joss-reviews
joss-reviews copied to clipboard
openjournals
[REVIEW]: PyMPDATA v1: Numba-accelerated Pythonic implementation of MPDATA with examples in Python, Julia and Matlab
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: Pending
:warning: JOSS reduced service mode :warning:
Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/10e7361e43785dbb1b3d659c5b01757a"><img src="https://joss.theoj.org/papers/10e7361e43785dbb1b3d659c5b01757a/status.svg"></a>
Markdown: [](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:
- Make sure you're logged in to your GitHub account
- Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mjsottile know.
✨ 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 ✨
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 :tada:.
:warning: JOSS reduced service mode :warning:
Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.
:star: Important :star:
If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿
To fix this do the following two things:
- Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:
- You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications
For a list of things I can do to help you, just type:
@whedon commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@whedon generate pdf
PDF failed to compile for issue #3896 with the following error:
Can't find any papers to compile :-(
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
Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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
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
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
And perhaps change the characters that are being encoded for example:
10.1175/1520-0493(1989)117<0102:TDSLTW>2.0.CO;2
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
thank you @danielskatz, indeed the URL escapes in the bib file were the cause - good job on the checker side!
:wave: @dmikushin, please update us on how your review is going (this is an automated reminder).
:wave: @olekravchenko, please update us on how your review is going (this is an automated reminder).
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.
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.
:wave: @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!
👋 @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!
Hi @mjsottile, unfortunately this is pretty far outside of my area of expertise. So much so, I don't think I would be able to provide any sort of useful review of the functionality of the software (but it does look like an interesting program).
Hi @slayoo , is there a performance comparison between Numba-based PyMPDATA and any other native code implementations of your choice? That would be really interesting to see!
@dmikushin Thanks for feedback. Very good point on including a performance comparison with other implementations,
We have so far:
- looked at wall times for these tests which have direct counterparts in libmpdata++ (Github Actions used in both projects - times on similar virtual machines are available for each CI build, but these include compilation times in the case of PyMPDATA, hence not straightforward to analyse "as is", but that would be the first candidate to start the analysis from);
- analysed execution times of various MPDATA varians versus upwind times for PyMPDATA and corroborated it with such wall-time ratios from literature, see Table 2 here: https://arxiv.org/pdf/2011.14726.pdf
Comparing with libmpdata++ times is certainly doable (February/March?). Any other suggestion on what to compare with?
wave @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!
Sorry for my late reply. This is not exactly my area of expertise and I'm well occupied with other reviews right now. So I would prefer to skip this one. Please let me know, if there is an urgent need for a comment. :)
@dmikushin Thanks for providing some feedback about this submission. Did you have a chance to look at over entries from the review checklist at the top of this issue?
wave @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!
Sorry for my late reply. This is not exactly my area of expertise and I'm well occupied with other reviews right now. So I would prefer to skip this one. Please let me know, if there is an urgent need for a comment. :)
@highlando No problem. Thanks for responding!