Release 0.3.1 changes (#270)

* Update __init__.py

* change branch in example colab links

* Update README.md

* Update README.md

* rename directory

* Update README.md

Author: waltsims

examples/README.md

@@ -6,12 +6,15 @@ Every example has a short readme.md file which briefly describes the purpose of
 
 ## List of Examples
 
-- [Array as a sensor](at_array_as_sensor/) ([original example](http://www.k-wave.org/documentation/example_at_array_as_sensor.php), [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/waltsims/k-wave-python/blob/migrate-examples-to-notebooks/examples/at_array_as_sensor/at_array_as_sensor.ipynb))
-- [Array as a source](at_array_as_source/) ([original example](http://www.k-wave.org/documentation/example_at_array_as_source.php), [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/waltsims/k-wave-python/blob/migrate-examples-to-notebooks/examples/at_array_as_source/at_array_as_source.ipynb))
+- [Array as a sensor](at_array_as_sensor/) ([original example](http://www.k-wave.org/documentation/example_at_array_as_sensor.php), [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/waltsims/k-wave-python/blob/master/examples/at_array_as_sensor/at_array_as_sensor.ipynb))
+- [Array as a source](at_array_as_source/) ([original example](http://www.k-wave.org/documentation/example_at_array_as_source.php), [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/waltsims/k-wave-python/blob/master/examples/at_array_as_source/at_array_as_source.ipynb))
 - [Linear array transducer](at_linear_array_transducer/)
-([original example](http://www.k-wave.org/documentation/example_at_linear_array_transducer.php), [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/waltsims/k-wave-python/blob/migrate-examples-to-notebooks/examples/at_linear_array_transducer/at_linear_array_transducer.ipynb))
-- [Photoacoustic Waveforms](ivp_photoacoustic_waveforms/) ([original example](http://www.k-wave.org/documentation/example_ivp_photoacoustic_waveforms.php), [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/waltsims/k-wave-python/blob/migrate-examples-to-notebooks/examples/ivp_photoacoustic_waveforms/ivp_photoacoustic_waveforms.ipynb))
-- [Linear transducer B-mode](us_bmode_linear_transducer/) ([original example](http://www.k-wave.org/documentation/example_us_bmode_linear_transducer.php), [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/waltsims/k-wave-python/blob/migrate-examples-to-notebooks/examples/us_bmode_linear_transducer/us_bmode_linear_transducer.ipynb))    
+([original example](http://www.k-wave.org/documentation/example_at_linear_array_transducer.php), [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/waltsims/k-wave-python/blob/master/examples/at_linear_array_transducer/at_linear_array_transducer.ipynb))
+- [Photoacoustic Waveforms](ivp_photoacoustic_waveforms/) ([original example](http://www.k-wave.org/documentation/example_ivp_photoacoustic_waveforms.php), [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/waltsims/k-wave-python/blob/master/examples/ivp_photoacoustic_waveforms/ivp_photoacoustic_waveforms.ipynb))
+- [Controling the PML](na_controlling_the_pml/)
+([original example](http://www.k-wave.org/documentation/example_na_controlling_the_pml.php), [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/waltsims/k-wave-python/blob/master/examples/na_controlling_the_pml/na_controlling_the_pml.ipynb))
+- [Linear transducer B-mode](us_bmode_linear_transducer/) ([original example](http://www.k-wave.org/documentation/example_us_bmode_linear_transducer.php), [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/waltsims/k-wave-python/blob/master/examples/us_bmode_linear_transducer/us_bmode_linear_transducer.ipynb))    
+
 
 ## Contributing new examples
 

…example_na_controlling_the_pml/README.md examples/na_controlling_the_pml/README.mdexamples/example_na_controlling_the_pml/README.md renamed to examples/na_controlling_the_pml/README.md examples/example_na_controlling_the_pml/README.md renamed to examples/na_controlling_the_pml/README.md

@@ -1,6 +1,6 @@
 # Using An Ultrasound Transducer As A Sensor Example
 
-<a target="_blank" href="https://colab.research.google.com/github/waltsims/k-wave-python/blob/master/examples/example_na_controlling_the_pml/example_na_controlling_the_pml.ipynb">
+<a target="_blank" href="https://colab.research.google.com/github/waltsims/k-wave-python/blob/master/examples/na_controlling_the_pml/example_na_controlling_the_pml.ipynb">
   <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
 </a>
 

…pml/example_na_controlling_the_pml.ipynb …pml/example_na_controlling_the_pml.ipynbexamples/example_na_controlling_the_pml/example_na_controlling_the_pml.ipynb renamed to examples/na_controlling_the_pml/example_na_controlling_the_pml.ipynb examples/example_na_controlling_the_pml/example_na_controlling_the_pml.ipynb renamed to examples/na_controlling_the_pml/example_na_controlling_the_pml.ipynb

@@ -7,7 +7,7 @@
 
 # Test installation with:
 # python3 -m pip install -i https://test.pypi.org/simple/ --extra-index-url=https://pypi.org/simple/ k-Wave-python==0.3.0
-VERSION = '0.3.0'
+VERSION = '0.3.1'
 # Set environment variable to binaries to get rid of user warning
 # This code is a crutch and should be removed when kspaceFirstOrder
 # is refactored