From 4272c015e1d2711af039672c062c4524032671f0 Mon Sep 17 00:00:00 2001
From: "Jason K. Moore" <moorepants@gmail.com>
Date: Sun, 5 Jan 2025 14:01:40 +0100
Subject: [PATCH 01/17] Make setuptools a required dependency, fixes #295.

---
 README.rst       | 5 +++--
 opty-dev-env.yml | 1 +
 setup.py         | 1 +
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/README.rst b/README.rst
index 54ad8c1e..235221c2 100644
--- a/README.rst
+++ b/README.rst
@@ -79,6 +79,7 @@ The required dependencies are as follows:
 - numpy >= 1.19.0
 - python 3.9-3.13
 - scipy >= 1.5.0
+- setuptools
 - sympy >= 1.6.0
 
 The optional dependencies are as follows:
@@ -136,7 +137,7 @@ set the ``LD_LIBRARY_PATH`` so that you can link to Ipopt when installing
 
 Once Ipopt is installed and accessible, install conda then create an environment::
 
-   $ conda create -n opty-custom -c conda-forge cython numpy pip scipy sympy
+   $ conda create -n opty-custom -c conda-forge cython numpy pip scipy setuptools sympy
    $ source activate opty-custom
    (opty-custom)$ pip install cyipopt  # this will compile cyipopt against the available ipopt
    (opty-custom)$ pip install opty
@@ -145,7 +146,7 @@ If you want to develop opty, create a conda environment with all of the
 dependencies installed::
 
    $ conda config --add channels conda-forge
-   $ conda create -n opty-dev python sympy numpy scipy cython ipopt cyipopt matplotlib pytables pydy pandas pytest sphinx sphinx-gallery numpydoc
+   $ conda create -n opty-dev python sympy numpy scipy cython ipopt cyipopt matplotlib pytables pydy pandas pytest setuptools sphinx sphinx-gallery numpydoc
    $ source activate opty-dev
 
 Next download the opty source files and install with::
diff --git a/opty-dev-env.yml b/opty-dev-env.yml
index e2e073a0..e995ba18 100644
--- a/opty-dev-env.yml
+++ b/opty-dev-env.yml
@@ -13,6 +13,7 @@ dependencies:
   - pytest-cov
   - python
   - scipy >=1.5.0
+  - setuptools
   - sphinx
   - sphinx-gallery
   - sympy >=1.13  # version required for the docs
diff --git a/setup.py b/setup.py
index 34f7b404..33d3eefc 100644
--- a/setup.py
+++ b/setup.py
@@ -20,6 +20,7 @@
         'cython>=0.29.19',
         'numpy>=1.19.0',
         'scipy>=1.5.0',
+        'setuptools',  # provides distutils for Python >=3.13
         'sympy>=1.6.0',
     ],
     extras_require={

From 4ee3cb80223e971248d67d4c11bc03c39377cc63 Mon Sep 17 00:00:00 2001
From: Peter Stahlecker <peter.stahlecker@gmail.com>
Date: Sat, 18 Jan 2025 16:27:51 +0100
Subject: [PATCH 02/17] changed a typo in line 434

---
 opty/direct_collocation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index c598695e..4c084b23 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -340,7 +340,7 @@ def jacobian(self, free):
 
         Returns
         =======
-        jac_vals : ndarray, shape((2*n + q + r + s)*(n*(N - 1) + o), )
+        jac_vals : ndarray, shape((2*n + q + r + s)*(n*(N - 1)) + o, )
             Non-zero Jacobian values in triplet format.
 
         """

From 10c0feb02e6b92fa33069836294f41c093e3117f Mon Sep 17 00:00:00 2001
From: Peter Stahlecker <peter.stahlecker@gmail.com>
Date: Tue, 21 Jan 2025 14:28:10 +0100
Subject: [PATCH 03/17] add parse_free method to Problem class, add test
 fubction

---
 opty/direct_collocation.py            |  56 ++++++++++++
 opty/tests/test_direct_collocation.py | 124 +++++++++++++++++++++++++-
 2 files changed, 179 insertions(+), 1 deletion(-)

diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index 4c084b23..3f60ffd0 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -597,6 +597,62 @@ def plot_objective_value(self):
 
         return ax
 
+    def parse_free(self, free):
+        """Parses the free parameters vector and returns it's components.
+
+        Parameters
+        ----------
+        free : ndarray, shape(n*N + q*N + r + s)
+            The free parameters of the system.
+
+        where:
+
+        - N : number of collocation nodes
+        - n : number of unknown state trajectories
+        - q : number of unknown input trajectories
+        - r : number of unknown parameters
+        - s : number of unknown time intervals (s=1 if variable duration, else s=0)
+
+
+        Returns
+        -------
+        states : ndarray, shape(n, N)
+            The array of n states through N time steps.
+        specified_values : ndarray, shape(q, N) or shape(N,), or None
+            The array of q specified inputs through N time steps.
+        constant_values : ndarray, shape(r,)
+            The array of r constants.
+        time_interval : float
+            The time between collocation nodes. Only returned if
+            ``variable_duration`` is ``True``.
+
+        """
+
+        n = self.collocator.num_states
+        N = self.collocator.num_collocation_nodes
+        q = self.collocator.num_unknown_input_trajectories
+        variable_duration = self.collocator._variable_duration
+
+        len_states = n * N
+        len_specified = q * N
+
+        free_states = free[:len_states].reshape((n, N))
+
+        if q == 0:
+            free_specified = None
+        else:
+            free_specified = free[len_states:len_states + len_specified]
+            if q > 1:
+                free_specified = free_specified.reshape((q, N))
+
+        if variable_duration:
+            free_time_interval = free[-1]
+            free_constants = free[len_states + len_specified:-1]
+            return free_states, free_specified, free_constants, free_time_interval
+        else:
+            free_constants = free[len_states + len_specified:]
+            return free_states, free_specified, free_constants
+
 
 class ConstraintCollocator(object):
     """This class is responsible for generating the constraint function and the
diff --git a/opty/tests/test_direct_collocation.py b/opty/tests/test_direct_collocation.py
index adc2f3f8..ec4e37f9 100644
--- a/opty/tests/test_direct_collocation.py
+++ b/opty/tests/test_direct_collocation.py
@@ -10,7 +10,7 @@
 from pytest import raises
 
 from ..direct_collocation import Problem, ConstraintCollocator
-from ..utils import create_objective_function, sort_sympy
+from ..utils import create_objective_function, sort_sympy, parse_free
 
 
 def test_pendulum():
@@ -1566,3 +1566,125 @@ def test_for_algebraic_eoms():
         )
 
     assert excinfo.type is ValueError
+
+
+def test_prob_parse_free():
+    """
+    Test for parse_free method of Problem class.
+    ===========================================
+
+    This test whether the parse_free method of the Problem class works as
+    the parse_free in utils.
+
+    **States**
+
+    - :math:`x_1, x_2, ux_1, ux_2` : state variables
+
+    **Control**
+
+    - :math:`u_1, u_2` : control variable
+
+    """
+
+    t = mech.dynamicsymbols._t
+
+    x1, x2, ux1, ux2 = mech.dynamicsymbols('x1 x2 ux1 ux2')
+    u1, u2 = mech.dynamicsymbols('u1 u2')
+    h = sym.symbols('h')
+    a, b = sym.symbols('a b')
+
+    # equations of motion.
+    # (No meaning, just for testing)
+    eom = sym.Matrix([
+            -x1.diff(t) + ux1,
+            -x2.diff(t) + ux2,
+            -ux1.diff(t) + a*u1,
+            -ux2.diff(t) + b*u2,
+    ])
+
+    # Set up and Solve the Optimization Problem
+    num_nodes = 11
+    t0, tf = 0.0, 0.9
+    state_symbols = (x1, x2, ux1, ux2)
+    control_symbols = (u1, u2)
+
+    interval_value = (tf - t0)/(num_nodes - 1)
+    times = np.linspace(t0, tf, num_nodes)
+
+    # Specify the symbolic instance constraints, as per the example.
+    instance_constraints = (
+        x1.func(t0) - 1.0,
+        x2.func(t0) + 1.0,
+    )
+
+    # Specify the objective function and form the gradient.
+
+    def obj(free):
+        return sum([free[i]**2 for i in range(2*num_nodes)])
+
+    def obj_grad(free):
+        grad = np.zeros_like(free)
+        grad[:2*num_nodes] = 2*free[:2*num_nodes]
+        return grad
+
+    # Create the optimization problem and set any options.
+    prob = Problem(
+            obj,
+            obj_grad,
+            eom,
+            state_symbols,
+            num_nodes,
+            interval_value,
+            instance_constraints=instance_constraints,
+)
+
+    # Give some estimates for the trajectory.
+    initial_guess = np.random.rand(prob.num_free)
+    initial_guess1 = initial_guess
+
+    # check whether same results.
+    statesu, controlsu, constantsu = parse_free(initial_guess1,
+            len(state_symbols), len(control_symbols), num_nodes)
+
+    states, controls, constants = prob.parse_free(initial_guess)
+    assert(np.all(states == statesu))
+    assert(np.all(controls == controlsu))
+    assert(np.all(constants == constantsu))
+
+
+    # test with variable interval_value
+    interval_value = h
+    t0, tf = 0.0, (num_nodes - 1)*interval_value
+    def obj(free):
+        return sum([free[i]**2 for i in range(2*num_nodes)])
+
+    def obj_grad(free):
+        grad = np.zeros_like(free)
+        grad[:2*num_nodes] = 2*free[:2*num_nodes]
+        return grad
+
+    # Create the optimization problem and set any options.
+    prob = Problem(
+            obj,
+            obj_grad,
+            eom,
+            state_symbols,
+            num_nodes,
+            interval_value,
+            instance_constraints=instance_constraints,
+)
+
+    # Give some estimates for the trajectory.
+    initial_guess = np.random.rand(prob.num_free)
+    initial_guess1 = initial_guess
+
+    # check whether same results.
+    statesu, controlsu, constantsu, timeu = parse_free(initial_guess1,
+        len(state_symbols), len(control_symbols),
+        num_nodes, variable_duration=True)
+
+    states, controls, constants, times = prob.parse_free(initial_guess)
+    assert(np.all(states == statesu))
+    assert(np.all(controls == controlsu))
+    assert(np.all(constants == constantsu))
+    assert(np.all(timeu == times))

From e7a22b2aa0ca61aa0a0ca23ac777f6d2cb999d50 Mon Sep 17 00:00:00 2001
From: Peter Stahlecker <peter.stahlecker@gmail.com>
Date: Tue, 21 Jan 2025 15:15:53 +0100
Subject: [PATCH 04/17] changed as per Timo's idea

---
 opty/direct_collocation.py | 21 +--------------------
 1 file changed, 1 insertion(+), 20 deletions(-)

diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index 3f60ffd0..50ef2be3 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -633,26 +633,7 @@ def parse_free(self, free):
         q = self.collocator.num_unknown_input_trajectories
         variable_duration = self.collocator._variable_duration
 
-        len_states = n * N
-        len_specified = q * N
-
-        free_states = free[:len_states].reshape((n, N))
-
-        if q == 0:
-            free_specified = None
-        else:
-            free_specified = free[len_states:len_states + len_specified]
-            if q > 1:
-                free_specified = free_specified.reshape((q, N))
-
-        if variable_duration:
-            free_time_interval = free[-1]
-            free_constants = free[len_states + len_specified:-1]
-            return free_states, free_specified, free_constants, free_time_interval
-        else:
-            free_constants = free[len_states + len_specified:]
-            return free_states, free_specified, free_constants
-
+        return parse_free(free, n, q, N, variable_duration)
 
 class ConstraintCollocator(object):
     """This class is responsible for generating the constraint function and the

From 29eaa2ca94fbf45333b7030e64b318b03f396059 Mon Sep 17 00:00:00 2001
From: Peter Stahlecker <peter.stahlecker@gmail.com>
Date: Tue, 21 Jan 2025 17:34:14 +0100
Subject: [PATCH 05/17] changed test function to np.allclose as per suggerstion

---
 opty/tests/test_direct_collocation.py | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/opty/tests/test_direct_collocation.py b/opty/tests/test_direct_collocation.py
index ec4e37f9..1a074144 100644
--- a/opty/tests/test_direct_collocation.py
+++ b/opty/tests/test_direct_collocation.py
@@ -1647,10 +1647,9 @@ def obj_grad(free):
             len(state_symbols), len(control_symbols), num_nodes)
 
     states, controls, constants = prob.parse_free(initial_guess)
-    assert(np.all(states == statesu))
-    assert(np.all(controls == controlsu))
-    assert(np.all(constants == constantsu))
-
+    assert(np.allclose(states, statesu))
+    assert(np.allclose(controls, controlsu))
+    assert(np.allclose(constants, constantsu))
 
     # test with variable interval_value
     interval_value = h
@@ -1684,7 +1683,7 @@ def obj_grad(free):
         num_nodes, variable_duration=True)
 
     states, controls, constants, times = prob.parse_free(initial_guess)
-    assert(np.all(states == statesu))
-    assert(np.all(controls == controlsu))
-    assert(np.all(constants == constantsu))
-    assert(np.all(timeu == times))
+    assert(np.allclose(states, statesu))
+    assert(np.allclose(controls, controlsu))
+    assert(np.allclose(constants, constantsu))
+    assert(np.allclose(timeu, times))

From 1516536c269e89c4eb944f141dc7731351e06b22 Mon Sep 17 00:00:00 2001
From: Peter Stahlecker <peter.stahlecker@gmail.com>
Date: Tue, 21 Jan 2025 18:10:33 +0100
Subject: [PATCH 06/17] changed to np.testing.assert_allclose(a, b)

---
 opty/tests/test_direct_collocation.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/opty/tests/test_direct_collocation.py b/opty/tests/test_direct_collocation.py
index 1a074144..ee598876 100644
--- a/opty/tests/test_direct_collocation.py
+++ b/opty/tests/test_direct_collocation.py
@@ -1647,9 +1647,9 @@ def obj_grad(free):
             len(state_symbols), len(control_symbols), num_nodes)
 
     states, controls, constants = prob.parse_free(initial_guess)
-    assert(np.allclose(states, statesu))
-    assert(np.allclose(controls, controlsu))
-    assert(np.allclose(constants, constantsu))
+    np.testing.assert_allclose(states, statesu)
+    np.testing.assert_allclose(controls, controlsu)
+    np.testing.assert_allclose(constants, constantsu)
 
     # test with variable interval_value
     interval_value = h
@@ -1683,7 +1683,7 @@ def obj_grad(free):
         num_nodes, variable_duration=True)
 
     states, controls, constants, times = prob.parse_free(initial_guess)
-    assert(np.allclose(states, statesu))
-    assert(np.allclose(controls, controlsu))
-    assert(np.allclose(constants, constantsu))
-    assert(np.allclose(timeu, times))
+    np.testing.assert_allclose(states, statesu)
+    np.testing.assert_allclose(controls, controlsu)
+    np.testing.assert_allclose(constants, constantsu)
+    np.testing.assert_allclose(timeu, times)

From 12966847b1b9a930065cec236ef5c69e12ba7119 Mon Sep 17 00:00:00 2001
From: Peter Stahlecker <peter.stahlecker@gmail.com>
Date: Wed, 22 Jan 2025 16:48:04 +0100
Subject: [PATCH 07/17]  improved HTML rendering

---
 opty/direct_collocation.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index 50ef2be3..e0feced2 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -601,21 +601,12 @@ def parse_free(self, free):
         """Parses the free parameters vector and returns it's components.
 
         Parameters
-        ----------
+        ==========
         free : ndarray, shape(n*N + q*N + r + s)
             The free parameters of the system.
 
-        where:
-
-        - N : number of collocation nodes
-        - n : number of unknown state trajectories
-        - q : number of unknown input trajectories
-        - r : number of unknown parameters
-        - s : number of unknown time intervals (s=1 if variable duration, else s=0)
-
-
         Returns
-        -------
+        =======
         states : ndarray, shape(n, N)
             The array of n states through N time steps.
         specified_values : ndarray, shape(q, N) or shape(N,), or None
@@ -626,6 +617,15 @@ def parse_free(self, free):
             The time between collocation nodes. Only returned if
             ``variable_duration`` is ``True``.
 
+        Notes
+        =====
+
+        - N : number of collocation nodes
+        - n : number of unknown state trajectories
+        - q : number of unknown input trajectories
+        - r : number of unknown parameters
+        - s : number of unknown time intervals (s=1 if ``variable duration`` is ``True`` else s=0)
+
         """
 
         n = self.collocator.num_states

From 2f6ccd0ba651348d4a7adcd24be76460001dd55c Mon Sep 17 00:00:00 2001
From: Peter Stahlecker <peter.stahlecker@gmail.com>
Date: Sat, 25 Jan 2025 09:00:47 +0100
Subject: [PATCH 08/17] trial push whether layout is o.k.

---
 opty/direct_collocation.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index e0feced2..1610c60e 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -727,6 +727,13 @@ def __init__(self, equations_of_motion, state_symbols,
             If True, STDOUT and STDERR of the Cython compilation call will be
             shown.
 
+        Attributes
+        ----------
+        eom : sympy.Matrix
+            The equations of motion used.
+        state_symbols : tuple
+            The state symbols used. Functions of time.
+
         """
         self.eom = equations_of_motion
 

From bd360fb77fe72f9c73901bd7b7cb3dff430a9146 Mon Sep 17 00:00:00 2001
From: Peter Stahlecker <peter.stahlecker@gmail.com>
Date: Sat, 25 Jan 2025 12:05:13 +0100
Subject: [PATCH 09/17] included all public attributes of ConstraintCollocator

---
 opty/direct_collocation.py | 70 ++++++++++++++++++++++++++++++++++++--
 1 file changed, 68 insertions(+), 2 deletions(-)

diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index 1610c60e..b4431569 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -128,6 +128,8 @@ class Problem(cyipopt.Problem):
                       eomn2, ... eomnN,
                       c1, ..., co]
 
+    The attributes may be accessed as follows: Problem_instance.collocator.name_of_attribute
+
     """
 
     INF = 10e19
@@ -729,10 +731,74 @@ def __init__(self, equations_of_motion, state_symbols,
 
         Attributes
         ----------
-        eom : sympy.Matrix
+        Some of the attributes are explained in more detail under Parameters above.
+
+        eom: sympy.Matrix
             The equations of motion used.
         state_symbols : tuple
-            The state symbols used. Functions of time.
+            The state symbols used. Functrion of time.
+        state_derivative_symbols : tuple
+            symbols for the time derivatives of the states.
+        num_states : int
+            The number of states = len(state_symbols).
+        num_collocation_nodes : int
+            Number of times spaced evenly between the initial and final time of the optimization.
+        node_time_interval : float or sympy.Symbol
+            The time interval between the collocation nodes. float if the time is fixed, sympy.Symbol if the time is a variable.
+        time_interval_symbol : sympy.Symbol
+            The symbol used to represent the time interval if it is variable, else the internal symbol.
+        known_parameter_map : dict
+            A mapping of known parameters to their values.
+        unknown_parameters : tuple
+            The unknown parameters in the problem, in the sequence in which they appear in the solution of the optimization.
+        num_unknown_parameters : int
+            The number of unknown parameters.
+        parameters : tuple
+            known_parameters + unknown_parameters
+        num_parameters : int
+            The number of parameters = len(parameters).
+        known_trajectory_map : dict
+            A mapping of known trajectories to their values, see also above in Parameters
+        known_trajectory_symbols : tuple
+            The known trajectory symbols.
+        num_known_trajectories : int
+            The number of known trajectories = len(known_trajectory_symbols).
+        unknown_input_trajectories : tuple
+            The unknown input trajectories symbols.
+        num_unknown_input_trajectories : int
+            The number of unknown input trajectories = len(unknown_input_trajectories).
+        input_trajectories : tuple
+            known_input_trajectories + unknown_input_trajectories
+        instance_constraints : tuple
+            The instance constraints used in the optimization.
+        num_constraints : int
+            The number of constraints = (num_collection_nodes-1)*num_states + len(instance_constraints).
+        num_instance_constraints : int
+            The number of instance constraints = len(instance_constraints).
+        previous_discrete_state_symbols : tuple
+            The symbols for the previous discrete states.
+        current_discrete_state_symbols : tuple
+            The symbols for the current discrete states.
+        next_discrete_state_symbols : tuple
+            The symbols for the next discrete states.
+        current_discrete_specified_symbols : tuple
+            The symbols for the current discrete specified inputs.
+        next_discrete_specified_symbols : tuple
+            The symbols for the next discrete specified inputs.
+        integration_method : str
+            The integration method used.
+        discrete_eom : sympy.Matrix
+            Discretized equations of motion. Depending on the integration method used.
+        num_free : int
+            Number of variables to be optimized
+        time_symbol : sympy.Symbol
+            The symbol used to represent time, usually `t`
+        tmp_dir
+            The temporary directory used to store files generated
+        parallel : bool
+            Whether to use parallel processing or not.
+        show_compile_output : bool
+            Whether to show the compile output or not.
 
         """
         self.eom = equations_of_motion

From 222505b241ed306cdc881c364802b75923e75ce9 Mon Sep 17 00:00:00 2001
From: Peter Stahlecker <peter.stahlecker@gmail.com>
Date: Sun, 26 Jan 2025 11:40:04 +0100
Subject: [PATCH 10/17] tried to address the suggestions given

---
 opty/direct_collocation.py | 150 +++++++++++++++++++------------------
 1 file changed, 78 insertions(+), 72 deletions(-)

diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index b4431569..c03063a4 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -656,9 +656,86 @@ class ConstraintCollocator(object):
     - o : number of instance constraints
     - nN + qN + r + s : number of free variables
     - n(N - 1) + o : number of constraints
+    - Some of the attributes are explained in more detail under Parameters below.
+
+    Attributes
+    ----------
+    ==========
+
+    current_discrete_state_symbols : n-tuple
+        The symbols for the current discrete states.
+    current_discrete_specified_symbols : q-tuple
+        The symbols for the current discrete specified inputs.
+    discrete_eom : sympy.Matrix, shape(n, 1)
+        Discretized equations of motion. Depending on the integration method
+        used.
+    eom: sympy.Matrix, shape(n, 1)
+        The equations of motion used.
+    input_trajectories : tuple
+        known_input_trajectories + unknown_input_trajectories.
+    instance_constraints : o-tuple
+        The instance constraints used in the optimization.
+    integration_method : str
+        The integration method used.
+    known_parameters : tuple
+        The symbols of the known parameters in the problem.
+    known_parameter_map : dict
+        A mapping of known parameters to their values.
+    known_trajectory_map : dict
+        A mapping of known trajectories to their values.
+    known_trajectory_symbols : (m-q)-tuple
+        The known trajectory symbols.
+    next_discrete_specified_symbols : q-tuple
+        The symbols for the next discrete specified inputs.
+    next_discrete_state_symbols : n-tuple
+        The symbols for the next discrete states.
+    node_time_interval : float or sympy.Symbol
+        The time interval between the collocation nodes. float if the interval
+        is fixed, sympy.Symbol if the interval is variable.
+    num_collocation_nodes : int
+        Number of times spaced evenly between the initial and final time of
+        the optimization = N.
+    num_constraints : int
+        The number of constraints = (num_collection_nodes-1)*num_states +
+        len(instance_constraints).
+    num_free : int
+        Number of variables to be optimized = n*N + q*N + r + s.
+    num_input_trajectories : int
+        The number of input trajectories = len(input_trajectories).
+    num_instance_constraints : int
+        The number of instance constraints = len(instance_constraints).
+    num_known_trajectories : int
+        The number of known trajectories = len(known_trajectory_symbols).
+    num_parameters : int
+        The number of parameters = len(parameters).
+    num_states : int
+        The number of states = len(state_symbols) = n.
+    num_unknown_input_trajectories : int
+        The number of unknown input trajectories =
+        len(unknown_input_trajectories).
+    num_unknown_parameters : int
+        The number of unknown parameters = r.
+    parameters : tuple
+        known_parameters + unknown_parameters.
+    parallel : bool
+        Whether to use parallel processing or not.
+    previous_discrete_state_symbols : n-tuple
+        The symbols for the previous discrete states.
+    show_compile_output : bool
+        Whether to show the compile output or not.
+    state_derivative_symbols : n-tuple
+        symbols for the time derivatives of the states.
+    time_symbol : sympy.Symbol
+        The symbol used to represent time, usually `t`.
+    tmp_dir
+        The temporary directory used to store files generated.
+    unknown_input_trajectories : q-tuple
+        The unknown input trajectories symbols.
+    unknown_parameters : r-tuple
+        The unknown parameters in the problem, in the sequence in which they
+        appear in the solution of the optimization.
 
     """
-
     def __init__(self, equations_of_motion, state_symbols,
                  num_collocation_nodes, node_time_interval,
                  known_parameter_map={}, known_trajectory_map={},
@@ -729,77 +806,6 @@ def __init__(self, equations_of_motion, state_symbols,
             If True, STDOUT and STDERR of the Cython compilation call will be
             shown.
 
-        Attributes
-        ----------
-        Some of the attributes are explained in more detail under Parameters above.
-
-        eom: sympy.Matrix
-            The equations of motion used.
-        state_symbols : tuple
-            The state symbols used. Functrion of time.
-        state_derivative_symbols : tuple
-            symbols for the time derivatives of the states.
-        num_states : int
-            The number of states = len(state_symbols).
-        num_collocation_nodes : int
-            Number of times spaced evenly between the initial and final time of the optimization.
-        node_time_interval : float or sympy.Symbol
-            The time interval between the collocation nodes. float if the time is fixed, sympy.Symbol if the time is a variable.
-        time_interval_symbol : sympy.Symbol
-            The symbol used to represent the time interval if it is variable, else the internal symbol.
-        known_parameter_map : dict
-            A mapping of known parameters to their values.
-        unknown_parameters : tuple
-            The unknown parameters in the problem, in the sequence in which they appear in the solution of the optimization.
-        num_unknown_parameters : int
-            The number of unknown parameters.
-        parameters : tuple
-            known_parameters + unknown_parameters
-        num_parameters : int
-            The number of parameters = len(parameters).
-        known_trajectory_map : dict
-            A mapping of known trajectories to their values, see also above in Parameters
-        known_trajectory_symbols : tuple
-            The known trajectory symbols.
-        num_known_trajectories : int
-            The number of known trajectories = len(known_trajectory_symbols).
-        unknown_input_trajectories : tuple
-            The unknown input trajectories symbols.
-        num_unknown_input_trajectories : int
-            The number of unknown input trajectories = len(unknown_input_trajectories).
-        input_trajectories : tuple
-            known_input_trajectories + unknown_input_trajectories
-        instance_constraints : tuple
-            The instance constraints used in the optimization.
-        num_constraints : int
-            The number of constraints = (num_collection_nodes-1)*num_states + len(instance_constraints).
-        num_instance_constraints : int
-            The number of instance constraints = len(instance_constraints).
-        previous_discrete_state_symbols : tuple
-            The symbols for the previous discrete states.
-        current_discrete_state_symbols : tuple
-            The symbols for the current discrete states.
-        next_discrete_state_symbols : tuple
-            The symbols for the next discrete states.
-        current_discrete_specified_symbols : tuple
-            The symbols for the current discrete specified inputs.
-        next_discrete_specified_symbols : tuple
-            The symbols for the next discrete specified inputs.
-        integration_method : str
-            The integration method used.
-        discrete_eom : sympy.Matrix
-            Discretized equations of motion. Depending on the integration method used.
-        num_free : int
-            Number of variables to be optimized
-        time_symbol : sympy.Symbol
-            The symbol used to represent time, usually `t`
-        tmp_dir
-            The temporary directory used to store files generated
-        parallel : bool
-            Whether to use parallel processing or not.
-        show_compile_output : bool
-            Whether to show the compile output or not.
-
         """
         self.eom = equations_of_motion
 

From 26681cafb98b7d22d31aebb06b523fda43e9136d Mon Sep 17 00:00:00 2001
From: Peter Stahlecker <peter.stahlecker@gmail.com>
Date: Sun, 26 Jan 2025 13:22:39 +0100
Subject: [PATCH 11/17] put attributes above notes, changed that sentence

---
 opty/direct_collocation.py | 33 +++++++++++++++++----------------
 1 file changed, 17 insertions(+), 16 deletions(-)

diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index c03063a4..45937c77 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -643,25 +643,9 @@ class ConstraintCollocator(object):
     for a non-linear programming problem where the essential constraints are
     defined from the equations of motion of the system.
 
-    Notes
-    =====
-
-    - N : number of collocation nodes
-    - n : number of states
-    - m : number of input trajectories
-    - q : number of unknown input trajectories
-    - r : number of unknown parameters
-    - s : number of unknown time intervals (0 or 1 if fixed duration or
-      variable duration)
-    - o : number of instance constraints
-    - nN + qN + r + s : number of free variables
-    - n(N - 1) + o : number of constraints
-    - Some of the attributes are explained in more detail under Parameters below.
 
     Attributes
-    ----------
     ==========
-
     current_discrete_state_symbols : n-tuple
         The symbols for the current discrete states.
     current_discrete_specified_symbols : q-tuple
@@ -735,6 +719,23 @@ class ConstraintCollocator(object):
         The unknown parameters in the problem, in the sequence in which they
         appear in the solution of the optimization.
 
+    Notes
+    =====
+
+    - N : number of collocation nodes
+    - n : number of states
+    - m : number of input trajectories
+    - q : number of unknown input trajectories
+    - r : number of unknown parameters
+    - s : number of unknown time intervals (0 or 1 if fixed duration or
+      variable duration)
+    - o : number of instance constraints
+    - nN + qN + r + s : number of free variables
+    - n(N - 1) + o : number of constraints
+
+    Some of the attributes are explained in more detail under Parameters below.
+
+
     """
     def __init__(self, equations_of_motion, state_symbols,
                  num_collocation_nodes, node_time_interval,

From 2f3ba013dee279beb4b7df2e2a5fce293d02660f Mon Sep 17 00:00:00 2001
From: "Jason K. Moore" <moorepants@gmail.com>
Date: Sun, 26 Jan 2025 14:28:26 +0100
Subject: [PATCH 12/17] Update opty/direct_collocation.py

---
 opty/direct_collocation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index 45937c77..da4bb6aa 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -128,7 +128,7 @@ class Problem(cyipopt.Problem):
                       eomn2, ... eomnN,
                       c1, ..., co]
 
-    The attributes may be accessed as follows: Problem_instance.collocator.name_of_attribute
+    The attributes may be accessed as follows: ``Problem_instance.collocator.name_of_attribute``
 
     """
 

From 7bed059c6390939d1409c8c51085931c5dcb21e9 Mon Sep 17 00:00:00 2001
From: "Jason K. Moore" <moorepants@gmail.com>
Date: Sun, 26 Jan 2025 14:29:18 +0100
Subject: [PATCH 13/17] Update opty/direct_collocation.py

---
 opty/direct_collocation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index da4bb6aa..a2db8848 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -675,7 +675,7 @@ class ConstraintCollocator(object):
         The symbols for the next discrete states.
     node_time_interval : float or sympy.Symbol
         The time interval between the collocation nodes. float if the interval
-        is fixed, sympy.Symbol if the interval is variable.
+        is fixed, ``sympy.Symbol`` if the interval is variable.
     num_collocation_nodes : int
         Number of times spaced evenly between the initial and final time of
         the optimization = N.

From da1214035fd4eb1d33fb021bcb0ef10a6a72bd4f Mon Sep 17 00:00:00 2001
From: "Jason K. Moore" <moorepants@gmail.com>
Date: Mon, 27 Jan 2025 07:53:42 +0100
Subject: [PATCH 14/17] Update readthedocs config.

---
 .readthedocs.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index f9514ee9..d514e60c 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -1,8 +1,8 @@
 version: 2
 build:
-  os: "ubuntu-22.04"
+  os: "ubuntu-24.04"
   tools:
-    python: "mambaforge-22.9"
+    python: "miniconda-latest"
 sphinx:
   configuration: docs/conf.py
 formats: all

From bffff7a1eeb5d17a7ec4a2957fa471999cdab127 Mon Sep 17 00:00:00 2001
From: "Jason K. Moore" <moorepants@gmail.com>
Date: Mon, 27 Jan 2025 07:59:36 +0100
Subject: [PATCH 15/17] Testing the RTD preview builds.

---
 docs/index.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/index.rst b/docs/index.rst
index 4721e1b2..bfbc5e29 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -6,6 +6,8 @@
 Welcome to opty's documentation!
 ================================
 
+Trying out a preview build.
+
 Contents
 --------
 

From f88480f8c792582edc5c0989ab8637395899d458 Mon Sep 17 00:00:00 2001
From: "Jason K. Moore" <moorepants@gmail.com>
Date: Mon, 27 Jan 2025 08:18:48 +0100
Subject: [PATCH 16/17] Docstring shuffling.

---
 docs/index.rst             |  2 --
 opty/direct_collocation.py | 12 +++++++-----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/docs/index.rst b/docs/index.rst
index bfbc5e29..4721e1b2 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -6,8 +6,6 @@
 Welcome to opty's documentation!
 ================================
 
-Trying out a preview build.
-
 Contents
 --------
 
diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index a2db8848..8f5d9f24 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -626,7 +626,8 @@ def parse_free(self, free):
         - n : number of unknown state trajectories
         - q : number of unknown input trajectories
         - r : number of unknown parameters
-        - s : number of unknown time intervals (s=1 if ``variable duration`` is ``True`` else s=0)
+        - s : number of unknown time intervals (s=1 if ``variable duration`` is
+          ``True`` else s=0)
 
         """
 
@@ -643,7 +644,6 @@ class ConstraintCollocator(object):
     for a non-linear programming problem where the essential constraints are
     defined from the equations of motion of the system.
 
-
     Attributes
     ==========
     current_discrete_state_symbols : n-tuple
@@ -719,6 +719,11 @@ class ConstraintCollocator(object):
         The unknown parameters in the problem, in the sequence in which they
         appear in the solution of the optimization.
 
+    Some of the attributes are explained in more detail under Parameters below.
+
+    It is best to treat ``ConstraintCollocator`` as immutable, changing
+    attributes after initialization will inevitably fail.
+
     Notes
     =====
 
@@ -733,9 +738,6 @@ class ConstraintCollocator(object):
     - nN + qN + r + s : number of free variables
     - n(N - 1) + o : number of constraints
 
-    Some of the attributes are explained in more detail under Parameters below.
-
-
     """
     def __init__(self, equations_of_motion, state_symbols,
                  num_collocation_nodes, node_time_interval,

From a77fedb1515ddd9db5bea92c76c0bb4dafd7f148 Mon Sep 17 00:00:00 2001
From: "Jason K. Moore" <moorepants@gmail.com>
Date: Mon, 27 Jan 2025 08:41:05 +0100
Subject: [PATCH 17/17] Move paragraph text back into notes.

---
 opty/direct_collocation.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/opty/direct_collocation.py b/opty/direct_collocation.py
index 8f5d9f24..47059a0f 100644
--- a/opty/direct_collocation.py
+++ b/opty/direct_collocation.py
@@ -719,11 +719,6 @@ class ConstraintCollocator(object):
         The unknown parameters in the problem, in the sequence in which they
         appear in the solution of the optimization.
 
-    Some of the attributes are explained in more detail under Parameters below.
-
-    It is best to treat ``ConstraintCollocator`` as immutable, changing
-    attributes after initialization will inevitably fail.
-
     Notes
     =====
 
@@ -738,6 +733,11 @@ class ConstraintCollocator(object):
     - nN + qN + r + s : number of free variables
     - n(N - 1) + o : number of constraints
 
+    Some of the attributes are explained in more detail under Parameters below.
+
+    It is best to treat ``ConstraintCollocator`` as immutable, changing
+    attributes after initialization will inevitably fail.
+
     """
     def __init__(self, equations_of_motion, state_symbols,
                  num_collocation_nodes, node_time_interval,