release as qsurface (#34)

(re)release as qsurface

.github/workflows/python-package.yml

@@ -39,14 +39,14 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest, check coverage
       run: |
-        pytest --cov=opensurfacesim tests/ --cov-report=xml -m "not plotting"
+        pytest --cov=qsurface tests/ --cov-report=xml -m "not plotting"
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
       with:
         file: ./coverage.xml
         flags: unittests
         env_vars: OS,PYTHON
-        name: codecov-opensurfacesim
+        name: codecov-qsurface
         fail_ci_if_error: false
         path_to_write_report: ./codecov_report.gz
         verbose: true

.gitignore

@@ -7,7 +7,8 @@
 !requirements.txt
 !pytest.ini
 test.py
-opensurfacesim/decoders/mwpm/blossom5-v2.05.src/
+qsurface/decoders/mwpm/blossom5-v2.05.src/
+!qsurface/decoders/decoders.ini
 
 .python-version
 .vscode/

README.md

@@ -1,22 +1,22 @@
 
-# opensurfacesim
-
-[![PyPI version](https://img.shields.io/pypi/v/opensurfacesim?color=blue)](https://pypi.org/project/opensurfacesim/)
-![Build](https://github.com/watermarkhu/opensurfacesim/workflows/Build/badge.svg)
-[![Documentation Status](https://readthedocs.org/projects/opensurfacesim/badge/?version=latest)](https://opensurfacesim.readthedocs.io/en/latest/?badge=latest)
-[![codecov](https://codecov.io/gh/watermarkhu/OpenSurfaceSim/branch/master/graph/badge.svg?token=CWLVPDFF2L)](https://codecov.io/gh/watermarkhu/OpenSurfaceSim)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/watermarkhu/opensurfacesim/master?filepath=examples.ipynb)
-![License](https://img.shields.io/pypi/l/opensurfacesim)
+# Qsurface
+
+[![PyPI version](https://img.shields.io/pypi/v/qsurface?color=blue)](https://pypi.org/project/qsurface/)
+![Build](https://github.com/watermarkhu/qsurface/workflows/Build/badge.svg)
+[![Documentation Status](https://readthedocs.org/projects/qsurface/badge/?version=latest)](https://qsurface.readthedocs.io/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/watermarkhu/Qsurface/branch/master/graph/badge.svg?token=CWLVPDFF2L)](https://codecov.io/gh/watermarkhu/qsurface)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/watermarkhu/qsurface/master?filepath=examples.ipynb)
+![License](https://img.shields.io/pypi/l/qsurface)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4247617.svg)](https://doi.org/10.5281/zenodo.4247617)
 [![Unitary Fund](https://img.shields.io/badge/Supported%20By-UNITARY%20FUND-brightgreen.svg?style=flat-the-badge)](http://unitary.fund)
 
-Opensurfacesim is a simulation package for the surface code, and is designed to modularize 3 aspects of a surface code simulation.
+Qsurface is a simulation package for the surface code, and is designed to modularize 3 aspects of a surface code simulation.
 
 1. The surface code
 2. The error model
 3. The used decoder
 
-New types of surface codes, error modules and decoders can be added to opensurfacesim by using the included templates for each of the three core module categories.
+New types of surface codes, error modules and decoders can be added to Qsurface by using the included templates for each of the three core module categories.
 
 The current included decoders are:
 
@@ -37,7 +37,7 @@ The compatibility of these decoders with the included surface codes are listed b
 All required packages can be installed through:
 
 ```bash
-pip install opensurfacesim
+pip install qsurface
 ```
 
 ## Requirements
@@ -48,10 +48,10 @@ pip install opensurfacesim
 
 ### MWPM decoder
 
-The MWPM decoder utilizes `networkx` for finding the minimal weights in a fully connected graph. This implementation is however rather slow compared to Kolmogorov's [Blossom V](https://pub.ist.ac.at/~vnk/software.html) algorithm. Blossom V has its own license and is thus not included with opensurfacesim. We do provided a single function to download and compile Blossom V, and to setup the integration with opensurfacesim automatically.
+The MWPM decoder utilizes `networkx` for finding the minimal weights in a fully connected graph. This implementation is however rather slow compared to Kolmogorov's [Blossom V](https://pub.ist.ac.at/~vnk/software.html) algorithm. Blossom V has its own license and is thus not included with Qsurface. We do provided a single function to download and compile Blossom V, and to setup the integration with Qsurface automatically.
 
 ```python
->>> from opensurfacesim.decoders import mwpm
+>>> from qsurface.decoders import mwpm
 >>> mwpm.get_blossomv()
 ```
 
@@ -60,7 +60,7 @@ The MWPM decoder utilizes `networkx` for finding the minimal weights in a fully
 To simulate the toric code and simulate with bitflip error for 10 iterations and decode with the MWPM decoder:
 
 ```python
->>> from opensurfacesim.main import initialize, run
+>>> from qsurface.main import initialize, run
 >>> code, decoder = initialize((6,6), "toric", "mwpm", enabled_errors=["pauli"])
 >>> run(code, decoder, iterations=10, error_rates = {"p_bitflip": 0.1})
 {'no_error': 8}
@@ -69,7 +69,7 @@ To simulate the toric code and simulate with bitflip error for 10 iterations and
 Benchmarking of decoders can be enabled by attaching a *benchmarker* object to the decoder. See the docs for the syntax and information to setup benchmarking.
 
 ```python
->>> from opensurfacesim.main import initialize, run
+>>> from qsurface.main import initialize, run
 >>> benchmarker = BenchmarkDecoder({"decode":"duration"})
 >>> run(code, decoder, iterations=10, error_rates = {"p_bitflip": 0.1}, benchmark=benchmarker)
 {'no_error': 8,
@@ -81,15 +81,15 @@ Benchmarking of decoders can be enabled by attaching a *benchmarker* object to t
 
 ## Plotting
 
-The figures in opensurfacesim allows for step-by-step visualization of the surface code simulation (and if supported the decoding process). Each figure logs its history such that the user can move backwards in time to view past states of the surface (and decoder). Press `h` when the figure is open for more information.
+The figures in Qsurface allows for step-by-step visualization of the surface code simulation (and if supported the decoding process). Each figure logs its history such that the user can move backwards in time to view past states of the surface (and decoder). Press `h` when the figure is open for more information.
 
 ```python
->>> from opensurfacesim.main import initialize, run
+>>> from qsurface.main import initialize, run
 >>> code, decoder = initialize((6,6), "toric", "mwpm", enabled_errors=["pauli"], plotting=True, initial_states=(0,0))
 >>> run(code, decoder, error_rates = {"p_bitflip": 0.1, "p_phaseflip": 0.1}, decode_initial=False)
 ```
 
-![Interactive plotting on a 6x6 toric code.](https://raw.githubusercontent.com/watermarkhu/OpenSurfaceSim/master/images/toric-2d.gif "Iteractive plotting on a 2d axis")
+![Interactive plotting on a 6x6 toric code.](https://raw.githubusercontent.com/watermarkhu/qsurface/master/images/toric-2d.gif "Iteractive plotting on a 2d axis")
 
 Plotting will be performed on a 3D axis if faulty measurements are enabled.
 
@@ -98,24 +98,24 @@ Plotting will be performed on a 3D axis if faulty measurements are enabled.
 >>> run(code, decoder, error_rates = {"p_bitflip": 0.05, "p_bitflip_plaq": 0.05}, decode_initial=False)
 ```
 
-![Interactive plotting on a toric code with faulty measurements.](https://raw.githubusercontent.com/watermarkhu/OpenSurfaceSim/master/images/toric-3d.gif "Iteractive plotting on a 3d axis")
+![Interactive plotting on a toric code with faulty measurements.](https://raw.githubusercontent.com/watermarkhu/qsurface/master/images/toric-3d.gif "Iteractive plotting on a 3d axis")
 
-In IPython, inline images are created for each iteration of the plot, which can be tested in the [example notebook](https://mybinder.org/v2/gh/watermarkhu/opensurfacesim/master?filepath=examples.ipynb).
+In IPython, inline images are created for each iteration of the plot, which can be tested in the [example notebook](https://mybinder.org/v2/gh/watermarkhu/qsurface/master?filepath=examples.ipynb).
 
 ## Command line interface
 
 Simulations can also be initiated from the command line
 
 ```bash
-$ python -m opensurfacesim -e pauli -D mwpm -C toric simulation --p_bitflip 0.1 -n 10
+$ python -m qsurface -e pauli -D mwpm -C toric simulation --p_bitflip 0.1 -n 10
 {'no_error': 8}
 ```
 
 For more information on command line interface:
 
 ```bash
-$ python -m opensurfacesim -h
-usage: opensurfacesim
+$ python -m qsurface -h
+usage: qsurface
 ...
 ```
 

docs/source/codes/elements.rst

@@ -1,7 +1,7 @@
 Code elements
 -------------
 
-.. automodule:: opensurfacesim.codes.elements
+.. automodule:: qsurface.codes.elements
     :member-order: bysource
     :inherited-members:
     :members:

docs/source/codes/planar.rst

@@ -4,22 +4,22 @@ Planar code
 Simulation
 ^^^^^^^^^^
 
-.. autoclass:: opensurfacesim.codes.planar.sim.PerfectMeasurements
+.. autoclass:: qsurface.codes.planar.sim.PerfectMeasurements
     :member-order: bysource
     :inherited-members:
     :members:
 
-.. autoclass:: opensurfacesim.codes.planar.sim.FaultyMeasurements
+.. autoclass:: qsurface.codes.planar.sim.FaultyMeasurements
     :member-order: bysource
     :inherited-members:
     :members:
 
 Plotting
 ^^^^^^^^
 
-.. autoclass:: opensurfacesim.codes.planar.plot.PerfectMeasurements
+.. autoclass:: qsurface.codes.planar.plot.PerfectMeasurements
     :member-order: bysource
     :inherited-members:
     :members:
 
-.. autoclass:: opensurfacesim.codes.planar.plot.FaultyMeasurements
+.. autoclass:: qsurface.codes.planar.plot.FaultyMeasurements

docs/source/codes/template.rst

@@ -4,22 +4,22 @@ Template code
 Simulation
 ^^^^^^^^^^
 
-.. autoclass:: opensurfacesim.codes._template.sim.PerfectMeasurements
+.. autoclass:: qsurface.codes._template.sim.PerfectMeasurements
     :member-order: bysource
     :inherited-members:
     :members:
 
-.. autoclass:: opensurfacesim.codes._template.sim.FaultyMeasurements
+.. autoclass:: qsurface.codes._template.sim.FaultyMeasurements
     :member-order: bysource
     :inherited-members:
     :members:
 
 Plotting
 ^^^^^^^^
 
-.. autoclass:: opensurfacesim.codes._template.plot.PerfectMeasurements
+.. autoclass:: qsurface.codes._template.plot.PerfectMeasurements
     :member-order: bysource
     :inherited-members:
     :members:
 
-.. autoclass:: opensurfacesim.codes._template.plot.FaultyMeasurements
+.. autoclass:: qsurface.codes._template.plot.FaultyMeasurements

docs/source/codes/toric.rst

@@ -4,22 +4,22 @@ Toric code
 Simulation
 ^^^^^^^^^^
 
-.. autoclass:: opensurfacesim.codes.toric.sim.PerfectMeasurements
+.. autoclass:: qsurface.codes.toric.sim.PerfectMeasurements
     :member-order: bysource
     :inherited-members:
     :members:
 
-.. autoclass:: opensurfacesim.codes.toric.sim.FaultyMeasurements
+.. autoclass:: qsurface.codes.toric.sim.FaultyMeasurements
     :member-order: bysource
     :inherited-members:
     :members:
 
 Plotting
 ^^^^^^^^
 
-.. autoclass:: opensurfacesim.codes.toric.plot.PerfectMeasurements
+.. autoclass:: qsurface.codes.toric.plot.PerfectMeasurements
     :member-order: bysource
     :inherited-members:
     :members:
 
-.. autoclass:: opensurfacesim.codes.toric.plot.FaultyMeasurements
+.. autoclass:: qsurface.codes.toric.plot.FaultyMeasurements

docs/source/conf.py

@@ -17,7 +17,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "Open Surface code Simulations"
+project = "Qsurface"
 copyright = "2020, Mark Shui Hu"
 author = "Mark Shui Hu"
 

docs/source/decoders/mwpm.rst

@@ -1,18 +1,18 @@
 Information
 -----------
 
-.. automodule:: opensurfacesim.decoders.mwpm
+.. automodule:: qsurface.decoders.mwpm
     :members:
 
 Simulation
 ----------
 
-.. autoclass:: opensurfacesim.decoders.mwpm.sim.Toric
+.. autoclass:: qsurface.decoders.mwpm.sim.Toric
     :member-order: bysource
     :inherited-members:
     :members:
 
-.. autoclass:: opensurfacesim.decoders.mwpm.sim.Planar
+.. autoclass:: qsurface.decoders.mwpm.sim.Planar
     :member-order: bysource
     :inherited-members:
     :members:
@@ -21,7 +21,7 @@ Simulation
 Plotting
 --------
 
-.. automodule:: opensurfacesim.decoders.mwpm.plot
+.. automodule:: qsurface.decoders.mwpm.plot
     :member-order: bysource
     :members:
 

docs/source/decoders/template.rst

@@ -1,7 +1,7 @@
 Template decoder
 ================
 
-.. automodule:: opensurfacesim.decoders._template
+.. automodule:: qsurface.decoders._template
     :member-order: bysource
     :inherited-members:
     :members:

docs/source/decoders/ufns.rst

@@ -1,10 +1,10 @@
 Information
 -----------
 
-.. automodule:: opensurfacesim.decoders.ufns
+.. automodule:: qsurface.decoders.ufns
     :members:
 
-.. automodule:: opensurfacesim.decoders.ufns.elements
+.. automodule:: qsurface.decoders.ufns.elements
     :member-order: bysource
     :members:
 
@@ -14,18 +14,18 @@ Simulation
 
 The following description also applies to `.ufns.sim.Planar`. 
 
-.. autoclass:: opensurfacesim.decoders.ufns.sim.Toric
+.. autoclass:: qsurface.decoders.ufns.sim.Toric
     :member-order: bysource
     :inherited-members:
     :members:
 
-.. autoclass:: opensurfacesim.decoders.ufns.sim.Planar
+.. autoclass:: qsurface.decoders.ufns.sim.Planar
 
 Plotting
 --------
 
-.. autoclass:: opensurfacesim.decoders.ufns.plot.Toric
+.. autoclass:: qsurface.decoders.ufns.plot.Toric
 
-.. autoclass:: opensurfacesim.decoders.ufns.plot.Planar
+.. autoclass:: qsurface.decoders.ufns.plot.Planar
 
 .. [hu2020thesis] Hu, Mark Shui, *Quasilinear Time Decoding Algorithm for Topological Codes with High Error Threshold*, DOI: 10.13140/RG.2.2.13495.96162, 2020.

docs/source/decoders/unionfind.rst

@@ -3,38 +3,38 @@
 Information
 -----------
 
-.. automodule:: opensurfacesim.decoders.unionfind
+.. automodule:: qsurface.decoders.unionfind
     :members:
 
-.. automodule:: opensurfacesim.decoders.unionfind.elements
+.. automodule:: qsurface.decoders.unionfind.elements
     :members:
 
 Simulation
 ----------
 
 The following description also applies to `.unionfind.sim.Planar`. 
 
-.. autoclass:: opensurfacesim.decoders.unionfind.sim.Toric
+.. autoclass:: qsurface.decoders.unionfind.sim.Toric
     :member-order: bysource
     :inherited-members:
     :members:
 
-.. autoclass:: opensurfacesim.decoders.unionfind.sim.Planar
+.. autoclass:: qsurface.decoders.unionfind.sim.Planar
 
 Plotting
 --------
 
-.. autoclass:: opensurfacesim.decoders.unionfind.plot.Toric
+.. autoclass:: qsurface.decoders.unionfind.plot.Toric
 
-    .. autoclass:: opensurfacesim.decoders.unionfind.plot::Toric.Figure2D
+    .. autoclass:: qsurface.decoders.unionfind.plot::Toric.Figure2D
 
-    .. autoclass:: opensurfacesim.decoders.unionfind.plot::Toric.Figure3D
+    .. autoclass:: qsurface.decoders.unionfind.plot::Toric.Figure3D
 
-.. autoclass:: opensurfacesim.decoders.unionfind.plot.Planar
+.. autoclass:: qsurface.decoders.unionfind.plot.Planar
 
-    .. autoclass:: opensurfacesim.decoders.unionfind.plot::Planar.Figure2D
+    .. autoclass:: qsurface.decoders.unionfind.plot::Planar.Figure2D
 
-    .. autoclass:: opensurfacesim.decoders.unionfind.plot::Planar.Figure3D
+    .. autoclass:: qsurface.decoders.unionfind.plot::Planar.Figure3D
 
 
 .. [delfosse2017almost] Delfosse, Nicolas and Nickerson, Naomi H., *Almost-linear time decoding algorithm for topological codes*, arXiv preprint arXiv:1709.06218, 2017. 

docs/source/errors/erasure.rst

@@ -1,5 +1,5 @@
 Erasure error
 -------------
 
-.. automodule:: opensurfacesim.errors.erasure
+.. automodule:: qsurface.errors.erasure
     :members:

docs/source/errors/pauli.rst

@@ -1,5 +1,5 @@
 Pauli error
 -----------
 
-.. automodule:: opensurfacesim.errors.pauli
+.. automodule:: qsurface.errors.pauli
     :members: