update citation bibtex and bump version to v2.7.0

Author: ytdHuang

CITATION.bib

@@ -1,13 +1,27 @@
-@article{HierarchicalEOM-jl2023,
-  doi = {10.1038/s42005-023-01427-2},
-  url = {https://doi.org/10.1038/s42005-023-01427-2},
-  year = {2023},
-  month = {Oct},
+@article{HierarchicalEOM.jl2023,
+  title = {An efficient {J}ulia framework for hierarchical equations of motion in open quantum systems},
+  author = {Huang, Yi-Te and Kuo, Po-Chen and Lambert, Neill and Cirio, Mauro and Cross, Simon and Yang, Shen-Liang and Nori, Franco and Chen, Yueh-Nan},  
+  journal = {Communications Physics},
   publisher = {Nature Portfolio},
   volume = {6},
   number = {1},
   pages = {313},
-  author = {Huang, Yi-Te and Kuo, Po-Chen and Lambert, Neill and Cirio, Mauro and Cross, Simon and Yang, Shen-Liang and Nori, Franco and Chen, Yueh-Nan},
-  title = {An efficient {J}ulia framework for hierarchical equations of motion in open quantum systems},
-  journal = {Communications Physics}
+  month = {Oct},
+  year = {2023},
+  doi = {10.1038/s42005-023-01427-2},
+  url = {https://doi.org/10.1038/s42005-023-01427-2}
+}
+
+@article{QuantumToolbox.jl2025,
+  title = {Quantum{T}oolbox.jl: {A}n efficient {J}ulia framework for simulating open quantum systems},
+  author = {Mercurio, Alberto and Huang, Yi-Te and Cai, Li-Xun and Chen, Yueh-Nan and Savona, Vincenzo and Nori, Franco},
+  journal = {{Quantum}},
+  issn = {2521-327X},
+  publisher = {{Verein zur F{\"{o}}rderung des Open Access Publizierens in den Quantenwissenschaften}},
+  volume = {9},
+  pages = {1866},
+  month = sep,
+  year = {2025},
+  doi = {10.22331/q-2025-09-29-1866},
+  url = {https://doi.org/10.22331/q-2025-09-29-1866}
 }

Project.toml

@@ -1,7 +1,7 @@
 name = "HierarchicalEOM"
 uuid = "a62dbcb7-80f5-4d31-9a88-8b19fd92b128"
 authors = ["Yi-Te Huang"]
-version = "2.6.0"
+version = "2.7.0"
 
 [deps]
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
@@ -37,7 +37,7 @@ LinearSolve = "2.4.2 - 3"
 OrdinaryDiffEqCore = "1"
 OrdinaryDiffEqLowOrderRK = "1"
 Pkg = "1"
-QuantumToolbox = "0.34, 0.35"
+QuantumToolbox = "0.36"
 Reexport = "1"
 SciMLBase = "2.105"
 SciMLOperators = "1.4"

README.md

@@ -75,34 +75,36 @@ The documentation can be found in :
 If you like `HierarchicalEOM.jl`, we would appreciate it if you starred the repository in order to help us increase its visibility. Furthermore, if you find the framework useful in your research, we would be grateful if you could cite our publication [ [Communications Physics 6, 313 (2023)](https://doi.org/10.1038/s42005-023-01427-2)  ] using the following bibtex entry:
 
 ```bib
-@article{HierarchicalEOM-jl2023,
-  doi = {10.1038/s42005-023-01427-2},
-  url = {https://doi.org/10.1038/s42005-023-01427-2},
-  year = {2023},
-  month = {Oct},
+@article{HierarchicalEOM.jl2023,
+  title = {An efficient {J}ulia framework for hierarchical equations of motion in open quantum systems},
+  author = {Huang, Yi-Te and Kuo, Po-Chen and Lambert, Neill and Cirio, Mauro and Cross, Simon and Yang, Shen-Liang and Nori, Franco and Chen, Yueh-Nan},  
+  journal = {Communications Physics},
   publisher = {Nature Portfolio},
   volume = {6},
   number = {1},
   pages = {313},
-  author = {Huang, Yi-Te and Kuo, Po-Chen and Lambert, Neill and Cirio, Mauro and Cross, Simon and Yang, Shen-Liang and Nori, Franco and Chen, Yueh-Nan},
-  title = {An efficient {J}ulia framework for hierarchical equations of motion in open quantum systems},
-  journal = {Communications Physics}
+  month = {Oct},
+  year = {2023},
+  doi = {10.1038/s42005-023-01427-2},
+  url = {https://doi.org/10.1038/s42005-023-01427-2}
 }
 ```
 
-Since this package is built on top of [`QuantumToolbox.jl`](https://qutip.org/QuantumToolbox.jl/), we would appreciate it if you could also cite the arXiv preprint [ [arXiv:2504.21440 (2025)](https://doi.org/10.48550/arXiv.2504.21440) ] using the following bibtex entry:
+Since this package is built on top of [`QuantumToolbox.jl`](https://qutip.org/QuantumToolbox.jl/), we would appreciate it if you could also cite the publication [ [Quantum 9, 1866 (2025)](https://doi.org/10.22331/q-2025-09-29-1866) ] using the following bibtex entry:
 
 ```bib
-@article{QuantumToolbox-jl2025,
-    title={{QuantumToolbox.jl}: An efficient {Julia} framework for simulating open quantum systems},
-    author={Mercurio, Alberto and Huang, Yi-Te and Cai, Li-Xun and Chen, Yueh-Nan and Savona, Vincenzo and Nori, Franco},
-    journal={arXiv preprint arXiv:2504.21440},
-    year={2025},
-    publisher = {arXiv},
-    eprint={2504.21440},
-    archivePrefix={arXiv},
-    primaryClass={quant-ph},
-    doi = {10.48550/arXiv.2504.21440}
+@article{QuantumToolbox.jl2025,
+  title = {Quantum{T}oolbox.jl: {A}n efficient {J}ulia framework for simulating open quantum systems},
+  author = {Mercurio, Alberto and Huang, Yi-Te and Cai, Li-Xun and Chen, Yueh-Nan and Savona, Vincenzo and Nori, Franco},
+  journal = {{Quantum}},
+  issn = {2521-327X},
+  publisher = {{Verein zur F{\"{o}}rderung des Open Access Publizierens in den Quantenwissenschaften}},
+  volume = {9},
+  pages = {1866},
+  month = sep,
+  year = {2025},
+  doi = {10.22331/q-2025-09-29-1866},
+  url = {https://doi.org/10.22331/q-2025-09-29-1866}
 }
 ```
 

docs/src/cite.md

@@ -3,33 +3,35 @@
 If you like `HierarchicalEOM.jl`, we would appreciate it if you could cite our publication [ [Communications Physics 6, 313 (2023)](https://doi.org/10.1038/s42005-023-01427-2) ] using the following bibtex entry:
 
 ```bib
-@article{HierarchicalEOM-jl2023,
-  doi = {10.1038/s42005-023-01427-2},
-  url = {https://doi.org/10.1038/s42005-023-01427-2},
-  year = {2023},
-  month = {Oct},
+@article{HierarchicalEOM.jl2023,
+  title = {An efficient {J}ulia framework for hierarchical equations of motion in open quantum systems},
+  author = {Huang, Yi-Te and Kuo, Po-Chen and Lambert, Neill and Cirio, Mauro and Cross, Simon and Yang, Shen-Liang and Nori, Franco and Chen, Yueh-Nan},  
+  journal = {Communications Physics},
   publisher = {Nature Portfolio},
   volume = {6},
   number = {1},
   pages = {313},
-  author = {Huang, Yi-Te and Kuo, Po-Chen and Lambert, Neill and Cirio, Mauro and Cross, Simon and Yang, Shen-Liang and Nori, Franco and Chen, Yueh-Nan},
-  title = {An efficient {J}ulia framework for hierarchical equations of motion in open quantum systems},
-  journal = {Communications Physics}
+  month = {Oct},
+  year = {2023},
+  doi = {10.1038/s42005-023-01427-2},
+  url = {https://doi.org/10.1038/s42005-023-01427-2}
 }
 ```
 
-Since this package is built on top of [`QuantumToolbox.jl`](https://qutip.org/QuantumToolbox.jl/), we would appreciate it if you could also cite the arXiv preprint [ [arXiv:2504.21440 (2025)](https://doi.org/10.48550/arXiv.2504.21440) ] using the following bibtex entry:
+Since this package is built on top of [`QuantumToolbox.jl`](https://qutip.org/QuantumToolbox.jl/), we would appreciate it if you could also cite the publication [ [Quantum 9, 1866 (2025)](https://doi.org/10.22331/q-2025-09-29-1866) ] using the following bibtex entry:
 
 ```bib
-@article{QuantumToolbox-jl2025,
-    title={{QuantumToolbox.jl}: An efficient {Julia} framework for simulating open quantum systems},
-    author={Mercurio, Alberto and Huang, Yi-Te and Cai, Li-Xun and Chen, Yueh-Nan and Savona, Vincenzo and Nori, Franco},
-    journal={arXiv preprint arXiv:2504.21440},
-    year={2025},
-    publisher = {arXiv},
-    eprint={2504.21440},
-    archivePrefix={arXiv},
-    primaryClass={quant-ph},
-    doi = {10.48550/arXiv.2504.21440}
+@article{QuantumToolbox.jl2025,
+  title = {Quantum{T}oolbox.jl: {A}n efficient {J}ulia framework for simulating open quantum systems},
+  author = {Mercurio, Alberto and Huang, Yi-Te and Cai, Li-Xun and Chen, Yueh-Nan and Savona, Vincenzo and Nori, Franco},
+  journal = {{Quantum}},
+  issn = {2521-327X},
+  publisher = {{Verein zur F{\"{o}}rderung des Open Access Publizierens in den Quantenwissenschaften}},
+  volume = {9},
+  pages = {1866},
+  month = sep,
+  year = {2025},
+  doi = {10.22331/q-2025-09-29-1866},
+  url = {https://doi.org/10.22331/q-2025-09-29-1866}
 }
 ```

docs/src/libraryAPI.md

@@ -130,6 +130,7 @@ DensityOfStates
 ```@docs
 HierarchicalEOM.versioninfo()
 HierarchicalEOM.about()
+HierarchicalEOM.cite()
 ```
 The outputs will be something like the following:
 ```@example

src/HeomBase.jl

@@ -118,7 +118,7 @@ function _get_pkg_version(pkg_name::String)
     end
 end
 
-"""
+@doc raw"""
     HierarchicalEOM.print_logo(io::IO=stdout)
 
 Print the Logo of HierarchicalEOM package
@@ -178,10 +178,10 @@ function print_logo(io::IO = stdout)
     return printstyled(io, "\n")
 end
 
-"""
+@doc raw"""
     HierarchicalEOM.versioninfo(io::IO=stdout)
 
-Command line output of information on HierarchicalEOM, dependencies, and system information.
+Command line output of information on HierarchicalEOM, dependencies, and system information, same as [`HierarchicalEOM.about`](@ref).
 """
 function versioninfo(io::IO = stdout)
     cpu = Sys.cpu_info()
@@ -218,22 +218,60 @@ function versioninfo(io::IO = stdout)
     )
 
     # print System information
-    println(io, "System information:")
-    println(io, "====================================")
-    println(io, """OS       : $(OS_name) ($(Sys.MACHINE))""")
-    println(io, """CPU      : $(length(cpu)) × $(cpu[1].model)""")
-    println(io, """Memory   : $(round(Sys.total_memory() / 2 ^ 30, digits=3)) GB""")
-    println(io, """WORD_SIZE: $(Sys.WORD_SIZE)""")
-    println(io, """LIBM     : $(Base.libm_name)""")
-    println(io, """LLVM     : libLLVM-$(Base.libllvm_version) ($(Sys.JIT), $(Sys.CPU_NAME))""")
-    println(io, """BLAS     : $(basename(BLAS_info.libname)) ($(BLAS_info.interface))""")
-    println(io, """Threads  : $(Threads.nthreads()) (on $(Sys.CPU_THREADS) virtual cores)""")
-    return print(io, "\n")
+    println(
+        io,
+        "System information:\n",
+        "====================================\n",
+        """OS       : $(OS_name) ($(Sys.MACHINE))\n""",
+        """CPU      : $(length(cpu)) × $(cpu[1].model)\n""",
+        """Memory   : $(round(Sys.total_memory() / 2 ^ 30, digits=3)) GB\n""",
+        """WORD_SIZE: $(Sys.WORD_SIZE)\n""",
+        """LIBM     : $(Base.libm_name)\n""",
+        """LLVM     : libLLVM-$(Base.libllvm_version) ($(Sys.JIT), $(Sys.CPU_NAME))\n""",
+        """BLAS     : $(basename(BLAS_info.libname)) ($(BLAS_info.interface))\n""",
+        """Threads  : $(Threads.nthreads()) (on $(Sys.CPU_THREADS) virtual cores)\n""",
+    )
+
+    # print citation information
+    println(
+        io,
+        "+----------------------------------------------------+\n",
+        "| Please cite HierarchicalEOM.jl in your publication |\n",
+        "+----------------------------------------------------+\n",
+        "For your convenience, a bibtex reference can be easily generated using `HierarchicalEOM.cite()`.\n",
+    )
+    return nothing
 end
 
-"""
-    QuantumToolbox.about(io::IO=stdout)
+@doc raw"""
+    HierarchicalEOM.about(io::IO=stdout)
 
 Command line output of information on HierarchicalEOM, dependencies, and system information, same as [`HierarchicalEOM.versioninfo`](@ref).
 """
 about(io::IO = stdout) = versioninfo(io)
+
+@doc raw"""
+    HierarchicalEOM.cite(io::IO = stdout)
+
+Command line output of citation information and bibtex generator for `HierarchicalEOM.jl`.
+"""
+function cite(io::IO = stdout)
+    citation = raw"""
+    @article{HierarchicalEOM.jl2023,
+      title = {An efficient {J}ulia framework for hierarchical equations of motion in open quantum systems},
+      author = {Huang, Yi-Te and Kuo, Po-Chen and Lambert, Neill and Cirio, Mauro and Cross, Simon and Yang, Shen-Liang and Nori, Franco and Chen, Yueh-Nan},  
+      journal = {Communications Physics},
+      publisher = {Nature Portfolio},
+      volume = {6},
+      number = {1},
+      pages = {313},
+      month = {Oct},
+      year = {2023},
+      doi = {10.1038/s42005-023-01427-2},
+      url = {https://doi.org/10.1038/s42005-023-01427-2}
+    }
+    """
+    print(io, citation)
+    QuantumToolbox.cite(io)
+    return nothing
+end

test/cite.jl

@@ -0,0 +1,21 @@
+@testitem "Citation Bibtex" begin
+    # citation bibtex
+    io_buffer = IOBuffer()
+    HierarchicalEOM.cite(io_buffer)
+    captured_output = String(take!(io_buffer))
+    @test captured_output ==
+          """@article{HierarchicalEOM.jl2023,\n""" *
+          """  title = {An efficient {J}ulia framework for hierarchical equations of motion in open quantum systems},\n""" *
+          """  author = {Huang, Yi-Te and Kuo, Po-Chen and Lambert, Neill and Cirio, Mauro and Cross, Simon and Yang, Shen-Liang and Nori, Franco and Chen, Yueh-Nan},\n""" *
+          """  journal = {Communications Physics},\n""" *
+          """  publisher = {Nature Portfolio},\n""" *
+          """  volume = {6},\n""" *
+          """  number = {1},\n""" *
+          """  pages = {313},\n""" *
+          """  month = {Oct},\n""" *
+          """  year = {2023},\n""" *
+          """  doi = {10.1038/s42005-023-01427-2},\n""" *
+          """  url = {https://doi.org/10.1038/s42005-023-01427-2}\n""" *
+          """}\n""" *
+          QuantumToolbox.cite(io_buffer)
+end