting.py
@@ -606,14 +606,14 @@ def test_plot_iterated_fluxes(
         compare_plots = {
             "shf": {
                 "title": "Sensible Heat Flux",
-                "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
-                "xlabel": "Time, CET",
+                "y_label": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
+                "x_label": "Time, CET",
                 "plot": (compare_plots[0]),
             },
             "comparison": {
                 "title": "Sensible Heat Flux from Free Convection and Iteration",
-                "ylabel": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
-                "xlabel": "Time, CET",
+                "y_label": r"Sensible Heat Flux, [W$\cdot$m$^{-2}$]",
+                "x_label": "Time, CET",
                 "plot": (compare_plots[1]),
             },
         }
diff --git a/tests/test_wrangler_data_parser.py b/tests/test_wrangler_data_parser.py
index 83d0ff0..77f3d05 100644
--- a/tests/test_wrangler_data_parser.py
+++ b/tests/test_wrangler_data_parser.py
@@ -891,7 +891,7 @@ def test_vertical_init(self):
     @pytest.mark.dependency(
         name="TestWranglerVertical::test_construct_hatpro_levels_error"
     )
-    @pytest.mark.parametrize("arg_levels", [[(0, 1), (0)], [1.0, 30]])
+    @pytest.mark.parametrize("arg_levels", [[(0, 1), 0], [1.0, 30]])
     def test_construct_hatpro_levels_error(self, arg_levels):
         """Raise error for incorrectly formatted scanning levels."""
 
@@ -910,7 +910,7 @@ def test_construct_hatpro_levels(self, arg_levels):
         compare_scan = self.test_wrangler_vertical.construct_hatpro_levels(
             levels=arg_levels
         )
-        assert isinstance(compare_scan, (list))
+        assert isinstance(compare_scan, list)
         assert all(isinstance(x, int) for x in compare_scan)
 
     @pytest.mark.dependency(

From cc9fedcaaa4bf7b34f40439eb3a486bf3944dd84 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Mon, 29 May 2023 16:20:04 +0200
Subject: [PATCH 15/17] merge: merge feat-ST128-deprecations module (#9)

* feat(backed): add decorators for deprecating objects

Call the decorator with:

    from scintillometry.backend.deprecations import Decorators

    @Decorators.deprecated(stage="...", reason="...", version="...")
    def some_function(foo=...):
        ...

Refs: ST-3, ST-6, ST-128

* feat(backend): deprecate individual arguments

Adds method to deprecate individual function arguments.

```
from scintillometry.backend.deprecations import Decorators

@Decorators.deprecated_argument(stage, old_argument="new_argument")
def some_function(new_argument):
    ...
```

Refs: ST-3, ST-6, ST-128

* refactor(visuals): start deprecating plot_iterated_fluxes

Marks `plot_iterated_fluxes` as pending deprecation. This function is
superseded by `MetricsFlux.plot_iterated_metrics`.

Refs: ST-3, ST-8, ST-126

* refactor(metrics): deprecate argument in plot_iterated_metrics

Marks `site_location` as pending deprecation. Argument is replaced by
`location`.

Refs: ST-3, ST-7, ST-126

* docs(metrics): updates docstring noting deprecation

Refs: ST-2, ST-126
---
 docs/source/scintillometry.backend.rst     |  10 +
 src/scintillometry/backend/deprecations.py | 339 +++++++++++++
 src/scintillometry/metrics/calculations.py |  19 +-
 src/scintillometry/visuals/plotting.py     |   6 +
 tests/test_backend_deprecations.py         | 543 +++++++++++++++++++++
 tests/test_metrics_calculations.py         |  16 +-
 tests/test_visuals_plotting.py             |  11 +-
 7 files changed, 930 insertions(+), 14 deletions(-)
 create mode 100644 src/scintillometry/backend/deprecations.py
 create mode 100644 tests/test_backend_deprecations.py

diff --git a/docs/source/scintillometry.backend.rst b/docs/source/scintillometry.backend.rst
index fb56779..97ef5a5 100644
--- a/docs/source/scintillometry.backend.rst
+++ b/docs/source/scintillometry.backend.rst
@@ -70,6 +70,16 @@ In: scintillometry.backend.iterations.py
    :undoc-members:
    :show-inheritance:
 
+Deprecations module
+-------------------
+
+In: scintillometry.backend.deprecations.py
+
+.. automodule:: scintillometry.backend.deprecations
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 References
 ----------
 
diff --git a/src/scintillometry/backend/deprecations.py b/src/scintillometry/backend/deprecations.py
new file mode 100644
index 0000000..2f6cb22
--- /dev/null
+++ b/src/scintillometry/backend/deprecations.py
@@ -0,0 +1,339 @@
+"""Copyright 2023 Scintillometry Contributors.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    https://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=====
+
+Handles deprecating, deprecated, and defunct code. The deprecation
+process takes one patch release cycle, the removal process takes two
+major release cycles.
+
+EOL Cycle
+---------
+
+Import the decorator
+:func:`~scintillometry.backend.deprecations.deprecated` from this
+module. Mark deprecating functions like so:
+
+.. code-block:: python
+
+    @deprecated(stage="deprecated", reason="Some reason", version="1.1.1")
+    def foobar(...)
+        ...
+
+Where ``stage`` is the stage in the function's deprecation cycle,
+``reason`` is an optional message, and ``version`` is the release number
+when ``stage`` was last updated.
+
+Update ``stage`` by following this schedule:
+
+1. A function pending deprecation is marked as **pending** and issues a
+PendingDeprecationWarning during patch development.
+
+2. The function is marked as **deprecated** and issues a
+DeprecationWarning from the next patch release. It must still work as
+intended.
+
+3. The function is marked as **eol** and issues a FutureWarning during
+the next minor release cycle. It must still work as intended.
+
+4. The function is marked as **defunct** and throws an error during the
+next major release cycle, but is not removed.
+
+5. The defunct function is entirely removed from release candidates in
+preparation for the subsequent major release.
+"""
+
+
+import functools
+import inspect
+import warnings
+from typing import Callable
+
+
+class DeprecationHandler:
+    """Methods for marking and handling deprecation cycles.
+
+    Attributes:
+        string_types (tuple): Supported string types (str and
+            byte literals).
+    """
+
+    def __init__(self):
+        super().__init__()
+        self.string_types = (type(b""), type(""))  # support byte literals
+
+    def get_stage(self, name):
+        """Gets stage in deprecation cycle.
+
+        Args:
+            name (str): Stage of deprecation cycle. Valid values
+                are:
+
+                    - pending
+                    - deprecated
+                    - eol
+                    - defunct
+
+        Returns:
+            tuple[str, Exception]: The description of the deprecation stage,
+            and the Exception subclass matching this stage.
+
+        Raises:
+            TypeError: <type(name)> is an invalid type. Use str instead.
+            ValueError: <name> is not a valid deprecation stage.
+        """
+
+        if isinstance(name, self.string_types):
+            stage_lower = name.lower()
+            if stage_lower == "deprecated":
+                stage_string = "deprecated."
+                category = DeprecationWarning
+            elif stage_lower == "pending":
+                stage_string = "pending deprecation."
+                category = PendingDeprecationWarning
+            elif stage_lower == "eol":
+                stage_string = "deprecated."
+                category = FutureWarning
+            elif stage_lower == "defunct":
+                stage_string = "defunct."
+                category = RuntimeError
+            else:
+                raise ValueError(f"{stage_lower} is not a valid deprecation stage.")
+        else:
+            raise TypeError(f"{type(name)} is an invalid type. Use {str} instead.")
+
+        return stage_string, category
+
+    def get_reason(self, **kwargs):
+        """Gets reason for deprecation.
+
+        Keyword Args:
+            reason (str): Reason for deprecation.
+
+        Returns:
+            str: The reason for deprecation if available, otherwise returns
+            an empty string.
+        """
+
+        reason = kwargs.get("reason", None)
+        if not isinstance(reason, self.string_types):
+            reason = ""
+
+        return reason
+
+    def get_version(self, **kwargs):
+        """Gets release number of latest stage in deprecation.
+
+        Keyword Args:
+            version (str): Release number of latest stage in deprecation.
+
+        Returns:
+            str: Formatted version number of latest stage in deprecation if
+            provided, otherwise returns an empty string.
+        """
+
+        version = kwargs.get("version", None)
+        if not isinstance(version, self.string_types):
+            version = ""
+        else:
+            version = f"Ver. {version}: "
+
+        return version
+
+    def raise_warning(self, obj, stage, details):
+        """Raises warning or error with informative message.
+
+        Raises a warning or error stating the function or class' stage in
+        its deprecation cycle. Optionally, lists a release number and
+        reason.
+
+        Args:
+            obj (Callable): The function or class being deprecated.
+            stage (str): The current stage in the deprecation cycle.
+            details (dict): A dictionary map optionally containing the
+                keys:
+
+                    - **reason**: the reason for deprecation.
+                    - **version**: the release number of the latest
+                      change in the deprecation cycle.
+
+        Raises:
+            RuntimeError: The function <obj.__name__> is <stage>.
+        """
+
+        stage_string, warn_class = self.get_stage(name=stage)
+        reason = self.get_reason(**details)
+        version = self.get_version(**details)
+        suffix = " ".join((stage_string, reason))
+
+        if inspect.isclass(obj):
+            warn_string = f"{version}The class {obj.__name__} is {suffix}"
+        else:
+            warn_string = f"{version}The function {obj.__name__} is {suffix}"
+
+        if stage.lower() != "defunct":
+            warnings.warn(
+                message=warn_string.strip(),
+                category=warn_class,
+                stacklevel=2,
+            )
+        else:
+            raise RuntimeError(warn_string.strip())
+
+    def rename_arguments(self, obj, stage, kwargs, alias, reason=None, version=None):
+        """Marks argument as deprecated and redirects to alias.
+
+        The wrapped function's arguments are wrapped into `kwargs` and
+        are safe from being overwritten by arguments in alias.
+
+        Args:
+            obj (Callable): The function or class being deprecated.
+            stage (str): The current stage in the deprecation cycle.
+            kwargs (dict): Keyword arguments.
+            alias (dict): A dictionary map optionally containing the
+                keys:
+
+            reason (str): The reason for deprecation. Default None.
+            version (str): The release number of the latest change in
+                the deprecation cycle. Default None.
+        """
+
+        stage_string, warn_class = self.get_stage(name=stage)
+        reason = self.get_reason(**{"reason": reason})
+        version = self.get_version(**{"version": version})
+
+        for old, new in alias.items():
+            if old in kwargs:
+                if new in kwargs:
+                    warn_string = (
+                        f"{version}{obj.__name__}",
+                        f"received both {old} and {new} as arguments. {old}",
+                        f"is {stage_string}",
+                        f"Use {new} instead.",
+                        f"{reason}",
+                    )
+                    raise TypeError(" ".join(warn_string).strip())
+                else:
+                    warn_string = (
+                        f"{version}The argument {old} in {obj.__name__}",
+                        f"is {stage_string}",
+                        f"Use {new} instead.",
+                        f"{reason}",
+                    )
+                    warnings.warn(
+                        message=" ".join(warn_string).strip(),
+                        category=warn_class,
+                        stacklevel=2,
+                    )
+                kwargs[new] = kwargs.pop(old)
+
+
+class Decorators:
+    def __init__(self):
+        super().__init__()
+
+    @staticmethod
+    def deprecated(stage="deprecated", **details):
+        """Decorator for deprecated function and method arguments.
+
+        Example:
+
+        .. code-block:: python
+
+            @deprecated(stage="pending", reason="Foobar", version="1.3.2")
+            def some_function(foo):
+                ...
+
+
+        Args:
+            stage(str): Stage of deprecation cycle. Valid values
+                are:
+
+                    - pending
+                    - deprecated
+                    - eol
+                    - defunct
+
+                Default "deprecated".
+        Keyword Args:
+            reason (str): Reason for deprecation.
+            version (str): Release number of latest stage in deprecation.
+
+        Returns:
+            Callable: Decorator for deprecated argument.
+        """
+
+        internals = DeprecationHandler()
+
+        def decorator(f: Callable):
+            @functools.wraps(f)
+            def wrapper(*args, **kwargs):
+                internals.raise_warning(f, stage, details)
+                return f(*args, **kwargs)
+
+            return wrapper
+
+        return decorator
+
+    @staticmethod
+    def deprecated_argument(stage="deprecated", reason=None, version=None, **aliases):
+        """Decorator for deprecated function and method arguments.
+
+        Use as follows:
+
+        .. code-block:: python
+
+            @deprecated_argument(old_argument="new_argument")
+            def myfunc(new_arg):
+                ...
+
+        Args:
+            stage(str): Stage of deprecation cycle. Valid values
+                are:
+
+                    - pending
+                    - deprecated
+                    - eol
+                    - defunct
+
+                Default "deprecated".
+            reason (str): Reason for deprecation. Default None.
+            version (str): Release number of latest stage in
+                deprecation. Default None.
+            aliases (dict[str, str]): Deprecated argument and its
+                alternative.
+
+        Returns:
+            Callable: Decorator for deprecated argument.
+
+        """
+
+        internals = DeprecationHandler()
+
+        def decorator(f: Callable):
+            @functools.wraps(f)
+            def wrapper(*args, **kwargs):
+                internals.rename_arguments(
+                    obj=f,
+                    stage=stage,
+                    reason=reason,
+                    version=version,
+                    kwargs=kwargs,
+                    alias=aliases,
+                )
+                return f(*args, **kwargs)
+
+            return wrapper
+
+        return decorator
diff --git a/src/scintillometry/metrics/calculations.py b/src/scintillometry/metrics/calculations.py
index 4b044d1..6eea166 100755
--- a/src/scintillometry/metrics/calculations.py
+++ b/src/scintillometry/metrics/calculations.py
@@ -27,6 +27,7 @@
 from scintillometry.backend.iterations import IterationMost
 from scintillometry.backend.transects import TransectParameters
 from scintillometry.visuals.plotting import FigurePlotter
+from scintillometry.backend.deprecations import Decorators
 
 
 class MetricsTopography:
@@ -824,20 +825,22 @@ def plot_derived_metrics(self, derived_data, time_id, regime=None, location=""):
 
         return derived_plots
 
-    def plot_iterated_metrics(self, iterated_data, time_stamp, site_location=""):
+    @Decorators.deprecated_argument(
+        stage="pending", version="1.0.5", site_location="location"
+    )
+    def plot_iterated_metrics(self, iterated_data, time_stamp, location=""):
         """Plots and saves iterated SHF, comparison to free convection.
 
         .. todo::
-            ST-126: Deprecate FigurePlotter.plot_iterated_fluxes in
-                favour of plot_iterated_metrics. `site_location` should
-                be deprecated in favour of `location`.
+            ST-126: Deprecate the argument `site_location` for
+                `location`.
 
         Args:
             iterated_data (pd.DataFrame): TZ-aware with columns for
                 sensible heat fluxes calculated for free convection
                 |H_free|, and by MOST |H|.
             time_stamp (pd.Timestamp): Local time of data collection.
-            site_location (str): Location of data collection. Default empty
+            location (str): Location of data collection. Default empty
                 string.
 
         Returns:
@@ -846,7 +849,7 @@ def plot_iterated_metrics(self, iterated_data, time_stamp, site_location=""):
             sensible heat flux under free convection.
         """
 
-        shf_plot = self.plotting.plot_generic(iterated_data, "shf", site=site_location)
+        shf_plot = self.plotting.plot_generic(iterated_data, "shf", site=location)
         self.plotting.save_figure(
             figure=shf_plot[0], timestamp=time_stamp, suffix="shf"
         )
@@ -856,7 +859,7 @@ def plot_iterated_metrics(self, iterated_data, time_stamp, site_location=""):
             df_02=iterated_data,
             keys=["H_free", "shf"],
             labels=["Free Convection", "Iteration"],
-            site=site_location,
+            site=location,
         )
         self.plotting.save_figure(
             figure=comparison_plot[0], timestamp=time_stamp, suffix="shf_comp"
@@ -974,7 +977,7 @@ def calculate_standard_metrics(
         self.plot_iterated_metrics(
             iterated_data=iterated_dataframe,
             time_stamp=data_timestamp,
-            site_location=location,
+            location=location,
         )
 
         data["derivation"] = derived_dataframe
diff --git a/src/scintillometry/visuals/plotting.py b/src/scintillometry/visuals/plotting.py
index 68f5ccf..2819747 100644
--- a/src/scintillometry/visuals/plotting.py
+++ b/src/scintillometry/visuals/plotting.py
@@ -25,6 +25,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
+from scintillometry.backend.deprecations import Decorators
 
 
 class FigureFormat:
@@ -582,6 +583,11 @@ def plot_comparison(self, df_01, df_02, keys, labels, site=""):
 
         return figure, axes
 
+    @Decorators.deprecated(
+        stage="pending",
+        reason="Superseded by MetricsFlux.plot_iterated_metrics.",
+        version="1.0.5",
+    )
     def plot_iterated_fluxes(self, iteration_data, time_id, location=""):
         """Plots and saves iterated SHF, comparison to free convection.
 
diff --git a/tests/test_backend_deprecations.py b/tests/test_backend_deprecations.py
new file mode 100644
index 0000000..8ed5e6a
--- /dev/null
+++ b/tests/test_backend_deprecations.py
@@ -0,0 +1,543 @@
+"""Copyright 2023 Scintillometry Contributors.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    https://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=====
+
+This module is used to test deprecation decorators, not deprecating
+functions.
+
+Use the `conftest_boilerplate` fixture to avoid duplicating tests.
+"""
+
+import inspect
+from typing import Callable
+
+import pytest
+
+from scintillometry.backend.deprecations import Decorators, DeprecationHandler
+
+
+class TestBackendDeprecationsMock:
+    """Test mock class targeted by decorators."""
+
+    class MockDeprecationsClass:
+        """Mock class to call when testing decorators."""
+
+        def add_one(self, a: int):
+            """Adds 1 to input integer."""
+
+            a += 1
+
+            return a
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsMock::test_mock_deprecations_class"
+    )
+    def test_mock_deprecations_class(self):
+        """Create mock class for testing deprecation."""
+        assert inspect.isclass(self.MockDeprecationsClass)
+        mock_class = self.MockDeprecationsClass
+        assert mock_class.__name__ == "MockDeprecationsClass"
+        mock_class_instance = self.MockDeprecationsClass()
+        assert mock_class_instance
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsMock::test_add_one",
+        depends=["TestBackendDeprecationsMock::test_mock_deprecations_class"],
+    )
+    def test_add_one(self):
+        """Add 1 to integer."""
+
+        mock_class_instance = self.MockDeprecationsClass()
+        test_integer = 3
+        compare_integer = mock_class_instance.add_one(a=test_integer)
+        assert isinstance(compare_integer, int)
+        assert compare_integer == test_integer + 1
+
+
+class TestBackendDeprecationsHandler:
+    """Handles deprecation methods.
+
+    Attributes:
+        test_stages (dict[str, tuple[str, Exception]]): Names of
+            deprecation labels and respective text and warning category.
+        test_details (dict[str, str]): Mock details for decorator.
+        test_mock (type): Mock class called when testing decorators.
+        test_mock_instance (MockDeprecationsClass): An instantiated mock
+            class called when testing methods.
+        test_handler (DeprecationHandler): Class called by decorator
+            marking deprecation.
+    """
+
+    test_stages = {
+        "pending": ("pending deprecation.", PendingDeprecationWarning),
+        "deprecated": ("deprecated.", DeprecationWarning),
+        "eol": ("deprecated.", FutureWarning),
+        "defunct": ("defunct.", RuntimeError),
+    }
+    test_details = {"version": "1.1.2", "reason": "Some reason."}
+    test_mock = TestBackendDeprecationsMock.MockDeprecationsClass
+    test_mock_instance = TestBackendDeprecationsMock.MockDeprecationsClass()
+    test_handler = DeprecationHandler()
+
+    def setup_warning(
+        self,
+        obj: Callable,
+        stage: str = "deprecated",
+        reason: bool = False,
+        version: bool = False,
+    ):
+        """Creates regex string for warning message."""
+
+        test_details = {}
+        suffix = ""
+        prefix = ""
+        if reason:
+            test_details["reason"] = self.test_details["reason"]
+            suffix = test_details["reason"]
+        if version:
+            test_details["version"] = self.test_details["version"]
+            prefix = f"Ver. {test_details['version']}: "
+
+        suffix_string = " ".join((self.test_stages[stage][0], suffix))
+        if inspect.isclass(obj):
+            assert obj.__name__ == "MockDeprecationsClass"
+            object_string = f"class {obj.__name__}"
+        else:
+            object_string = f"function {obj.__name__}"
+
+        regex = f"{prefix}The {object_string} is {suffix_string}".strip()
+
+        return regex, prefix, suffix, test_details
+
+    @pytest.mark.parametrize("arg_stage", ["pending", "deprecated"])
+    @pytest.mark.parametrize("arg_class", [True, False])
+    @pytest.mark.parametrize("arg_reason", [True, False])
+    @pytest.mark.parametrize("arg_version", [True, False])
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsHandler::test_setup_warning",
+        depends=["TestBackendDeprecationsMock::test_add_one"],
+    )
+    def test_setup_warning(self, arg_class, arg_stage, arg_reason, arg_version):
+        """Create regex string to test warning message."""
+
+        if arg_class:
+            test_object = self.test_mock
+            assert isinstance(test_object, type)
+            assert inspect.isclass(test_object)
+        else:
+            test_object = self.test_mock_instance.add_one
+            assert not isinstance(test_object, type)
+            assert not inspect.isclass(test_object)
+            assert isinstance(test_object, Callable)
+
+        warn_params = self.setup_warning(
+            obj=test_object,
+            stage=arg_stage,
+            reason=arg_reason,
+            version=arg_version,
+        )
+        assert isinstance(warn_params[0], str)
+        if arg_version:
+            assert warn_params[1] == f"Ver. {self.test_details['version']}: "
+            assert "version" in warn_params[3]
+        else:
+            assert warn_params[1] == ""
+            assert "version" not in warn_params[3]
+        if arg_reason:
+            assert warn_params[2] == self.test_details["reason"]
+            assert "reason" in warn_params[3]
+        else:
+            assert warn_params[2] == ""
+            assert "reason" not in warn_params[3]
+
+    def get_mock_object(self, is_class: bool = False):
+        """Gets mock class or function."""
+
+        if is_class:
+            obj = self.test_mock
+        else:
+            obj = self.test_mock_instance.add_one
+
+        return obj
+
+    @pytest.mark.dependency(name="TestBackendDeprecationsHandler::test_get_mock_object")
+    @pytest.mark.parametrize("arg_class", [True, False])
+    def test_get_mock_object(self, arg_class):
+        """Get mock class or function."""
+
+        compare_object = self.get_mock_object(is_class=arg_class)
+        if arg_class:
+            assert inspect.isclass(compare_object)
+        else:
+            assert not inspect.isclass(compare_object)
+
+    @pytest.mark.dependency(name="TestBackendDeprecationsHandler::test_get_stage_error")
+    def test_get_stage_error(self):
+        """Raise error for incorrect or missing stage argument."""
+
+        test_stage = "incorrect stage"
+        with pytest.raises(
+            ValueError, match=f"{test_stage} is not a valid deprecation stage."
+        ):
+            self.test_handler.get_stage(name=test_stage)
+        with pytest.raises(
+            TypeError, match=f"{int} is an invalid type. Use {str} instead."
+        ):
+            self.test_handler.get_stage(name=1)
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsHandler::test_get_stage",
+        depends=["TestBackendDeprecationsHandler::test_get_stage_error"],
+    )
+    def test_get_stage(self):
+        """Get deprecation stage and warning category."""
+
+        for key, value in self.test_stages.items():
+            compare_stage, compare_warning = self.test_handler.get_stage(name=key)
+            assert compare_stage == value[0]
+            assert compare_warning == value[1]
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsHandler::test_get_reason_invalid"
+    )
+    def test_get_reason_invalid(self):
+        """Return empty string for missing value or invalid type."""
+
+        test_kwargs = {"stage": "pending"}
+        compare_reason = self.test_handler.get_reason(**test_kwargs)
+        assert compare_reason == ""
+        compare_reason = self.test_handler.get_reason(reason=1)
+        assert compare_reason == ""
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsHandler::test_get_reason",
+        depends=["TestBackendDeprecationsHandler::test_get_reason_invalid"],
+    )
+    def test_get_reason(self):
+        """Get reason for deprecation."""
+
+        test_kwargs = {"stage": "pending", "reason": "Some reason."}
+
+        compare_reason = self.test_handler.get_reason(**test_kwargs)
+        assert compare_reason == test_kwargs["reason"]
+        compare_reason = self.test_handler.get_reason(reason=test_kwargs["reason"])
+        assert compare_reason == test_kwargs["reason"]
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsHandler::test_get_version_invalid"
+    )
+    def test_get_version_invalid(self):
+        """Return empty string for missing version or invalid type."""
+
+        test_kwargs = {"stage": "pending"}
+        compare_reason = self.test_handler.get_version(**test_kwargs)
+        assert compare_reason == ""
+        compare_reason = self.test_handler.get_version(reason=1)
+        assert compare_reason == ""
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsHandler::test_get_version",
+        depends=["TestBackendDeprecationsHandler::test_get_version_invalid"],
+    )
+    def test_get_version(self):
+        """Get release number of last deprecation update."""
+
+        test_kwargs = {"stage": "pending", "version": "1.1.0"}
+
+        compare_version = self.test_handler.get_version(**test_kwargs)
+        assert compare_version == f"Ver. {test_kwargs['version']}: "
+        compare_version = self.test_handler.get_version(version=test_kwargs["version"])
+        assert compare_version == f"Ver. {test_kwargs['version']}: "
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsHandler::test_raise_warning",
+        depends=["TestBackendDeprecationsHandler::test_setup_warning"],
+    )
+    @pytest.mark.parametrize("arg_stage", ["pending", "deprecated", "eol"])
+    @pytest.mark.parametrize("arg_class", [True, False])
+    @pytest.mark.parametrize("arg_reason", [True, False])
+    @pytest.mark.parametrize("arg_version", [True, False])
+    def test_raise_warning(self, arg_class, arg_stage, arg_reason, arg_version):
+        """Raise warning for deprecated object."""
+
+        assert arg_stage in self.test_stages
+        test_object = self.get_mock_object(is_class=arg_class)
+        test_warning = self.setup_warning(
+            obj=test_object, stage=arg_stage, reason=arg_reason, version=arg_version
+        )
+
+        with pytest.warns(self.test_stages[arg_stage][1], match=test_warning[0]):
+            self.test_handler.raise_warning(
+                obj=test_object, stage=arg_stage, details=test_warning[3]
+            )
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsHandler::test_raise_warning_error",
+        depends=["TestBackendDeprecationsHandler::test_setup_warning"],
+    )
+    @pytest.mark.parametrize("arg_class", [True, False])
+    @pytest.mark.parametrize("arg_reason", [True, False])
+    @pytest.mark.parametrize("arg_version", [True, False])
+    def test_raise_warning_error(self, arg_reason, arg_version, arg_class):
+        """Raise RuntimeError when stage="defunct."""
+
+        assert "defunct" in self.test_stages
+        test_object = self.get_mock_object(is_class=arg_class)
+        test_warning = self.setup_warning(
+            obj=test_object, stage="defunct", reason=arg_reason, version=arg_version
+        )
+
+        with pytest.raises(self.test_stages["defunct"][1], match=test_warning[0]):
+            self.test_handler.raise_warning(
+                obj=test_object, stage="defunct", details=test_warning[3]
+            )
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsHandler::test_rename_arguments",
+        depends=["TestBackendDeprecationsHandler::test_setup_warning"],
+    )
+    @pytest.mark.parametrize("arg_stage", ["pending", "deprecated", "eol"])
+    @pytest.mark.parametrize("arg_reason", [True, False])
+    @pytest.mark.parametrize("arg_version", [True, False])
+    def test_rename_arguments(self, arg_stage, arg_reason, arg_version):
+        """Raise warning and redirect deprecated argument."""
+
+        assert arg_stage in self.test_stages
+        test_object = self.get_mock_object(is_class=False)
+        test_warning = self.setup_warning(
+            obj=test_object, stage=arg_stage, reason=arg_reason, version=arg_version
+        )
+        test_alias_old = "a"
+        test_alias_new = "b"
+        test_regex = (
+            f"{test_warning[1]}The argument {test_alias_old} in {test_object.__name__}",
+            f"is {self.test_stages[arg_stage][0]}",
+            f"Use {test_alias_new} instead.",
+            f"{test_warning[3].get('reason','')}",
+        )
+        test_kwargs = {test_alias_old: 2, "extra_arg": 3}
+        test_alias = {test_alias_old: test_alias_new}
+
+        with pytest.warns(
+            self.test_stages[arg_stage][1], match=" ".join(test_regex).strip()
+        ):
+            self.test_handler.rename_arguments(
+                obj=test_object,
+                stage=arg_stage,
+                kwargs=test_kwargs,
+                alias=test_alias,
+                version=test_warning[3].get("version", None),
+                reason=test_warning[3].get("reason", None),
+            )
+        assert test_alias_old not in test_kwargs  # argument is replaced
+        assert test_alias_new in test_kwargs
+        assert test_kwargs[test_alias_new] == 2
+        assert "extra_arg" in test_kwargs
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsHandler::test_rename_arguments_error",
+        depends=["TestBackendDeprecationsHandler::test_setup_warning"],
+    )
+    @pytest.mark.parametrize("arg_stage", ["pending", "deprecated", "eol"])
+    @pytest.mark.parametrize("arg_reason", [True, False])
+    @pytest.mark.parametrize("arg_version", [True, False])
+    def test_rename_arguments_error(self, arg_stage, arg_reason, arg_version):
+        """Raise warning and redirect deprecated argument."""
+
+        assert arg_stage in self.test_stages
+        test_object = self.get_mock_object(is_class=False)
+        test_warning = self.setup_warning(
+            obj=test_object, stage=arg_stage, reason=arg_reason, version=arg_version
+        )
+        test_alias_old = "a"
+        test_alias_new = "b"
+        test_regex = (
+            f"{test_warning[1]}{test_object.__name__}",
+            f"received both {test_alias_old} and {test_alias_new} as arguments.",
+            f"{test_alias_old} is {self.test_stages[arg_stage][0]} "
+            f"Use {test_alias_new} instead.",
+            f"{test_warning[3].get('reason','')}",
+        )
+        test_kwargs = {test_alias_old: 1, test_alias_new: 3, "extra_arg": 2}
+        test_alias = {test_alias_old: test_alias_new}
+
+        with pytest.raises(TypeError, match=" ".join(test_regex).strip()):
+            self.test_handler.rename_arguments(
+                obj=test_object,
+                stage=arg_stage,
+                kwargs=test_kwargs,
+                alias=test_alias,
+                version=test_warning[3].get("version", None),
+                reason=test_warning[3].get("reason", None),
+            )
+        assert test_alias_old in test_kwargs
+        assert test_alias_new in test_kwargs
+        assert test_kwargs[test_alias_new] == 3  # argument is not replaced
+        assert "extra_arg" in test_kwargs
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsHandler::test_rename_arguments_missing",
+        depends=["TestBackendDeprecationsHandler::test_setup_warning"],
+    )
+    @pytest.mark.parametrize("arg_stage", ["pending", "deprecated", "eol"])
+    @pytest.mark.parametrize("arg_reason", [True, False])
+    @pytest.mark.parametrize("arg_version", [True, False])
+    def test_rename_arguments_missing(self, arg_stage, arg_reason, arg_version):
+        """Raise warning and redirect deprecated argument."""
+
+        assert arg_stage in self.test_stages
+        test_object = self.get_mock_object(is_class=False)
+        test_warning = self.setup_warning(
+            obj=test_object, stage=arg_stage, reason=arg_reason, version=arg_version
+        )
+        test_alias_old = "a"
+        test_alias_new = "b"
+        test_kwargs = {test_alias_new: 3, "extra_arg": 2}
+        test_alias = {test_alias_old: test_alias_new}
+
+        self.test_handler.rename_arguments(
+            obj=test_object,
+            stage=arg_stage,
+            kwargs=test_kwargs,
+            alias=test_alias,
+            version=test_warning[3].get("version", None),
+            reason=test_warning[3].get("reason", None),
+        )
+        assert test_alias_old not in test_kwargs
+        assert test_alias_new in test_kwargs
+        assert test_kwargs[test_alias_new] == 3  # argument is not replaced
+        assert "extra_arg" in test_kwargs
+
+
+class TestBackendDeprecationsDecorator(TestBackendDeprecationsHandler):
+    """Tests decorators marking deprecated objects."""
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsDecorator::test_decorators_init"
+    )
+    def test_decorators_init(self):
+        test_instance = Decorators()
+        assert test_instance
+        assert inspect.isclass(Decorators)
+        assert inspect.isfunction(Decorators.deprecated)
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsDecorator::test_deprecated_decorator",
+        depends=["TestBackendDeprecationsMock::test_add_one"],
+    )
+    @pytest.mark.parametrize("arg_stage", ["pending", "deprecated", "eol"])
+    @pytest.mark.parametrize("arg_reason", [True, False])
+    @pytest.mark.parametrize("arg_version", [True, False])
+    def test_deprecated_decorator(self, arg_stage, arg_reason, arg_version):
+        """Use decorator to raise warning."""
+
+        assert arg_stage in self.test_stages
+        test_details = {}
+        if arg_version:
+            test_details["version"] = self.test_details["version"]
+        if arg_reason:
+            test_details["reason"] = self.test_details["reason"]
+
+        @Decorators.deprecated(stage=arg_stage, **test_details)
+        def deprecated_one(x):  # pragma: no cover
+            b = self.test_mock_instance.add_one(a=x)
+            return b
+
+        test_warning = self.setup_warning(
+            obj=deprecated_one, stage=arg_stage, reason=arg_reason, version=arg_version
+        )
+
+        with pytest.warns(self.test_stages[arg_stage][1], match=test_warning[0]):
+            y = deprecated_one(x=1)
+            assert y == 2
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsDecorator::test_deprecated_error",
+        depends=[
+            "TestBackendDeprecationsMock::test_add_one",
+            "TestBackendDeprecationsHandler::test_raise_warning",
+            "TestBackendDeprecationsHandler::test_raise_warning_error",
+        ],
+    )
+    @pytest.mark.parametrize("arg_reason", [True, False])
+    @pytest.mark.parametrize("arg_version", [True, False])
+    def test_deprecated_error(self, arg_reason, arg_version):
+        """Raise RuntimeError when stage="defunct."""
+
+        assert "defunct" in self.test_stages
+        test_details = {}
+        if arg_version:
+            test_details["version"] = self.test_details["version"]
+        if arg_reason:
+            test_details["reason"] = self.test_details["reason"]
+
+        @Decorators.deprecated(stage="defunct", **test_details)
+        def deprecated_one(x):  # pragma: no cover
+            b = self.test_mock_instance.add_one(a=x)
+            return b
+
+        test_warning = self.setup_warning(
+            obj=deprecated_one, stage="defunct", reason=arg_reason, version=arg_version
+        )
+
+        with pytest.raises(
+            self.test_stages["defunct"][1],
+            match=test_warning[0],
+        ):
+            deprecated_one(x=1)
+
+    @pytest.mark.dependency(
+        name="TestBackendDeprecationsDecorator::test_deprecated_argument_decorator",
+        depends=["TestBackendDeprecationsMock::test_add_one"],
+    )
+    @pytest.mark.parametrize("arg_stage", ["pending", "deprecated", "eol"])
+    @pytest.mark.parametrize("arg_reason", [True, False])
+    @pytest.mark.parametrize("arg_version", [True, False])
+    def test_deprecated_argument_decorator(self, arg_stage, arg_reason, arg_version):
+        """Use decorator to raise warning."""
+
+        assert arg_stage in self.test_stages
+        test_details = {}
+        if arg_version:
+            test_details["version"] = self.test_details["version"]
+        if arg_reason:
+            test_details["reason"] = self.test_details["reason"]
+        test_alias_new = "a"
+
+        @Decorators.deprecated_argument(
+            stage=arg_stage,
+            reason=test_details.get("reason", ""),
+            version=test_details.get("version", ""),
+            x=test_alias_new,
+        )
+        def deprecated_one(a):  # pragma: no cover
+            b = self.test_mock_instance.add_one(a=a)
+            return b
+
+        test_warning = self.setup_warning(
+            obj=deprecated_one, stage=arg_stage, reason=arg_reason, version=arg_version
+        )
+        test_regex = (
+            f"{test_warning[1]}The argument x in {deprecated_one.__name__}",
+            f"is {self.test_stages[arg_stage][0]}",
+            f"Use {test_alias_new} instead.",
+            f"{test_warning[3].get('reason','')}",
+        )
+
+        with pytest.warns(
+            self.test_stages[arg_stage][1], match=" ".join(test_regex).strip()
+        ):
+            y = deprecated_one(x=1)  # pylint:disable=no-value-for-parameter
+            assert y == 2
diff --git a/tests/test_metrics_calculations.py b/tests/test_metrics_calculations.py
index 468ed2c..98e75c0 100644
--- a/tests/test_metrics_calculations.py
+++ b/tests/test_metrics_calculations.py
@@ -908,7 +908,7 @@ def test_plot_iterated_metrics(
         compare_plots = self.test_metrics.plot_iterated_metrics(
             iterated_data=test_frame,
             time_stamp=test_stamp,
-            site_location=arg_location,
+            location=arg_location,
         )
         assert isinstance(compare_plots, list)
         assert all(isinstance(compare_tuple, tuple) for compare_tuple in compare_plots)
@@ -932,6 +932,20 @@ def test_plot_iterated_metrics(
 
         plt.close("all")
 
+        # site_location is pending deprecation
+        with pytest.warns(PendingDeprecationWarning):
+            compare_plots = self.test_metrics.plot_iterated_metrics(
+                iterated_data=test_frame,
+                time_stamp=test_stamp,
+                site_location=arg_location,  # pylint:disable=unexpected-keyword-arg
+            )
+        assert isinstance(compare_plots, list)
+        assert all(isinstance(compare_tuple, tuple) for compare_tuple in compare_plots)
+        for params in compare_params.values():
+            conftest_boilerplate.check_plot(plot_params=params, title=test_title)
+
+        plt.close("all")
+
     @pytest.mark.dependency(
         name="TestMetricsFlux::test_iterate_fluxes",
         depends=["TestMetricsFlux::test_append_vertical_variables"],
diff --git a/tests/test_visuals_plotting.py b/tests/test_visuals_plotting.py
index 7fd3f4c..043ba21 100644
--- a/tests/test_visuals_plotting.py
+++ b/tests/test_visuals_plotting.py
@@ -595,11 +595,12 @@ def test_plot_iterated_fluxes(
         test_title = f"{test_location},\n{self.test_date}"
         timestamp = test_data.index[0]
 
-        compare_plots = self.test_plotting.plot_iterated_fluxes(
-            iteration_data=test_data,
-            time_id=timestamp,
-            location=arg_location,
-        )
+        with pytest.deprecated_call():
+            compare_plots = self.test_plotting.plot_iterated_fluxes(
+                iteration_data=test_data,
+                time_id=timestamp,
+                location=arg_location,
+            )
         assert isinstance(compare_plots, list)
         assert all(isinstance(compare_tuple, tuple) for compare_tuple in compare_plots)
 

From 70f9d9832ee4383dc9690128ec6951b326c5cdb6 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Mon, 29 May 2023 16:24:09 +0200
Subject: [PATCH 16/17] build: toml license refers to name instead of file

Refs: ST-1, ST-2
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7ff6d7a..ee0c88c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ authors = [
 description = "Analyse data & 2D flux footprints from Scintec's BLS scintillometers."
 readme = "README.md"
 requires-python = ">=3.8"
-license = {file = "LICENSE"}
+license = Apache-2.0
 classifiers = [
     "Private :: Do Not Upload",
     "License :: OSI Approved :: Apache Software License",

From c948a21661057343ff49513cb09ff226f8996595 Mon Sep 17 00:00:00 2001
From: gampnico <45390064+gampnico@users.noreply.github.com>
Date: Mon, 29 May 2023 16:26:35 +0200
Subject: [PATCH 17/17] fix: incorrect toml syntax

Refs: ST-1
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ee0c88c..4ddb4c2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ authors = [
 description = "Analyse data & 2D flux footprints from Scintec's BLS scintillometers."
 readme = "README.md"
 requires-python = ">=3.8"
-license = Apache-2.0
+license = "Apache-2.0"
 classifiers = [
     "Private :: Do Not Upload",
     "License :: OSI Approved :: Apache Software License",