README changed to PyTheus/pytheus.

Author: cruizgo

README.md

@@ -1,5 +1,5 @@
-# Theseus
-Theseus, a highly-efficient inverse-design algorithm for quantum optical experiments
+# PyTheus
+PyTheus, a highly-efficient inverse-design algorithm for quantum optical experiments
 
 ## Installation
 
@@ -9,24 +9,24 @@ When published it will be possible to install via `pip install`. Untill then, in
 python setup.py install
 ```
 
-## Running Theseus
+## Running PyTheus
 
 To list the included examples, type
 
 ```
-theseus list
+pytheus list
 ```
 
 To run one of the included examples, type e.g.
 
 ```
-theseus run --example ghz_346
+pytheus run --example ghz_346
 ```
 
 To run your own input file, type
 
 ```
-theseus run PATH_TO_YOUR_INPUT_FILE
+pytheus run PATH_TO_YOUR_INPUT_FILE
 ```
 
 Output of optimization is saved to a directory called `output`. Names of the subdirectorie are specified by the name
@@ -35,17 +35,17 @@ and content of the config file.
 To plot the graph corresponding to one result saved as a json file, execute 
 
 ```
-theseus plot PATH_TO_RESULT_FILE
+pytheus plot PATH_TO_RESULT_FILE
 ```
 
 To analyze a subdirectory corresponding to one run, type
 
 ```
-theseus analyze -d outputs/ghz_346/ghz_346 
+pytheus analyze -d outputs/ghz_346/ghz_346 
 ```
 or just 
 ```
-theseus analyze  
+pytheus analyze  
 ```
 then an overview of all available folders that can be selected is given.
 After that one can choose which run (if there exists different run-folders having different
@@ -55,7 +55,7 @@ that can be declared via ```-i```. With ```-pm``` a pdf can be created that show
 When one wants to set all weights to plus minus one one can choose the option ```-one```.
 Everthing together:
 ```
-theseus analyze -d your/directory -one -pm -i 'norm' -i 'ent' -i 'k'  
+pytheus analyze -d your/directory -one -pm -i 'norm' -i 'ent' -i 'k'  
 ```
 ```norm``` shows the normalization of the state, ```ent``` gives information about entanglement for 
 the different bipartitions and ```k``` gives information if there is a k-uniform state and which
@@ -64,9 +64,9 @@ the different bipartitions and ```k``` gives information if there is a k-uniform
 To get help, add the `--help` option to any command. For instance
 
 ```
-> theseus run --help
+> pytheus run --help
 
-Usage: theseus run [OPTIONS] FILENAME
+Usage: pytheus run [OPTIONS] FILENAME
 
   Run an input file.
 
@@ -80,7 +80,7 @@ Options:
 ### Clone repository
 
 ```
-git clone https://github.com/artificial-scientist-lab/Theseus.git
+git clone https://github.com/artificial-scientist-lab/PyTheus.git
 ```
 
 ### Create virtual environment
@@ -141,7 +141,7 @@ pip install coverage
 Then run coverage scan:
 
 ```
-coverage run --source=theseus -m unittest discover tests 
+coverage run --source=pytheus -m unittest discover tests 
 ```
 
 After that, create the coverage report: