[PRE REVIEW]: A Framework to Quality Control Oceanographic Data

[whedon]

Submitting author: @castelao (Guilherme Castelao)
Repository: https://github.com/castelao/CoTeDe
Version: 0.21.0
Editor: @kthyng
Reviewers: @jessicaaustin, @evanleeturner

Author instructions

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

@castelao 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.

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[whedon]

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This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience 😸

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[whedon]

Attempting to check references...

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1985 with the following error:

Can't find any papers to compile :-(

[Kevin-Mattheus-Moerman]

@castelao our bot @whedon cannot find the paper.md file. Where is it located?

[Kevin-Mattheus-Moerman]

@openjournals/dev the paper is here, on a different branch: https://github.com/castelao/CoTeDe/tree/joss/joss
What is the process for handling this again? Thanks

[danielskatz]

@whedon generate pdf from branch joss

[whedon]

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

[whedon]

👉 Check article proof 📄 👈

[castelao]

Thanks @Kevin-Mattheus-Moerman . I can merge the joss branch into the master if that helps.

A suggestion of reviewers: efiring and koldunovn

[whedon]

OK DOIs

-  http://dx.doi.org/10.13155/33951 is OK
- 10.1016/j.mio.2014.09.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[castelao]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

[castelao]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[castelao]

Hi @Kevin-Mattheus-Moerman and @danielskatz , do I need to do anything else or just wait? Thanks!

[danielskatz]

@castelao - the action is now for @Kevin-Mattheus-Moerman to find reviewers - you don't need to do anything more at this point

[castelao]

Great, thanks!

[danielskatz]

no, sorry, my mistake - we first need an editor - @Kevin-Mattheus-Moerman started handling this as the rotating associate editor-in-chief, not as the editor

[danielskatz]

👋 @kthyng - would you be willing to edit this submission?

[kthyng]

@whedon assign @kthyng as editor

[whedon]

OK, the editor is @kthyng

[kthyng]

@koldunovn and @efiring You've been suggested as a potential reviewer for this submission to the Journal for Open Source Software, which is largely code-review based for software with scientific applications. Are you interested in reviewing this submission? We ask for reviews within about 3 weeks if possible, and you can find more information about the process here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

[kthyng]

@castelao I see that your package is self-described as "old" and doesn't use more modern packages like pandas and xarray. As a potential user of your package but also a pythonista who is trying to stay modern in my code, can you justify this more to me and others? If there is a small amount of work that could make your package at least able to tie into these other packages, that would be hugely useful to the community using your package. A number of other packages have been updating over time to be able to, for example, recognize and use data when it is input as a pandas dataframe or xarray dataarray/dataset.

[castelao]

@kthyng, thanks for raising this point. I see CoTeDe as an old package but not outdated. Yes, I also use and appreciate pandas and xarray, so I intend to provide a direct connection to them, but that will be an optional resource, so I do not force more dependencies than required. A few groups and packages already use CoTeDe, and I do not want to impose more dependencies than necessary. For instance, to Quality Control WOD on its binary files, QC a PostgreSQL database or QC directly cnv (CTD) files (https://github.com/castelao/seabird/blob/master/docs/notebooks/QualityControl.ipynb), there is no need for more.

Note that at some point, I changed my standard from .attributes to .attrs to match xarray so that CoTeDe could read directly from a dataset (xarray object). I still need to make a few adjustments to be fully transparent, but I think it is better to keep the CoTeDe data model simple so that a dictionary of np.array or an xr.dataset would both work.

[koldunovn]

@kthyng Thank you for the nomination, but I am afraid I can't do it fast due to the huge amount of work and family commitments I have at the moment. Moreover, observations are not really my thing anymore, I am in the modeling business for over 15 years now, and the set of problems is quite different. I suggest to contact @ocefpaf @ledm @zklaus . They have experience in both python and oceanography.

[ooo]

👋 Hey @castelao...

Letting you know, @kthyng is currently OOO until Thursday, January 23rd 2020. ❤️

[kthyng]

@castelao Let's try then.

@seagrinch If you don't think you'll have time, it's probably best to not review. If we end up needing to push back anyway, though, I would probably reach out again in that case.

@gmaze JOSS is the Journal for Open Source Software, which involves largely code-review based for software with research applications. Are you interested in reviewing this submission? We ask for reviews within about 3 weeks if possible, and you can find more information about the process here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

I'm looking for experience with Python and quality controlling oceanographic data.

In total, we need two reviewers. Thanks.

[gmaze]

Hi @karthik
Yes I'd like to review this paper,
But like many I'll be very busy to the end of February because of the Ocean Sciences meeting (and many other commitments)
So I can't guarantee to finish the review within 3 weeks.
g

[castelao]

@gmaze, thanks!

[kthyng]

Hi @gmaze, that is certainly a trend right now!

@callumrollo I see you are on the JOSS reviewer list with an expertise in Marine Technology. Do you work with oceanographic data? This submission to JOSS is about quality control of ocean data so I'm looking for reviewers with this background plus Python expertise. I'm hoping to move through reviews in the next 3 weeks if possible. Any interest?

[kthyng]

@castelao I'm willing to keep recruiting reviewers to try to review your submission before Ocean Sciences, but I could use more suggestions. I'd really like to include people with data experience in particular. If you have suggestions, please list them without @-mentioning them here.

@gmaze Just to be clear, I am going to see if I can find reviewers who can work on this sooner, but if not I would like to be able to call on you! Thanks.

[ocefpaf]

@kthyng I spoke with Jessica Austin (@jessicaaustin), from Axiom DataScience, and she is willing to review it. Jessica a lot of experience with scientific Software development applied to oceanography and is the lead developer for the IOOS QA/QC QARTOD implementation.

[kthyng]

Awesome, thanks @ocefpaf!

@jessicaaustin JOSS is the Journal for Open Source Software, which involves largely code-review based for software with research applications. Are you interested in reviewing this submission? We ask for reviews within about 3 weeks if possible, and you can find more information about the process here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

I'm looking for experience with Python and quality controlling oceanographic data.

In total, we need two reviewers. Thanks.

[jessicaaustin]

@kthyng Yes, I am happy to review this submission

[kthyng]

@evanleeturner JOSS is the Journal for Open Source Software, which involves largely code-review based for software with research applications. Are you interested in reviewing this submission? We ask for reviews within about 3 weeks if possible, and you can find more information about the process here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html
I'm looking for one more reviewer! Thanks for your consideration.

[kthyng]

Thanks @jessicaaustin! I've also had confirmation by email from @evanleeturner so let's start this review!

[kthyng]

@whedon assign @jessicaaustin as reviewer

[whedon]

OK, @jessicaaustin is now a reviewer

[kthyng]

@whedon add @evanleeturner as reviewer

[whedon]

OK, @evanleeturner is now a reviewer

[kthyng]

@whedon start review

[whedon]

OK, I've started the review over in #2063.

[kthyng]

@jessicaaustin and @evanleeturner Please to go #2063 for the actual review. You'll find a reviewer checklist for each of you and some instructions. Please open new issues in the software repo and link back to the review issue for items that arise, and let me know if you have any questions!

[evanleeturner]

Thanks for the invite. This is a whole new experience to do a review in github, so bear with me pls! Looking forward to taking a look at the work. -evan

[castelao]

@jessicaaustin and @evanleeturner, thank you for accepting to review my submission.

@kthyng, I do appreciate your effort and time to keep this review moving forward considering this pre-OSM busy times. Thanks!

@gmaze and @seagrinch, I would be very much interested in hearing any comments or questions that you might have. Please feel free to contact me by opening an issue in the CoTeDe repository or directly by email. Thanks!

[callumrollo]

Hi @kthyng sorry for missing this, I was at sea for 6 weeks with no internet. Just the kind of thing I would be happy to review in future though. @castelao I'll have a proper dig into the code once I'm caught up on post cruise admin. Looks like an awesome tool!

[ooo]

👋 Hey @callumrollo...

Letting you know, @kthyng is currently OOO until Sunday, March 15th 2020. ❤️