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Sign up[REVIEW]: MetSim: A Python package for estimation anddisaggregation of meteorological data #2042
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Chilipp, @dsryberg it looks like you're currently assigned to review this paper 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:
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Thanks @sjpfenninger! I am busy this week with other appointments, but I will do the review on monday in a week. |
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Hey everyone! My apologies for the delay! I am done with the review and I highly appreciate your work here! MetSim seems to be a very valuable tool for downscaling meterology and I hope that you will provide a methodologic paper (i.e. where you describe the scientific details of your method) at some point as well! The code-base and the documentation of this package is in a good condition and I could install and run the software on my local laptop (Linux). I did not try it on OS X and Ubuntu, and the authors do not state anything about OS-specific requirements (which is something that could be added to the installation instructions). I came across UW-Hydro/MetSim#200 and UW-Hydro/MetSim#201 during the review, and besides that, I have the following comments with reference to the checklist above:
In the paper you state:
In what sense does MetSim improve the performance compared to the previous tools?
The documentation of the
There are tests but it is not described in the documentation, how to run them. This should be mentioned somewhere (e.g. the README file, in the installation instructions or in the Contribution guidelines). I also strongly recommend to measure the coverage of the tests (e.g. using pytest-cov and some free service, such as codecov.io).
Is this enough for a review here? This paragraph does not describe the state of the field, but at least it highlights what is special about MetSim compared to other tools (modern workflow, improved performance, new IO routines, etc., although the statement about improving perfomance has to be revised, see Performance above).
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Hi @Chilipp - thank you for your review! I have addressed your comments above on the master branch. Thanks for catching that timestamp bug! Regarding tests: we do show how to run the tests when installing from source. I'm not 100% sure if that's enough, but because our tests rely on sample datasets, it seems like the easiest way to recommend running them. Let me know if you have other ideas. Regarding performance/state of the field: I added a bit to the performance claim, but the main takeaway is that we have implemented scalable parallelism, which is why we included a section on it. For the section on the state of the field, we hope it is clear that MetSim really does not aim to implement any new methods, but simply improve the infrastructure of some of the common methods that already existed in ad-hoc frameworks. |
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Hey @arbennett! Thanks for your quick actions!
Can you point me to the URL? I could not find it, neither in the installation instructions in the docs nor in the README
Thanks for the clarification! Otherwise, only the part about State of the field is unclear for me (see my comment above @sjpfenninger) |
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@Chilipp I updated the readme so that the line containing |
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Ha, thanks @arbennett. Sorry, I must have overlooked that line |
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@Chillipp thanks for the review and @arbennett thanks for addressing them so rapidly! @arbennett can you make sure to address the point raised about covering State of the field -- i.e., referring to other published packages that MetSim is comparable, complements, or goes beyond? From your response above it sounds like this kind of code is usually set up on an ad-hoc basis and there are no published packages - if so, I would also point that out in the paper. |
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@dsryberg looking forward to your review as well! |
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Thanks @sjpfenninger - I have updated the text to include a paragraph discussing the state of the field! |
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Thanks @arbennett! For me, this paper is ready for publication @sjpfenninger |
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Hi all! Sorry for the delay/confusion on my part. I have now also completed the review, but I am unable to adjust the checklist since I cannot complete this step:
I am told that the invitation has expired. Is this easy to fix? |
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I've just re-invited you. The link at https://github.com/openjournals/joss-reviews/invitations should work again now. |
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Unfortunately I am still told "Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account." Although I have also made sure I am logging into the account by trying this on three different devices |
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Can you try again right now @dsryberg? |
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Everything seems to be working now. I will input my comments now... |
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Overall: I agree that MetSim is a well structured, well documented, and sufficiently tested package, and I would definitely support it being published via JOSS. I nevertheless had a few hiccups during the review/testing process, and I also have trouble understanding who are the intended users of MetSim and what issue it is meant to resolve. I also suggest reworking some of the example scripts, as aspects of these failed for me. Finally, I think more detail should be given regarding MetSim's "Disaggregation of daily simulation values to sub-daily timesteps". I'll go into more detail below: Functionality
Documentation
Software paper
Other thoughts
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@whedon generate pdf |
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@dsryberg thanks for the thorough review! I have updated the text of the paper as well as the documentation here to reflect the algorithms used to disaggregate. The more recent version of the article proof contains additional text about the state of the field, particularly with respect to MTCLIM and VIC. Regarding your point number 1, I want to be clear that we aren't trying to say that MetSim is preferable to something like ERA5, but is complementary. MetSim can be used to generate sub-daily timeseries when something like ERA5 cannot be used (pre-1950, smaller spatial scales, etc). This actually brings up your point 3 as well. MetSim can be used at any spatial scale or mesh arrangement. I have also added a sentence to the paper to address this. I have also updated the tutorial setup so that the Pandas error no longer occurs. |
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@sjpfenninger - I just released a new version, 2.2.1, to fix the timestamp bug as well as another bug found by a user when simulating polar regions. Is is possible to update the version for this paper? @dsryberg - Thanks for the followup. I have released a new version to deal with the bug you describe in 4, along with an additional bug. On the topic of tests, we don't have much bandwidth to improve the tests at this time. Specifically, for the time it takes to run the tests, I agree it is longer than necessary, but only a minor detriment in our view. Improving the For the examples, this was the reason we came up with the tutorial in a separate repo with a Binder setup for interactive use, as well as a filmed walkthrough (which I finally just updated the tutorial repo to link to). It provides background as well as some further exposition about how/why things are set up. |
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@arbennett Thanks for the detailed response. In my opinion, the bug I came across was the most crucial issue to fix, so thanks for dealing with that. I've also just checked out the video walkthrough, and it is definitely very informative and well made. Maybe eventually this information should be put into a text form (so that one doesn't need to search through a 1.2 hr video to find the information they need) but, for the time being, I think it is sufficient. For the other issues, I think opening an issue for future improvements to the testing and examples is a good solution for now. After all, continued development is within the spirit of opensource software :) With that being said, @sjpfenninger, I am satisfied with the state of this software and I support it being published within JOSS. Please let me know if there is anything more you need from me? |
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Dear authors and reviewers We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required. Thanks in advance for your understanding. Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team. |
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@dsryberg and @Chilipp thanks to both of you for the really constructive reviews! I definitely feel like this whole process has made MetSim more accessible and uncovered a couple of bugs that are now fixed. @sjpfenninger - let me know if there's anything else to do whenever you get around to looking at this again. @arfon (and really the rest of you) - I just wanted to say how nice this review format is, I really appreciate the workflows and how clearly laid out everything is. This is my first submission to JOSS and the experience has been really pleasant! |
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@whedon generate pdf |
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@arbennett - I found an issue with your figure labels (Pandoc numbers these automatically). UW-Hydro/MetSim#214 fixes this. I'm not sure if @sjpfenninger is online currently but I'd like to give him a little time to wrap make his final checks on this before handing it off to the EiCs for publishing. |
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@arbennett Apologies for the delay and thanks for your work addressing the reviewer comments. It looks like this is ready for acceptance. Just one quick question - you mentioned updating the version, but I'm not sure what you mean, can you clarify? |
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@sjpfenninger Up on the header of this review it has: Version: v2.2.0 I'm wondering if it's possible/necessary to change this to v2.2.1 since we've fixed some bugs since submission. It seems it's not really referenced in the paper or my submission on the JOSS website so maybe this isn't needed. |
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@whedon generate pdf |
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@whedon set version as v2.2.1 |
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I'm sorry human, I don't understand that. You can see what commands I support by typing:
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@whedon set v2.2.1 as version |
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OK. v2.2.1 is the version. |
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@whedon check references |
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@arbennett Almost there, thanks for your patience. I have updated the version to v2.2.1. I've also noticed a couple small issues with the bibliography:
Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive. For the Zenodo/figshare archive, please make sure that:
Once that's done, we can move forward with accepting this! |
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@sjpfenninger - thanks again for your efforts in editing this paper. I've updated the DOIs for the dask and pandas citations. I've also uploaded to Zenodo. The DOI is 10.5281/zenodo.3728015 |
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@whedon set 10.5281/zenodo.3728015 as archive |
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OK. 10.5281/zenodo.3728015 is the archive. |
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@whedon accept |
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Check final proof If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1390, then you can now move forward with accepting the submission by compiling again with the flag
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@sjpfenninger - this is ready to go? All final proofreading is done? |
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@arbennett - I've suggested some changes in UW-Hydro/MetSim#216 and UW-Hydro/MetSim#217 |
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@danielskatz I was going to say yes, but it looks like you found a couple of remaining issues. Other than those, it's ready to go as far as I'm concerned! |
whedon commentedJan 27, 2020
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edited
Submitting author: @arbennett (Andrew Bennett)
Repository: https://github.com/UW-Hydro/MetSim
Version: v2.2.1
Editor: @sjpfenninger
Reviewer: @Chilipp, @dsryberg
Archive: 10.5281/zenodo.3728015
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Review checklist for @Chilipp
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Review checklist for @dsryberg
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