Merge pull request #254 from GazzolaLab/doc_patch

Doc patch

docs/conf.py

@@ -22,7 +22,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'PyElastica'
-copyright = '2022, Gazzola Lab'
+copyright = '2023, Gazzola Lab'
 author = 'Gazzola Lab'
 
 # The full version, including alpha/beta/rc tags

docs/index.rst

@@ -36,6 +36,7 @@ If you are interested to contribute, please read `contribution-guide`_ first.
 
    overview/welcome_page
    overview/installation
+   overview/FAQs
 
 .. toctree::
    :maxdepth: 1
@@ -50,7 +51,7 @@ If you are interested to contribute, please read `contribution-guide`_ first.
 .. toctree::
    :maxdepth: 2
    :caption: API Documentation
-   
+
    api/rods
    api/rigidbody
    api/constraints

docs/intro_page.rst.inc

@@ -6,28 +6,43 @@ More information about Elastica is available at the `project website`_
 PyElastica
 ~~~~~~~~~~
 .. image:: https://travis-ci.com/GazzolaLab/PyElastica.svg?branch=master
-	:target: https://travis-ci.com/gazzolalab 
+	:target: https://travis-ci.com/gazzolalab
 	:alt: Build_status
 
 .. image:: https://codecov.io/gh/gazzolalab/PyElastica/branch/master/graph/badge.svg
 	:target: https://codecov.io/gh/gazzolalab/PyElastica
 	:alt: codecov
-	
+
 .. image:: https://readthedocs.org/projects/pyelastica/badge/?version=latest
 	:target: https://pyelastica.readthedocs.io/en/latest/?badge=latest
 	:alt: Documentation Status
 
-PyElastica is the python implementation of Elastica. The easiest way to install PyElastica is with PIP: 
+PyElastica is the python implementation of Elastica. The easiest way to install PyElastica is with PIP:
+
+.. code-block:: bash
+
+   $ 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.
 
-.. code:: console
+.. code-block:: bash
 
-    $ pip install pyelastica
+    $ pip install "pyelastica[magnetism,examples,docs]"
 
-Or download the source code from the `GitHub repo`_ 
 
 Elastica++
 ==========
-Elastica++ is a C++ implementation of Elastica. The expected release date for the beta version is 2022 Q2.
+Elastica++ is a C++ implementation of Elastica. The expected release date for the beta version is 2023 Q4.
 
 .. _project website: https://cosseratrods.org
 .. _GitHub repo: https://github.com/GazzolaLab/PyElastica

docs/overview/FAQs.md

@@ -1,12 +1,7 @@
+# FAQs
+
 If you have a question not answered here, leave an issue on our [github-issue](https://github.com/GazzolaLab/PyElastica/issues).
 
-### Q. Is there support available for Elastica?
+## Q. Is there support available for Elastica?
 
 If you open an issue on [GitHub](https://github.com/GazzolaLab/PyElastica), we will look and respond within 24-48 hours.
-
-<!--
-### Q2. Do PyElastica and Elastica++ have the same features?
-Almost. Due to development cycles, they may not always be equally up to date. If there is a feature in one that you would like to see in the other, let us know on [GitHub](https://github.com/GazzolaLab/PyElastica). 
--->
-
-[link-citation]: https://github.com/GazzolaLab/PyElastica#citation

docs/overview/installation.md

@@ -2,18 +2,30 @@
 
 ## Instruction
 
-PyElastica requires Python 3.5 - 3.8, which needs to be installed prior to using PyElastica. For information on installing Python, see [here](https://realpython.com/installing-python/). If you are interested in using a package manager like Conda, see [here](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html).
+PyElastica requires Python 3.8 - 3.10, which needs to be installed prior to using PyElastica. For information on installing Python, see [here](https://realpython.com/installing-python/). If you are interested in using a package manager like Conda, see [here](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html).
 
 :::{note}
 Python version above 3.8 is tested only in Ubuntu and Mac OS. For Windows 10, some of the dependencies were not yet compatible.
 :::
 
 The easiest way to install PyElastica is with `pip`:
 
-```sh
+```bash
 $ pip install pyelastica
 ```
-You can also download the source code for PyElastica directly from [GitHub](https://github.com/GazzolaLab/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]"
+```
 
 ## Dependencies
 
@@ -26,4 +38,4 @@ The core of PyElastica is developed using:
 - matplotlib (visualization)
 
 Above packages will be installed along with PyElastica if you used `pip` to install.
-If you have directly downloaded the source code, you must install these packages separately. 
+If you have directly downloaded the source code, you must install these packages separately.

elastica/boundary_conditions.py

@@ -481,7 +481,7 @@ class FixedConstraint(GeneralConstraint):
 
     >>> simulator.constrain(rod).using(
     ...    FixedConstraint,
-    ...    constrained_position_idx=(10)
+    ...    constrained_position_idx=(10,)
     ... )
 
     See Also