fix:remove circular dependency of magnetopyelastica

GazzolaLab · May 12, 2023 · 9d53228 · 9d53228
1 parent 5ffa54e
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -63,9 +63,6 @@ make pre-commit-install
 If you are planning to contribute to the examples,
 extra dependencies can be installed using `poetry install -E examples`.
 
-If you are planning to contribute on the functionality for simulating magnetic Cosserat rods,
-implementation details can be found [here](https://github.com/armantekinalp/MagnetoPyElastica).
-
 If you are planning to contribute on documentation, extra dependencies can be installed
 using `poetry install -E docs`.
 The detail instruction is included

diff --git a/README.md b/README.md
@@ -22,20 +22,25 @@ $ pip install pyelastica
 With this you get a minimal version with very little dependencies.
 
 All options:
-- `magnetism`: use this if you want to simulate magnetic Cosserat rods
-interacting with external magnetic environments (details can be found [here](https://github.com/armantekinalp/MagnetoPyElastica)) .
 - `examples`: installs dependencies to run example cases,
-found under the folder `examples`.
+found under the folder [`examples`](https://github.com/GazzolaLab/PyElastica/tree/master/examples).
 - `docs`: packages to build documentation
 
 Options can be combined e.g.
 ```bash
-pip install "pyelastica[magnetism,examples,docs]"
+$ pip install "pyelastica[examples,docs]"
 ```
 
 Documentation of PyElastica is available [here][link-docs-website].
 
-Example cases for simulating magnetic Cosserat rods can be found [here](https://github.com/armantekinalp/MagnetoPyElastica).
+If you want to simulate magnetic Cosserat rods interacting with external magnetic environments you can install the derived package using
+
+```bash
+$ pip install magneto_pyelastica
+```
+
+Details can be found [here](https://github.com/armantekinalp/MagnetoPyElastica).
+
 ## Citation
 
 We ask that any publications which use Elastica cite as following:

diff --git a/docs/intro_page.rst.inc b/docs/intro_page.rst.inc
@@ -27,8 +27,6 @@ You can also download the source code for PyElastica directly from `GitHub <http
 
 All options:
 
-- ``magnetism``: use this if you want to simulate magnetic Cosserat rods
-  interacting with external magnetic environments (details can be found `here <https://github.com/armantekinalp/MagnetoPyElastica>`__).
 - ``examples``: installs dependencies to run example cases,
   found under the folder `examples <https://github.com/GazzolaLab/PyElastica/tree/master/examples>`__.
 - ``docs``: packages to build documentation
@@ -37,7 +35,15 @@ Options can be combined, e.g.
 
 .. code-block:: bash
 
-    $ pip install "pyelastica[magnetism,examples,docs]"
+    $ pip install "pyelastica[examples,docs]"
+
+If you want to simulate magnetic Cosserat rods interacting with external magnetic environments you can install the derived package using
+
+.. code-block:: bash
+
+    $ pip install magneto_pyelastica
+
+Details can be found `here <https://github.com/armantekinalp/MagnetoPyElastica>`__.
 
 
 Elastica++

diff --git a/docs/overview/installation.md b/docs/overview/installation.md
@@ -16,17 +16,23 @@ $ pip install pyelastica
 You can also download the source code for PyElastica directly from [GitHub](https://github.com/GazzolaLab/PyElastica).
 
 All options:
-- `magnetism`: use this if you want to simulate magnetic Cosserat rods
-interacting with external magnetic environments (details can be found [here](https://github.com/armantekinalp/MagnetoPyElastica)) .
 - `examples`: installs dependencies to run example cases,
 found under the folder [`examples`](https://github.com/GazzolaLab/PyElastica/tree/master/examples).
 - `docs`: packages to build documentation
 
 Options can be combined e.g.
 ```bash
-$ pip install "pyelastica[magnetism,examples,docs]"
+$ pip install "pyelastica[examples,docs]"
 ```
 
+If you want to simulate magnetic Cosserat rods interacting with external magnetic environments you can install the derived package using
+
+```bash
+$ pip install magneto_pyelastica
+```
+
+Details can be found [here](https://github.com/armantekinalp/MagnetoPyElastica).
+
 ## Dependencies
 
 The core of PyElastica is developed using:

diff --git a/elastica/transformations.py b/elastica/transformations.py
@@ -17,6 +17,7 @@
 def format_vector_shape(vector_collection):
     """
     Function for formatting vector shapes into correct format
+
     Parameters
     ----------
     vector_collection: numpy.ndarray
@@ -61,6 +62,7 @@ def format_vector_shape(vector_collection):
 def format_matrix_shape(matrix_collection):
     """
     Formats input matrix into correct format
+
     Parameters
     ----------
     matrix_collection: numpy.ndarray

diff --git a/elastica/utils.py b/elastica/utils.py
@@ -145,7 +145,10 @@ def grouper(iterable, n):
 
 
 def extend_instance(obj, cls):
-    """Apply mixins to a class instance after creation
+    """
+
+    Apply mixins to a class instance after creation
+
     Parameters
     ----------
     obj : object (not class!) targeted for interface extension
@@ -159,6 +162,7 @@ def extend_instance(obj, cls):
     Credits
     -------
     https://stackoverflow.com/a/31075641
+
     """
     base_cls = obj.__class__
     base_cls_name = obj.__class__.__name__

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -52,7 +52,6 @@ numpydoc = {version = "^1.3.1", optional = true}
 docutils = {version = "^0.18", optional = true}
 cma = {version = "^3.2.2", optional = true}
 matplotlib = {version = "^3.3.2", optional = true}
-magneto_pyelastica = {version = "^0.0.1", optional = true}
 
 [tool.poetry.dev-dependencies]
 black = "21.12b0"
@@ -80,9 +79,6 @@ examples = [
   "cma",
   "matplotlib",
 ]
-magnetism = [
-  "magneto_pyelastica",
-]
 
 [tool.black]
 # https://github.com/psf/black