[REVIEW]: PyMPDATA v1: Numba-accelerated Pythonic implementation of MPDATA with examples in Python, Julia and Matlab

[whedon]

Submitting author: @slayoo (Sylwester Arabas)
Repository: https://github.com/atmos-cloud-sim-uj/PyMPDATA
Branch with paper.md (empty if default branch):
Version: v1
Editor: @arfon
Reviewers: @Chiil, @wdeconinck
Archive: 10.5281/zenodo.6934418

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Status

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Markdown: [![status](https://joss.theoj.org/papers/10e7361e43785dbb1b3d659c5b01757a/status.svg)](https://joss.theoj.org/papers/10e7361e43785dbb1b3d659c5b01757a)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@dmikushin & @olekravchenko, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dmikushin, @olekravchenko it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[whedon]

PDF failed to compile for issue #3896 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.11 s (659.4 files/s, 49581.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          60            586            375           3462
Markdown                         1             93              0            527
YAML                            10             33              6            257
-------------------------------------------------------------------------------
SUM:                            71            712            381           4246
-------------------------------------------------------------------------------


Statistical information for the repository '8066b4e37f38bca61302e6b0' was
gathered on 2021/11/07.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Maciej Manna                     9           196            263            1.06
Michael                         93          1687           1332            6.97
Michaeldz36                     38          3704           1752           12.60
Sylwester Arabas               334         14308           9780           55.61
kruci-no                         2            22              4            0.06
piotrbartman                     1            37           1207            2.87
prbartman                       42          3780           5245           20.83

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Michael                     109            6.5         17.4               10.09
Sylwester Arabas           4095           28.6          5.4                8.03
kruci-no                      4           18.2         14.6                0.00
piotrbartman                215          581.1         17.5                2.33

[mjsottile]

@whedon generate pdf from branch JOSS

[whedon]

Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...

[whedon]

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

[mjsottile]

@whedon check references

[mjsottile]

@whedon check references from branch JOSS

[whedon]

Attempting to check references... from custom branch JOSS

[whedon]

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

OK DOIs

- 10.1175/1520-0493(1983)111<0479:ASPDAS>2.0.CO;2 is OK
- 10.1016/0021-9991(84)90121-9 is OK
- 10.1016/0021-9991(86)90270-6  is OK
- 10.1016/0021-9991(90)90105-A is OK
- 10.1175/1520-0493(1993)121<1847:OFITDF>2.0.CO;2 is OK
- 10.1201/9780203711194 is OK
- 10.1006/jcph.1998.5901 is OK
- 10.1137/S106482759324700X is OK
- 10.1016/j.jcp.2004.12.021 is OK
- 10.1002/fld.1070 is OK
- doi:10.1002/fld.1071 is OK
- 10.1002/qj.1913 is OK
- 10.3233/SPR-140379 is OK
- 10.1016/j.jcp.2015.02.003 is OK
- 10.5194/gmd-8-1005-2015 is OK
- 10.1007/978-3-319-93864-6_5 is OK
- 10.5194/gmd-12-651-2019 is OK
- 10.1016/j.cam.2019.05.023 is OK
- 10.5194/gmd-2020-404 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1175/1520-0450(1968)007%3C0160:AOFDMA%3E2.0.CO;2 is INVALID
- 10.1175/1520-0493(1989)117%3C0102:TDSLTW%3E2.0.CO;2 is INVALID

[slayoo]

it's puzzling as the above "INVALID DOIs" seem correct, at leat both of the below URLs redirect correctly to the journal site:

• https://doi.org/10.1175/1520-0450(1968)007%3C0160:AOFDMA%3E2.0.CO;2
• https://doi.org/10.1175/1520-0493(1989)117%3C0102:TDSLTW%3E2.0.CO;2

[danielskatz]

Please make sure the DOIs are in doi entries in the bib file rather than url entries, and that they don't include the https://doi.org part

[danielskatz]

And perhaps change the characters that are being encoded for example:

10.1175/1520-0493(1989)117<0102:TDSLTW>2.0.CO;2

[slayoo]

@whedon check references from branch JOSS

[whedon]

Attempting to check references... from custom branch JOSS

[whedon]

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

OK DOIs

- 10.1175/1520-0450(1968)007<0160:AOFDMA>2.0.CO;2 is OK
- 10.1175/1520-0493(1983)111<0479:ASPDAS>2.0.CO;2 is OK
- 10.1016/0021-9991(84)90121-9 is OK
- 10.1016/0021-9991(86)90270-6  is OK
- 10.1175/1520-0493(1989)117<0102:TDSLTW>2.0.CO;2 is OK
- 10.1016/0021-9991(90)90105-A is OK
- 10.1175/1520-0493(1993)121<1847:OFITDF>2.0.CO;2 is OK
- 10.1201/9780203711194 is OK
- 10.1006/jcph.1998.5901 is OK
- 10.1137/S106482759324700X is OK
- 10.1016/j.jcp.2004.12.021 is OK
- 10.1002/fld.1070 is OK
- doi:10.1002/fld.1071 is OK
- 10.1002/qj.1913 is OK
- 10.3233/SPR-140379 is OK
- 10.1016/j.jcp.2015.02.003 is OK
- 10.5194/gmd-8-1005-2015 is OK
- 10.1007/978-3-319-93864-6_5 is OK
- 10.5194/gmd-12-651-2019 is OK
- 10.1016/j.cam.2019.05.023 is OK
- 10.5194/gmd-2020-404 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[slayoo]

thank you @danielskatz, indeed the URL escapes in the bib file were the cause - good job on the checker side!

[whedon]

👋 @dmikushin, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @olekravchenko, please update us on how your review is going (this is an automated reminder).

[mjsottile]

Hello @dmikushin and @olekravchenko - I was wondering if you needed anything in starting the reviews? I noticed that there hasn't been activity since the review was initiated. I'm happy to help or answer questions in getting started.

[mjsottile]

Hi @slayoo : it appears that the reviewers who agreed to review have vanished and are unresponsive (unless you’ve heard from them outside this review thread). This unfortunately happens sometimes. I will identify alternative reviewers to replace them so the review doesn’t go idle. Give me a day or so to find people to take their place.

[slayoo]

Thank you, @mjsottile. (I haven't heard from the reviewers)

[mjsottile]

👋 @d-chambers Would you be willing to perform a review for this submission to the Journal of Open Source Software? I identified you based on your areas of expertise as listed on the spreadsheet of potential JOSS reviewers. Please let me know if you would be interested. Thank you!

[mjsottile]

👋 @highlando Would you be willing to perform a review for this submission to the Journal of Open Source Software? I identified you based on your areas of expertise as listed on the spreadsheet of potential JOSS reviewers. Please let me know if you would be interested. Thank you!

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03896 joss-papers#3503
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03896
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[slayoo]

@arfon Thank you!
Unfortunately, we have an issue with a non-breaking space in the title that is wrongly displayed on the JOSS website here:

[arfon]

Can you remove the   from the title text please and I'll reprocess.

[arfon]

@slayoo fixed in open-atmos/PyMPDATA#338

[slayoo]

Merged, thank you, @arfon!

[slayoo]

BTW, we have an analogous problem in #4326

[arfon]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#3506

[arfon]

OK, this should be fixed now.

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03896/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03896/status.svg
   :target: https://doi.org/10.21105/joss.03896

This is how it will look in your documentation:

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[slayoo]

Thank you, @arfon !

[slayoo]

@arfon I've noticed that there were three more nbsps in the author list that also go through into the paper metadata and JOSS website:

Just removed it in the repo: open-atmos/PyMPDATA@a35a159

Let me ask for one more regeneration of the metadata.
Thank you!
Sylwester

[slayoo]

@arfon, please let us know if it would be possible to fix the remaining nbsp problems in the author list (already fixed in the project repo) - see above, thanks, Sylwester

[kthyng]

@openjournals/dev Could you take a look at this?

[slayoo]

@kthyng, is there any better place to report such issues? (this issue is closed, so it's perhaps not the best place)
Thanks,
Sylwester

[xuanxu]

@kthyng if the paper is already updated in the original repo, the reaccept command should regenerate the metadata

[kthyng]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#3530

[kthyng]

@slayoo How does your paper look now?

[slayoo]

@kthyng it's now fixed:

Thank you for your help!