Fixed formatting issue in documentation

docs/conf.py

@@ -39,6 +39,7 @@
     "sphinx.ext.viewcode",
     "sphinx_rtd_theme",
     "sphinx.ext.mathjax",
+    "recommonmark",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -49,17 +50,28 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
-autodoc_default_flags = [
-    "members",
-    "private-members",
-    "special-members",
-    "show-inheritance",
-]
+# autodoc_default_flags = [
+#     "members",
+#     "private-members",
+#     "special-members",
+#     "show-inheritance",
+# ]
+
+autodoc_default_options = {
+    'members': True,
+    'private-members': True,
+    'special-members': True,
+    'show-inheritance': True,
+}
 
-source_parsers = {
-    ".md": "recommonmark.parser.CommonMarkParser",
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.txt': 'markdown',
+    '.md': 'markdown',
 }
-source_suffix = [".rst", ".md"]
+
+# source_parsers = { ".md": "recommonmark.parser.CommonMarkParser",}
+# source_suffix = [".rst", ".md"]
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -70,4 +82,4 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+# html_static_path = ["_static"]

docs/intro_page.rst

@@ -18,6 +18,7 @@ PyElastica
 .. image:: https://codecov.io/gh/mattialabteam/elastica-python/branch/master/graph/badge.svg?token=O8nBw9I5vr
 	:target: https://codecov.io/gh/mattialabteam/elastica-python
 	:alt: codecov
+
 PyElastica is the python implementation of Elastica. The easiest way to install PyElastica is with PIP: 
 
 .. code:: console
@@ -28,4 +29,4 @@ Elastica++
 ~~~~~~~~~~
 Elastica++ is a C++ implementation of Elastica. 
 
-.. _project website: https://cosseratrods.org
+.. _project website: https://cosseratrods.org

elastica/boundary_conditions.py

@@ -65,12 +65,12 @@ class OneEndFixedRod(FreeRod):
     this boundary condition fixes position and directors
     at the first node and first element of the rod.
 
-        Attributes
-        ----------
-        fixed_positions : numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type.
-        fixed_directors : numpy.ndarray
-            3D (dim, dim, 1) array containing data with 'float' type.
+    Attributes
+    ----------
+    fixed_positions : numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type.
+    fixed_directors : numpy.ndarray
+        3D (dim, dim, 1) array containing data with 'float' type.
     """
 
     def __init__(self, fixed_position, fixed_directors):
@@ -103,28 +103,28 @@ class HelicalBucklingBC(FreeRod):
     The applied boundary condition is twist and slack on to
     the first and last nodes and elements of the rod.
 
-        Attributes
-        ----------
-        twisting_time: float
-            Time to complete twist.
-        final_start_position: numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type.
-            Position of first node of rod after twist completed.
-        final_end_position: numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type.
-            Position of last node of rod after twist completed.
-        ang_vel: numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type.
-            Angular velocity of rod during twisting time.
-        shrink_vel: numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type.
-            Shrink velocity of rod during twisting time.
-        final_start_directors: numpy.ndarray
-            3D (dim, dim, blocksize) array containing data with 'float' type.
-            Directors of first element of rod after twist completed.
-        final_end_directors: numpy.ndarray
-            3D (dim, dim, blocksize) array containing data with 'float' type.
-            Directors of last element of rod after twist completed.
+    Attributes
+    ----------
+    twisting_time: float
+        Time to complete twist.
+    final_start_position: numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type.
+        Position of first node of rod after twist completed.
+    final_end_position: numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type.
+        Position of last node of rod after twist completed.
+    ang_vel: numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type.
+        Angular velocity of rod during twisting time.
+    shrink_vel: numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type.
+        Shrink velocity of rod during twisting time.
+    final_start_directors: numpy.ndarray
+        3D (dim, dim, blocksize) array containing data with 'float' type.
+        Directors of first element of rod after twist completed.
+    final_end_directors: numpy.ndarray
+        3D (dim, dim, blocksize) array containing data with 'float' type.
+        Directors of last element of rod after twist completed.
 
 
     """

elastica/callback_functions.py

@@ -47,12 +47,12 @@ class MyCallBack(CallBackBaseClass):
     This is just an example of a callback class, this class as an example/template to write
     new call back classes in your client file.
 
-        Attributes
-        ----------
-        sample_every: int
-            Collect data using make_callback method every sampling step.
-        callback_params: dict
-            Collected callback data is saved in this dictionary.
+    Attributes
+    ----------
+    sample_every: int
+        Collect data using make_callback method every sampling step.
+    callback_params: dict
+        Collected callback data is saved in this dictionary.
     """
 
     def __init__(self, step_skip: int, callback_params):

elastica/external_forces.py

@@ -65,10 +65,10 @@ class GravityForces(NoForces):
     """
     This class applies a constant gravitational force to the entire rod.
 
-        Attributes
-        ----------
-        acc_gravity: numpy.ndarray
-            1D (dim) array containing data with 'float' type. Gravitational acceleration vector.
+    Attributes
+    ----------
+    acc_gravity: numpy.ndarray
+        1D (dim) array containing data with 'float' type. Gravitational acceleration vector.
 
     """
 
@@ -92,14 +92,14 @@ class EndpointForces(NoForces):
     """
     This class applies constant forces on the endpoint nodes.
 
-        Attributes
-        ----------
-        start_force: numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type. Force applied to first node of the rod-like object.
-        end_force: numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type. Force applied to last node of the rod-like object.
-        ramp_up_time: float
-            Applied forces are ramped up until ramp up time.
+    Attributes
+    ----------
+    start_force: numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type. Force applied to first node of the rod-like object.
+    end_force: numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type. Force applied to last node of the rod-like object.
+    ramp_up_time: float
+        Applied forces are ramped up until ramp up time.
 
     """
 
@@ -135,10 +135,10 @@ class UniformTorques(NoForces):
     """
     This class applies a uniform torque to the entire rod.
 
-        Attributes
-        ----------
-        torque: numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type. Total torque applied to a rod-like object.
+    Attributes
+    ----------
+    torque: numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type. Total torque applied to a rod-like object.
 
     """
 
@@ -167,10 +167,10 @@ class UniformForces(NoForces):
     """
     This class applies a uniform force to the entire rod.
 
-        Attributes
-        ----------
-        force:  numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type. Total force applied to a rod-like object.
+    Attributes
+    ----------
+    force:  numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type. Total force applied to a rod-like object.
     """
 
     def __init__(self, force, direction=np.array([0.0, 0.0, 0.0])):
@@ -205,20 +205,20 @@ class MuscleTorques(NoForces):
     as a traveling wave. For implementation details refer to Gazzola et. al.
     RSoS. (2018).
 
-        Attributes
-        ----------
-        direction: numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type. Muscle torque direction.
-        angular_frequency: float
-            Angular frequency of traveling wave.
-        wave_number: float
-            Wave number of traveling wave.
-        phase_shift: float
-            Phase shift of traveling wave.
-        ramp_up_time: float
-            Applied muscle torques are ramped up until ramp up time.
-        my_spline: numpy.ndarray
-            1D (blocksize) array containing data with 'float' type. Generated spline.
+    Attributes
+    ----------
+    direction: numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type. Muscle torque direction.
+    angular_frequency: float
+        Angular frequency of traveling wave.
+    wave_number: float
+        Wave number of traveling wave.
+    phase_shift: float
+        Phase shift of traveling wave.
+    ramp_up_time: float
+        Applied muscle torques are ramped up until ramp up time.
+    my_spline: numpy.ndarray
+        1D (blocksize) array containing data with 'float' type. Generated spline.
 
     """
 

elastica/interaction.py

@@ -75,20 +75,20 @@ class InteractionPlane:
     force on a rod-like object.  For more details regarding the contact module refer to
     Eqn 4.8 of Gazzola et al. RSoS (2018).
 
-        Attributes
-        ----------
-        k: float
-            Stiffness coefficient between the plane and the rod-like object.
-        nu: float
-            Dissipation coefficient between the plane and the rod-like object.
-        plane_origin: numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type.
-            Origin of the plane.
-        plane_normal: numpy.ndarray
-           2D (dim, 1) array containing data with 'float' type.
-           The normal vector of the plane.
-        surface_tol: float
-            Penetration tolerance between the plane and the rod-like object.
+    Attributes
+    ----------
+    k: float
+        Stiffness coefficient between the plane and the rod-like object.
+    nu: float
+        Dissipation coefficient between the plane and the rod-like object.
+    plane_origin: numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type.
+        Origin of the plane.
+    plane_normal: numpy.ndarray
+       2D (dim, 1) array containing data with 'float' type.
+       The normal vector of the plane.
+    surface_tol: float
+        Penetration tolerance between the plane and the rod-like object.
 
     """
 
@@ -212,26 +212,26 @@ class AnisotropicFrictionalPlane(NoForces, InteractionPlane):
     A detailed explanation of the implemented equations
     can be found in Gazzola et al. RSoS. (2018).
 
-        Attributes
-        ----------
-        k: float
-            Stiffness coefficient between the plane and the rod-like object.
-        nu: float
-            Dissipation coefficient between the plane and the rod-like object.
-        plane_origin: numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type.
-            Origin of the plane.
-        plane_normal: numpy.ndarray
-            2D (dim, 1) array containing data with 'float' type.
-            The normal vector of the plane.
-        slip_velocity_tol: float
-            Velocity tolerance to determine if the element is slipping or not.
-        static_mu_array: numpy.ndarray
-            1D (3,) array containing data with 'float' type.
-            [forward, backward, sideways] static friction coefficients.
-        kinetic_mu_array: numpy.ndarray
-            1D (3,) array containing data with 'float' type.
-            [forward, backward, sideways] kinetic friction coefficients.
+    Attributes
+    ----------
+    k: float
+        Stiffness coefficient between the plane and the rod-like object.
+    nu: float
+        Dissipation coefficient between the plane and the rod-like object.
+    plane_origin: numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type.
+        Origin of the plane.
+    plane_normal: numpy.ndarray
+        2D (dim, 1) array containing data with 'float' type.
+        The normal vector of the plane.
+    slip_velocity_tol: float
+        Velocity tolerance to determine if the element is slipping or not.
+    static_mu_array: numpy.ndarray
+        1D (3,) array containing data with 'float' type.
+        [forward, backward, sideways] static friction coefficients.
+    kinetic_mu_array: numpy.ndarray
+        1D (3,) array containing data with 'float' type.
+        [forward, backward, sideways] kinetic friction coefficients.
     """
 
     def __init__(
@@ -661,10 +661,10 @@ class SlenderBodyTheory(NoForces):
     forces on the body using the slender body theory given in
     Eq. 4.13 of Gazzola et al. RSoS (2018).
 
-        Attributes
-        ----------
-        dynamic_viscosity: float
-            Dynamic viscosity of the fluid.
+    Attributes
+    ----------
+    dynamic_viscosity: float
+        Dynamic viscosity of the fluid.
 
     """