[PRE REVIEW]: MDCraft: A Python assistant for performing and analyzing molecular dynamics simulations of soft matter systems

[editorialbot]

Submitting author: @pw0908 (Pierre Walker)
Repository: https://github.com/bbye98/mdcraft
Branch with paper.md (empty if default branch): main
Version: v1.1.0
Editor: @srmnitc
Reviewers: @raynol-dsouza, @aazocar
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/fa65dcce626157b3f2b0b396c43adfed/status.svg)](https://joss.theoj.org/papers/fa65dcce626157b3f2b0b396c43adfed)

Author instructions

Thanks for submitting your paper to JOSS @pw0908. Currently, there isn't a JOSS editor assigned to your paper.

@pw0908 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.13 s (868.9 files/s, 196582.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          54           4293           8453           7681
C++                              8            139             52           1020
CUDA                             5            199             63           1006
Markdown                         6            134              0            360
C/C++ Header                    10            107            345            300
TeX                              1             13              0            210
Jupyter Notebook                 3              0            384            177
CMake                            4             60             51            156
YAML                             5             12             21            135
SWIG                             1             19             11             90
TOML                             1              2              0             36
SVG                              4              0              0             24
reStructuredText                 7             51            142             20
Bourne Shell                     2              2              0             10
CSS                              1              0              0              8
JSON                             1              0              0              4
INI                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                           114           5031           9522          11240
-------------------------------------------------------------------------------

Commit count by author:

    38	bbye98
     5	pw0908
     2	Benjamin Ye

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/1.457481 is OK
- 10.1063/1.479595 is OK
- 10.1063/1.3216473 is OK
- 10.1021/acs.macromol.0c02001 is OK
- 10.1371/journal.pcbi.1005659 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1002/jcc.21787 is OK
- 10.1016/j.bpj.2015.08.015 is OK
- 10.1021/acs.macromol.3c02437 is OK
- 10.1021/acs.langmuir.3c03640 is OK
- 10.21203/rs.3.rs-3643582/v1 is OK
- 10.48550/ARXIV.2403.08148 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 767

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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[Kevin-Mattheus-Moerman]

@editorialbot invite @srmnitc as editor

[editorialbot]

Invitation to edit this submission sent!

[pw0908]

Hi! I am submitting on behalf of @bbye98.

I also recommend the following reviewers:

1. Joe Greener (jgreener64)
2. Peter Eastman (peastman)
3. Lorenzo Rovigatti (lorenzo-rovigatti)
4. Jakub Krajniak (jkrajniak)

[srmnitc]

@editorialbot assign me as editor

[editorialbot]

Assigned! @srmnitc is now the editor

[srmnitc]

@bbye98 @bbye98 Thanks for this nice submission, I will be handling editor here. The next step would be to find some reviewers. Thank you for your reviewer suggestions. I will also take a look, and start finding some reviewers in the next few days. Meanwhile feel free to ask any questions that you might have.

[pw0908]

Thank you @srmnitc! Are we allowed to help with contacting reviewers? I’ve seen in a few other submissions we '@‘ them on the GitHub issue.

[srmnitc]

Thank you @srmnitc! Are we allowed to help with contacting reviewers? I’ve seen in a few other submissions we '@‘ them on the GitHub issue.

@pw0908 You can suggest withwithout @ here, and I will contact them. That would be the way to go.

[pw0908]

Just to confirm, you'd be fine with me @{username} directly?

[srmnitc]

Just to confirm, you'd be fine with me @{username} directly?

I realise I said 'with' instead of 'without'; sorry! I edited my comment above now. Please suggest only without @, and I will contact them. Sorry for the confusion, thanks again!

[pw0908]

Ok! I think the four I suggested are still suitable. If you need anymore I can look for alternatives.

[srmnitc]

@pw0908 meanwhile, the user guide does not seem to have any content at the moment, could you please take a look, or point me to where we I can find some examples?

[pw0908]

@srmnitc Oh, we need to update this. We have added examples as part of the quick start page: https://mdcraft.readthedocs.io/en/latest/notebooks/getting_started/quick_start.html

We were going to populate the User guide with the content from this repository, which is for a separate paper: https://github.com/bbye98/gcme

The API docs are very rigorous however.

[srmnitc]

@editorialbot add @raynol-dsouza as reviewer

[editorialbot]

@raynol-dsouza added to the reviewers list!

[srmnitc]

@peastman @lorenzo-rovigatti would any of you have time and be willing to review this submission for JOSS? As you might know, we carry out our checklist-driven reviews here in GitHub issues and follow these guidelines. Thanks for your time!

[lorenzo-rovigatti]

Hi! This looks like a great submission that aligns well with my expertise (and interests...), but unfortunately I'm rather fully booked right now. Feel free to ping me again if you can't find anyone else though!

[pw0908]

@srmnitc Some alternative reviewers: Irfan Alibay (IAlibay), Tyler Reddy (tylerjereddy) and Jeff Wagner (j-wags)

[raynol-dsouza]

Hello! If I am also allowed to suggest a reviewer: Petr Grigorev (pgrigorev) :)

[srmnitc]

👋🏽 @aazocar @pgrigorev would any of you have time and be willing to review this submission for JOSS? As you might know, we carry out our checklist-driven reviews here in GitHub issues and follow these guidelines. Thanks for your time!

[aazocar]

@srmnitc 👋🏽 Thanks for the invite! Looks interesting, I'd be happy to participate in the review process. Please let me know further steps.

[srmnitc]

Thanks a lot for agreeing to review @aazocar !

[srmnitc]

@editorialbot add @aazocar as reviewer

[editorialbot]

@aazocar added to the reviewers list!

[srmnitc]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7013.

[pgrigorev]

@srmnitc thanks a lot for the invitation and sorry for the late reply. I am afraid I cannot devote enough time to have a thorough review in coming weeks. Good luck!