Repository: NREL/floris

Issue:
Bug report: `WindRose.plot()` argument `legend_kwargs` are said to be passed to `legend` in the doc strings, but they are passed to `colorbar` instead
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# Bug report: `WindRose.plot()` argument `legend_kwargs` are said to be passed to `legend` in the doc strings, but they are passed to `colorbar` instead
<!--
A clear and concise description of the bug including what happened
and what you expected to happen.
-->
`WindRose.plot()` argument `legend_kwargs` are said to be passed to `legend` in the doc strings, but they are passed to `colorbar` instead. This makes usage non-intuitive.

## How to reproduce
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Describe how another person with no context can recreate this issue.
It is typically very helpful to reduce the problem as much as possible
and share a minimum working example. See the note above on including
code as text rather than screenshots.
-->
Pass typical legend arguments to `WindRose.plot()`
```python

    import matplotlib.pyplot as plt

    wind_data = fmodel.wind_data
  
    time_series = TimeSeries(
        wind_directions=wind_data.wind_directions,
        wind_speeds=wind_data.wind_speeds,
        turbulence_intensities=wind_data.turbulence_intensities,
    )
          
    wind_rose = time_series.to_WindRose(wd_edges=np.arange(0, 360, 3.0), ws_edges=np.arange(2, 20, 2.0))
      
    fig, ax = plt.subplots(1, figsize=(4,4), subplot_kw={'projection': 'polar'})

    ax = wind_rose.plot(ax=ax, wd_step=10, legend_kwargs={"title": "Wind Speed (m/s)", "frameon": True})
```

## Relevant output
<!--
Include any output, plots, or other means of communication here to add context to the problem.
 -->
```text
  File "floris/floris/wind_data.py", line 782, in plot
    ax.figure.colorbar(sm_ws, ax=ax, **legend_kwargs)
  File "matplotlib/figure.py", line 1253, in colorbar
    cb = cbar.Colorbar(cax, mappable, **{
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

## Floris version
<!--
Share your floris version and how you installed it. You can print the floris version from
a Python REPL or script with these commands:
```python
import floris
print(floris.__version__)
```
 -->
4.2

## System Information
<!-- Add your information here. -->
 - OS: macOS 14.7.1
 - Python version: 3.11
 - Library versions
   - matplotlib: 3.9.2

Hints from issue comments:
@misi9170: Hi @jaredthomas68 , thanks for raising this. I believe the problem was introduced in #969. I think you can get around this for now by setting `legend_kwargs` to `{"label": Wind Speed (m/s)"}` (and dropping the `frameon` argument). But this is a user-interface change that we should have handled more thoroughly in a minor release, so I'll look into a more robust bugfix.@misi9170: Hi @jaredthomas68 , I've believe I've now addressed this in #1028 

Solution patch:
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index ead77afce..9281f86c0 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -20,11 +20,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build twine
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
         twine upload dist/*
diff --git a/docs/dev_guide.md b/docs/dev_guide.md
index 4a7c5dd76..a4a08e195 100644
--- a/docs/dev_guide.md
+++ b/docs/dev_guide.md
@@ -210,7 +210,7 @@ is located at `floris/.github/workflows/continuous-integration-workflow.yaml`.
 The online documentation is built with Jupyter Book which uses Sphinx
 as a framework. It is automatically built and hosted by GitHub, but it
 can also be compiled locally. Additional dependencies are required
-for the documentation, and they are listed in the `EXTRAS` of `setup.py`.
+for the documentation, and they are listed in the `project.optional-dependencies` of `pyproject.toml`.
 The commands to build the docs are given below. After successfully
 compiling, a file should be located at ``docs/_build/html/index.html``.
 This file can be opened in any browser.
@@ -246,7 +246,7 @@ Be sure to complete each step in the sequence as described.
     with a commit message such as "Update version to vN.M".
     The version number must be updated in the following two files:
     - [floris/README.md](https://github.com/NREL/floris/blob/main/README.md)
-    - [floris/floris/version.py](https://github.com/NREL/floris/blob/main/floris/version.py)
+    - [pyproject.toml](https://github.com/NREL/floris/blob/main/pyproject.toml)
     Note that a `.0` version number is left off meaning that valid versions
     are `v3`, `v3.1`, `v3.1.1`, etc.
 
diff --git a/examples/examples_control_optimization/008_optimize_yaw_with_disabled_turbines.py b/examples/examples_control_optimization/008_optimize_yaw_with_disabled_turbines.py
new file mode 100644
index 000000000..bd4d80b7b
--- /dev/null
+++ b/examples/examples_control_optimization/008_optimize_yaw_with_disabled_turbines.py
@@ -0,0 +1,48 @@
+"""Example: Optimizing yaw angles with disabled turbines
+
+This example demonstrates how to optimize yaw angles in FLORIS, when some turbines are disabled.
+The example optimization is run using both YawOptimizerSR and YawOptimizerGeometric, the two
+yaw optimizers that support disabling turbines.
+"""
+
+import numpy as np
+
+from floris import FlorisModel
+from floris.optimization.yaw_optimization.yaw_optimizer_geometric import YawOptimizationGeometric
+from floris.optimization.yaw_optimization.yaw_optimizer_sr import YawOptimizationSR
+
+
+# Load a 3-turbine model
+fmodel = FlorisModel("../inputs/gch.yaml")
+
+# Set wind conditions to be the same for two cases
+fmodel.set(wind_directions=[270.]*2, wind_speeds=[8.]*2, turbulence_intensities=[.06]*2)
+
+# First run the case where all turbines are active and print results
+yaw_opt = YawOptimizationSR(fmodel)
+df_opt = yaw_opt.optimize()
+print("Serial Refine optimized yaw angles (all turbines active) [deg]:\n", df_opt.yaw_angles_opt)
+
+yaw_opt = YawOptimizationGeometric(fmodel)
+df_opt = yaw_opt.optimize()
+print("\nGeometric optimized yaw angles (all turbines active) [deg]:\n", df_opt.yaw_angles_opt)
+
+# Disable turbines (different pattern for each of the two cases)
+# First case: disable the middle turbine
+# Second case: disable the front turbine
+fmodel.set_operation_model('mixed')
+fmodel.set(disable_turbines=np.array([[False, True, False], [True, False, False]]))
+
+# Rerun optimizations and print results
+yaw_opt = YawOptimizationSR(fmodel)
+df_opt = yaw_opt.optimize()
+print(
+    "\nSerial Refine optimized yaw angles (some turbines disabled) [deg]:\n",
+    df_opt.yaw_angles_opt
+)
+# Note that disabled turbines are assigned a zero yaw angle, but their yaw angle is arbitrary as it
+# does not affect the total power output.
+
+yaw_opt = YawOptimizationGeometric(fmodel)
+df_opt = yaw_opt.optimize()
+print("\nGeometric optimized yaw angles (some turbines disabled) [deg]:\n", df_opt.yaw_angles_opt)
diff --git a/floris/__init__.py b/floris/__init__.py
index d97bb24eb..717ea3175 100644
--- a/floris/__init__.py
+++ b/floris/__init__.py
@@ -1,9 +1,9 @@
 
+from importlib.metadata import version
 from pathlib import Path
 
 
-with open(Path(__file__).parent / "version.py") as _version_file:
-    __version__ = _version_file.read().strip()
+__version__ = version("floris")
 
 
 from .floris_model import FlorisModel
diff --git a/floris/core/turbine/operation_models.py b/floris/core/turbine/operation_models.py
index a6c1ff160..066e26b04 100644
--- a/floris/core/turbine/operation_models.py
+++ b/floris/core/turbine/operation_models.py
@@ -382,22 +382,22 @@ def axial_induction(
 @define
 class MixedOperationTurbine(BaseOperationModel):
 
+    @staticmethod
     def power(
         yaw_angles: NDArrayFloat,
         power_setpoints: NDArrayFloat,
         **kwargs
     ):
-        # Yaw angles mask all yaw_angles not equal to zero
-        yaw_angles_mask = yaw_angles != 0.0
-        power_setpoints_mask = power_setpoints < POWER_SETPOINT_DEFAULT
-        neither_mask = np.logical_not(yaw_angles_mask) & np.logical_not(power_setpoints_mask)
-
-        if (power_setpoints_mask & yaw_angles_mask).any():
-            raise ValueError((
-                "Power setpoints and yaw angles are incompatible."
-                "If yaw_angles entry is nonzero, power_setpoints must be greater than"
-                " or equal to {0}.".format(POWER_SETPOINT_DEFAULT)
-            ))
+        (
+            yaw_angles,
+            power_setpoints,
+            yaw_angles_mask,
+            power_setpoints_mask,
+            neither_mask
+        ) = MixedOperationTurbine._handle_mixed_operation_setpoints(
+            yaw_angles=yaw_angles,
+            power_setpoints=power_setpoints
+        )
 
         powers = np.zeros_like(power_setpoints)
         powers[yaw_angles_mask] += CosineLossTurbine.power(
@@ -414,21 +414,22 @@ def power(
 
         return powers
 
+    @staticmethod
     def thrust_coefficient(
         yaw_angles: NDArrayFloat,
         power_setpoints: NDArrayFloat,
         **kwargs
     ):
-        yaw_angles_mask = yaw_angles != 0.0
-        power_setpoints_mask = power_setpoints < POWER_SETPOINT_DEFAULT
-        neither_mask = np.logical_not(yaw_angles_mask) & np.logical_not(power_setpoints_mask)
-
-        if (power_setpoints_mask & yaw_angles_mask).any():
-            raise ValueError((
-                "Power setpoints and yaw angles are incompatible."
-                "If yaw_angles entry is nonzero, power_setpoints must be greater than"
-                " or equal to {0}.".format(POWER_SETPOINT_DEFAULT)
-            ))
+        (
+            yaw_angles,
+            power_setpoints,
+            yaw_angles_mask,
+            power_setpoints_mask,
+            neither_mask
+        ) = MixedOperationTurbine._handle_mixed_operation_setpoints(
+            yaw_angles=yaw_angles,
+            power_setpoints=power_setpoints
+        )
 
         thrust_coefficients = np.zeros_like(power_setpoints)
         thrust_coefficients[yaw_angles_mask] += CosineLossTurbine.thrust_coefficient(
@@ -445,21 +446,22 @@ def thrust_coefficient(
 
         return thrust_coefficients
 
+    @staticmethod
     def axial_induction(
         yaw_angles: NDArrayFloat,
         power_setpoints: NDArrayFloat,
         **kwargs
     ):
-        yaw_angles_mask = yaw_angles != 0.0
-        power_setpoints_mask = power_setpoints < POWER_SETPOINT_DEFAULT
-        neither_mask = np.logical_not(yaw_angles_mask) & np.logical_not(power_setpoints_mask)
-
-        if (power_setpoints_mask & yaw_angles_mask).any():
-            raise ValueError((
-                "Power setpoints and yaw angles are incompatible."
-                "If yaw_angles entry is nonzero, power_setpoints must be greater than"
-                " or equal to {0}.".format(POWER_SETPOINT_DEFAULT)
-            ))
+        (
+            yaw_angles,
+            power_setpoints,
+            yaw_angles_mask,
+            power_setpoints_mask,
+            neither_mask
+        ) = MixedOperationTurbine._handle_mixed_operation_setpoints(
+            yaw_angles=yaw_angles,
+            power_setpoints=power_setpoints
+        )
 
         axial_inductions = np.zeros_like(power_setpoints)
         axial_inductions[yaw_angles_mask] += CosineLossTurbine.axial_induction(
@@ -476,6 +478,34 @@ def axial_induction(
 
         return axial_inductions
 
+    @staticmethod
+    def _handle_mixed_operation_setpoints(
+        yaw_angles: NDArrayFloat,
+        power_setpoints: NDArrayFloat,
+    ):
+        """
+        Check for incompatible yaw angles and power setpoints and raise an error if found.
+        Return masks and updated setpoints.
+        """
+        # If any turbines are disabled, set their yaw angles to zero
+        yaw_angles[power_setpoints <= POWER_SETPOINT_DISABLED] = 0.0
+
+        # Create masks for whether yaw angles and power setpoints are set
+        yaw_angles_mask = yaw_angles != 0.0
+        power_setpoints_mask = power_setpoints < POWER_SETPOINT_DEFAULT
+        neither_mask = np.logical_not(yaw_angles_mask) & np.logical_not(power_setpoints_mask)
+
+        # Check for incompatibility and raise error if found.
+        if (power_setpoints_mask & yaw_angles_mask).any():
+            raise ValueError((
+                "Power setpoints and yaw angles are incompatible."
+                "If yaw_angles entry is nonzero, power_setpoints must be greater than"
+                " or equal to {0}.".format(POWER_SETPOINT_DEFAULT)
+            ))
+
+        # Return updated setpoints as well as masks
+        return yaw_angles, power_setpoints, yaw_angles_mask, power_setpoints_mask, neither_mask
+
 @define
 class AWCTurbine(BaseOperationModel):
     """
diff --git a/floris/floris_model.py b/floris/floris_model.py
index 1f92fa092..83610e993 100644
--- a/floris/floris_model.py
+++ b/floris/floris_model.py
@@ -453,10 +453,7 @@ def set(
         # previous setting
         if not (_yaw_angles == 0).all():
             self.core.farm.set_yaw_angles(_yaw_angles)
-        if not (
-            (_power_setpoints == POWER_SETPOINT_DEFAULT)
-            | (_power_setpoints == POWER_SETPOINT_DISABLED)
-        ).all():
+        if not (_power_setpoints == POWER_SETPOINT_DEFAULT).all():
             self.core.farm.set_power_setpoints(_power_setpoints)
         if _awc_modes is not None:
             self.core.farm.set_awc_modes(_awc_modes)
diff --git a/floris/optimization/yaw_optimization/yaw_optimization_base.py b/floris/optimization/yaw_optimization/yaw_optimization_base.py
index 07a2f7e11..1949d132c 100644
--- a/floris/optimization/yaw_optimization/yaw_optimization_base.py
+++ b/floris/optimization/yaw_optimization/yaw_optimization_base.py
@@ -5,6 +5,7 @@
 import numpy as np
 import pandas as pd
 
+from floris.core.turbine.operation_models import POWER_SETPOINT_DISABLED
 from floris.logging_manager import LoggingManager
 
 from .yaw_optimization_tools import derive_downstream_turbines
@@ -99,7 +100,7 @@ def __init__(
         """
 
         # Save turbine object to self
-        self.fmodel = fmodel.copy()
+        self.fmodel = copy.deepcopy(fmodel)
         self.nturbs = len(self.fmodel.layout_x)
 
         # # Check floris options
@@ -131,6 +132,11 @@ def __init__(
         self.minimum_yaw_angle = self._unpack_variable(minimum_yaw_angle)
         self.maximum_yaw_angle = self._unpack_variable(maximum_yaw_angle)
 
+        # Limit yaw angles to zero for disabled turbines
+        active_turbines = fmodel.core.farm.power_setpoints > POWER_SETPOINT_DISABLED
+        self.minimum_yaw_angle[~active_turbines] = 0.0
+        self.maximum_yaw_angle[~active_turbines] = 0.0
+
         # Set initial condition for optimization
         if x0 is not None:
             self.x0 = self._unpack_variable(x0)
@@ -224,7 +230,7 @@ def _reduce_control_problem(self):
         self.turbs_to_opt = (self.maximum_yaw_angle - self.minimum_yaw_angle >= 0.001)
 
         # Initialize subset variables as full set
-        self.fmodel_subset = self.fmodel.copy()
+        self.fmodel_subset = copy.deepcopy(self.fmodel)
         n_findex_subset = copy.deepcopy(self.fmodel.core.flow_field.n_findex)
         minimum_yaw_angle_subset = copy.deepcopy(self.minimum_yaw_angle)
         maximum_yaw_angle_subset = copy.deepcopy(self.maximum_yaw_angle)
@@ -301,6 +307,7 @@ def _calculate_farm_power(
             ti_array=None,
             turbine_weights=None,
             heterogeneous_speed_multipliers=None,
+            power_setpoints=None,
         ):
         """
         Calculate the wind farm power production assuming the predefined
@@ -353,6 +360,7 @@ def _calculate_farm_power(
             wind_speeds=ws_array,
             turbulence_intensities=ti_array,
             yaw_angles=yaw_angles,
+            power_setpoints=power_setpoints,
         )
         fmodel_subset.run()
         turbine_power = fmodel_subset.get_turbine_powers()
diff --git a/floris/optimization/yaw_optimization/yaw_optimizer_geometric.py b/floris/optimization/yaw_optimization/yaw_optimizer_geometric.py
index ea68204b4..68c687512 100644
--- a/floris/optimization/yaw_optimization/yaw_optimizer_geometric.py
+++ b/floris/optimization/yaw_optimization/yaw_optimizer_geometric.py
@@ -1,6 +1,7 @@
 
 import numpy as np
 
+from floris.core.turbine.operation_models import POWER_SETPOINT_DISABLED
 from floris.utilities import rotate_coordinates_rel_west
 
 from .yaw_optimization_base import YawOptimization
@@ -46,10 +47,11 @@ def optimize(self):
         # Loop through every WD individually. WS ignored!
         wd_array = self.fmodel_subset.core.flow_field.wind_directions
 
+        active_turbines = self.fmodel_subset.core.farm.power_setpoints > POWER_SETPOINT_DISABLED
         for nwdi, wd in enumerate(wd_array):
-            self._yaw_angles_opt_subset[nwdi, :] = geometric_yaw(
-                self.fmodel_subset.layout_x,
-                self.fmodel_subset.layout_y,
+            self._yaw_angles_opt_subset[nwdi, active_turbines[nwdi]] = geometric_yaw(
+                self.fmodel_subset.layout_x[active_turbines[nwdi]],
+                self.fmodel_subset.layout_y[active_turbines[nwdi]],
                 wd,
                 self.fmodel.core.farm.turbine_definitions[0]["rotor_diameter"],
                 top_left_yaw_upper=self.maximum_yaw_angle[0, 0],
diff --git a/floris/optimization/yaw_optimization/yaw_optimizer_scipy.py b/floris/optimization/yaw_optimization/yaw_optimizer_scipy.py
index cdde87656..810144c50 100644
--- a/floris/optimization/yaw_optimization/yaw_optimizer_scipy.py
+++ b/floris/optimization/yaw_optimization/yaw_optimizer_scipy.py
@@ -30,6 +30,12 @@ def __init__(
         Instantiate YawOptimizationScipy object with a FlorisModel object
         and assign parameter values.
         """
+        valid_op_models = ["cosine-loss"]
+        if fmodel.get_operation_model() not in valid_op_models:
+            raise ValueError(
+                "YawOptimizationScipy is currently limited to the following operation models: "
+                + ", ".join(valid_op_models)
+            )
         if opt_options is None:
             # Default SciPy parameters
             opt_options = {
diff --git a/floris/optimization/yaw_optimization/yaw_optimizer_sr.py b/floris/optimization/yaw_optimization/yaw_optimizer_sr.py
index 2b5b7ad1b..127cca01b 100644
--- a/floris/optimization/yaw_optimization/yaw_optimizer_sr.py
+++ b/floris/optimization/yaw_optimization/yaw_optimizer_sr.py
@@ -93,6 +93,7 @@ def _calc_powers_with_memory(self, yaw_angles_subset, use_memory=True):
         wd_array_subset = self.fmodel_subset.core.flow_field.wind_directions
         ws_array_subset = self.fmodel_subset.core.flow_field.wind_speeds
         ti_array_subset = self.fmodel_subset.core.flow_field.turbulence_intensities
+        power_setpoints_subset = self.fmodel_subset.core.farm.power_setpoints
         turbine_weights_subset = self._turbine_weights_subset
 
         # Reformat yaw_angles_subset, if necessary
@@ -108,6 +109,7 @@ def _calc_powers_with_memory(self, yaw_angles_subset, use_memory=True):
             wd_array_subset = np.tile(wd_array_subset, Ny)
             ws_array_subset = np.tile(ws_array_subset, Ny)
             ti_array_subset = np.tile(ti_array_subset, Ny)
+            power_setpoints_subset = np.tile(power_setpoints_subset, (Ny, 1))
             turbine_weights_subset = np.tile(turbine_weights_subset, (Ny, 1))
 
         # Initialize empty matrix for floris farm power outputs
@@ -143,7 +145,8 @@ def _calc_powers_with_memory(self, yaw_angles_subset, use_memory=True):
                 ti_array=ti_array_subset[~idx],
                 turbine_weights=turbine_weights_subset[~idx, :],
                 yaw_angles=yaw_angles_subset[~idx, :],
-                heterogeneous_speed_multipliers=het_sm
+                heterogeneous_speed_multipliers=het_sm,
+                power_setpoints=power_setpoints_subset[~idx, :],
             )
             self.time_spent_in_floris += (timerpc() - start_time)
 
diff --git a/floris/version.py b/floris/version.py
deleted file mode 100644
index bf77d5496..000000000
--- a/floris/version.py
+++ /dev/null
@@ -1 +0,0 @@
-4.2
diff --git a/floris/wind_data.py b/floris/wind_data.py
index b470fe515..3d49dec4b 100644
--- a/floris/wind_data.py
+++ b/floris/wind_data.py
@@ -779,8 +779,12 @@ def plot(
                 )
 
         # Configure the plot
-        ax.figure.colorbar(sm_ws, ax=ax, **legend_kwargs)
-        ax.figure.tight_layout()
+        try:
+           ax.figure.colorbar(sm_ws, ax=ax, **legend_kwargs)
+           ax.figure.tight_layout()
+        except TypeError:
+           ax.legend(reversed(rects), ws_bins, **legend_kwargs)
+           ax.figure.get_children()[-1].remove() # Remove the empty colorbar
         ax.set_theta_direction(-1)
         ax.set_theta_offset(np.pi / 2.0)
         ax.set_theta_zero_location("N")
@@ -1822,8 +1826,12 @@ def plot(
                 )
 
         # Configure the plot
-        ax.figure.colorbar(sm_wv, ax=ax, **legend_kwargs)
-        ax.figure.tight_layout()
+        try:
+            ax.figure.colorbar(sm_wv, ax=ax, **legend_kwargs)
+            ax.figure.tight_layout()
+        except TypeError:
+            ax.legend(reversed(rects), var_bins, **legend_kwargs)
+            ax.figure.get_children()[-1].remove() # Remove the empty colorbar
         ax.set_theta_direction(-1)
         ax.set_theta_offset(np.pi / 2.0)
         ax.set_theta_zero_location("N")
diff --git a/pyproject.toml b/pyproject.toml
index 330c5a2d8..dea224866 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,6 +2,71 @@
 requires = ["setuptools >= 40.6.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "floris"
+version = "4.2"
+description = "A controls-oriented engineering wake model."
+readme = "README.md"
+requires-python = ">=3.8"
+authors = [
+    { name = "Rafael Mudafort", email = "rafael.mudafort@nrel.gov" },
+    { name = "Paul Fleming", email = "paul.fleming@nrel.gov" },
+    { name = "Michael (Misha) Sinner", email = "Michael.Sinner@nrel.gov" },
+    { name = "Eric Simley", email = "Eric.Simley@nrel.gov" },
+    { name = "Christopher Bay", email = "Christopher.Bay@nrel.gov" },
+]
+license = { file = "LICENSE.txt" }
+keywords = ["floris"]
+classifiers = [
+        "License :: OSI Approved :: BSD License",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: Implementation :: CPython",
+        "Programming Language :: Python :: Implementation :: PyPy"
+]
+dependencies = [
+    "attrs",
+    "pyyaml~=6.0",
+    "numexpr~=2.0",
+    "numpy~=1.20",
+    "scipy~=1.1",
+    "matplotlib~=3.0",
+    "pandas~=2.0",
+    "shapely~=2.0",
+    "coloredlogs~=15.0",
+    "pathos~=0.3",
+]
+
+[project.optional-dependencies]
+docs = [
+    "jupyter-book",
+    "sphinx-book-theme",
+    "sphinx-autodoc-typehints",
+    "sphinxcontrib-autoyaml",
+    "sphinxcontrib.mermaid",
+]
+develop = [
+    "pytest",
+    "pre-commit",
+    "ruff",
+    "isort"
+]
+
+[tool.setuptools.packages.find]
+include = ["floris*"]
+
+[tool.setuptools.package-data]
+floris = [
+    "turbine_library/*.yaml",
+    "core/wake_velocity/turbopark_lookup_table.mat"
+]
+
+[project.urls]
+Homepage = "https://github.com/NREL/floris"
+Documentation = "https://nrel.github.io/floris/"
 
 [coverage.run]
 # Coverage.py configuration file
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 7e3a11be4..000000000
--- a/setup.py
+++ /dev/null
@@ -1,89 +0,0 @@
-
-from pathlib import Path
-
-from setuptools import find_packages, setup
-
-
-# Package meta-data.
-NAME = "FLORIS"
-DESCRIPTION = "A controls-oriented engineering wake model."
-URL = "https://github.com/NREL/FLORIS"
-EMAIL = "rafael.mudafort@nrel.gov"
-AUTHOR = "NREL National Wind Technology Center"
-REQUIRES_PYTHON = ">=3.8.0"
-
-# What packages are required for this module to be executed?
-REQUIRED = [
-    # simulation
-    "attrs",
-    "pyyaml~=6.0",
-    "numexpr~=2.0",
-    "numpy~=1.20",
-    "scipy~=1.1",
-
-    # tools
-    "matplotlib~=3.0",
-    "pandas~=2.0",
-    "shapely~=2.0",
-
-    # utilities
-    "coloredlogs~=15.0",
-    "pathos~=0.3",
-]
-
-# What packages are optional?
-# To use:
-#   pip install -e ".[docs,develop]"    install both sets of extras in editable install
-#   pip install -e ".[develop]"         installs only developer packages in editable install
-#   pip install "floris[develop]"       installs developer packages in non-editable install
-EXTRAS = {
-    "docs": {
-        "jupyter-book",
-        "sphinx-book-theme",
-        "sphinx-autodoc-typehints",
-        "sphinxcontrib-autoyaml",
-        "sphinxcontrib.mermaid",
-    },
-    "develop": {
-        "pytest",
-        "pre-commit",
-        "ruff",
-        "isort",
-    },
-}
-
-ROOT = Path(__file__).parent
-with open(ROOT / "floris" / "version.py") as version_file:
-    VERSION = version_file.read().strip()
-
-setup(
-    name=NAME,
-    version=VERSION,
-    description=DESCRIPTION,
-    long_description=DESCRIPTION,
-    long_description_content_type="text/markdown",
-    author=AUTHOR,
-    author_email=EMAIL,
-    python_requires=REQUIRES_PYTHON,
-    url=URL,
-    packages=find_packages(exclude=["tests", "*.tests", "*.tests.*", "tests.*"]),
-    package_data={
-        'floris': ['turbine_library/*.yaml', 'core/wake_velocity/turbopark_lookup_table.mat']
-    },
-    install_requires=REQUIRED,
-    extras_require=EXTRAS,
-    include_package_data=True,
-    license_files = ('LICENSE.txt',),
-    classifiers=[
-        # Trove classifiers
-        # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
-        "License :: OSI Approved :: BSD License",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: Implementation :: CPython",
-        "Programming Language :: Python :: Implementation :: PyPy"
-    ],
-)


Test patch:
diff --git a/tests/floris_model_integration_test.py b/tests/floris_model_integration_test.py
index 395ff03a1..88a242c56 100644
--- a/tests/floris_model_integration_test.py
+++ b/tests/floris_model_integration_test.py
@@ -10,7 +10,7 @@
     TimeSeries,
     WindRose,
 )
-from floris.core.turbine.operation_models import POWER_SETPOINT_DEFAULT
+from floris.core.turbine.operation_models import POWER_SETPOINT_DEFAULT, POWER_SETPOINT_DISABLED
 
 
 TEST_DATA = Path(__file__).resolve().parent / "data"
@@ -44,7 +44,24 @@ def test_assign_setpoints():
 
     # power_setpoints and disable_turbines (disable_turbines overrides power_setpoints)
     fmodel.set(power_setpoints=[[1e6, 2e6]], disable_turbines=[[True, False]])
-    assert np.allclose(fmodel.core.farm.power_setpoints, np.array([[0.001, 2e6]]))
+    assert np.allclose(fmodel.core.farm.power_setpoints, np.array([[POWER_SETPOINT_DISABLED, 2e6]]))
+
+    # Setting sequentially is equivalent to setting together
+    fmodel.reset_operation()
+    fmodel.set(disable_turbines=[[True, False]])
+    fmodel.set(yaw_angles=[[0, 30]])
+    assert np.allclose(
+        fmodel.core.farm.power_setpoints,
+        np.array([[POWER_SETPOINT_DISABLED, POWER_SETPOINT_DEFAULT]])
+    )
+    assert np.allclose(fmodel.core.farm.yaw_angles, np.array([[0, 30]]))
+
+    fmodel.set(disable_turbines=[[True, False]], yaw_angles=[[0, 30]])
+    assert np.allclose(
+        fmodel.core.farm.power_setpoints,
+        np.array([[POWER_SETPOINT_DISABLED, POWER_SETPOINT_DEFAULT]])
+    )
+    assert np.allclose(fmodel.core.farm.yaw_angles, np.array([[0, 30]]))
 
 def test_set_run():
     """
diff --git a/tests/geometric_yaw_unit_test.py b/tests/geometric_yaw_unit_test.py
new file mode 100644
index 000000000..2fb0452bb
--- /dev/null
+++ b/tests/geometric_yaw_unit_test.py
@@ -0,0 +1,115 @@
+
+import numpy as np
+import pandas as pd
+
+from floris import FlorisModel
+from floris.optimization.yaw_optimization.yaw_optimizer_geometric import YawOptimizationGeometric
+
+
+DEBUG = False
+VELOCITY_MODEL = "gauss"
+DEFLECTION_MODEL = "gauss"
+
+# Inputs for basic yaw optimizations
+WIND_DIRECTIONS = [0.0, 90.0, 180.0, 270.0]
+WIND_SPEEDS = [8.0] * 4
+TURBULENCE_INTENSITIES = [0.06] * 4
+LAYOUT_X = [0.0, 600.0, 1200.0]
+LAYOUT_Y = [0.0, 0.0, 0.0]
+MAXIMUM_YAW_ANGLE = 25.0
+
+def test_basic_optimization(sample_inputs_fixture):
+    """
+    The Serial Refine (SR) method optimizes yaw angles based on a sequential, iterative yaw
+    optimization scheme. This test checks basic properties of the optimization result.
+    """
+    sample_inputs_fixture.core["wake"]["model_strings"]["velocity_model"] = VELOCITY_MODEL
+    sample_inputs_fixture.core["wake"]["model_strings"]["deflection_model"] = DEFLECTION_MODEL
+
+    fmodel = FlorisModel(sample_inputs_fixture.core)
+
+    fmodel.set(
+        layout_x=LAYOUT_X,
+        layout_y=LAYOUT_Y,
+        wind_directions=WIND_DIRECTIONS,
+        wind_speeds=WIND_SPEEDS,
+        turbulence_intensities=TURBULENCE_INTENSITIES
+    )
+    fmodel.set_operation_model("cosine-loss")
+
+    yaw_opt = YawOptimizationGeometric(
+        fmodel,
+        minimum_yaw_angle=0.0,
+        maximum_yaw_angle=MAXIMUM_YAW_ANGLE
+    )
+    df_opt = yaw_opt.optimize()
+
+    # Unaligned conditions
+    assert np.allclose(df_opt.loc[0, "yaw_angles_opt"], 0.0)
+    assert np.allclose(df_opt.loc[2, "yaw_angles_opt"], 0.0)
+
+    # Check aligned conditions
+    # Check maximum and minimum are respected
+    assert (df_opt.loc[1, "yaw_angles_opt"] <= MAXIMUM_YAW_ANGLE).all()
+    assert (df_opt.loc[3, "yaw_angles_opt"] <= MAXIMUM_YAW_ANGLE).all()
+    assert (df_opt.loc[1, "yaw_angles_opt"] >= 0.0).all()
+    assert (df_opt.loc[3, "yaw_angles_opt"] >= 0.0).all()
+
+    # Check 90.0 and 270.0 are symmetric
+    assert np.allclose(df_opt.loc[1, "yaw_angles_opt"], np.flip(df_opt.loc[3, "yaw_angles_opt"]))
+
+    # Check last turbine's angles are zero at 270.0
+    assert np.allclose(df_opt.loc[3, "yaw_angles_opt"][-1], 0.0)
+
+    # YawOptimizationGeometric does not compute farm powers
+
+def test_disabled_turbines(sample_inputs_fixture):
+    """
+    Tests SR when some turbines are disabled and checks that the results are equivalent to removing
+    those turbines from the wind farm. Need a tight layout to ensure that the front-to-back distance
+    is not too large.
+    """
+
+    sample_inputs_fixture.core["wake"]["model_strings"]["velocity_model"] = VELOCITY_MODEL
+    sample_inputs_fixture.core["wake"]["model_strings"]["deflection_model"] = DEFLECTION_MODEL
+
+    fmodel = FlorisModel(sample_inputs_fixture.core)
+
+    fmodel.set(
+        layout_x=LAYOUT_X,
+        layout_y=LAYOUT_Y,
+        wind_directions=WIND_DIRECTIONS,
+        wind_speeds=WIND_SPEEDS,
+        turbulence_intensities=TURBULENCE_INTENSITIES
+    )
+    fmodel.set_operation_model("mixed")
+
+    # Disable the middle turbine in all wind conditions, run optimization, and extract results
+    fmodel.set(disable_turbines=[[False, True, False]]*4)
+    yaw_opt = YawOptimizationGeometric(
+        fmodel,
+        minimum_yaw_angle=0.0,
+        maximum_yaw_angle=MAXIMUM_YAW_ANGLE
+    )
+    df_opt = yaw_opt.optimize()
+    yaw_angles_opt_disabled = df_opt.loc[3, "yaw_angles_opt"]
+
+    # Set up a new wind farm with the middle turbine removed
+    fmodel = FlorisModel(sample_inputs_fixture.core)
+    fmodel.set(
+        layout_x=np.array(LAYOUT_X)[[0, 2]],
+        layout_y=np.array(LAYOUT_Y)[[0, 2]],
+        wind_directions=WIND_DIRECTIONS,
+        wind_speeds=WIND_SPEEDS,
+        turbulence_intensities=TURBULENCE_INTENSITIES
+    )
+    fmodel.set_operation_model("cosine-loss")
+    yaw_opt = YawOptimizationGeometric(
+        fmodel,
+        minimum_yaw_angle=0.0,
+        maximum_yaw_angle=MAXIMUM_YAW_ANGLE
+    )
+    df_opt = yaw_opt.optimize()
+    yaw_angles_opt_removed = df_opt.loc[3, "yaw_angles_opt"]
+
+    assert np.allclose(yaw_angles_opt_disabled[[0, 2]], yaw_angles_opt_removed)
diff --git a/tests/serial_refine_unit_test.py b/tests/serial_refine_unit_test.py
new file mode 100644
index 000000000..cfda030a7
--- /dev/null
+++ b/tests/serial_refine_unit_test.py
@@ -0,0 +1,107 @@
+
+import numpy as np
+import pandas as pd
+
+from floris import FlorisModel
+from floris.optimization.yaw_optimization.yaw_optimizer_sr import YawOptimizationSR
+
+
+DEBUG = False
+VELOCITY_MODEL = "gauss"
+DEFLECTION_MODEL = "gauss"
+
+# Inputs for basic yaw optimizations
+WIND_DIRECTIONS = [0.0, 90.0, 180.0, 270.0]
+WIND_SPEEDS = [8.0] * 4
+TURBULENCE_INTENSITIES = [0.06] * 4
+LAYOUT_X = [0.0, 600.0, 1200.0]
+LAYOUT_Y = [0.0, 0.0, 0.0]
+MAXIMUM_YAW_ANGLE = 25.0
+
+def test_basic_optimization(sample_inputs_fixture):
+    """
+    The Serial Refine (SR) method optimizes yaw angles based on a sequential, iterative yaw
+    optimization scheme. This test checks basic properties of the optimization result.
+    """
+    sample_inputs_fixture.core["wake"]["model_strings"]["velocity_model"] = VELOCITY_MODEL
+    sample_inputs_fixture.core["wake"]["model_strings"]["deflection_model"] = DEFLECTION_MODEL
+
+    fmodel = FlorisModel(sample_inputs_fixture.core)
+
+    fmodel.set(
+        layout_x=LAYOUT_X,
+        layout_y=LAYOUT_Y,
+        wind_directions=WIND_DIRECTIONS,
+        wind_speeds=WIND_SPEEDS,
+        turbulence_intensities=TURBULENCE_INTENSITIES
+    )
+    fmodel.set_operation_model("cosine-loss")
+
+    yaw_opt = YawOptimizationSR(fmodel, minimum_yaw_angle=0.0, maximum_yaw_angle=MAXIMUM_YAW_ANGLE)
+    df_opt = yaw_opt.optimize()
+
+    # Unaligned conditions
+    assert np.allclose(df_opt.loc[0, "yaw_angles_opt"], 0.0)
+    assert np.allclose(df_opt.loc[2, "yaw_angles_opt"], 0.0)
+
+    # Check aligned conditions
+    # Check maximum and minimum are respected
+    assert (df_opt.loc[1, "yaw_angles_opt"] <= MAXIMUM_YAW_ANGLE).all()
+    assert (df_opt.loc[3, "yaw_angles_opt"] <= MAXIMUM_YAW_ANGLE).all()
+    assert (df_opt.loc[1, "yaw_angles_opt"] >= 0.0).all()
+    assert (df_opt.loc[3, "yaw_angles_opt"] >= 0.0).all()
+
+    # Check 90.0 and 270.0 are symmetric
+    assert np.allclose(df_opt.loc[1, "yaw_angles_opt"], np.flip(df_opt.loc[3, "yaw_angles_opt"]))
+
+    # Check last turbine's angles are zero at 270.0
+    assert np.allclose(df_opt.loc[3, "yaw_angles_opt"][-1], 0.0)
+
+    # Check that optimizer reports a power improvement
+    assert (df_opt["farm_power_opt"] >= df_opt["farm_power_baseline"]).all()
+
+def test_disabled_turbines(sample_inputs_fixture):
+    """
+    Tests SR when some turbines are disabled and checks that the results are equivalent to removing
+    those turbines from the wind farm. Need a tight layout to ensure that the front-to-back distance
+    is not too large.
+    """
+
+    sample_inputs_fixture.core["wake"]["model_strings"]["velocity_model"] = VELOCITY_MODEL
+    sample_inputs_fixture.core["wake"]["model_strings"]["deflection_model"] = DEFLECTION_MODEL
+
+    fmodel = FlorisModel(sample_inputs_fixture.core)
+
+    fmodel.set(
+        layout_x=LAYOUT_X,
+        layout_y=LAYOUT_Y,
+        wind_directions=WIND_DIRECTIONS,
+        wind_speeds=WIND_SPEEDS,
+        turbulence_intensities=TURBULENCE_INTENSITIES
+    )
+    fmodel.set_operation_model("mixed")
+
+    # Disable the middle turbine in all wind conditions, run optimization, and extract results
+    fmodel.set(disable_turbines=[[False, True, False]]*4)
+    yaw_opt = YawOptimizationSR(fmodel, minimum_yaw_angle=0.0, maximum_yaw_angle=MAXIMUM_YAW_ANGLE)
+    df_opt = yaw_opt.optimize()
+    yaw_angles_opt_disabled = df_opt.loc[3, "yaw_angles_opt"]
+    farm_power_opt_disabled = df_opt.loc[3, "farm_power_opt"]
+
+    # Set up a new wind farm with the middle turbine removed
+    fmodel = FlorisModel(sample_inputs_fixture.core)
+    fmodel.set(
+        layout_x=np.array(LAYOUT_X)[[0, 2]],
+        layout_y=np.array(LAYOUT_Y)[[0, 2]],
+        wind_directions=WIND_DIRECTIONS,
+        wind_speeds=WIND_SPEEDS,
+        turbulence_intensities=TURBULENCE_INTENSITIES
+    )
+    fmodel.set_operation_model("cosine-loss")
+    yaw_opt = YawOptimizationSR(fmodel, minimum_yaw_angle=0.0, maximum_yaw_angle=MAXIMUM_YAW_ANGLE)
+    df_opt = yaw_opt.optimize()
+    yaw_angles_opt_removed = df_opt.loc[3, "yaw_angles_opt"]
+    farm_power_opt_removed = df_opt.loc[3, "farm_power_opt"]
+
+    assert np.allclose(yaw_angles_opt_disabled[[0, 2]], yaw_angles_opt_removed)
+    assert np.allclose(farm_power_opt_disabled, farm_power_opt_removed)