MontePy Submission

[MicahGale]

Submitting Author: @MicahGale
All current maintainers: @MicahGale, @tjlaboss
Package Name: MontePy
One-Line Description of Package: MontePy is a python library for reading, editing, and writing MCNP input files.
Repository Link: https://github.com/idaholab/MontePy
Version submitted: 0.2.10
EiC: @cmarmo
Editor: @kellyrowland
Reviewer 1: @munkm
Reviewer 2: @jpmorgan98
Archive:
JOSS DOI: https://joss.theoj.org/papers/10.21105/joss.07951
Version accepted: 0.5.5
Date accepted (month/day/year): 03/19/2025

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Description

• Include a brief paragraph describing what your package does:

MontePy is a Python library for reading, editing, and writing MCNP input files. MCNP is the Monte Carlo N-Particle radiation transport code that supports 37 particle types, and is widely used in Nuclear Engineering, and Medical Physics. MontePy provides an object-oriented interface for MCNP input files. This allows for easy automation of many different tasks for working with MCNP input files. MontePy does not support MCNP output files

Scope

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  Check out our package scope page to learn more about our
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  • Data retrieval
  • Data extraction
  • Data processing/munging
  • Data deposition
  • Data validation and testing
  • Data visualization¹
  • Workflow automation
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  • Scientific software wrappers
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• Geospatial
• Education

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    • Scientists and engineers who use MCNP and know python are the primary audience. This will be mostly nuclear engineers, and medical physicists. Use cases are:

    • Automating tedious updates of simulation models (e.g., renumbering all materials to merge two models)

    • Automating generating many permutations of the model for optimization, sensitivity analysis, etc.

    • Extracting information from an existing model in a more legible way.

  • Are there other Python packages that accomplish the same thing? If so, how does yours differ?

    • There is also MCNPy, which reports to provide similar features. I have been unable to verify this as I have been unable to install it. MontePy is different by being written purely in python, and not java, and having a publicly accessible github, that anyone can open an issue for.

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[cmarmo]

Editor in Chief checks

Hi @MicahGale ! Thank you for submitting your package for pyOpenSci review.
Below are the basic checks that your package needs to pass to begin our review.
If some of these are missing, we will ask you to work on them before the review process begins.

Please check our Python packaging guide for more information on the elements
below.

• Installation The package can be installed from a community repository such as PyPI (preferred), and/or a community channel on conda (e.g. conda-forge, bioconda).
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Editor comments

MontePy is in very good shape, congratulations to all the maintainers for your hard work!

Some comments about the checklist above.

• In the documentation about the installation of a specific version : I strongly recommend to remove any manual process creating symbolic links and installing requirements in a folder. Virtual environments should always be preferred and you can install specific versions/tags/branches or commit in them with

pip install git+https://github.com/idaholab/MontePy.git@<your-version/tag/branch/commit>

• The README.md redirects to the documentation for details about the installation: may I suggest to explicitely add the command pip install? This will clarify that the package is available from pypi but not from any conda channel.
• The code of conduct is linked in contributing.md (btw thanks for expliciting the contact e-mail) but the file is missing and the link gives a "404 not found".

Minor comments not needed to start the review:

• the documentation generally moves from more readable contents to more technical and detailed contents: I would have put the API at the end of the documentation.
• wearing my data processing engineer hat, I would be grateful to have a safe default option backupping original files when overwriting ... I was checking basic usage documentation and the behaviour of your writing function really scared me.... 😅

Final note: I enjoyed this quote from your documentation 🪄

Creating a new universe is very straight forward. You just need to initialize it with a new number

[MicahGale]

@cmarmo thank you for the feedback!

I have opened this PR: idaholab/MontePy#440 to address this feedback.

In the documentation about the installation of a specific version : I strongly recommend to remove any manual process creating symbolic links and installing requirements in a folder. Virtual environments should always be preferred and you can install specific versions/tags/branches or commit in them with

These directions are old and from when this was an internal tool. I just removed them and instead pointed to using pip install montepy==<version>. Most versions are on PyPI, and those that aren't, can't be because they don't have an OSS license yet. So if someone really wants that old of a version I think they will figure it out on their own how to manage.

The README.md redirects to the documentation for details about the installation: may I suggest to explicitely add the command pip install? This will clarify that the package is available from pypi but not from any conda channel.

Added the command.

The code of conduct is linked in contributing.md (btw thanks for expliciting the contact e-mail) but the file is missing and the link gives a "404 not found".

Corrected this and actually added a boilerplate code of conduct.

the documentation generally moves from more readable contents to more technical and detailed contents: I would have put the API at the end of the documentation.

Good point. I updated the index to list the API documentation last.

wearing my data processing engineer hat, I would be grateful to have a safe default option backupping original files when overwriting ... I was checking basic usage documentation and the behaviour of your writing function really scared me.... 😅

This warning was written when MontePy used to discard user formatting and comments, which is no longer the case. write_to_file has no default option that would override the original file. I think now the only real risk with overwriting the original file is having a script that is buggy and accidentally changing the model. I changed the warning to discourage this sort of workflow for making script development easier.

After more consideration (mostly from others) I think this behavior should be changed, and an issue has been opened: idaholab/MontePy#442.

Final note: I enjoyed this quote from your documentation 🪄

Creating a new universe is very straight forward. You just need to initialize it with a new number

I forget sometimes about how silly the concept of universes are in these models is sometimes especially when working with them.

[cmarmo]

Thank you @MicahGale for your prompt response to my comments.
Let me know when your PR is merged so I can start looking for an editor.

[MicahGale]

Ok this PR has been merged.

[cmarmo]

Thank you @MicahGale !
Your package looks ready for review to me.

I noticed that you submitted to JOSS independently (see openjournals/joss-reviews#6977): may I suggest to merge the two submissions, as pyOpenSci has a partnership with JOSS.
This will also lower the pression on our two communities, as both pyOpenSci and JOSS are based on volounteer engagement.
If you are ok with that I can comment on the related JOSS issue and we can follow up here.

[MicahGale]

Yes let's merge them if that makes sense. I just did things in a bit of a different order.

[cmarmo]

Hello @MicahGale , I'm glad to announce that @kellyrowland has accepted to be editor for the MontePy review.
Thank you so much Kelly!

I'm letting her introduce herself here and I wish to all of you a happy review process! 🚀 :

[kellyrowland]

Hi -

This is my first engagement with pyOpenSci, so thanks in advance for your patience. 😅 I've been an editor for JOSS for a few years, and that's how we've arrived here.

@MicahGale before I get started on finding reviewers, I see there are a set of JOSS-related boxes to tick off - can you take a look at those and check them off/open PRs/etc. and let me know about the status of those items?

Thanks for tagging some possible reviewers over in openjournals/joss-reviews#6977 - I'll ping folks in this issue and make a post with the editor template once we've got two reviewers on board.

-Kelly

[MicahGale]

Thank you for being willing to do this new role for this package. :)

Ok I updated the JOSS section accordingly.

The one concern I had was about getting a DOI for archiving the software. Under the JOSS guidelines it seems like that's a final step?

Upon successful completion of the review, authors will make a tagged release of the software, and deposit a copy of the repository with a data-archiving service such as Zenodo or figshare, get a DOI for the archive, and update the review issue thread with the version number and DOI.

Are you alright with following the JOSS order for this?

[kellyrowland]

Good point, thanks. I think archiving the release and getting a DOI is a logical last step since it's often the case that changes are made to the software during the review process.

[kellyrowland]

@cmarmo it looks like the remaining "Core GitHub repository Files" item is set - could you please take a look and check that off at your earliest convenience? I think I should be set to ping potential reviewers at that point.

[cmarmo]

Done! Thank you Kelly!

[kellyrowland]

hi @paulromano @munkm 👋 would you be interested in and available to review this pyOpenSci submission?

the reviewer template that you would use can be seen at https://www.pyopensci.org/software-peer-review/appendices/templates.html#peer-review-template .

if you're not available for the review, could you suggest other potential reviewers for the package?

[munkm]

I would love to! But I won't be able to review until after September 15th. Will that be an issue? If it is, I'll suggest an alternate.

[kellyrowland]

@MicahGale does the above timeline work for you?

[MicahGale]

@munkm I don't think you get notified when we tag you in the MontePy repository. I have taken a first draft at addressing your comments. When you are able to, could you please review them? I just wanted to link to the PRs here as well for your convenience:

• Address review comments from PyOpenSci idaholab/MontePy#647
• Add munkm feedback to JOSS paper idaholab/MontePy#649

[munkm]

Hey @MicahGale thanks for tagging me there and here. I did get notified by your tags, but this extra linking is helpful. I'll review them asap.

[kellyrowland]

hi @munkm have you been able to take a look at the recent round of updates?

[munkm]

Hi @MicahGale and @kellyrowland ! I've reviewed the PRs that were submitted to MontePy by @MicahGale and they satisfy all of my comments from review. I'm happy to approve with those additions included.

@MicahGale I think I've reviewed the PRs that you tagged me in, but let me know if I missed anything.

[MicahGale]

@munkm, no you got them all. Thank you for the review!

[MicahGale]

@kellyrowland it sounds like we've got all the review comments addressed.

What are the next steps? I think we might be ready for step 6: package acceptance.

[kellyrowland]

yep, I think it's about that time. 🚀

@MicahGale please create a new Github release with the changes if you haven't already; ideally since we're going to do the companion JOSS paper this will be the release and version to which the archive and DOI that you'll create will match up with so that's all done in one fell swoop. I'll note here that we ask authors to put the archive on somewhere like Zenodo and then post the DOI (that can go in the JOSS issue and we can follow up there on JOSS specifics).

@cmarmo are there any steps for you to take now?

[MicahGale]

@kellyrowland I found this checklist/template in the editor guide for you. It looks like there's just a few things to wrap up.

I am checking with our organization admin on github for adding the Zenodo integration, and will hopefully get that figured out in the next few days. I'll be doing the release to finalize this review later today (that will be version 0.5.5).

Update: 0.5.5 has been released to PyPI. TODO list:

• enable Zenodo
• publish draft release on GH
• Publish to conda-forge

[MicahGale]

MontePy has been published on Zenodo:

Note: however, we had a previous DOI for MontePy, so the DOI link does not go to Zenodo. The Zenodo archive is here. Is this an issue?

[cmarmo]

@cmarmo are there any steps for you to take now?

Not really... :) a part thank you all for all your work!
I am not sure though that the zenodo archive is necessary as MontePy was already declared on the U.S. Department of Energy Office of Scientific and Technical Information archive...
I guess it's up to the author to decide which one they prefer keeping updated.

[lwasser]

hi everyone 👋🏻 i wasn't able to find the acceptance checklist here to finish updating the YAML file and close this review. i'm going to paste it here. (UNLESS I MISSED IT) and then ask for some help filling it out 🚀 (We parse these issues so this information is needed!!)

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🎉 MontePy has been approved by pyOpenSci! Thank you @MicahGale, @tjlaboss for submitting MontePy and many thanks to @munkm @jpmorgan98 for reviewing this package! 😸

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[lwasser]

@MicahGale @kellyrowland can you kindly fill me in here.
✅ I think the package was accepted on 19 march. But I also see that it went through JOSS.
✅ it looks like zenodo was added to the top and the version is 0.5.5 (thank you Micah!
✅ it also looks like you filled out the post survey -- THANK YOU. ✨

I think we are in good shape. i've added the JOSS doi, version accepted etc to the yaml header!

[lwasser]

@MicahGale and EVERYONE involved in this review, if you are interested in joining our slack (if you aren't already there!) please email me at leah at pyopensci.org and i'll shoot you a link! Thank you for all of your collective time in running this review!! 🚀 i hope that you are all well and taking good care of yourselves during these tricky times. 💓

[MicahGale]

Thank you @lwasser for finishing this up, and your support. I see that you have mention of a promotion blog post. Going through the blogs I haven't seen any recent package blogs. Is this still a thing? If so is there any guide on the process for this?

[lwasser]

hi @MicahGale of course!! Blog posts are definitely still a thing and we welcome you to submit one!

• Here is an overview of how to submit one to us .
• Here is a blog post submitted a few months ago as an example.

If you have any questions, feel free to ask here OR you can also ask in Slack in our #software-review channel.
I'm open to updating our docs if you have questions so please do ask if things in the docs could be more clear!