[Docs] Update outdated docs, wiki, and contributor guidelines

CONTRIBUTING.md

@@ -0,0 +1,58 @@
+## How to contribute to RMG-Py
+
+Thank you for contributing to RMG-Py! Please take a moment to review our guidelines:
+
+### **Did you find a bug? Do you want to see a new feature?**
+
+* Please open an Issue to the corresponding repository:
+    * [RMG-Py](https://github.com/ReactionMechanismGenerator/RMG-Py/issues): For functionality of the RMG and Arkane software packages
+    * [RMG-database](https://github.com/ReactionMechanismGenerator/RMG-database/issues): For issues related to the data available to RMG
+    * [RMG-website](https://github.com/ReactionMechanismGenerator/RMG-website/issues): For issues related to the [RMG website](https://rmg.mit.edu)
+
+
+### **Did you write code that fixes a bug or adds a new feature?**
+
+* Open a new GitHub PR to merge into the main branch. Make sure the PR clearly describes the problem + solution. If applicable, include the relevant issue.
+
+* Your PR must pass unit tests, regression tests, and code coverage, and receive approval from at least one reviewer before it can be merged in.
+
+* If you wrote a new feature, please [add unit tests](https://github.com/ReactionMechanismGenerator/RMG-Py/tree/main/test/rmgpy). We currently use [pytest](https://docs.pytest.org/en/stable/) for our unit testing.
+
+* If you wrote a significant new feature, please add a regression test:
+    * First, please create an input file that includes your new feature. Ensure `saveEdgeSpecies` is set to `True` so that the edge model will also be saved to a file. If applicable, include diverse sets of input conditions to test compatibility with other features.
+    * Generate the reaction mechanism corresponding to the input file. Ensure that the simulation does not take more than 15 minutes maximum. You can reduce simulation times in multiple ways, e.g. by increasing the `toleranceMoveToCore` flag.
+    * In the `test/regression` folder, create a new folder with a relevant name, and copy the RMG-Py simulation input file in this folder. Include this new folder in your PR.
+    * In `.github/workflows/CI.yml`, edit the two lists of regression tests in the `Regression Tests - Execution` and `Regression Tests - Compare to Baseline` steps to add the name of your folder. Be sure to follow BASH syntax.
+
+    * > Warning: This will __fail__ CI because of directory not found errors. This is because the baseline files used for comparison in the regression tests do not exist yet. Your PR will need to be merged by bypassing branch protection restrictions.
+
+
+### **Do you want to contribute to the documentation?**
+
+* Documentation is [hosted here](http://reactionmechanismgenerator.github.io/RMG-Py/) using [Sphinx](https://www.sphinx-doc.org/en/master/). 
+
+* The live version of the documentation is hosted on the `gh-pages` branch which is updated upon pushes to the `main` branch of RMG-Py.
+
+* To add new documentation, create or modify `.rst` (reStructuredText) files under the `documentation` directory and create a PR to push to `main`. For a primer on how to write `.rst` markup, please [check out the Sphinx documentation.](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html)
+
+* Please test the documentation on a local build (e.g., via `make html` in the `documentation` directory) before pushing changes.
+
+### **Do you have questions?**
+
+* Email us at [email protected].
+
+###  **Best practices for PRs**
+
+* Rebase to the main branch before working, to avoid merge conflicts.
+
+* Keep PRs small and aim to merge quickly.
+
+* Commits should be specific and as small as required; commit messages should be descriptive and as long as required. Commit messages should explain *why* the change is needed. We recommend following [these guidelines.](https://wiki.openstack.org/wiki/GitCommitMessages) 
+
+* Submit a PR only when the code is polished and ready for review. Consider opening a draft PR for work in progress that requires collaborator input.
+
+* Please follow the [PEP8 Python style guide.](https://peps.python.org/pep-0008/)
+
+Thank you!
+
+RMG Developers

documentation/source/theory/rmg/dynamics.rst

@@ -67,31 +67,31 @@ for movement from surface to bulk core based on flux or dynamics criterion.
 Key Parameters for Dynamics Criterion and Surface Algorithm
 ===========================================================
 
-* **toleranceMoveEdgeReactionToCore**
+* ``toleranceMoveEdgeReactionToCore``
 
   An edge reaction will be pulled directly into the bulk core if its dynamics number
   ever exceeds this value.
 
-* **toleranceMoveEdgeReactionToSurface**
+* ``toleranceMoveEdgeReactionToSurface``
 
   An edge reaction will be pulled into the surface if its dynamics number
   ever exceeds this value.
 
-* **toleranceMoveEdgeReactionToCoreInterrupt**
+* ``toleranceMoveEdgeReactionToCoreInterrupt``
 
   When any reaction's dynamics number exceeds this value the simulation will be interrupted.
 
-* **toleranceMoveEdgeReactionToSurfaceInterrupt**
+* ``toleranceMoveEdgeReactionToSurfaceInterrupt``
 
   When the dynamics number of any reaction that would be valid for movement to the surface
   exceeds this value the simulation will be interrupted
 
-* **toleranceMoveSurfaceReactionToCore**
+* ``toleranceMoveSurfaceReactionToCore``
 
   A surface reaction will be pulled into the bulk core if its dynamics number
   ever exceeds this value.  Note this is done on the fly during simulation.
 
-* **toleranceMoveSurfaceSpeciesToCore**
+* ``toleranceMoveSurfaceSpeciesToCore``
 
   A surface species will be pulled into the bulk core if it's rate ratio
   ever exceeds this value.  Note this is done on the fly during simulation.

documentation/source/theory/rmg/prune.rst

@@ -12,30 +12,30 @@ in order to achieve both low memory consumption and mechanism accuracy. Pruning
 Key Parameters in Pruning
 =========================
 
-* toleranceKeepInEdge
+* ``toleranceKeepInEdge``
 
-  Any edge species to prune should have peak flux along the whole conversion course lower than toleranceKeepInEdge :math:`*` characteristic flux. Thus, larger values will lead to smaller edge mechanisms.
+  Any edge species to prune should have peak flux along the whole conversion course lower than ``toleranceKeepInEdge`` :math:`*` characteristic flux. Thus, larger values will lead to smaller edge mechanisms.
 
-* toleranceMoveToCore
+* ``toleranceMoveToCore``
 
-  Any edge species to enter core model should have flux at some point larger than toleranceMoveToCore :math:`*` characteristic flux Thus, in general, smaller values will lead to larger core mechanisms.
+  Any edge species to enter core model should have flux at some point larger than ``toleranceMoveToCore`` :math:`*` characteristic flux. Thus, in general, smaller values will lead to larger core mechanisms.
 
-* toleranceInterrupSimulation
+* ``toleranceInterruptSimulation``
 
-  Once flux of any edge species exceeds toleranceInterruptSimulation :math:`*` characteristic flux, dynamic simulation will be stopped.
+  Once flux of any edge species exceeds ``toleranceInterruptSimulation`` :math:`*` characteristic flux, dynamic simulation will be stopped.
   Usually this tolerance will be set a very high value so that any flux's exceeding that means mechanism is too incomplete to continue 
   dynamic simulation.
 
-* maximumEdgeSpecies
+* ``maximumEdgeSpecies``
 
   If dynamic simulation isn't interrupted in half way and total number of the edge species whose peak fluxes are higher than 
-  toleranceKeepInEdge :math:`*` characteristic flux exceeds maximumEdgeSpecies, such excessive amount of edge species with lowest peak fluxes will be pruned.
+  ``toleranceKeepInEdge`` :math:`*` characteristic flux exceeds ``maximumEdgeSpecies``, such excessive amount of edge species with lowest peak fluxes will be pruned.
 
-* minCoreSizeForPrune
+* ``minCoreSizeForPrune``
 
   Ensures that a minimum number of species are in the core before pruning occurs, in order to avoid pruning the model when it is far away from completeness.  The default value is set to 50 species. 
 
-* minSpeciesExistIterationsForPrune
+* ``minSpeciesExistIterationsForPrune``
 
   Set the number of iterations an edge species must stay in the job before it can be pruned.  The default value is 2 iterations.  
 
@@ -46,20 +46,20 @@ How Pruning Works
 
   The goal of pruning is to delete those "useless" edge species. So "usefulness" should be defined and it's natural to have flux as a 
   criterion for "usefulness". Since flux changes with reactant conversion, peak flux is chosen here to make decision of pruning or not.
-  Every time pruning is triggered, edge species with peak flux lower than toleranceKeepInEdge :math:`*` characteristic flux will be deleted.
+  Every time pruning is triggered, edge species with peak flux lower than ``toleranceKeepInEdge`` :math:`*` characteristic flux will be deleted.
 
 .. figure:: fluxDiagramWithTolerance.png
 
-  However, pruning is not always triggered because of toleranceInterruptSimulation. As mentioned above, in order to prune, RMG needs to figure out
+  However, pruning is not always triggered because of ``toleranceInterruptSimulation``. As mentioned above, in order to prune, RMG needs to figure out
   the peak flux of each edge species, which requires dynamic simulation to complete. If some run of dynamic simulation is terminated in half way
-  by toleranceInterruptSimulation, pruning is rejected although there might be some edge species with peak fluxes lower than 
-  toleranceKeepInEdge :math:`*` characteristic flux. Since pruning requires to complete dynamic simulation, setting toleranceInterruptSimulation to be positive infinity, 
-  as an extreme case, means always enabling pruning. Another extreme case would be that it has same value as toleranceMoveToCore where 
+  by ``toleranceInterruptSimulation``, pruning is rejected although there might be some edge species with peak fluxes lower than 
+  ``toleranceKeepInEdge`` :math:`*` characteristic flux. Since pruning requires to complete dynamic simulation, setting ``toleranceInterruptSimulation`` to be positive infinity, 
+  as an extreme case, means always enabling pruning. Another extreme case would be that it has same value as ``toleranceMoveToCore`` where 
   no pruning occurs.
 
-  In summary, each run of dynamic simulation will proceed towards terminationConversion unless some flux exceeds 
-  toleranceInterruptSimulation :math:`*` characteristic flux.Following complete simulation is the pruning of edge species whose flux is not high enough be kept
-  in the edge, which is followed by pruning of excessive amount of edge species to make sure total edge species number is no greater than maximumEdgeSpecies.
+  In summary, each run of dynamic simulation will proceed towards ``terminationConversion`` unless some flux exceeds 
+  ``toleranceInterruptSimulation`` :math:`*` characteristic flux. Following complete simulation is the pruning of edge species whose flux is not high enough be kept
+  in the edge, which is followed by pruning of excessive amount of edge species to make sure total edge species number is no greater than ``maximumEdgeSpecies``.
 
 
 

documentation/source/users/arkane/credits.rst

@@ -9,7 +9,7 @@ Project Supervisors:
 - Prof. William H. Green ([email protected])
 - Prof. Richard H. West ([email protected])
 - Prof. C. Franklin Goldsmith ([email protected])
-- Asst. Prof. Alon Grinberg Dana ([email protected])
+- Prof. Alon Grinberg Dana ([email protected])
 
 Developers: ([email protected])
 
@@ -24,10 +24,10 @@ Developers: ([email protected])
 - Dr. D.S. Ranasinghe
 - Dr. R.J. Gillis
 - Dr. A.M. Payne
-- Asst. Prof. Y.-P. Li
-- X. Dong
-- K.A. Spiekermann
-- H. Wu
+- Prof. Y.-P. Li
+- Dr. X. Dong
+- Dr. K.A. Spiekermann
+- Mr. H. Wu
 - Dr. E.E. Dames
 - Dr. Z.J. Buras,
 - Dr. N.M. Vandewiele
@@ -41,11 +41,4 @@ Developers: ([email protected])
 How to Cite
 ***********
 
-A. Grinberg Dana, M.S. Johnson, J.W. Allen, S. Sharma, S. Raman, M. Liu, C.W. Gao, C.A. Grambow, M.J. Goldman,
-D.S. Ranasinghe, R.J. Gillis, A.M. Payne, Y.-P. Li, X. Dong, K.A. Spiekermann, H. Wu, E.E. Dames, Z.J. Buras,
-N.M. Vandewiele, N.W. Yee, S.S. Merchant, B. Buesser, C.A. Class, C.F. Goldsmith, R.H. West, W.H. Green,
-"Automated reaction kinetics and network exploration (Arkane):
-A statistical mechanics, thermodynamics, transition state theory, and master equation software",
-*International Journal of Chemical Kinetics* 2023, 55(6), 300-323.
-
-DOI: `10.1002/kin.21637 <https://doi.org/10.1002/kin.21637>`_
+Please refer to the ``Arkane`` reference in the `CITATIONS.bib file <https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/CITATIONS.bib>`_.

documentation/source/users/rmg/credits.rst

@@ -16,26 +16,29 @@ Project Supervisors:
 
 Current Developers: ([email protected])
 
-- Dr. Alon Grinberg Dana
+- Prof. Alon Grinberg Dana
 - Dr. Matt Johnson
-- Yen-Ting Wang
-- Xiaorui Dong
-- Hao-Wei Pang
+- Dr. Anna Doner
 - Oscar Wu
-- Kevin Spiekermann
 - Jonathan Zheng
 - Jackson Burns
 - Nathan Morgan
+- Prof. Richard H. West
 - Prof. C. Franklin Goldsmith
-- Dr. Katrin Blondal
 - Dr. Bjarne Kreitz
+- Chao Xu
 - Chris Blais
 - Sevy Harris
 - Nora Khalil
 
 Previous Developers: 
 
+- Dr. Xiaorui Dong
+- Dr. Hao-Wei Pang
+- Dr. Kevin Spiekermann
+- Yen-Ting Wang
 - Dr. Joshua W. Allen
+- Dr. Katrin Blondal
 - Dr. Yunsie Chung
 - Dr. David Farina
 - Dr. Mark Goldman
@@ -66,25 +69,4 @@ Previous Developers:
 How to Cite
 ***********
 
-C.W. Gao, J.W. Allen, W.H. Green, R.H. West,
-"Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms",
-*Computer Physics Communications* 2016, 203, 212-225.
-
-DOI: `10.1016/j.cpc.2016.02.013 <https://doi.org/10.1016/j.cpc.2016.02.013>`_
-
-
-M. Liu, A. Grinberg Dana, M.S. Johnson, M.J. Goldman, A. Jocher, A.M. Payne, C.A. Grambow, K. Han, N.W. Yee,
-E.J. Mazeau, K. Blondal, R.H. West, C.F. Goldsmith, W.H. Green,
-"Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation",
-*Journal of Chemical Information and Modeling* 2021, 61(6), 2686–2696.
-
-DOI: `10.1021/acs.jcim.0c01480 <https://doi.org/10.1021/acs.jcim.0c01480>`_
-
-
-
-M.S. Johnson, X. Dong, A. Grinberg Dana, Y. Chung, D. Farina, R.J. Gillis, M. Liu, N.W. Yee, K. Blondal,
-E. Mazeau, C.A. Grambow, A.M. Payne, K.A. Spiekermann, H.-W. Pang, C.F. Goldsmith, R.H. West, W.H. Green,
-"The RMG Database for Chemical Property Prediction",
-*Chemical Information* 2022, 62(20), 4906–4915.
-
-DOI: `10.1021/acs.jcim.2c00965 <https://doi.org/10.1021/acs.jcim.2c00965>`_
+Please refer to the ``RMG``, ``RMG3``, and ``RMG_Database`` citations in the `CITATIONS.bib file <https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/CITATIONS.bib>`_.