Cleanup docs.

Author: shyuep

README.md

@@ -40,12 +40,24 @@ Pymatgen is free to use. However, we also welcome your help to improve this libr
 
 ## Why use `pymatgen`?
 
-1. **It is (fairly) robust.** Pymatgen is used by thousands of researchers and is the analysis code powering the [Materials Project]. The analysis it produces survives rigorous scrutiny every single day. Bugs tend to be found and corrected quickly. Pymatgen also uses Github Actions for continuous integration, which ensures that every new code passes a comprehensive suite of unit tests.
-2. **It is well documented.** A fairly comprehensive documentation has been written to help you get to grips with it quickly.
-3. **It is open.** You are free to use and contribute to `pymatgen`. It also means that `pymatgen` is continuously being improved. We will attribute any code you contribute to any publication you specify. Contributing to `pymatgen` means your research becomes more visible, which translates to greater impact.
-4. **It is fast.** Many of the core numerical methods in `pymatgen` have been optimized by vectorizing in `numpy`/`scipy`. This means that coordinate manipulations are fast. Pymatgen also comes with a complete system for handling periodic boundary conditions.
-5. **It will be around.** Pymatgen is not a pet research project. It is used in the well-established Materials Project. It is also actively being developed and maintained by the [Materials Virtual Lab], the ABINIT group and many other research groups.
-6. **A growing ecosystem of developers and add-ons**. Pymatgen has contributions from materials scientists all over the world. We also now have an architecture to support add-ons that expand `pymatgen`'s functionality even further. Check out the [contributing page](https://pymatgen.org/contributing) and [add-ons page](https://pymatgen.org/addons) for details and examples.
+1. **It is (fairly) robust.** Pymatgen is used by thousands of researchers and is the analysis code powering the
+   [Materials Project]. The analysis it produces survives rigorous scrutiny every single day. Bugs tend to be found
+   and corrected quickly. Pymatgen also uses Github Actions for continuous integration, which ensures that every
+   new code passes a comprehensive suite of unit tests.
+2. **It is well documented.** A fairly comprehensive documentation has been written to help you get to grips with
+   it quickly.
+3. **It is open.** You are free to use and contribute to `pymatgen`. It also means that `pymatgen` is continuously
+   being improved. We will attribute any code you contribute to any publication you specify. Contributing to
+   `pymatgen` means your research becomes more visible, which translates to greater impact.
+4. **It is fast.** Many of the core numerical methods in `pymatgen` have been optimized by vectorizing in
+   `numpy`/`scipy`. This means that coordinate manipulations are fast. Pymatgen also comes with a complete system
+   for handling periodic boundary conditions.
+5. **It will be around.** Pymatgen is not a pet research project. It is used in the well-established Materials
+   Project. It is also actively being developed and maintained by the [Materials Virtual Lab], the ABINIT group and
+   many other research groups.
+6. **A growing ecosystem of developers and add-ons**. Pymatgen has contributions from materials scientists all over
+   the world. We also now have an architecture to support add-ons that expand `pymatgen`'s functionality even
+   further. Check out the [contributing page](https://pymatgen.org/contributing) and [add-ons page](https://pymatgen.org/addons) for details and examples.
 
 ## Installation
 
@@ -63,7 +75,7 @@ If you'd like to use the latest unreleased changes on the main branch, you can i
 pip install -U git+https://github.com/materialsproject/pymatgen
 ```
 
-The minimum Python version is 3.10. Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the [`pymatgen` docs]).
+Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the [`pymatgen` docs]).
 
 ## Change Log
 
@@ -72,39 +84,42 @@ See [GitHub releases](https://github.com/materialsproject/pymatgen/releases), [`
 ## Using pymatgen
 
 Please refer to the official [`pymatgen` docs] for tutorials and examples. Dr Anubhav Jain (@computron) has also created
-a series of [tutorials](https://github.com/computron/pymatgen_tutorials)
-and [YouTube videos](https://www.youtube.com/playlist?list=PL7gkuUui8u7_M47KrV4tS4pLwhe7mDAjT), which is a good
-resource, especially for beginners.
+a series of [tutorials](https://github.com/computron/pymatgen_tutorials) and [YouTube videos](https://www.youtube.com/playlist?list=PL7gkuUui8u7_M47KrV4tS4pLwhe7mDAjT), which is a good resource, especially for beginners.
 
 ## How to cite pymatgen
 
-If you use `pymatgen` in your research, please consider citing the following work:
+If you use `pymatgen` in your research, please consider citing the following [work](https://doi.org/10.1016/j.commatsci.2012.10.028):
 
-> Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy
-> Hautier, Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent Chevrier,
-> Kristin A. Persson, Gerbrand Ceder. *Python Materials Genomics
-> (pymatgen): A Robust, Open-Source Python Library for Materials
-> Analysis.* Computational Materials Science, 2013, 68, 314-319.
-> [doi:10.1016/j.commatsci.2012.10.028](https://doi.org/10.1016/j.commatsci.2012.10.028)
-
-In addition, some of `pymatgen`'s functionality is based on scientific advances/principles developed by the computational materials scientists in our team. Please refer to the [`pymatgen` docs] on how to cite them.
-
-### Soliciting contributions to 2nd `pymatgen` paper
+```txt
+Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy Hautier, Michael Kocher, Shreyas Cholia, Dan
+Gunter, Vincent Chevrier, Kristin A. Persson, Gerbrand Ceder. Python Materials Genomics (pymatgen): A Robust,
+Open-Source Python Library for Materials Analysis. Computational Materials Science, 2013, 68, 314-319.
+doi:10.1016/j.commatsci.2012.10.028
+```
 
-If you are a long-standing `pymatgen` contributor and would like to be involved in working on an updated `pymatgen` publication,
-please fill out this [co-author registration form](https://docs.google.com/forms/d/e/1FAIpQLSecIhD2YjdPGldrRTM8Go3VxVg_vjKjZAOXtIKDG7qckHLYaQ/viewform) or contact [@shyuep, @mkhorton and @janosh](mailto:[email protected],[email protected],[email protected]?subject=Contributing%20to%20updated%20pymatgen%20paper) with questions.
+In addition, some of `pymatgen`'s functionality is based on scientific advances/principles developed by the
+computational materials scientists in our team. Please refer to the [`pymatgen` docs] on how to cite them.
 
 ## License
 
 Pymatgen is released under the MIT License. The terms of the license are as follows:
 
-> The MIT License (MIT) Copyright (c) 2011-2012 MIT & LBNL
->
-> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
->
-> The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
->
-> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+```txt
+The MIT License (MIT) Copyright (c) 2011-2012 MIT & LBNL
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
+documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
+rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of
+the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO
+THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+```
 
 ## About the Pymatgen Development Team
 
@@ -115,7 +130,12 @@ The [`pymatgen` development team] is the set of all contributors to the `pymatge
 
 ## Our Copyright Policy
 
-Pymatgen uses a shared copyright model. Each contributor maintains copyright over their contributions to `pymatgen`. But, it is important to note that these contributions are typically only changes to the repositories. Thus, the `pymatgen` source code, in its entirety is not the copyright of any single person or institution. Instead, it is the collective copyright of the entire [`pymatgen` Development Team]. If individual contributors want to maintain a record of what changes/contributions they have specific copyright on, they should indicate their copyright in the commit message of the change, when they commit the change to one of the `pymatgen` repositories.
+Pymatgen uses a shared copyright model. Each contributor maintains copyright over their contributions to `pymatgen`.
+But, it is important to note that these contributions are typically only changes to the repositories. Thus, the
+`pymatgen` source code, in its entirety is not the copyright of any single person or institution. Instead, it is the
+collective copyright of the entire [`pymatgen` Development Team]. If individual contributors want to maintain a
+record of what changes/contributions they have specific copyright on, they should indicate their copyright in the
+commit message of the change, when they commit the change to one of the `pymatgen` repositories.
 
 [`pymatgen` docs]: https://pymatgen.org
 [materials project]: https://materialsproject.org