Joss-reviews: [PRE REVIEW]: OpenSCM Two Layer Model: A Python implementation of the two-layer climate model
Submitting author: @znicholls (Zebedee Nicholls)
Repository: https://github.com/openscm/openscm-twolayermodel
Version: v0.1.2
Editor: @leouieda
Reviewers: @sadielbartholomew, @ashiklom
Managing EiC: Kristen Thyng
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Author instructions
Thanks for submitting your paper to JOSS @znicholls. Currently, there isn't an JOSS editor assigned to your paper.
The author's suggestion for the handling editor is @kthyng.
@znicholls 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
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All 33 comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.
: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.
For a list of things I can do to help you, just type:
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In addition, this list of people
Looking through the list, these people list climate or atmospheric science as areas so could be willing
- DamienIrving
- jtmiclat
- ritwikagarwal
- koldunovn
- eviatarbach
- arbennett
- bradyrx
- OmarShehata
- marvinjonathcn
- rchg
- andreas-h
- dhhagan
- josephhardinee
- ashwinvis
- ali-ramadhan
- rchg
- capitalaslash
- slayoo
- simonom
- rabernat
- sadielbartholomew
- sarats
znicholls
on 7 Oct 2020
To the editors, I've just read the review criteria properly. Apologies that I missed the description of effort! I am very happy to close this request if it appears to be out of scope because of its limited size. Having said that, this implementation (albeit in a different repository at the time) has already been used in the academic literature and is likely to be used again in future given the prominence of this model.
In the event that this submission is deemed out of scope, is it possible to reopen if/when we've been working on the implementation for more time and added more features or would we have to start fresh (not an overly difficult task I agree, just thought I should ask)?
znicholls
on 7 Oct 2020
@whedon check repository
kthyng
on 8 Oct 2020
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1175/JCLI-D-12-00195.1 is OK
- 10.1175/JCLI-D-12-00196.1 is OK
- 10.1175/2009JCLI3466.1 is OK
- 10.1002/2015GL064240 is OK
- 10.5194/gmd-11-2273-2018 is OK
- 10.5194/gmd-2019-375 is OK
MISSING DOIs
- 10.1007/s10584-011-0156-z may be a valid DOI for title: The RCP greenhouse gas concentrations and their extensions from 1765 to 2300
- 10.1007/s00382-019-04686-4 may be a valid DOI for title: On simple representations of the climate response to external radiative forcing
INVALID DOIs
- None
Software report (experimental):
github.com/AlDanial/cloc v 1.84 T=0.58 s (93.6 files/s, 15857.2 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 24 974 1350 3248
reStructuredText 13 135 77 193
Jupyter Notebook 4 0 2380 175
YAML 5 17 7 159
TeX 1 17 0 117
make 2 29 10 113
Markdown 4 33 0 81
DOS Batch 1 8 1 26
-------------------------------------------------------------------------------
SUM: 54 1213 3825 4112
-------------------------------------------------------------------------------
Statistical information for the repository '5791e613b1a54ddc2799fe0a' was
gathered on 2020/10/07.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Robert Gieseke 2 43 31 0.97
Zebedee Nicholls 55 6563 1003 99.03
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
Robert Gieseke 29 67.4 4.8 0.00
Zebedee Nicholls 5543 84.5 2.4 10.81
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
whedon
on 8 Oct 2020
Software report (experimental):
github.com/AlDanial/cloc v 1.84 T=0.47 s (115.5 files/s, 19564.4 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 24 974 1350 3248
reStructuredText 13 135 77 193
Jupyter Notebook 4 0 2380 175
YAML 5 17 7 159
TeX 1 17 0 117
make 2 29 10 113
Markdown 4 33 0 81
DOS Batch 1 8 1 26
-------------------------------------------------------------------------------
SUM: 54 1213 3825 4112
-------------------------------------------------------------------------------
Statistical information for the repository '0e07756652e2e9f655e0335a' was
gathered on 2020/10/07.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Robert Gieseke 2 43 31 0.97
Zebedee Nicholls 55 6563 1003 99.03
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
Robert Gieseke 29 67.4 4.8 0.00
Zebedee Nicholls 5543 84.5 2.4 10.81
@whedon invite @leouieda as editor
danielskatz
on 12 Oct 2020
@leouieda has been invited to edit this submission.
whedon
on 12 Oct 2020
👋 @leouieda - is there a chance you might be able to edit this submission?
danielskatz
on 12 Oct 2020
@danielskatz I'd be happy to 👌🏽
leouieda
on 12 Oct 2020
@whedon assign @leouieda as editor
leouieda
on 12 Oct 2020
OK, the editor is @leouieda
whedon
on 12 Oct 2020
thanks @danielskatz and @leouieda — I meant to get back to this over the weekend but didn't manage to.
kthyng
on 12 Oct 2020
👋🏽 Hi @znicholls thank you for the review suggestions!
I am very happy to close this request if it appears to be out of scope because of its limited size. Having said that, this implementation (albeit in a different repository at the time) has already been used in the academic literature and is likely to be used again in future given the prominence of this model.
I had a look at the software repository and the paper. This does seem more than "3 months of work" to me given that you have invested in a decent amount of testing and the model has been used in research already. Bare in mind that I'm not a climate scientist, though. We can investigate further if any reviewers have concerns but otherwise I'm happy to proceed with the review.
Please have a look at the "missing DOIs" report above and add the relevant DOIs to your paper.bib. I have also submitted a PR with some quick fixes to the paper format.
leouieda
on 12 Oct 2020
:wave: @sadielbartholomew @kdorheim @bradyrx would you be willing to review this submission for JOSS? Reviews are done entirely through GitHub (issues and pull requests). These are the reviewer guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html
This is a pre-review issue in which I will assign reviewers. Once there are sufficient reviewers (usually 2-3), I will open a new issue where the review will take place. If you agree to review, you will be notified when the review process if formally started.
If you are not able to review at this time, please let me know if you have recommendations for other reviewers. Please recommend without mentioning a handle to avoid notifying the person (e.g., you would refer to me as leouieda instead of @leouieda). This way we attempt to reduce the number of people who are subscribed to this thread.
leouieda
on 12 Oct 2020
leouieda unfortunately I am unable to review this at the moment given other time commitments. I am not sure if he is registered to review for JOSS but Alexey Shimnokol (https://github.com/ashiklom) comes to mind as someone who has worked on SCMs, is a good reviewer, a python user, and champion of open source science.
kdorheim
on 12 Oct 2020
Thanks leouieda. I am very busy this October but in November I will have a lot more free time. I am happy to review assuming the editor and authors wouldn't mind waiting on my review until early November, but that is still a number of weeks away so I appreciate that may be longer than reasonable or desired to wait.
So feel free to assign me to review or not depending on timescales required. Certainly if someone else is free to review more quickly, it would be better to choose them.
sadielbartholomew
on 12 Oct 2020
@kdorheim thank you for the suggestion! I'll ping Alexey and see if he's available/interested.
@sadielbartholomew early November is still within the 4-6 weeks we usually recommend for review turn around. I'm happy to assign you as reviewer 🙂
leouieda
on 12 Oct 2020
:wave: @ashiklom would you be willing to review this submission for The Journal of Open Source Software (JOSS)? JOSS is a developer-friendly open-access journal and reviews are done entirely through GitHub (issues and pull requests). These are our reviewer guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html Please see the previous comments in this thread for more context. The software submission is https://github.com/openscm/openscm-twolayermodel Thank you for your time 🙂
leouieda
on 12 Oct 2020
Sure, I'd be happy to review this! To confirm, the review deadline is in the first week or two of November? And, there will be a separate GitHub issue where I do the review?
ashiklom
on 12 Oct 2020
@ashiklom thank you for agreeing to review! 🎉 We don't have strict deadlines but we aim to have the reviews done or well under way within 4-6 weeks. Of course, these are not normal times for most of us so it's completely understandable if you require longer. There will be a separate issue for the review and I'll post some instructions there as soon as I start the review.
leouieda
on 22 Oct 2020
@whedon generate pdf
leouieda
on 22 Oct 2020
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
whedon
on 22 Oct 2020
@whedon assign @sadielbartholomew as reviewer
leouieda
on 22 Oct 2020
OK, @sadielbartholomew is now a reviewer
whedon
on 22 Oct 2020
@whedon add @ashiklom as reviewer
leouieda
on 22 Oct 2020
OK, @ashiklom is now a reviewer
whedon
on 22 Oct 2020
@whedon start review
leouieda
on 22 Oct 2020
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2766.
whedon
on 22 Oct 2020
@ashiklom @sadielbartholomew thank you both for offering your time to review this submission! @znicholls I have now started the review in #2766. I'll post some instructions there. From now on, please use that issue instead.
leouieda
on 22 Oct 2020
@ashiklom @sadielbartholomew if this is your first time reviewing for JOSS, you should get an invitation to join the openjournals GitHub organization (usually by email). Please accept the invitation so that you can edit your checklists in the JOSS review. The invitation will expire so it's best to do this as soon as possible. If you have any issues, we can issue the invitation again (just let me know).
leouieda
on 22 Oct 2020
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Most helpful comment
Sure, I'd be happy to review this! To confirm, the review deadline is in the first week or two of November? And, there will be a separate GitHub issue where I do the review?