[PRE REVIEW]: qgs: A flexible Python framework of reduced-order multiscale climate models

[whedon]

Submitting author: @jodemaey (Jonathan Demaeyer)
Repository: https://github.com/Climdyn/qgs
Version: v0.2.0
Editor: @harpolea
Reviewers: @eviatarbach, @sadielbartholomew
Managing EiC: Daniel S. Katz

⚠️ 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.

Author instructions

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

@jodemaey if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

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]

PDF failed to compile for issue #2549 with the following error:

Can't find any papers to compile :-(

[danielskatz]

@whedeon check repository from branch joss

[danielskatz]

@whedon generate pdf from branch joss

[whedon]

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

[whedon]

👉 Check article proof 📄 👈

[danielskatz]

@whedon check references from branch joss

[whedon]

Attempting to check references... from custom branch joss

[whedon]

Reference check summary:

OK DOIs

- 10.1016/j.physd.2015.07.006 is OK
- 10.5194/gmd-9-2793-2016 is OK
- 10.1007/s13351-018-8012-y is OK
- 10.1145/2833157.2833162 is OK
- 10.5194/npg-27-307-2020 is OK
- 10.1175/1520-0469(1963)020<0130:DNF>2.0.CO;2 is OK
- 10.1111/j.1600-0870.1984.tb00230.x is OK
- 10.1109/MCSE.2011.37 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.3233/978-1-61499-649-1-87 is OK
- 10.5334/jors.151 is OK
- 10.1029/2019MS001652 is OK
- 10.1007/s10955-020-02525-z is OK
- 10.1002/qj.3594 is OK
- 10.1007/s00382-020-05313-3 is OK
- 10.3402/tellusa.v41i4.11842 is OK

MISSING DOIs

- https://doi.org/10.2142/biophys.48.324 may be missing for title: Isca
- https://doi.org/10.1017/cbo9780511617652.004 may be missing for title: Predictability: A problem partly solved

INVALID DOIs

- 10.1175/1520-0469(1987)044%3C3282:TOMEAW%3E2.0.CO;2 is INVALID
- 10.1175/1520-0493(1982)110%3C1105:DOWRQS%3E2.0.CO;2 is INVALID

[danielskatz]

@whedon check repository

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.30 s (193.9 files/s, 45590.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              4              4           2937
Python                          17           1058           1792           2480
reStructuredText                20            373            387            454
Jupyter Notebook                 8              0           3037            439
TeX                              1             34              0            385
Markdown                         1             46              0             97
DOS Batch                        1              8              1             26
YAML                             2              5              4             23
Bourne Shell                     3              8              0             15
make                             1              4              9              9
-------------------------------------------------------------------------------
SUM:                            58           1540           5234           6865
-------------------------------------------------------------------------------


Statistical information for the repository '2549' was gathered on 2020/08/05.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jonathan Demaeyer               18          6983           1653          100.00

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
Jonathan Demaeyer          5330           76.3          4.0                6.45

[danielskatz]

👋 @jodemaey

• please check the DOIs as mentioned in a previous comment - whedon is not always right, but makes suggestions. If you make changes in your bib, enter the whedon commands I used above to regenerate the PDF and recheck the references
• In the paper, in the state of the field section, please explain how your work is different/related

[danielskatz]

👋 @harpolea - The authors suggested you as the editor - are you willing to take on another submission?

[danielskatz]

@whedon invited @harpolea as editor

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[harpolea]

@danielskatz I'd be happy to edit this submission!

[harpolea]

@whedon assign me as editor

[whedon]

OK, the editor is @harpolea

[harpolea]

@jodemaey do you have any suggestions for potential reviewers? If so, then please mention them here in this thread (without tagging them with an @). This list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

[jodemaey]

We suggest Eviatar Bach (eviatarbach) and Ryan Abernathey (rabernat).

[harpolea]

@jodemaey thanks!

👋 @eviatarbach & @rabernat, would either of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[eviatarbach]

Yes, I would be happy to review!

[harpolea]

Great, thanks @eviatarbach!

[harpolea]

@whedon assign @eviatarbach as reviewer

[whedon]

OK, @eviatarbach is now a reviewer

[jodemaey]

* please check the DOIs as mentioned in a previous comment - whedon is not always right, but makes suggestions.  If you make changes in your bib, enter the whedon commands I used above to regenerate the PDF and recheck the references

Here whedon is not right about the missing DOIs. The one for the reference to the Lorenz 96 paper points in fact to a re-edition of it in 2006 and I want to point to the original 1996 paper which has no DOI. The one about Isca is also wrong. To my knowledge, the Isca model doesn't have a DOI yet.

About the DOI that whedon claims to be wrong, if I click on all of them they lead me to the correct articles. All of them contains semicolons and weird characters so I guess that whedon has a problem with that.

[eviatarbach]

Just a comment regarding Isca: there is a paper about it published in Geoscientific Model Development that should be cited.

[jodemaey]

Huh ! Yes, we have completely overlooked this one, thank you.

[jodemaey]

Do we still need to do something for the paper to move to the REVIEW phase?
We will address the comment of @danielskatz :

In the paper, in the state of the field section, please explain how your work is different/related

in the revised manuscript.

[harpolea]

@jodemaey we still require a second reviewer before we can move ahead. As rabernat has not responded, do you have any other suggestions for people who may be suitable?

[jodemaey]

Ok, we suggest Sadie Bartholomew (sadielbartholomew) then.

[harpolea]

Thanks!

👋 @sadielbartholomew, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[rabernat]

Hi all--sorry for the slow response. I have been on vacation for most of August.

I am not able to review this submission right now. Some great alternatives might be @MFJansen, @francispoulin, @navidcy, @pittwolfe, and @mbueti, all of whom have worked on pyqg.

[sadielbartholomew]

wave @sadielbartholomew, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Hi, thanks for the request and yes I am happy to review this, assuming you are happy to wait one week or so for me to start reviewing since I am currently a JOSS reviewer for another library and will need to devote a little more time to that review before I should accept another.

[harpolea]

@sadielbartholomew great, thanks! And yes, that's totally fine – we typically ask that reviews are completed within 6 weeks or so, so that should give you plenty of time to finish up with the other review first!

[harpolea]

@whedon add @sadielbartholomew as reviewer

[whedon]

OK, @sadielbartholomew is now a reviewer

[harpolea]

@whedon start review

[whedon]

OK, I've started the review over in #2597.