Merge pull request #86 from GazzolaLab/update-0.2.3

Release 0.2.3
GazzolaLab · May 19, 2022 · 5f15801 · 5f15801
2 parents fee87b9 + 39e02ec
commit 5f15801
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diff --git a/.coveragerc b/.coveragerc
@@ -4,6 +4,12 @@ exclude_lines =
     # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:
+    ...
+    pass
+    def __repr__
+    from
+    import
+
 
 [run]
 branch = True

diff --git a/.flake8 b/.flake8
@@ -3,4 +3,8 @@ ignore = E203, E266, E501, W503, F403, F401, W191
 max-line-length = 88
 max-complexity = 18
 select = B,C,E,F,W,T4,B9
-exclude = .git,__pycache__,elastica/rod.py
+exclude =
+    .git,
+    __pycache__,
+    docs/conf.py
+    tests
diff --git a/Makefile b/Makefile
@@ -1,6 +1,6 @@
 black:
 	@black --version
-	@black --required-version 21.12b0 elastica tests
+	@black --required-version 21.12b0 elastica tests examples
 
 
 black_check:
@@ -12,6 +12,8 @@ flake8:
 	@flake8 --version
 	@flake8 elastica tests
 
+test:
+	@python -m pytest
 
 all:black flake8
 ci:black_check flake8
diff --git a/RELEASE.md b/RELEASE.md
@@ -1,3 +1,15 @@
+# Release Note (version 0.2.3)
+
+
+## Developer Note
+The major updates are knot theory module added to the Cosserat rod as *mixin*, and muscular snake example is added. 
+
+## Notable Changes
+- #70: Knot theory module to compute topological quantities.
+- #71: Reorganize rod constructor warning messages and collect messages in log.  
+- #72: Muscular snake example is added.
+---
+
 # Release Note (version 0.2.2)
 
 ## Developer Note

diff --git a/docs/api/external_forces.rst b/docs/api/external_forces.rst
@@ -8,7 +8,7 @@ External Forces / Interactions
 Description
 -----------
 
-External force and environmental interaction are represented as force/torque bounaary condition at different location.
+External force and environmental interaction are represented as force/torque boundary condition at different location.
 
 .. rubric:: Available Forcing
 

diff --git a/docs/api/rods.rst b/docs/api/rods.rst
@@ -1,12 +1,12 @@
 Rods
-=====
+====
 
 .. automodule:: elastica.rod.rod_base
    :members:
    :exclude-members: __weakref__
 
 Cosserat Rod
-~~~~~~~~~~~~
+------------
 
 +------------+-------------------+----------------------------------------+-----------------------------+
 |            |   On Nodes (+1)   |        On Elements (n_elements)        |       On Voronoi (-1)       |
@@ -39,9 +39,22 @@ Cosserat Rod
 .. automodule:: elastica.rod.cosserat_rod
    :exclude-members: __weakref__, __init__, update_accelerations, zeroed_out_external_forces_and_torques, compute_internal_forces_and_torques
    :members:
+   :inherited-members:
 
 .. Constitutive Models
 .. ~~~~~~~~~~~~~~~~~~~
 .. .. automodule:: elastica.rod.constitutive_model
 ..    :members:
 ..    :exclude-members: __weakref__
+
+
+Knot Theory (Mixin)
+~~~~~~~~~~~~~~~~~~~
+
+.. .. autoclass:: elastica.rod.knot_theory.KnotTheory
+
+.. .. autoclass:: elastica.rod.knot_theory.KnotTheoryCompatibleProtocol
+
+.. automodule:: elastica.rod.knot_theory
+   :exclude-members: __init__
+   :members:
diff --git a/docs/conf.py b/docs/conf.py
@@ -80,8 +80,13 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 
-html_theme = 'sphinx_rtd_theme'
-html_logo = "https://github.com/GazzolaLab/PyElastica/blob/assets/docs/assets/Logo.png?raw=true"
+html_theme = 'sphinx_book_theme'
+html_theme_options = {
+    "repository_url": "https://github.com/GazzolaLab/PyElastica",
+    "use_repository_button": True,
+}
+html_title = "PyElastica"
+html_logo = "_static/assets/Logo.png"
 #pygments_style = "sphinx"
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -90,5 +95,8 @@
 html_static_path = ['_static']
 html_css_files = ['css/*', 'css/logo.css']
 
+# -- Options for autodoc  ---------------------------------------------------
+autodoc_member_order = 'bysource'
+
 # -- Options for numpydoc ---------------------------------------------------
 numpydoc_show_class_members = False
diff --git a/docs/guide/pybind.md → docs/guide/binder.md b/docs/guide/pybind.md → docs/guide/binder.md
@@ -1,4 +1,4 @@
-# PyBind Tutorials
+# Binder Tutorials
 
 <!-- 
 <a href="https://mybinder.org/v2/gh/GazzolaLab/PyElastica/master?filepath=examples%2FBinder%2F0_PyElastica_Tutorials_Overview.ipynb">

diff --git a/docs/index.rst b/docs/index.rst
@@ -44,7 +44,7 @@ If you are interested to contribute, please read `contribution-guide`_ first.
    guide/workflow
    guide/discretization
    guide/example_cases
-   guide/pybind
+   guide/binder
    guide/visualization
 
 .. toctree::

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,7 +1,8 @@
 # File: docs/requirements.txt
 
 sphinx==4.4.0
-sphinx_rtd_theme==1.0.0
+#sphinx_rtd_theme==1.0.0
+sphinx-book-theme
 readthedocs-sphinx-search==0.1.1
 sphinx-autodoc-typehints
 myst-parser

diff --git a/elastica/__init__.py b/elastica/__init__.py
@@ -1,9 +1,7 @@
-import os
-import numpy as np
-import numba
 from collections import defaultdict
 from elastica.wrappers import *
 from elastica.rod.cosserat_rod import *
+from elastica.rod.knot_theory import *
 from elastica.rigidbody import *
 from elastica.boundary_conditions import *
 from elastica.external_forces import *