[PRE REVIEW]: PyMPDATA v1: Numba-accelerated Pythonic implementation of MPDATA with examples in Python, Julia and Matlab #3855

whedon · 2021-10-26T17:23:37Z

Submitting author: @slayoo (Sylwester Arabas)
Repository: https://github.com/atmos-cloud-sim-uj/PyMPDATA
Version: v1
Editor: @mjsottile
Reviewers: @dmikushin, @olekravchenko
Managing EiC: Kristen Thyng

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

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The text was updated successfully, but these errors were encountered:

whedon · 2021-10-26T17:23:40Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

⚠️ JOSS reduced service mode ⚠️

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.

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

whedon · 2021-10-26T17:23:49Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (1078.4 files/s, 78866.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          56            551            223           3330
Markdown                         1             78              0            432
YAML                            10             32              6            248
-------------------------------------------------------------------------------
SUM:                            67            661            229           4010
-------------------------------------------------------------------------------


Statistical information for the repository '2c3f65c96231f1a0c041c758' was
gathered on 2021/10/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Maciej Manna                     9           196            263            1.11
Michael                         93          1687           1332            7.29
Michaeldz36                     38          3704           1752           13.17
Sylwester Arabas               326         13200           8991           53.58
kruci-no                         2            22              4            0.06
piotrbartman                     1            37           1207            3.00
prbartman                       42          3780           5245           21.79

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                     145            8.6         17.5                7.59
Sylwester Arabas           3698           28.0          7.1                5.25
kruci-no                     11           50.0         14.4                0.00
piotrbartman                250          675.7         17.6                2.00

whedon · 2021-10-26T17:23:49Z

PDF failed to compile for issue #3855 with the following error:

 Can't find any papers to compile :-(

kthyng · 2021-10-26T17:32:14Z

@whedon generate pdf from branch JOSS

whedon · 2021-10-26T17:32:17Z

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

whedon · 2021-10-26T17:32:25Z

PDF failed to compile for issue #3855 with the following error:

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:155:in `block in check_orcids': Problem with ORCID (0000-0003-0361-0082) for Sylwester Arabas (RuntimeError)
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:153:in `each'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:153:in `check_orcids'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:90:in `initialize'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
	from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

kthyng · 2021-10-26T17:36:52Z

Hi @slayoo! It looks a little strange to be submitting to JOSS with a fork of a repo (from piotrbartman/PyMPDATA) so just wanted to inquire about this. Are there plans to merge together ultimately?

Can you also take a look at the paper compilation error above?

kthyng · 2021-10-26T17:37:49Z

@meg-simula Are you interested in editing this submission?

kthyng · 2021-10-26T17:37:57Z

@whedon invite @meg-simula as editor

whedon · 2021-10-26T17:38:00Z

@meg-simula has been invited to edit this submission.

slayoo · 2021-10-26T18:01:09Z

Hi @slayoo! It looks a little strange to be submitting to JOSS with a fork of a repo (from piotrbartman/PyMPDATA) so just wanted to inquire about this. Are there plans to merge together ultimately?

@kthyng thank you for handling the paper!
@piotrbartman could you delete your original PyMPDATA repo and create a new fork (as we did with PySDM), thanks!

slayoo · 2021-10-26T18:02:35Z

@whedon generate pdf from branch JOSS

whedon · 2021-10-26T18:02:37Z

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

whedon · 2021-10-26T18:03:06Z

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

slayoo · 2021-10-26T18:04:05Z

Can you also take a look at the paper compilation error above?

there was a typo in the orcid ID, fixed: open-atmos/PyMPDATA@dea9545
Thanks

meg-simula · 2021-10-26T20:46:33Z

@kthyng My plate is full for the next two weeks, but I'd be happy to take it on if it can wait until after then.

kthyng · 2021-10-26T22:40:58Z

@meg-simula thanks for letting me know! I'll see if I can find someone else.

kthyng · 2021-10-26T22:41:18Z

@mjsottile Are you willing to edit this submission?

kthyng · 2021-10-26T22:41:26Z

@whedon invite @mjsottile as editor

whedon · 2021-10-26T22:41:29Z

@mjsottile has been invited to edit this submission.

mjsottile · 2021-10-26T22:52:00Z

@kthyng I am going on travel for a week. If it's OK for me to wait to start the editorial/review process until next week then I can do it.

kthyng · 2021-10-27T16:28:46Z

@mjsottile Thanks for letting me know. Yes, I think that is soon enough. I'll go ahead and assign this to you for when you return and get to it, assuming you don't mind.

kthyng · 2021-10-27T16:28:53Z

@whedon assign @mjsottile as editor

whedon · 2021-10-27T16:28:57Z

OK, the editor is @mjsottile

slayoo · 2021-10-28T23:18:54Z

Hi @slayoo! It looks a little strange to be submitting to JOSS with a fork of a repo (from piotrbartman/PyMPDATA) so just wanted to inquire about this. Are there plans to merge together ultimately?

@kthyng thank you for handling the paper! @piotrbartman could you delete your original PyMPDATA repo and create a new fork (as we did with PySDM), thanks!

this is now fixed - all forks originate from the main atmos-cloud-sim-uj repo, thanks @piotrbartman:

slayoo · 2021-11-01T20:16:36Z

@whedon generate pdf from branch JOSS

whedon · 2021-11-01T20:16:38Z

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

whedon · 2021-11-01T20:17:10Z

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

slayoo · 2021-11-01T20:17:12Z

(updated the paper.md with a figure and sample code snippets in Python, Julia and Matlab)

mjsottile · 2021-11-03T23:57:40Z

👋 @slayoo Before I get started looking for reviewers I want to check to see if you have any specific people in mind that you would recommend be invited to review. If so, please list them and I'll reach out.

slayoo · 2021-11-04T03:17:03Z

Hello, @mjsottile,
At the bottom of the PyMPDATA README file, we have listed several related projects (https://github.com/atmos-cloud-sim-uj/PyMPDATA#other-open-source-mpdata-implementations). Among contributors to these projects, and excluding folks we have co-authored with, there are the following Github users - perhaps potential reviewers:

hilaryweller0 (hilaryweller0/AtmosFOAM@947b192)
dmikushin (https://github.com/apc-llc/mpdata/graphs/contributors)
anilzen, olekravchenko (https://github.com/olekravchenko/centpy/graphs/contributors)
ThanasisMattas (https://github.com/ThanasisMattas/mattflow/graphs/contributors)
stefanmeili (https://github.com/stefanmeili/FastFD/graphs/contributors)
https://github.com/orgs/clawpack/people

Browsing through Github topics, some other projects can be found and filtered by language, e.g.:

HTH, thank you,
Sylwester

mjsottile · 2021-11-06T00:27:24Z

👋 @hilaryweller0, @dmikushin, @olekravchenko - you were suggested by the author of this submission to JOSS as potential reviewers. Would you be interested in providing a review? If you haven't reviewed for JOSS before, you can see the review criteria here : https://joss.readthedocs.io/en/latest/review_criteria.html

Please let me know if you are interested and I can add you as a reviewer to the submission.

dmikushin · 2021-11-06T01:35:16Z

Hi thanks for reaching out, I'm new to JOSS but will be happy to help!

mjsottile · 2021-11-07T02:49:25Z

@dmikushin Great - once we get another reviewer I can initiate the review. Then you'll see the checklist in the review issue that gets created. The process is pretty straightforward, and I'm happy to help or answer questions along the way.

olekravchenko · 2021-11-07T04:54:49Z

@mjsottile Hi, sure. I'm glad to take a part.

mjsottile · 2021-11-07T07:01:51Z

@whedon assign @dmikushin as reviewer

whedon · 2021-11-07T07:01:56Z

OK, @dmikushin is now a reviewer

mjsottile · 2021-11-07T07:02:22Z

@whedon add @olekravchenko as reviewer

whedon · 2021-11-07T07:02:27Z

OK, @olekravchenko is now a reviewer

mjsottile · 2021-11-07T07:03:10Z

@whedon start review

whedon · 2021-11-07T07:03:14Z

OK, I've started the review over in #3896.

whedon added the pre-review label Oct 26, 2021

whedon added the Python label Oct 26, 2021

whedon assigned mjsottile Oct 27, 2021

whedon unassigned mjsottile Nov 7, 2021

whedon assigned dmikushin and mjsottile Nov 7, 2021

whedon assigned dmikushin, mjsottile and olekravchenko and unassigned mjsottile and dmikushin Nov 7, 2021

whedon closed this as completed Nov 7, 2021

slayoo mentioned this issue Feb 18, 2022

[REVIEW]: PyMPDATA v1: Numba-accelerated Pythonic implementation of MPDATA with examples in Python, Julia and Matlab #3896

Closed

editorialbot added the Track: 3 (PE) Physics and Engineering label Aug 12, 2022

[PRE REVIEW]: PyMPDATA v1: Numba-accelerated Pythonic implementation of MPDATA with examples in Python, Julia and Matlab #3855

[PRE REVIEW]: PyMPDATA v1: Numba-accelerated Pythonic implementation of MPDATA with examples in Python, Julia and Matlab #3855

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