Add arXiv reference.

BIBLIOGRAPHY.md

@@ -8,7 +8,7 @@ The code in this project is based on ideas from the following publications:
   (2018).
 - **[Pollock2018]** Pollock et al., *Non-Markovian quantum processes: Complete framework and efficient characterization*, [Phys. Rev. A 97, 012127](https://doi.org/10.1103/PhysRevA.97.012127) (2018).
 - **[Jorgensen2019]** Jørgensen and Pollock, *Exploiting the causal tensor network structure of quantum processes to efficiently simulate non-Markovian path integrals*, [Phys. Rev. Lett. 123, 240602](https://doi.org/10.1103/PhysRevLett.123.240602) (2019).
-- **[Strathearn2019]** Strathearn, *Modelling Non-Markovian Quantum Systems Using Tensor Networks*, [Springer Theses](https://doi.org/10.1007/978-3-030-54975-6) (2020).
+- **[Strathearn2020]** Strathearn, *Modelling Non-Markovian Quantum Systems Using Tensor Networks*, [Springer Theses](https://doi.org/10.1007/978-3-030-54975-6) (2020).
 - **[Fux2021]** Fux et al., *Efficient exploration of Hamiltonian parameter space for optimal control of non-Markovian open quantum systems*, [Phys. Rev. Lett. 126, 200401](https://doi.org/10.1103/PhysRevLett.126.200401) (2021).
 - **[Gribben2022a]** Gribben et al., *Exact dynamics of non-additive environments in non-Markovian open quantum systems*, [PRX Quantum 3, 10321](https://doi.org/10.1103/PRXQuantum.3.010321) (2022).
 - **[Gribben2022b]** Gribben et al., *Using the Environment to Understand non-Markovian Open Quantum Systems*,  [Quantum, 6, 847](https://doi.org/10.22331/q-2022-10-25-847) (2022).
@@ -142,14 +142,22 @@ BibTeX:
   url = {https://doi.org/10.1103/PhysRevLett.123.240602}
 }
 
-@misc{OQuPy,
+@misc{OQuPy-code-v0.5.0,
   author={{The TEMPO collaboration}},
-  title={{OQuPy: A Python 3 package to efficiently compute
-          non-Markovian open quantum systems.}},
-  year=2020,
+  title={{OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors.}},
+  year=2024,
   publisher={GitHub},
-  doi={10.5281/zenodo.4428316}
-  url={https://github.com/tempoCollaboration/TimeEvolvingMPO}
+  doi={10.5281/zenodo.12517767}
+  url={https://github.com/tempoCollaboration/OQuPy}
+}
+
+@misc{OQuPy-paper,
+  title={OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors}, 
+  author={Gerald E. Fux and Piper Fowler-Wright and Joel Beckles and Eoin P. Butler and Paul R. Eastham and Dominic Gribben and Jonathan Keeling and Dainius Kilda and Peter Kirton and Ewen D. C. Lawrence and Brendon W. Lovett and Eoin O'Neill and Aidan Strathearn and Roosmarijn de Wit},
+  year={2024},
+  eprint={2406.16650},
+  archivePrefix={arXiv},
+  doi = {https://doi.org/10.48550/arXiv.2406.16650}
 }
 
 @article{Pollock2018,
@@ -168,7 +176,7 @@ BibTeX:
   year = {2018}
 }
 
-@article{Strathearn_2017,
+@article{Strathearn2017,
 	doi = {10.1088/1367-2630/aa8744},
 	url = {https://doi.org/10.1088/1367-2630/aa8744},
 	year = 2017,
@@ -199,7 +207,7 @@ BibTeX:
   year = {2018}
 }
 
-@book{Strathearn2019,
+@book{Strathearn2020,
   address = {Cham},
   author = {Strathearn, Aidan},
   doi = {10.1007/978-3-030-54975-6},

HOW_TO_CITE.md

@@ -1,17 +1,18 @@
 How to Cite this Project
 ========================
 
+If you publish work using OQuPy, please cite the paper
 
-Citing the Code
----------------
+- **[OQuPy-paper]** G. E. Fux, P. Fowler-Wright, J.Beckles, E. P. Butler, P. R. Eastham, D. Gribben, J. Keeling, D. Kilda, P. Kirton, E. D. C. Lawrence, B. W. Lovett, E. O'Neill, A. Strathearn, R. de Wit, *OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors*, [arXiv:2406.16650](https://doi.org/10.48550/arXiv.2406.16650).
 
-- **[OQuPy]** The TEMPO collaboration, *OQuPy: A Python 3 package to efficiently compute non-Markovian open quantum systems*, [GitHub](https://doi.org/10.5281/zenodo.4428316) (2020).
+and the code version you used
 
+- **[OQuPy-code-v0.5.0]** The TEMPO collaboration, *OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors*, [doi: 10.5281/zenodo.12517767](https://doi.org/10.5281/zenodo.12517767) (2024).
 
-Please consider citing
-----------------------
 
-- TEMPO algorithm: **[Strathearn2018]**, **[Strathearn2019]**
+Also, please consider citing:
+
+- TEMPO algorithm: **[Strathearn2018]**, **[Strathearn2020]**
 - Process tensor approach: **[Pollock2018]**, **[Jorgensen2019]**
 - Optimization: **[Fux2021]**, **[Bulter2024]**
 - Multiple environments: **[Gribben2022a]**

README.md

@@ -1,8 +1,7 @@
 
 # OQuPy: Open Quantum Systems in Python
 
-**A Python package to efficiently simulate non-Markovian open quantum systems
-with process tensors.**
+[**ArXiv:2406.16650 - A Python package to efficiently simulate non-Markovian open quantum systems with process tensors.**](https://doi.org/10.48550/arXiv.2406.16650)
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/tempoCollaboration/OQuPy/main?filepath=tutorials%2Fquickstart.ipynb)
 [![Tests status](https://github.com/tempoCollaboration/OQuPy/actions/workflows/python-package-tests.yml/badge.svg)](https://github.com/tempoCollaboration/OQuPy/actions/workflows/python-package-tests.yml)
@@ -13,6 +12,8 @@ with process tensors.**
 
 [![Unitary Fund](https://img.shields.io/badge/Supported%20By-UNITARY%20FUND-brightgreen.svg?style=for-the-badge)](http://unitary.fund)
 
+
+
 This open source project aims to facilitate versatile numerical tools to efficiently compute the dynamics of quantum systems that are possibly strongly coupled to structured environments. It facilitates the convenient application of several numerical methods that combine the conceptional advantages of the process tensor framework [1], with the numerical efficiency of tensor networks.
 
 OQuPy includes numerically exact methods (i.e. employing only numerically well controlled approximations) for the non-Markovian dynamics and multi-time correlations of ...

docs/index.rst

@@ -1,8 +1,7 @@
-OQuPy - Open Quantum Systems in Python
-======================================
+OQuPy: Open Quantum Systems in Python
+=====================================
 
-**A Python package to efficiently simulate non-Markovian open quantum systems
-with process tensors.**
+`ArXiv:2406.16650 <https://doi.org/10.48550/arXiv.2406.16650>`__ - **A Python package to efficiently simulate non-Markovian open quantum systems with process tensors.**
 
 .. image:: https://img.shields.io/badge/Supported%20By-UNITARY%20FUND-brightgreen.svg?style=for-the-badge
  :target: http://unitary.fund

docs/pages/bibliography.rst

@@ -18,7 +18,7 @@ publications:
    tensor network structure of quantum processes to efficiently simulate
    non-Markovian path integrals*, `Phys. Rev. Lett. 123,
    240602 <https://doi.org/10.1103/PhysRevLett.123.240602>`__ (2019).
--  **[Strathearn2019]** Strathearn, *Modelling Non-Markovian Quantum
+-  **[Strathearn2020]** Strathearn, *Modelling Non-Markovian Quantum
    Systems Using Tensor Networks*, `Springer
    Theses <https://doi.org/10.1007/978-3-030-54975-6>`__ (2020).
 -  **[Fux2021]** Fux et al., *Efficient exploration of Hamiltonian
@@ -173,14 +173,22 @@ BibTeX:
      url = {https://doi.org/10.1103/PhysRevLett.123.240602}
    }
 
-   @misc{OQuPy,
-     author={{The TEMPO collaboration}},
-     title={{OQuPy: A Python 3 package to efficiently compute
-             non-Markovian open quantum systems.}},
-     year=2020,
-     publisher={GitHub},
-     doi={10.5281/zenodo.4428316}
-     url={https://github.com/tempoCollaboration/TimeEvolvingMPO}
+   @misc{OQuPy-code-v0.5.0,
+      author={{The TEMPO collaboration}},
+      title={{OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors.}},
+      year=2024,
+      publisher={GitHub},
+      doi={10.5281/zenodo.12517767}
+      url={https://github.com/tempoCollaboration/OQuPy}
+   }
+
+   @misc{OQuPy-paper,
+      title={OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors}, 
+      author={Gerald E. Fux and Piper Fowler-Wright and Joel Beckles and Eoin P. Butler and Paul R. Eastham and Dominic Gribben and Jonathan Keeling and Dainius Kilda and Peter Kirton and Ewen D. C. Lawrence and Brendon W. Lovett and Eoin O'Neill and Aidan Strathearn and Roosmarijn de Wit},
+      year={2024},
+      eprint={2406.16650},
+      archivePrefix={arXiv},
+      doi = {https://doi.org/10.48550/arXiv.2406.16650}
    }
 
    @article{Pollock2018,
@@ -199,7 +207,7 @@ BibTeX:
      year = {2018}
    }
 
-   @article{Strathearn_2017,
+   @article{Strathearn2017,
        doi = {10.1088/1367-2630/aa8744},
        url = {https://doi.org/10.1088/1367-2630/aa8744},
        year = 2017,
@@ -230,7 +238,7 @@ BibTeX:
      year = {2018}
    }
 
-   @book{Strathearn2019,
+   @book{Strathearn2020,
      address = {Cham},
      author = {Strathearn, Aidan},
      doi = {10.1007/978-3-030-54975-6},

docs/pages/how_to_cite.rst

@@ -1,17 +1,18 @@
 How to Cite this Project
 ========================
 
-Citing the Code
----------------
+If you publish work using OQuPy, please cite the paper
 
--  **[OQuPy]** The TEMPO collaboration, *OQuPy: A Python 3 package to
-   efficiently compute non-Markovian open quantum systems*,
-   `GitHub <https://doi.org/10.5281/zenodo.4428316>`__ (2020).
+- **[OQuPy-paper]** G. E. Fux, P. Fowler-Wright, J.Beckles, E. P. Butler, P. R. Eastham, D. Gribben, J. Keeling, D. Kilda, P. Kirton, E. D. C. Lawrence, B. W. Lovett, E. O'Neill, A. Strathearn, R. de Wit, *OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors*, `arXiv:2406.16650 <https://doi.org/10.48550/arXiv.2406.16650>`__.
 
-Please consider citing
-----------------------
+and the code version you used
 
--  TEMPO algorithm: **[Strathearn2018]**, **[Strathearn2019]**
+- **[OQuPy-code-v0.5.0]** The TEMPO collaboration, *OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors*, `doi: 10.5281/zenodo.12517767 <https://doi.org/10.5281/zenodo.12517767>`__ (2024).
+
+
+Also, please consider citing:
+
+-  TEMPO algorithm: **[Strathearn2018]**, **[Strathearn2020]**
 -  Process tensor approach: **[Pollock2018]**, **[Jorgensen2019]**
 -  Optimization: **[Fux2021]**, **[Bulter2024]**
 -  Multiple environments: **[Gribben2022a]**

oqupy/__init__.py

@@ -2,6 +2,8 @@
 A Python package to efficiently simulate non-Markovian open quantum systems
 with process tensors.
 
+--> see ArXiv:2406.16650 (https://doi.org/10.48550/arXiv.2406.16650)
+
 This open source project aims to facilitate versatile numerical tools to
 efficiently compute the dynamics of quantum systems that are possibly strongly
 coupled to structured environments. It facilitates the convenient application