readme: fix broken link and add initialize instruction (#431)

Updates the example usage in the README to include initialization of
AMReX. This is not strictly required for the example, but avoids the
potential for users to follow the example for more complex usage that
causes segfaults when AMReX is not initialized (#327).

Also fixes a broken link.

Author: baperry2

README.md

@@ -3,10 +3,10 @@
 [![Python3][api-py3]](https://www.python.org/)
 ![Python3 API: Beta][dev-beta]
 [![Documentation Status](https://readthedocs.org/projects/pyamrex/badge/?version=latest)](https://pyamrex.readthedocs.io)
-[![Discussions](https://img.shields.io/badge/chat-discussions-turquoise.svg)](https://github.com/AMReX-Codes/pyamrex/discussions)  
+[![Discussions](https://img.shields.io/badge/chat-discussions-turquoise.svg)](https://github.com/AMReX-Codes/pyamrex/discussions)
 ![Linux](https://github.com/AMReX-Codes/pyamrex/actions/workflows/ubuntu.yml/badge.svg?branch=development)
 ![macOS](https://github.com/AMReX-Codes/pyamrex/actions/workflows/macos.yml/badge.svg?branch=development)
-![Windows](https://github.com/AMReX-Codes/pyamrex/actions/workflows/windows.yml/badge.svg?branch=development)  
+![Windows](https://github.com/AMReX-Codes/pyamrex/actions/workflows/windows.yml/badge.svg?branch=development)
 [![License pyAMReX](https://img.shields.io/badge/license-BSD--3--Clause--LBNL-blue.svg)](https://spdx.org/licenses/BSD-3-Clause-LBNL.html)
 [![DOI (source)](https://img.shields.io/badge/DOI%20(source)-10.5281/zenodo.8408733-blue.svg)](https://doi.org/10.5281/zenodo.8408733)
 
@@ -24,21 +24,27 @@ pyAMReX [can be installed](https://pyamrex.readthedocs.io/en/latest/install/user
 
 ### Usage
 
-Please see the [manual](https://pyamrex.readthedocs.io/en/latest/usage/how_to_run.html) and our [test cases](https://github.com/AMReX-Codes/pyamrex/tree/development/tests) for detailed examples.
+Please see the [manual](https://pyamrex.readthedocs.io/en/latest/usage/examples.html) and our [test cases](https://github.com/AMReX-Codes/pyamrex/tree/development/tests) for detailed examples.
 
 Use AMReX objects and APIs from Python:
 ```python
 import amrex.space3d as amr
 
+amr.initialize([])
+
 small_end = amr.IntVect()
 big_end = amr.IntVect(2, 3, 4)
 
 b = amr.Box(small_end, big_end)
 print(b)
 
 # ...
+
+amr.finalize()
 ```
 
+Note that many AMReX functions may cause a segmentation fault if run without first initializing AMReX (`amr.initialize([])`).
+
 ## Developers
 
 If you are new to CMake, [this short tutorial](https://hsf-training.github.io/hsf-training-cmake-webpage/) from the HEP Software foundation is the perfect place to get started with it.
@@ -241,6 +247,6 @@ If you have questions about your rights to use or distribute this software,
 please contact Berkeley Lab's Intellectual Property Office at
 [email protected].
 
-Please see the full license agreement in [LICENSE](LICENSE).  
-Please see the notices in [NOTICE](NOTICE).  
+Please see the full license agreement in [LICENSE](LICENSE).
+Please see the notices in [NOTICE](NOTICE).
 The SPDX license identifier is `BSD-3-Clause-LBNL`.