From f2aa2e8a7006986830c8ef4af7154718b0367c10 Mon Sep 17 00:00:00 2001
From: btol <btol@dtu.dk>
Date: Wed, 25 Feb 2026 15:53:12 +0100
Subject: [PATCH 1/7] Make all wrapped tools optional dependencies

Move pywake, floris, foxes, wayve, and code_saturne from hard
dependencies to optional extras in pyproject.toml. Users can now
install only the tools they need: `pip install wifa[pywake]`,
`pip install wifa[foxes]`, etc., or all at once with `wifa[all]`.

- Add `wifa/_optional.py` with `require()` helper that gives clear
  install instructions when an optional tool is missing
- Add `require()` checks at the top of each `run_*` function
- Add `pytest.importorskip()` to test modules so tests skip cleanly
  when a tool is not installed
- Move matplotlib and mpmath to lazy imports in wayve_api.py
- Move FoxesWakeModel import into the foxes branch of wake_model_setup()
- Add scipy and pyyaml as core dependencies (used at module level)
- Add missing run_floris export in __init__.py

Closes #50

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 pyproject.toml       | 21 ++++++++++++++++-----
 tests/test_floris.py |  5 ++++-
 tests/test_foxes.py  |  4 ++++
 tests/test_pywake.py |  3 +++
 tests/test_wayve.py  |  4 ++++
 wifa/__init__.py     |  1 +
 wifa/_optional.py    | 10 ++++++++++
 wifa/floris_api.py   |  3 +++
 wifa/foxes_api.py    |  3 +++
 wifa/pywake_api.py   |  4 ++++
 wifa/wayve_api.py    | 14 ++++++++++----
 11 files changed, 62 insertions(+), 10 deletions(-)
 create mode 100644 wifa/_optional.py

diff --git a/pyproject.toml b/pyproject.toml
index 5d64209..728106e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,16 +38,27 @@ classifiers = [
 ]
 requires-python = ">=3.9,<3.12"
 dependencies = [
-    "py_wake>=2.6.5",
-    "foxes>=1.6.2",
     "windIO @ git+https://github.com/EUFlow/windIO.git",
-    "wayve @ git+https://gitlab.kuleuven.be/TFSO-software/wayve@dev_foxes",
-    "floris @ git+https://github.com/lejeunemax/floris.git@windIO",
     "xarray>=2022.0.0,<2025",
-    "mpmath",
+    "scipy",
+    "pyyaml",
 ]
 
 [project.optional-dependencies]
+pywake = ["py_wake>=2.6.5"]
+foxes = ["foxes>=1.6.2"]
+floris = ["floris @ git+https://github.com/lejeunemax/floris.git@windIO"]
+wayve = [
+    "wayve @ git+https://gitlab.kuleuven.be/TFSO-software/wayve@dev_foxes",
+    "mpmath",
+]
+cs = []  # code_saturne is a subprocess, no pip dependency
+all = [
+    "wifa[pywake]",
+    "wifa[foxes]",
+    "wifa[floris]",
+    "wifa[wayve]",
+]
 test = [
     "pytest",
     "pytest-cov",
diff --git a/tests/test_floris.py b/tests/test_floris.py
index 2f8cd8e..c4fb51b 100644
--- a/tests/test_floris.py
+++ b/tests/test_floris.py
@@ -11,10 +11,13 @@
 import shutil
 from pathlib import Path
 
-import floris
 import numpy as np
 import pytest
 import xarray as xr
+
+pytest.importorskip("floris", reason="floris not installed, install with: pip install wifa[floris]")
+
+import floris
 from floris.turbine_library import build_cosine_loss_turbine_dict
 from windIO import __path__ as wiop
 from windIO import load_yaml
diff --git a/tests/test_foxes.py b/tests/test_foxes.py
index deb17de..2c3e8b7 100644
--- a/tests/test_foxes.py
+++ b/tests/test_foxes.py
@@ -3,6 +3,10 @@
 from shutil import rmtree
 
 import numpy as np
+import pytest
+
+pytest.importorskip("foxes", reason="foxes not installed, install with: pip install wifa[foxes]")
+
 from windIO import __path__ as wiop
 from windIO import validate as validate_yaml
 
diff --git a/tests/test_pywake.py b/tests/test_pywake.py
index 3c01eb2..a0414b0 100644
--- a/tests/test_pywake.py
+++ b/tests/test_pywake.py
@@ -4,6 +4,9 @@
 import numpy as np
 import pytest
 import xarray as xr
+
+pytest.importorskip("py_wake", reason="py_wake not installed, install with: pip install wifa[pywake]")
+
 from py_wake.deficit_models.gaussian import BastankhahGaussian
 from py_wake.examples.data.dtu10mw._dtu10mw import DTU10MW
 from py_wake.examples.data.hornsrev1 import Hornsrev1Site
diff --git a/tests/test_wayve.py b/tests/test_wayve.py
index 902edf0..07024d3 100644
--- a/tests/test_wayve.py
+++ b/tests/test_wayve.py
@@ -1,6 +1,10 @@
 import os
 from pathlib import Path
 
+import pytest
+
+pytest.importorskip("wayve", reason="wayve not installed, install with: pip install wifa[wayve]")
+
 from windIO import __path__ as wiop
 from windIO import validate as validate_yaml
 
diff --git a/wifa/__init__.py b/wifa/__init__.py
index 88be468..005a376 100644
--- a/wifa/__init__.py
+++ b/wifa/__init__.py
@@ -1,6 +1,7 @@
 # __init__.py
 
 from .cs_api.cs_modules.csLaunch.cs_run_function import run_code_saturne
+from .floris_api import run_floris
 from .foxes_api import run_foxes
 from .main_api import run_api
 from .pywake_api import run_pywake
diff --git a/wifa/_optional.py b/wifa/_optional.py
new file mode 100644
index 0000000..0870f42
--- /dev/null
+++ b/wifa/_optional.py
@@ -0,0 +1,10 @@
+import importlib.util
+
+
+def require(package_name: str, extra_name: str) -> None:
+    """Raise a clear ImportError if an optional dependency is missing."""
+    if importlib.util.find_spec(package_name) is None:
+        raise ImportError(
+            f"'{package_name}' is required for this functionality but is not installed. "
+            f"Install it with: pip install wifa[{extra_name}]"
+        )
diff --git a/wifa/floris_api.py b/wifa/floris_api.py
index b5d5812..7a23c94 100644
--- a/wifa/floris_api.py
+++ b/wifa/floris_api.py
@@ -5,6 +5,8 @@
 import windIO
 from windIO import load_yaml
 
+from wifa._optional import require
+
 if TYPE_CHECKING:
     from floris import FlorisModel
 
@@ -30,6 +32,7 @@ def run_floris(yaml_input):
     - Some advanced windIO properties may not be fully supported. These include:
       blockage_model, rotor_averaging, and axial_induction_model.
     """
+    require("floris", "floris")
 
     from floris import FlorisModel
     from floris.read_windio import TrackedDict
diff --git a/wifa/foxes_api.py b/wifa/foxes_api.py
index 8c97417..09f240a 100644
--- a/wifa/foxes_api.py
+++ b/wifa/foxes_api.py
@@ -3,6 +3,8 @@
 
 from windIO import load_yaml
 
+from wifa._optional import require
+
 
 def run_foxes(
     input_yaml,
@@ -54,6 +56,7 @@ def run_foxes(
         foxes output class
 
     """
+    require("foxes", "foxes")
 
     from foxes.input.yaml import run_dict
     from foxes.input.yaml.windio import read_windio_dict
diff --git a/wifa/pywake_api.py b/wifa/pywake_api.py
index 703f5dd..2f3c02f 100644
--- a/wifa/pywake_api.py
+++ b/wifa/pywake_api.py
@@ -11,6 +11,8 @@
 from windIO import dict_to_netcdf, load_yaml
 from windIO import validate as validate_yaml
 
+from wifa._optional import require
+
 # Define default values for wind_deficit_model parameters
 DEFAULTS = {
     "wind_deficit_model": {
@@ -1052,6 +1054,8 @@ def run_pywake(yaml_input, output_dir="output"):
         float: Total AEP in GWh
     """
     # Step 1: Load and validate configuration
+    require("py_wake", "pywake")
+
     system_dat, output_dir = load_and_validate_config(yaml_input, output_dir)
 
     # Step 2: Create turbine objects
diff --git a/wifa/wayve_api.py b/wifa/wayve_api.py
index 768df92..79601b1 100644
--- a/wifa/wayve_api.py
+++ b/wifa/wayve_api.py
@@ -3,16 +3,18 @@
 import warnings
 from pathlib import Path
 
-import matplotlib.pyplot as plt
-import mpmath
 import numpy as np
 import xarray as xr
 from scipy.interpolate import interp1d
 from scipy.special import gamma as scipy_gamma
 from windIO import load_yaml
 
+from wifa._optional import require
+
 
 def run_wayve(yamlFile, output_dir="output", debug_mode=False):
+    require("wayve", "wayve")
+
     # General APM setup
     from wayve.apm import APM
     from wayve.grid.grid import Stat2Dgrid
@@ -271,6 +273,8 @@ def run_wayve(yamlFile, output_dir="output", debug_mode=False):
 
 def nieuwstadt83_profiles(zh, v, wd, z0=1.0e-1, h=1.5e3, fc=1.0e-4, ust=0.666):
     """Set up the cubic analytical profile from Nieuwstadt (1983), based on hub height velocity information"""
+    import mpmath
+
     # Atmospheric state setup
     from wayve.abl.abl_tools import Cg_cubic, alpha_cubic
 
@@ -393,6 +397,8 @@ def rotate_xy_arrays(xs, ys, angle):
 def ci_fitting(
     zs, ths, l_mo=5.0e3, blh=1.0e3, dh_max=300.0, serz=True, plot_fits=False
 ):
+    import matplotlib.pyplot as plt
+
     # Atmospheric state setup
     from wayve.abl import ci_methods
 
@@ -638,8 +644,6 @@ def wm_coupling_setup(analysis_dat, wake_model):
 
 
 def wake_model_setup(analysis_dat, debug_mode=False):
-    # WAYVE imports
-    from wayve.couplings.foxes_coupling import FoxesWakeModel
     from wayve.forcing.wind_farms.wake_model_coupling.wake_models.lanzilao_merging import (
         Lanzilao,
     )
@@ -666,6 +670,8 @@ def wake_model_setup(analysis_dat, debug_mode=False):
         # Use wake merging method of Lanzilao and Meyers (2021)
         wake_model = Lanzilao(ka=k_a, kb=k_b, eps_beta=ceps)
     elif wake_tool == "foxes":
+        require("foxes", "foxes")
+        from wayve.couplings.foxes_coupling import FoxesWakeModel
         from foxes import ModelBook
         from foxes.input.yaml.windio.read_attributes import _read_analysis
         from foxes.utils import Dict

From 4dd492c1493612ae62430717358203316373e646 Mon Sep 17 00:00:00 2001
From: btol <btol@dtu.dk>
Date: Wed, 25 Feb 2026 15:56:52 +0100
Subject: [PATCH 2/7] Fix pre-commit: black line length and isort import order

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 tests/test_floris.py | 4 +++-
 tests/test_foxes.py  | 4 +++-
 tests/test_pywake.py | 4 +++-
 tests/test_wayve.py  | 4 +++-
 wifa/wayve_api.py    | 2 +-
 5 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/tests/test_floris.py b/tests/test_floris.py
index c4fb51b..653deed 100644
--- a/tests/test_floris.py
+++ b/tests/test_floris.py
@@ -15,7 +15,9 @@
 import pytest
 import xarray as xr
 
-pytest.importorskip("floris", reason="floris not installed, install with: pip install wifa[floris]")
+pytest.importorskip(
+    "floris", reason="floris not installed, install with: pip install wifa[floris]"
+)
 
 import floris
 from floris.turbine_library import build_cosine_loss_turbine_dict
diff --git a/tests/test_foxes.py b/tests/test_foxes.py
index 2c3e8b7..54791a3 100644
--- a/tests/test_foxes.py
+++ b/tests/test_foxes.py
@@ -5,7 +5,9 @@
 import numpy as np
 import pytest
 
-pytest.importorskip("foxes", reason="foxes not installed, install with: pip install wifa[foxes]")
+pytest.importorskip(
+    "foxes", reason="foxes not installed, install with: pip install wifa[foxes]"
+)
 
 from windIO import __path__ as wiop
 from windIO import validate as validate_yaml
diff --git a/tests/test_pywake.py b/tests/test_pywake.py
index a0414b0..5bd4003 100644
--- a/tests/test_pywake.py
+++ b/tests/test_pywake.py
@@ -5,7 +5,9 @@
 import pytest
 import xarray as xr
 
-pytest.importorskip("py_wake", reason="py_wake not installed, install with: pip install wifa[pywake]")
+pytest.importorskip(
+    "py_wake", reason="py_wake not installed, install with: pip install wifa[pywake]"
+)
 
 from py_wake.deficit_models.gaussian import BastankhahGaussian
 from py_wake.examples.data.dtu10mw._dtu10mw import DTU10MW
diff --git a/tests/test_wayve.py b/tests/test_wayve.py
index 07024d3..4957f04 100644
--- a/tests/test_wayve.py
+++ b/tests/test_wayve.py
@@ -3,7 +3,9 @@
 
 import pytest
 
-pytest.importorskip("wayve", reason="wayve not installed, install with: pip install wifa[wayve]")
+pytest.importorskip(
+    "wayve", reason="wayve not installed, install with: pip install wifa[wayve]"
+)
 
 from windIO import __path__ as wiop
 from windIO import validate as validate_yaml
diff --git a/wifa/wayve_api.py b/wifa/wayve_api.py
index 79601b1..d0ae9d3 100644
--- a/wifa/wayve_api.py
+++ b/wifa/wayve_api.py
@@ -671,10 +671,10 @@ def wake_model_setup(analysis_dat, debug_mode=False):
         wake_model = Lanzilao(ka=k_a, kb=k_b, eps_beta=ceps)
     elif wake_tool == "foxes":
         require("foxes", "foxes")
-        from wayve.couplings.foxes_coupling import FoxesWakeModel
         from foxes import ModelBook
         from foxes.input.yaml.windio.read_attributes import _read_analysis
         from foxes.utils import Dict
+        from wayve.couplings.foxes_coupling import FoxesWakeModel
 
         verbosity = 1 if debug_mode else 0
 

From fc824f3424b4e04765a08101284dc69281a0e621 Mon Sep 17 00:00:00 2001
From: btol <btol@dtu.dk>
Date: Wed, 25 Feb 2026 16:01:06 +0100
Subject: [PATCH 3/7] Install all tool extras in CI so all tests run

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 .github/workflows/run_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index 330cdeb..1fee02d 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -44,7 +44,7 @@ jobs:
         apt-get update && apt-get install -y git-lfs
         git lfs install
         pip install --upgrade pip
-        pip install -e .[test]
+        pip install -e ".[all,test]"
     - name: Test with pytest
       run: |
         py.test --durations=0 tests/

From 3b75ad62883dfab319a988fddf897afd54a5c613 Mon Sep 17 00:00:00 2001
From: btol <btol@dtu.dk>
Date: Wed, 25 Feb 2026 16:04:41 +0100
Subject: [PATCH 4/7] Fix numpy 2.x compatibility: replace np.trapz with
 np.trapezoid

np.trapz was removed in numpy 2.0. Use np.trapezoid with fallback
for older numpy versions.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 wifa/wayve_api.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/wifa/wayve_api.py b/wifa/wayve_api.py
index d0ae9d3..b933d59 100644
--- a/wifa/wayve_api.py
+++ b/wifa/wayve_api.py
@@ -830,8 +830,9 @@ def flow_io_abl(wind_resource_dat, time_index, zh, h1, dh_max=None, serz=True):
             )
         # Geostrophic wind speed
         z = np.linspace(h, 15.0e3, 1000)
-        U3 = np.trapz(np.interp(z, zs, us), z) / (15.0e3 - h)
-        V3 = np.trapz(np.interp(z, zs, vs), z) / (15.0e3 - h)
+        _trapz = getattr(np, "trapezoid", np.trapz)
+        U3 = _trapz(np.interp(z, zs, us), z) / (15.0e3 - h)
+        V3 = _trapz(np.interp(z, zs, vs), z) / (15.0e3 - h)
     # Upper layer thickness
     h2 = h - h1
     if (

From 928c81a18ac7a58df4252f7c3822705ca62427ce Mon Sep 17 00:00:00 2001
From: btol <btol@dtu.dk>
Date: Wed, 25 Feb 2026 16:07:28 +0100
Subject: [PATCH 5/7] Skip floris tests on Python < 3.10

floris uses PEP 604 union types (str | Path) which require Python 3.10+.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 tests/test_floris.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/test_floris.py b/tests/test_floris.py
index 653deed..1495535 100644
--- a/tests/test_floris.py
+++ b/tests/test_floris.py
@@ -9,12 +9,16 @@
 
 import os
 import shutil
+import sys
 from pathlib import Path
 
 import numpy as np
 import pytest
 import xarray as xr
 
+if sys.version_info < (3, 10):
+    pytest.skip("floris requires Python >= 3.10", allow_module_level=True)
+
 pytest.importorskip(
     "floris", reason="floris not installed, install with: pip install wifa[floris]"
 )

From 7e174e91f5c701c12cb96a5b358f8ba94fb51645 Mon Sep 17 00:00:00 2001
From: btol <btol@dtu.dk>
Date: Wed, 25 Feb 2026 16:12:33 +0100
Subject: [PATCH 6/7] Pin numpy<2 for wayve extra (wayve uses removed np.trapz)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 728106e..51481ba 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,6 +51,7 @@ floris = ["floris @ git+https://github.com/lejeunemax/floris.git@windIO"]
 wayve = [
     "wayve @ git+https://gitlab.kuleuven.be/TFSO-software/wayve@dev_foxes",
     "mpmath",
+    "numpy<2",  # wayve uses np.trapz, removed in numpy 2.0
 ]
 cs = []  # code_saturne is a subprocess, no pip dependency
 all = [

From c7d34c6a8722c593c277917b82927e63eee19182 Mon Sep 17 00:00:00 2001
From: btol <btol@dtu.dk>
Date: Wed, 25 Feb 2026 16:17:56 +0100
Subject: [PATCH 7/7] Remove numpy<2 pin: wayve main branch has np.trapz fix

Also update wayve URL to main branch.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 pyproject.toml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 51481ba..56c5d0f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,9 +49,8 @@ pywake = ["py_wake>=2.6.5"]
 foxes = ["foxes>=1.6.2"]
 floris = ["floris @ git+https://github.com/lejeunemax/floris.git@windIO"]
 wayve = [
-    "wayve @ git+https://gitlab.kuleuven.be/TFSO-software/wayve@dev_foxes",
+    "wayve @ git+https://gitlab.kuleuven.be/TFSO-software/wayve",
     "mpmath",
-    "numpy<2",  # wayve uses np.trapz, removed in numpy 2.0
 ]
 cs = []  # code_saturne is a subprocess, no pip dependency
 all = [