refactor: fix flake8 and documentation formatting errors

This commit fixes several flake8 and doc formatting errors.
rickstaa · Feb 14, 2024 · f2a097b · f2a097b
1 parent 668f3ef
commit f2a097b
Show file tree

Hide file tree

Showing 8 changed files with 92 additions and 44 deletions.
diff --git a/setup.cfg b/setup.cfg
@@ -1,8 +1,11 @@
 [flake8]
 max-line-length = 89
-extend-ignore = E266
 exclude =
+    docs/source/conf.py,
     build,
-    node_modules
+    node_modules,
+    tests,
+    stable_gym/version.py
 per-file-ignores =
     __init__.py: F401, E501
+extend-ignore = E266, D400, D401, D205
diff --git a/stable_gym/common/utils.py b/stable_gym/common/utils.py
@@ -228,7 +228,7 @@ def inject_value(input_item, value, round_accuracy=2, order=False, axis=0):
     Returns:
         union[list,dict]: The list or dictionary that contains the value.
     """
-    order_op = lambda *args, **kwargs: (
+    order_op = lambda *args, **kwargs: (  # noqa: E731
         sorted(*args, **kwargs) if order else list(*args, **kwargs)
     )
     if isinstance(input_item, dict):
@@ -263,7 +263,7 @@ def verify_number_and_cast(x):
 
 
 def maybe_parse_reset_bounds(options, default_low, default_high):
-    """sThis function can be called during a reset() to customize the sampling
+    """This function can be called during a reset() to customize the sampling
     ranges for setting the initial state distributions.
 
     Args:

diff --git a/stable_gym/envs/biological/oscillator/oscillator.py b/stable_gym/envs/biological/oscillator/oscillator.py
@@ -37,7 +37,7 @@ class Oscillator(gym.Env):
               presented in `Han et al. 2020`_, which was not possible with the original
               code's observation space.
             - Added an adjustable ``max_cost`` threshold for episode termination,
-              defaulting to $100$ to match the original environment.
+              defaulting to 100 to match the original environment.
 
     .. _`Han et al. 2020`: https://arxiv.org/abs/2004.14288
 
@@ -47,24 +47,24 @@ class Oscillator(gym.Env):
         +-----+-----------------------------------------------+-------------------+-------------------+
         | Num | Observation                                   | Min               | Max               |
         +=====+===============================================+===================+===================+
-        | 0   | Lacl mRNA transcripts concentration           | 0                 | $\infty$          |
+        | 0   | Lacl mRNA transcripts concentration           | 0                 | :math:`\infty`    |
         +-----+-----------------------------------------------+-------------------+-------------------+
-        | 1   | tetR mRNA transcripts concentration           | 0                 | $\infty$          |
+        | 1   | tetR mRNA transcripts concentration           | 0                 | :math:`\infty`    |
         +-----+-----------------------------------------------+-------------------+-------------------+
-        | 2   | CI mRNA transcripts concentration             | 0                 | $\infty$          |
+        | 2   | CI mRNA transcripts concentration             | 0                 | :math:`\infty`    |
         +-----+-----------------------------------------------+-------------------+-------------------+
-        | 3   || lacI (repressor) protein concentration       | 0                 | $\infty$          |
+        | 3   || lacI (repressor) protein concentration       | 0                 | :math:`\infty`    |
         |     || (Inhibits transcription of the tetR gene)    |                   |                   |
         +-----+-----------------------------------------------+-------------------+-------------------+
-        | 4   || tetR (repressor) protein concentration       | 0                 | $\infty$          |
+        | 4   || tetR (repressor) protein concentration       | 0                 | :math:`\infty`    |
         |     || (Inhibits transcription of CI gene)          |                   |                   |
         +-----+-----------------------------------------------+-------------------+-------------------+
-        | 5   || CI (repressor) protein concentration         | 0                 | $\infty$          |
+        | 5   || CI (repressor) protein concentration         | 0                 | :math:`\infty`    |
         |     || (Inhibits transcription of lacI gene)        |                   |                   |
         +-----+-----------------------------------------------+-------------------+-------------------+
-        | 6   | The reference we want to follow               | 0                 | $\infty$          |
+        | 6   | The reference we want to follow               | 0                 | :math:`\infty`    |
         +-----+-----------------------------------------------+-------------------+-------------------+
-        | (7) || **Optional** - The error between the current | $-\infty$         | $\infty$          |
+        | (7) || **Optional** - The error between the current | :math:`-\infty`   | :math:`\infty`    |
         |     || value of protein 1 and the reference         |                   |                   |
         +-----+-----------------------------------------------+-------------------+-------------------+
 
@@ -96,7 +96,8 @@ class Oscillator(gym.Env):
 
     Episode Termination:
         - An episode is terminated when the maximum step limit is reached.
-        - The step exceeds a threshold (default is $100$). This threshold can be adjusted using the `max_cost` environment argument.
+        - The step exceeds a threshold (default is 100). This threshold can be
+          adjusted using the `max_cost` environment argument.
 
     Solved Requirements:
         Considered solved when the average cost is lower than 300.

diff --git a/stable_gym/envs/biological/oscillator_complicated/oscillator_complicated.py b/stable_gym/envs/biological/oscillator_complicated/oscillator_complicated.py
@@ -43,7 +43,7 @@ class is based on the :class:`~stable_gym.envs.biological.oscillator.oscillator.
               presented in `Han et al. 2020`_, which was not possible with the original
               code's observation space.
             - Added an adjustable ``max_cost`` threshold for episode termination,
-              defaulting to $\infty$ to match the original environment.
+              defaulting to :math:`\infty` to match the original environment.
 
     .. _`Han et al. 2020`: https://arxiv.org/abs/2004.14288
 
@@ -53,29 +53,29 @@ class is based on the :class:`~stable_gym.envs.biological.oscillator.oscillator.
         +-----+-------------------------------------------------+-------------------+-------------------+
         | Num | Observation                                     | Min               | Max               |
         +=====+=================================================+===================+===================+
-        | 0   | Lacl mRNA transcripts concentration             | 0                 | $\infty$               |
+        | 0   | Lacl mRNA transcripts concentration             | 0                 | :math:`\infty`    |
         +-----+-------------------------------------------------+-------------------+-------------------+
-        | 1   | tetR mRNA transcripts concentration             | 0                 | $\infty$               |
+        | 1   | tetR mRNA transcripts concentration             | 0                 | :math:`\infty`    |
         +-----+-------------------------------------------------+-------------------+-------------------+
-        | 2   | CI mRNA transcripts concentration               | 0                 | $\infty$               |
+        | 2   | CI mRNA transcripts concentration               | 0                 | :math:`\infty`    |
         +-----+-------------------------------------------------+-------------------+-------------------+
-        | 3   | Extra protein mRNA transcripts concentration    | 0                 | $\infty$               |
+        | 3   | Extra protein mRNA transcripts concentration    | 0                 | :math:`\infty`    |
         +-----+-------------------------------------------------+-------------------+-------------------+
-        | 4   || lacI (repressor) protein concentration         | 0                 | $\infty$               |
+        | 4   || lacI (repressor) protein concentration         | 0                 | :math:`\infty`    |
         |     || (Inhibits transcription of the tetR gene)      |                   |                   |
         +-----+-------------------------------------------------+-------------------+-------------------+
-        | 5   || tetR (repressor) protein concentration         | 0                 | $\infty$               |
+        | 5   || tetR (repressor) protein concentration         | 0                 | :math:`\infty`    |
         |     || (Inhibits transcription of CI gene)            |                   |                   |
         +-----+-------------------------------------------------+-------------------+-------------------+
-        | 6   || CI (repressor) protein concentration           | 0                 | $\infty$               |
+        | 6   || CI (repressor) protein concentration           | 0                 | :math:`\infty`    |
         |     || (Inhibits transcription of extra protein gene) |                   |                   |
         +-----+-------------------------------------------------+-------------------+-------------------+
-        | 7   || Extra (repressor) protein concentration        | 0                 | $\infty$               |
+        | 7   || Extra (repressor) protein concentration        | 0                 | :math:`\infty`    |
         |     || (Inhibits transcription of lacI gene)          |                   |                   |
         +-----+-------------------------------------------------+-------------------+-------------------+
-        | 8   | The reference we want to follow                 | 0                 | $\infty$               |
+        | 8   | The reference we want to follow                 | 0                 | :math:`\infty`    |
         +-----+-------------------------------------------------+-------------------+-------------------+
-        | (9) || **Optional** - The error between the current   | -$\infty$              | $\infty$               |
+        | (9) || **Optional** - The error between the current   | -:math:`\infty`   | :math:`\infty`    |
         |     || value of protein 1 and the reference           |                   |                   |
         +-----+-------------------------------------------------+-------------------+-------------------+
 
@@ -110,7 +110,8 @@ class is based on the :class:`~stable_gym.envs.biological.oscillator.oscillator.
 
     Episode Termination:
         - An episode is terminated when the maximum step limit is reached.
-        - The step exceeds a threshold (default is $\infty$). This threshold can be adjusted using the `max_cost` environment argument.
+        - The step exceeds a threshold (default is :math:`\infty`). This threshold can
+          be adjusted using the `max_cost` environment argument.
 
     Solved Requirements:
         Considered solved when the average cost is lower than 300.

diff --git a/stable_gym/envs/classic_control/ex3_ekf/__init__.py b/stable_gym/envs/classic_control/ex3_ekf/__init__.py
@@ -1,26 +1,70 @@
-"""Noisy master slave system (Ex3EKF) gymnasium environment.
+r"""Noisy master slave system (Ex3EKF) gymnasium environment.
 
-The dynamic system whose state is to be estimated:
+Dynamics
+========
+
+The dynamics of the system whose state is to be estimated are given by:
+
+.. math::
+   :nowrap:
+
+   \[
+   \begin{split}
+   x(k+1) &= A x(k) + w(k) \\
+   \end{split}
+   \]
+
+In which the state vector :math:`(x(k)` is given by:
 
 .. math::
+   :nowrap:
+
+   \[
+   \begin{align*}
+   x_1 &: \text{angle} \\
+   x_2 &: \text{frequency} \\
+   x_3 &: \text{amplitude}
+   \end{align*}
+   \]
 
-    x(k+1)=Ax(k)+w(k)
-    x_1: angle
-    x_2: frequency
-    x_3: amplitude
+and the measurement vector :math:`(y(k))` is given by:
+
+.. math::
+   :nowrap:
 
-    y(k)=x_3(k)*sin(x_1(k))+v(k)
-    A=[1,dt,0;0,1,0;0,0,1]
-    x(0)~N([0;10;1],[3,0,0;0,3,0;0,0,3])
-    w(k)~N([0;0;0],[1/3*(dt)^3*q_1,1/2*(dt)^2*q_1,0;1/2*(dt)^2*q_1,dt*q_1,0;0,0,dt*q_2])
-    v(k)~N(0,1)
+   \[
+   \begin{split}
+   y(k) &= x_3(k) \cdot \sin(x_1(k)) + v(k) \\
+   A &= \begin{bmatrix}
+       1 & dt & 0 \\
+       0 & 1 & 0 \\
+       0 & 0 & 1
+       \end{bmatrix} \\
+   x(0) &\sim \mathcal{N}\left(\begin{bmatrix}0 \\ 10 \\ 1\end{bmatrix}, \begin{bmatrix}
+       3 & 0 & 0 \\
+       0 & 3 & 0 \\
+       0 & 0 & 3
+       \end{bmatrix}\right) \\
+   w(k) &\sim \mathcal{N}\left(\begin{bmatrix}0 \\ 0 \\ 0\end{bmatrix}, \begin{bmatrix}
+       \frac{1}{3}dt^3 q_1 & \frac{1}{2}dt^2 q_1 & 0 \\
+       \frac{1}{2}dt^2 q_1 & dt q_1 & 0 \\
+       0 & 0 & dt q_2
+       \end{bmatrix}\right) \\
+   v(k) &\sim \mathcal{N}(0, 1)
+   \end{split}
+   \]
 
 Estimator design:
 
 .. math::
+   :nowrap:
 
-    \\hat(x)(k+1)=A\\hat(x)(k)+u
-    where u=[u1,u2,u3]', u=l(\\hat(x)(k),y(k)) come from the policy network l(.,.)
+   \[
+   \begin{split}
+   \hat{x}(k+1) &= A \hat{x}(k) + u \\
+   \text{where } u &= [u1, u2, u3]', \ u = l(\hat{x}(k), y(k)) \text{ come from the policy network } l(.,.).
+   \end{split}
+   \]
 """
 
 from stable_gym.envs.classic_control.ex3_ekf.ex3_ekf import Ex3EKF
diff --git a/stable_gym/envs/classic_control/ex3_ekf/ex3_ekf.py b/stable_gym/envs/classic_control/ex3_ekf/ex3_ekf.py
@@ -10,7 +10,7 @@
 
 
 class Ex3EKF(gym.Env):
-    """Noisy master slave system
+    r"""Noisy master slave system
 
     Description:
         The goal of the agent in the Ex3EKF environment is to act in such a way that
@@ -48,7 +48,7 @@ class Ex3EKF(gym.Env):
 
         .. math::
 
-            C = {(\\hat{x}_1 - x_1)}^2 + {(\\hat{x}_2 - x_2)}^2
+            C = {(\hat{x}_1 - x_1)}^2 + {(\hat{x}_2 - x_2)}^2
 
     Starting State:
         All observations are assigned a uniform random value in ``[-0.05..0.05]``

diff --git a/stable_gym/envs/robotics/fetch/fetch_reach_cost/fetch_reach_cost.py b/stable_gym/envs/robotics/fetch/fetch_reach_cost/fetch_reach_cost.py
@@ -12,7 +12,7 @@
 
 # TODO: Update solving criteria after training.
 class FetchReachCost(MujocoFetchReachEnv, utils.EzPickle):
-    """Custom FetchReach gymnasium robotics environment.
+    r"""Custom FetchReach gymnasium robotics environment.
 
     .. note::
         Can also be used in a vectorized manner. See the
@@ -41,7 +41,7 @@ class FetchReachCost(MujocoFetchReachEnv, utils.EzPickle):
 
         .. math::
 
-            cost = \\left | reward \\right |
+            cost = \left | reward \right |
 
     Solved Requirements:
         Considered solved when the average cost is less than or equal to 50 over

diff --git a/stable_gym/envs/robotics/quadrotor/quadx_waypoints_cost/quadx_waypoints_cost.py b/stable_gym/envs/robotics/quadrotor/quadx_waypoints_cost/quadx_waypoints_cost.py
@@ -331,7 +331,6 @@ def compute_target_deltas(self, ang_pos, lin_pos, quarternion):
         Returns:
             (np.ndarray): The waypoints target deltas.
         """  # noqa: E501
-
         # Store waypoints targets, distances and yaw error scalar.
         waypoints_targets = copy.copy(self.waypoints.targets)
         old_waypoints_distance = copy.copy(self.waypoints.old_distance)