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updated docs and locked sphinx=6.2.1 until error fixed #59

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Jul 4, 2023
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updated docs and locked sphinx=6.2.1 until error fixed #59

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dc2dc8a
updated docs and locked sphinx=6.1.1 until error fixed
bc118 Jul 4, 2023
3dfc329
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 4, 2023
6320212
updated docs and locked sphinx=6.1.1 until error fixed
bc118 Jul 4, 2023
de5edaf
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 4, 2023
2a3ee09
updated docs and locked sphinx=6.1.1 until error fixed
bc118 Jul 4, 2023
a920bcf
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 4, 2023
c0fadd8
updated docs and locked sphinx=6.1.1 until error fixed
bc118 Jul 4, 2023
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2 changes: 1 addition & 1 deletion docs/environment_docs.yml
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Expand Up @@ -23,7 +23,7 @@ dependencies:
- gmso>=0.9.1
- mbuild>=0.16.0
- pre-commit
- sphinx
- sphinx=6.2.1
- pip
- pip:
- bump2version
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39 changes: 35 additions & 4 deletions docs/reference/citing_mosdef_gomc_python.rst
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Expand Up @@ -6,17 +6,48 @@ Citing

If you use this code for your research, please cite for following sources:


`The Journal website <https://pubs.acs.org/doi/abs/10.1021/acs.jcim.2c01498>`_:

**ACS**

Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey. MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC. J. Chem. Inf. Model. 2023, 63(4), 1218-1228.

**BibTeX**

.. code-block:: bibtex

@article{MOSDEF_GOMC_2023_paper,
author = {Crawford, Brad and Timalsina, Umesh and Quach, Co D. and Craven, Nicholas C. and Gilmer, Justin B. and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey J.},
title = {MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC},
journal = {Journal of Chemical Information and Modeling},
volume = {63},
number = {4},
pages = {1218-1228},
year = {2023},
doi = {10.1021/acs.jcim.2c01498},
note ={PMID: 36791286},

url = {
https://doi.org/10.1021/acs.jcim.2c01498

},
}

Download as :download:`BibTeX <mosdef_gomc_paper.bib>` or :download:`RIS <mosdef_gomc_paper.ris>`


`The GitHub repository <https://github.com/GOMC-WSU/MoSDeF-GOMC>`_:

**ACS**

Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and Cummings, Peter T. and Potoff, Jeffrey. MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC, https://github.com/GOMC-WSU/MoSDeF-GOMC, 2022.
Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey. MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC, https://github.com/GOMC-WSU/MoSDeF-GOMC, 2022.

**BibTeX**

.. code-block:: bibtex

@Inbook{MOSDEF_GOMC_PYTHON_2022,
@Inbook{MOSDEF_GOMC_2022_python,
author = "Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey",
title = "MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC",
year = "2022",
Expand All @@ -31,14 +62,14 @@ Download as :download:`BibTeX <mosdef_gomc_python.bib>` or :download:`RIS <mosde

**ACS**

Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and Cummings, Peter T. and Potoff, Jeffrey. MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC, https://doi.org/10.5281/zenodo.7217632, 2022.
Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey. MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC, https://doi.org/10.5281/zenodo.7217632, 2022.

**BibTeX**

.. code-block:: bibtex

@software{MOSDEF_GOMC_2022_zenodo,
author = "Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and Cummings, Peter T. and Potoff, Jeffrey",
author = "Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey",
title = "MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC",
year = "2022",
publisher = "Zenodo",
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21 changes: 21 additions & 0 deletions docs/reference/mosdef_gomc_paper.bib
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@@ -0,0 +1,21 @@
@article{MOSDEF_GOMC_2023_paper,
author = {Crawford, Brad and Timalsina, Umesh and Quach, Co D. and Craven, Nicholas C. and Gilmer, Justin B. and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey J.},
title = {MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC},
journal = {Journal of Chemical Information and Modeling},
volume = {63},
number = {4},
pages = {1218-1228},
year = {2023},
doi = {10.1021/acs.jcim.2c01498},
note ={PMID: 36791286},

URL = {
https://doi.org/10.1021/acs.jcim.2c01498

},
eprint = {
https://doi.org/10.1021/acs.jcim.2c01498

}

}
27 changes: 27 additions & 0 deletions docs/reference/mosdef_gomc_paper.ris
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@@ -0,0 +1,27 @@
TY - JOUR
T1 - MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC
AU - Crawford, Brad
AU - Timalsina, Umesh
AU - Quach, Co D.
AU - Craven, Nicholas C.
AU - Gilmer, Justin B.
AU - McCabe, Clare
AU - Cummings, Peter T.
AU - Potoff, Jeffrey J.
Y1 - 2023/02/27
PY - 2023
DA - 2023/02/27
N1 - doi: 10.1021/acs.jcim.2c01498
DO - 10.1021/acs.jcim.2c01498
T2 - Journal of Chemical Information and Modeling
JF - Journal of Chemical Information and Modeling
JO - J. Chem. Inf. Model.
SP - 1218
EP - 1228
VL - 63
IS - 4
PB - American Chemical Society
SN - 1549-9596
M3 - doi: 10.1021/acs.jcim.2c01498
UR - https://doi.org/10.1021/acs.jcim.2c01498
ER -
2 changes: 1 addition & 1 deletion docs/reference/mosdef_gomc_python.bib
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@@ -1,4 +1,4 @@
@Inbook{MOSDEF_GOMC_2022,
@Inbook{MOSDEF_GOMC_2022_github,
author = "Crawford, Brad and Timalsina, Umesh and Quach, Co and Craven, Nicholas and Gilmer, Justin and McCabe, Clare and Cummings, Peter T. and Potoff, Jeffrey",
title = "MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC",
year = "2022",
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2 changes: 1 addition & 1 deletion environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ dependencies:
- gmso>=0.9.1
- mbuild>=0.16.0
- pre-commit
- sphinx
- sphinx=6.2.1
- pip
- pip:
- bump2version
Expand Down