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: 0.5.2
EiC: @cmarmo
Editor: @kellyrowland
Reviewer 1: @munkm
Reviewer 2: @jpmorgan98
Archive: TBD
JOSS DOI: TBD
Version accepted: TBD
Date accepted (month/day/year): TBD

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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

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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:

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[cmarmo]

Editor in Chief checks

Hi @MicahGale ! Thank you for submitting your package for pyOpenSci review.
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If some of these are missing, we will ask you to work on them before the review process begins.

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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]

Yes, @kellyrowland, @munkm that timeline works me.

[kellyrowland]

hello @jpmorgan98 @gwenchee 👋 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 .

[jpmorgan98]

@kellyrowland I am willing! However, I will not be available until Sept. 31st. Let me know if that's an issue

[MicahGale]

@jpmorgan98, I am fine with that. I understand end of the federal fiscal year crunch time.

[kellyrowland]

thanks all! I think we can assign the reviewers and then I'll check back in...

@cmarmo is that something you could do, edit the anchor post to add the reviewers? I don't think I'm able to as a drop-in editor here.

[kellyrowland]

@MicahGale @munkm @jpmorgan98 @cmarmo just FYI I will be out of office starting September 30 and will return on October 21.

[MicahGale]

@munkm, @jpmorgan98 I just wanted to check in with you both and see if you might have some time for this review now that we are in a new fiscal year.

[jpmorgan98]

@MicahGale I had this penciled in for Monday of next week. If you'd like I can move some stuff around and start tomorrow evening, sorry about the delays and thanks for your understanding!

[MicahGale]

No that's great. I just wanted to check in.

[jpmorgan98]

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Estimated hours spent reviewing:
4

Review Comments

A very well developed package with well written clear documentation. It always makes me happy to see open source work supporting radiation transport! I am not the most avid MCNP user but have had my fair share of evenings lost to unknown syntax errors in my input decks, so it's exciting to see a project address that in a well developed and thought out way.

Doc strings are very well written and integrate nicely into a well thought out documentation cite. They seem to be associated with every function at all depths.

I have some comments expanding on unchecked boxes above.

Itemized issues

• Version test not passing on local machine (github issue 572)
• Demo notebook failing on local machine (github issue 571)
• Specific requested badges (specifically: Docs building, repostatus.org badge, Python versions supported)
• Vignette from README not working locally. I have no foo.imcnp to compare too, maybe putting one in the demo directory and linking it might be nice
• Citation information needed at the bottom of the README. I am guessing this will be the JOSS paper once approved so just an acknowledgment that you'll do this once MontePy is accepted should suffice to check this off.
• Noting similar packages. You mention in the paper ARMI, WATTS, and MCNPy but they should also be mentioned on your README with a quick note about how MontePy is different.

NOTE I do not have access to an installation of MCNP. So for the purposes of this review I cannot validate that the output decks that MontePy provides, work.

You mention in the paper some of the other packages that do this but are less general purpose. I think PyNE also has some limited functionality to do this, tho I could be mistaken. Also another thing of note is that the other LANL Monte Carlo rad transport app MCATK has a built in Python interface which only further demonstrates the need for something general purpose like this for MCNP.

I also noticed that you just did a version release to 0.5.0, first off congrats, second should we change which version we are reviewing?

Great job again on such a well developed package!

[MicahGale]

Thank you @jpmorgan98 for your review and feedback!

re:version

I have been updating the submitted version with every release since this was started. However, I'm not sure if I should keep doing this though. Depending on what branch you were looking at you were either review 0.4.1 or 0.4.2devNNN (dev versions default to a patch release, so 0.4.2.devNNN became 0.5.0 on release because it was a minor release.) So I'll leave it to @kellyrowland on how we should deal with this once she is able to return.

re: Competitors.

Yes PyNE is definitely worth mentioning in the paper, and not just because Paul Wilson is my advisor. Since writing the first draft of this we have come across a lot more packages, and opened a lazy issue (433) to track these. This should be finalized prior to finalizing this review, right?

re: Validating if the MCNP input files work

Can't you just run python -m montepy -c :P. Yes this is a bit of a challenge sometimes and would require tedious manual review of the input files against the manual to see if the file makes sense. We do actually have a cyclical test where a file read-written-read to make sure nothing breaks. Obviously this isn't perfect, that it does catch a lot of low hanging fruit.

[kellyrowland]

Fair question on versioning - my experience with JOSS is that folks usually submit version X.Y which is reviewed, and then when any edits have gone in, we have the submitter cut a new release X.Z which contains the edits and then that gets an associated archive that goes with the publication. So, the JOSS publication is associated with some specific version of the software.

@MicahGale is there a pinned branch or version that you would preferably have the reviewers look at for being tagged along with the manuscript? For the JOSS review process it's generally not the case that the codebase gets a major overhaul for functionality, interface, etc. (often just manuscript edits), so any recent tag or version would be sufficient IMO. Let me know if you have any questions.

[MicahGale]

I think it should be fine if everyone reviews develop. The latest release was a minor one that added a new feature, and fixed a few bugs. We won't do a major release during this review that would remove any current functionality. So I think just keeping up with the current releases should be fine, and will reduce the amount of duplicate issues that reviewers find.

[kellyrowland]

Sounds good to me, thanks.

[kellyrowland]

hi @munkm checking in here if you're able to get started on your review. if you need to hand it off, just let me know.

[munkm]

Thanks for checking in! I'm around, just a little bit behind where I'd like to be. I will try to complete my review this week.

[MicahGale]

@jpmorgan98, I believe we have addressed all of you concerns through #578, and #573. Could you double check our develop branch and make sure we did properly address them all?

[jpmorgan98]

Great job I just marked my approval above. Great job again!

@kellyrowland: does that finalize my review or is there anything else I need to do on my end. Thanks!

[kellyrowland]

@jpmorgan98 I think that's good here, but please stay tuned just in case anything else is needed in the wrap-up stages later on.

@munkm just checking in 👋 please let me know if you need to set this down.

[MicahGale]

@kellyrowland, this week is the ANS Winter metting, and I saw that @munkm is chairing some sessions, so I don't think she'll be able to review this this week.

[kellyrowland]

Thanks for the note! I'm more active in the HPC space than the nuclear engineering space these days, so not so plugged into the immediate ANS calendar. 🙂

[munkm]

@MicahGale you were right! Last week I was busy with ANS. I work on this this week. If not M-W, then before the Monday following the holiday. I'm sorry for my delay!