331 update readme

CONTRIBUTING.md

@@ -12,8 +12,8 @@ of Conduct](CODE_OF_CONDUCT.md). Please report any unacceptable behavior to mgal
 ## Resources
 
 - [GitHub Repository](https://github.com/idaholab/montepy)
-- [Documentation](https://idaholab.github.io/MontePy/)
-- [Developer's Guide](https://idaholab.github.io/MontePy/developing.html)
+- [Documentation](https://www.montepy.org/)
+- [Developer's Guide](https://www.montepy.org/developing.html)
 
 ## How to Report Bugs
 
@@ -29,12 +29,11 @@ Please review the package philosophy to see if the feature would be a good fit.
 
 ## How to Submit Changes
 
-All changes to OpenMC happen through pull requests. For a full overview of the
-process, see the developer's guide section on [Contributing to
-OpenMC](https://docs.openmc.org/en/latest/devguide/contributing.html).
+All changes to MontePy happen through pull requests. For a full overview of the
+process, see the developer's guide section on [MontePy's documentation](https://www.montepy.org/developing.html)
 
 ## Code Style
 
 Before you run off to make changes to the code, please review the [design 
-philosophy](https://idaholab.github.io/MontePy/developing.html#design-philosophy),
+philosophy](https://www.montepy.org/developing.html#design-philosophy),
 and make sure to also use [black](https://black.readthedocs.io/en/stable/index.html).

README.md

@@ -5,9 +5,14 @@
 [![license](https://img.shields.io/github/license/idaholab/MontePy.svg)](https://github.com/idaholab/MontePy/blob/develop/LICENSE)
 [![JOSS article status](https://joss.theoj.org/papers/e5b5dc8cea19605a1507dd4d420d5199/status.svg)](https://joss.theoj.org/papers/e5b5dc8cea19605a1507dd4d420d5199)
 [![Coverage Status](https://coveralls.io/repos/github/idaholab/MontePy/badge.svg?branch=develop)](https://coveralls.io/github/idaholab/MontePy?branch=develop)
-[![PyPI version](https://badge.fury.io/py/montepy.svg)](https://badge.fury.io/py/montepy)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 
+
+[![PyPI version](https://badge.fury.io/py/montepy.svg)](https://badge.fury.io/py/montepy)
+[![Docs Deployment](https://github.com/idaholab/MontePy/actions/workflows/deploy.yml/badge.svg?branch=main)](https://www.montepy.org/)
+[![PyPI pyversions](https://img.shields.io/pypi/pyversions/montepy.svg)](https://pypi.org/project/montepy/)
+
+
 MontePy is the most user friendly Python library for reading, editing, and writing MCNP input files. 
 
 ## Installing
@@ -40,41 +45,40 @@ and the Python API documentation.
 * Can quickly [access cells, surfaces, and materials by their numbers](https://www.montepy.org/starting.html#collections-are-accessible-by-number). For example: `cell = problem.cells[105]`.
 * Can quickly update cell parameters, [such as importances](https://www.montepy.org/starting.html#setting-cell-importances). For example `cell.importance.neutron = 2.0`.
 * Can easily [create universes, and fill other cells with universes](https://www.montepy.org/starting.html#universes).
-* Currently has over 430 test cases.
+* Currently has over 550 test cases.
 
 
 Here is a quick example showing multiple tasks in MontePy:
 
 ```python
-import montepy
-# read in file
-problem = montepy.read_input("foo.imcnp")
+>>> import montepy
+>>> # read in file
+>>> problem = montepy.read_input("tests/inputs/test.imcnp")
 
-# set photon importance for multiple cells
-importances = {1: 0.005,
-    2: 0.1,
-    3: 1.0,
-    99: 1.235
-}
-for cell_num, importance in importances.items():
-    problem.cells[cell_num].importance.photon = importance
-
-#create a universe and fill another cell with it
-universe = montepy.Universe(123)
-problem.univeres.append(universe)
-# add all cells with numbers between 1 and 4
-universe.claim(problem.cells[1:5])
-# fill cell 99 with universe 123
-problem.cells[99].fill.universe = universe
-
-# update all surfaces numbers by adding 1000 to them
-for surface in problem.surfaces:
-    surface.number += 1000
-# all cells using these surfaces will be automatically updated as well
-
-#write out an updated file
-problem.write_problem("foo_update.imcnp")
-
+>>> # set photon importance for multiple cells
+>>> importances = {1: 0.005,
+...    2: 0.1,
+...    3: 1.0,
+...    99: 1.235
+... }
+>>> for cell_num, importance in importances.items():
+...    problem.cells[cell_num].importance.photon = importance
+
+>>> #create a universe and fill another cell with it
+>>> universe = montepy.Universe(123)
+>>> problem.universes.append(universe)
+>>> # add all cells with numbers between 1 and 4
+>>> universe.claim(problem.cells[1:5])
+>>> # fill cell 99 with universe 123
+>>> problem.cells[99].fill.universe = universe
+
+>>> # update all surfaces numbers by adding 1000 to them
+>>> for surface in problem.surfaces:
+...    surface.number += 1000
+>>> # all cells using these surfaces will be automatically updated as well
+
+>>> #write out an updated file
+>>> problem.write_problem("foo_update.imcnp")
 ```
 
 ## Limitations
@@ -89,6 +93,39 @@ Here a few of the known bugs and limitations:
     keyword-value pairs show up after the nuclide definitions. For example:
    * `M1 1001.80c 1.0 plib=80p` can be parsed.
    * `M1 plib=80p 1001.80c 1.0` cannot be parsed; despite it being a valid input.
+
+## Alternatives
+
+There are some python packages that offer some of the same features as MontePy,
+    but don't offer the same level of robustness, ease of installation, and user friendliness.
+
+Many of the competitors do not offer the robustness that MontePy does becuase,
+    they do not utilize context-free parsing (as of 2024). 
+These packages are:
+
+* [pyMCNP](https://github.com/FSIBT/PyMCNP)
+
+* [MCNP-Input-Reader](https://github.com/ENEA-Fusion-Neutronics/MCNP-Input-Reader)
+
+* [numjuggler](https://github.com/inr-kit/numjuggler)
+
+The only other library that does utilize context-free parsing that we are aware is
+[MCNP™y](https://github.rpi.edu/NuCoMP/mcnpy). MontePy differs by being:
+* On PyPI, and can be installed via pip.
+* Only requires a python interpreter, and not a Java virtual machine. 
+* Allowing contributions from anyone with a public GitHub account
+
+
+For only writing, or templating an input file there are also some great tools out there. 
+These packages don't provide the same functionality as MontePy inherently,
+    but could be the right tool for the job depending on the user's needs.
+
+* [Workflow and Template Toolkit for Simulation (WATTS)](https://github.com/watts-dev/watts)
+* [Advanced Reactor Modeling Interface (ARMI)](https://github.com/terrapower/armi)
+
+Another honorable mention that doesn't replicate the features of MontePy,
+    but could be a great supplement to MontePy for defining materials, performing activations, etc.
+    is [PyNE --- the Nuclear Engineering Toolkit](https://pyne.io/).
 
 ## Bugs, Requests and Development
 
@@ -98,5 +135,15 @@ The system is very modular and you should be able to develop it pretty quickly.
 Read the [developer's guide](https://www.montepy.org/developing.html) for more details.
 If you have any questions feel free to ask [@micahgale](mailto:[email protected]).
 
+## Citation
+
+For citing MontePy in a publication a [Journal of Open Source Software](https://joss.readthedocs.io/en/latest/) article is under review. 
+In the meantime there is a DOI for the software from [OSTI](https://osti.gov): [DOI:10.11578/dc.20240115.1](https://doi.org/10.11578/dc.20240115.1).
+
+You can cite MontePy as:
+
+> M. Gale, T. Labossiere-Hickman, B. Carbno, A. Bascom, and MontePy contributors, "MontePy", 2024, [doi: 10.11578/dc.20240115.1](https://doi.org/10.11578/dc.20240115.1).
+
+
 
 # Finally: make objects, not regexes!