fixing doc compilation

cocofest/dynamics/initial_guess_warm_start.py

@@ -2,6 +2,8 @@
 This class is meant to determine the initial states and control guesses of an optimization problem.
 """
 
+from __future__ import annotations
+
 import numpy as np
 
 import biorbd

cocofest/integration/ivp_fes.py

@@ -2,6 +2,8 @@
 Code used to determine the Initial Value Problem.
 """
 
+from __future__ import annotations
+
 import numpy as np
 from bioptim import (
     ControlType,

cocofest/misc/fourier_approx.py

@@ -2,6 +2,8 @@
 This class enables the creation of a Fourier serie, to track a position, a force position with the optimization problem.
 """
 
+from __future__ import annotations
+
 from casadi import cos, sin
 import matplotlib.pyplot as plt
 import numpy as np

cocofest/models/ding2003/ding2003.py

@@ -5,6 +5,8 @@
 during functional electrical stimulation. Journal of Electromyography and Kinesiology, 13(6), 575-588.
 """
 
+from __future__ import annotations
+
 from typing import Callable, List
 from math import gcd
 from fractions import Fraction

cocofest/models/ding2003/ding2003_with_fatigue.py

@@ -5,6 +5,8 @@
 during functional electrical stimulation. Journal of Electromyography and Kinesiology, 13(6), 575-588.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 
 from casadi import MX, vertcat

cocofest/models/ding2007/ding2007.py

@@ -5,6 +5,8 @@
 force-intensity and force-frequency relationships after spinal cord injuries. Muscle & Nerve, 36(2), 214-222.
 """
 
+from __future__ import annotations
+
 from typing import Callable, List
 
 from casadi import MX, vertcat, exp

cocofest/models/ding2007/ding2007_with_fatigue.py

@@ -5,6 +5,8 @@
 force-intensity and force-frequency relationships after spinal cord injuries. Muscle & Nerve, 36(2), 214-222.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 
 from casadi import MX, vertcat

cocofest/models/dynamical_model.py

@@ -2,6 +2,8 @@
 Musculoskeletal model driven by one or more FES muscle models.
 """
 
+from __future__ import annotations
+
 from typing import Callable, List
 import numpy as np
 

cocofest/models/fes_model.py

@@ -2,6 +2,8 @@
 Abstract interface every FES model must implement to be usable within bioptim.
 """
 
+from __future__ import annotations
+
 from abc import ABC, abstractmethod
 
 from casadi import MX

cocofest/models/hill_coefficients.py

@@ -6,6 +6,8 @@
 Annals of biomedical engineering, 44, 2922-2936.
 """
 
+from __future__ import annotations
+
 from casadi import exp, log, sqrt
 
 

cocofest/models/hmed2018/hmed2018.py

@@ -6,6 +6,8 @@
 Computers in Biology and Medicine, 101, 218-228.
 """
 
+from __future__ import annotations
+
 from typing import Callable, List
 
 from casadi import MX, vertcat, tanh

cocofest/models/hmed2018/hmed2018_with_fatigue.py

@@ -6,6 +6,8 @@
 Computers in Biology and Medicine, 101, 218-228.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 
 from casadi import MX, vertcat

cocofest/models/marion2009/marion2009.py

@@ -5,6 +5,8 @@
 muscle length on fatigue during electrical stimulation. Muscle & Nerve, 40(4), 573-581.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 
 from casadi import MX, vertcat

cocofest/models/marion2009/marion2009_modified.py

@@ -5,6 +5,8 @@
 muscle length on fatigue during electrical stimulation. Muscle & Nerve, 40(4), 573-581.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 
 from casadi import MX, vertcat

cocofest/models/marion2009/marion2009_modified_with_fatigue.py

@@ -5,6 +5,8 @@
 muscle length on fatigue during electrical stimulation. Muscle & Nerve, 40(4), 573-581.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 
 import numpy as np

cocofest/models/marion2009/marion2009_with_fatigue.py

@@ -5,6 +5,8 @@
 muscle length on fatigue during electrical stimulation. Muscle & Nerve, 40(4), 573-581.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 
 import numpy as np

cocofest/models/marion2013/marion2013.py

@@ -6,6 +6,8 @@
 and Rehabilitation, 10, 1-16.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 from casadi import MX, vertcat, exp, cos, pi
 import numpy as np

cocofest/models/marion2013/marion2013_modified.py

@@ -6,6 +6,8 @@
 and Rehabilitation, 10, 1-16.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 from casadi import MX, vertcat, exp, cos, pi
 import numpy as np

cocofest/models/marion2013/marion2013_modified_with_fatigue.py

@@ -6,6 +6,8 @@
 and Rehabilitation, 10, 1-16.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 from casadi import MX, vertcat
 import numpy as np

cocofest/models/marion2013/marion2013_with_fatigue.py

@@ -6,6 +6,8 @@
 and Rehabilitation, 10, 1-16.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 from casadi import MX, vertcat
 import numpy as np

cocofest/models/state_configure.py

@@ -2,6 +2,8 @@
 Registers the bioptim states/controls used by Cocofest's FES and musculoskeletal models.
 """
 
+from __future__ import annotations
+
 from bioptim import (
     ConfigureVariables,
     NonLinearProgram,

cocofest/models/veltink1992/veltink1992.py

@@ -5,6 +5,8 @@
 for artificially stimulated muscle. IEEE Transactions on Biomedical Engineering, 39(4), 368-380.
 """
 
+from __future__ import annotations
+
 from typing import Callable, List
 from casadi import MX, vertcat
 import numpy as np

cocofest/models/veltink1992/veltink1992_and_riener1998.py

@@ -7,6 +7,8 @@
 fatigue during electrical stimulation. IEEE Transactions on Biomedical Engineering, 45(1), 105-113.
 """
 
+from __future__ import annotations
+
 from typing import Callable
 from casadi import MX, vertcat
 import numpy as np

cocofest/optimization/fes_id_ocp.py

@@ -2,6 +2,8 @@
 Builds the optimal control problem used to identify FES model parameters by fitting a tracked force curve.
 """
 
+from __future__ import annotations
+
 import numpy as np
 
 from bioptim import (

cocofest/optimization/fes_mhe.py

@@ -2,6 +2,8 @@
 Moving horizon estimation (MHE) for a single-muscle FES model.
 """
 
+from __future__ import annotations
+
 import numpy as np
 
 from casadi import SX

cocofest/optimization/fes_mhe_multibody.py

@@ -2,6 +2,8 @@
 Moving horizon estimation (MHE) for a musculoskeletal model (FesMskModel) driven by FES.
 """
 
+from __future__ import annotations
+
 import numpy as np
 from copy import deepcopy
 from casadi import SX

cocofest/optimization/fes_ocp.py

@@ -2,6 +2,8 @@
 Builds the optimal control problem used to optimize a single-muscle FES model.
 """
 
+from __future__ import annotations
+
 import numpy as np
 
 from bioptim import (

cocofest/optimization/fes_ocp_multibody.py

@@ -2,6 +2,8 @@
 Builds the optimal control problem for a musculoskeletal model driven by one or more FES muscle models.
 """
 
+from __future__ import annotations
+
 import numpy as np
 
 from bioptim import (

cocofest/optimization/penalties/custom_constraints.py

@@ -3,6 +3,8 @@
 By adding definitions to this class, you can create your own custom constraints.
 """
 
+from __future__ import annotations
+
 from casadi import MX, SX, vertcat
 from bioptim import PenaltyController
 

cocofest/optimization/penalties/custom_objectives.py

@@ -3,6 +3,8 @@
 By adding definitions to this class, you can create your own custom objective.
 """
 
+from __future__ import annotations
+
 from casadi import MX, vertcat
 from bioptim import PenaltyController
 from ...models.fes_model import FesModel

cocofest/result/graphics.py

@@ -3,6 +3,8 @@
 model identification.
 """
 
+from __future__ import annotations
+
 from bioptim import Solution, SolutionMerge, InterpolationType
 import matplotlib.pyplot as plt
 import numpy as np

cocofest/result/pickle.py

@@ -2,6 +2,8 @@
 Exports a bioptim Solution's time, states, controls and parameters to a pickle file for later reuse.
 """
 
+from __future__ import annotations
+
 import pickle
 import numpy as np
 from bioptim import SolutionMerge

cocofest/result/plot.py

@@ -2,6 +2,8 @@
 Plots the muscle stimulation angle and related quantities of a cycling motion.
 """
 
+from __future__ import annotations
+
 import numpy as np
 import matplotlib
 

docs/sphinx/conf.py

@@ -1,9 +1,16 @@
+import importlib.util
 import pathlib
 import sys
 
-sys.path.insert(0, str(pathlib.Path(__file__).resolve().parent.parent.parent))
+repo_root = pathlib.Path(__file__).resolve().parent.parent.parent
+sys.path.insert(0, str(repo_root))
 
-from cocofest.misc.__version__ import __version__ as release
+_version_spec = importlib.util.spec_from_file_location(
+    "cocofest_version", repo_root / "cocofest" / "misc" / "__version__.py"
+)
+_version_module = importlib.util.module_from_spec(_version_spec)
+_version_spec.loader.exec_module(_version_module)
+release = _version_module.__version__
 
 project = "Cocofest"
 author = "Kev1Co"
@@ -27,9 +34,7 @@
     ".md": "markdown",
 }
 
-# cocofest.result.animate is not needed to build the docs and depends on
-# pyorerun, which is not installed in the docs environment.
-autodoc_mock_imports = ["pyorerun"]
+autodoc_mock_imports = ["bioptim", "biorbd", "casadi", "pyorerun"]
 
 autosummary_generate = True
 autodoc_default_options = {"undoc-members": True}

docs/sphinx/environment.yml

@@ -3,4 +3,3 @@ channels:
 - conda-forge
 dependencies:
 - python=3.11
-- bioptim=3.4.0