Merge pull request #245 from bhosale2/244_magnetic_cosserat_rods

(#244) magnetic cosserat rods functionality
GazzolaLab · May 3, 2023 · 39d3ae9 · 39d3ae9
2 parents 24f301a + 35879fd
commit 39d3ae9
Show file tree

Hide file tree

Showing 4 changed files with 52 additions and 7 deletions.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -60,8 +60,15 @@ make install
 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
+using `poetry install -E docs`.
+The detail instruction is included
 [here](https://github.com/GazzolaLab/PyElastica/blob/master/docs/README.md).
 
 4. Now your working environment is set!

diff --git a/README.md b/README.md
@@ -3,24 +3,39 @@
 
 [![Build_status][badge-travis]][link-travis] [![CI][badge-CI]][link-CI] [![Documentation Status][badge-docs-status]][link-docs-status] [![codecov][badge-codecov]][link-codecov] [![Downloads][badge-pepy-download-count]][link-pepy-download-count] [![DOI][badge-doi]][link-doi] [![Binder][badge-binder]][link-binder] [![Gitter][badge-gitter]][link-gitter]
  </div>
- 
+
 PyElastica is the python implementation of **Elastica**: an *open-source* project for simulating assemblies of slender, one-dimensional structures using Cosserat Rod theory.
 
 [![gallery][link-readme-gallary]][link-project-website]
 
 Visit [cosseratrods.org][link-project-website] for more information and learn about Elastica and Cosserat rod theory.
 
-## How to Start 
+## How to Start
 [![PyPI version][badge-pypi]][link-pypi] [![Documentation Status][badge-docs-status]][link-docs-status]
 
 PyElastica is compatible with Python 3.7 - 3.10.
 
 ~~~bash
-$ pip install pyelastica 
+$ 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`.
+- `docs`: packages to build documentation
+
+Options can be combined e.g.
+```bash
+pip install "pyelastica[magnetism,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).
 ## Citation
 
 We ask that any publications which use Elastica cite as following:
@@ -36,7 +51,7 @@ We ask that any publications which use Elastica cite as following:
                   Zhi Dou and
                   Chia-Hsien (Cathy) Shih and
                   Mattia Gazzola},
-  title        = {{PyElastica: Open-source software for the 
+  title        = {{PyElastica: Open-source software for the
                    simulation of assemblies of slender, one-
                    dimensional structures using Cosserat Rod theory}},
   month        = feb,
@@ -50,7 +65,7 @@ We ask that any publications which use Elastica cite as following:
 
 <details>
   <summary><h4>References</h4></summary>
- 
+
 - Gazzola, Dudte, McCormick, Mahadevan, <strong>Forward and inverse problems in the mechanics of soft filaments</strong>, Royal Society Open Science, 2018. doi: [10.1098/rsos.171628](https://doi.org/10.1098/rsos.171628)
 - Zhang, Chan, Parthasarathy, Gazzola, <strong>Modeling and simulation of complex dynamic musculoskeletal architectures</strong>, Nature Communications, 2019. doi: [10.1038/s41467-019-12759-5](https://doi.org/10.1038/s41467-019-12759-5)
 

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -52,6 +52,7 @@ 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"
@@ -79,6 +80,9 @@ examples = [
   "cma",
   "matplotlib",
 ]
+magnetism = [
+  "magneto_pyelastica",
+]
 
 [tool.black]
 # https://github.com/psf/black