ObsPy: Software Submission for Review

[megies]

Submitting Author: @megies
Package Name: ObsPy
One-Line Description of Package: A Python Toolbox for seismology/seismological observatories.
Repository Link: https://github.com/obspy/obspy
Version submitted: 1.1.1
Editor: @lwasser
Reviewer 1: @canyon289
Reviewer 2: @raoulcollenteur
Archive: TBD
Version accepted: TBD

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Description

ObsPy is an open-source project dedicated to provide a Python framework for processing seismological data. It provides parsers for common file formats, clients to access data centers and seismological signal processing routines which allow the manipulation of seismological time series (see Beyreuther et al. 2010, Megies et al. 2011, Krischer et al. 2015).

The goal of the ObsPy project is to facilitate rapid application development for seismology.

ObsPy is licensed under the GNU Lesser General Public License (LGPL) v3.0.

Scope

• Please indicate which category or categories this package falls under:
  • Data retrieval
  • Data extraction
  • Data munging
  • Data deposition
  • Reproducibility
  • Geospatial
  • Education
  • Data visualization* <-- didn't tick this, because the benefit of a 'pre-submission inquiry' didn't become obvious for me, the issue form seems to be largely the same

* Please fill out a pre-submission inquiry before submitting a data visualization package. For more info, see this section of our guidebook.

• Explain how the and why the package falls under these categories (briefly, 1-2 sentences):

It falls under these categories, because we retrieve and munge data. Also loads of the functionality is concerning geospatial aspects (can't be avoided in seismology). Being as high-level as we are in functionality, I'd also consider it to be educational, since you can illustrate how to do many processing steps (and what pitfalls there are) in a few lines of code.
If this is more about the core aspects of the software, I guess you could also argue for only retrieval and munging, and the other are rather side aspects.. although it's unclear to me in which bullet item signal processing is included (munging I guess?).

• Who is the target audience and what are scientific applications of this package?

Mainly scientists/researchers, but we know that obspy is also used in industry (no idea about numbers, though). Scientific applications span most fields of seismology that involve real or synthetic data, basically only excluding purely theoretical, pen and paper seismology.

• Are there other Python packages that accomplish the same thing? If so, how does yours differ?

There are various packages with I/O of up to a handful file formats at a time, usually concerned only with 1-3 file formats used by the authors. I am not aware of other packages that offer access clients for all important protocols like we do (FDSN web services, SeedLink, Earthworm, Arclink, NRL, syngine, ...). Most important point would be the widespread use in projects built on top of obspy, most likely.

• If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted:

no pre-submission enquiry filed.

Technical checks

For details about the pyOpenSci packaging requirements, see our packaging guide. Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
  • this feels a bit unclear, but in any case I'm not aware of any ToSs we would violate
• has an OSI approved license
  • LGPLv3
• contains a README with instructions for installing the development version.
  • these instructions are in the wiki which is linked in the README to keep it more concise
• includes documentation with examples for all functions.
  • docs.obspy.org built from source with sphinx
• contains a vignette with examples of its essential functions and uses.
  • submodule API landing pages (i.e. __init__.pys) hold the submodules' most important functions with explanations and usage examples,
• has a test suite.
  • see http://tests.obspy.org/
• has continuous integration, such as Travis CI, AppVeyor, CircleCI, and/or others.
  • Travis for Linux + Mac tests
  • Appveyor for Windows tests
  • Circle for quick linting and Flake8

Publication options

• Do you wish to automatically submit to the Journal of Open Source Software? If so:

We have citable papers out, so no need for this I think. If anything we might do a "history of obspy" short story?

JOSS Checks

• The package has an obvious research application according to JOSS's definition in their submission requirements. Be aware that completing the pyOpenSci review process does not guarantee acceptance to JOSS. Be sure to read their submission requirements (linked above) if you are interested in submitting to JOSS.
• The package is not a "minor utility" as defined by JOSS's submission requirements: "Minor ‘utility’ packages, including ‘thin’ API clients, are not acceptable." pyOpenSci welcomes these packages under "Data Retrieval", but JOSS has slightly different criteria.
• The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
• The package is deposited in a long-term repository with the DOI:

Note: Do not submit your package separately to JOSS

Are you OK with Reviewers Submitting Issues and/or pull requests to your Repo Directly?

This option will allow reviewers to open smaller issues that can then be linked to PR's rather than submitting a more dense text based review. It will also allow you to demonstrate addressing the issue via PR links.

• Yes I am OK with reviewers submitting requested changes as issues to my repo. Reviewers will then link to the issues in their submitted review.

Code of conduct

• I agree to abide by pyOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

We're using Contributor Covenant Code of Conduct v1.4

P.S. Have feedback/comments about our review process? Leave a comment here

Editor and Review Templates

Editor and review templates can be found here

[megies]

Code of conduct was added after last stable release, it's in master and will be part of soon-to-be-released 1.2.0.

[lwasser]

awesome! thanks @megies for this submission. we will get back to you soon!! likely after agu :) in the meantime are there people who you could suggest as reviewers? i can also dig into our spreadsheets but if you know of folks, please feel free to suggest here. now that i'm writing this i'm realizing we might consider adding this question to our template as well.

Editor's Template

Editor checks:

• Fit: The package meets criteria for fit and overlap.
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has an OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

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Editor comments

I asked the submitter below if they were interested in JOSS!

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Reviewers: Listed above with a due date of feb 24
Due date:

note: i think it might be good to add the editor checks somewhere in the issue ?? it seems redundant to list reviewers twice and a due date at the bottom.

[megies]

are there people who you could suggest as reviewers?

That'd be somebody working in seismonology, good in Python and not using obspy? Is that even possible?

👆 just kidding 😜 but yeah, most people I could come up with would be biased 😉

[lwasser]

hey there @megies !! i'm just catching up on things with the holidays, and beginning of the semester here... so my apologies for the delay. Our next meeting is this thursday so i'll be sure to get this review going.

I'll put a few calls out to try to find some reviewers. it seems to me that someone who uses obspy could be ok?! but if they are closely related to the development already that would not be ok. let's see if we can use a combo of twitter and our forum to find a few reviewers. more in a bit. i'm hoping to play catch up over the next week and this is a priority for me as it's been sitting for a month. thank you for your patience!!

[megies]

Like I said, it's all good, we're in no hurry about this at all. 👍

[canyon289]

Hi, I saw the call for reviewers on twitter, all for open source science, would like to be helpful. I'm not in seismology and don't use ObsPy, but do help maintain ArviZ and PyMC3 which I hope qualifies me enough. Let me know if I meet the bar.

[raoulcollenteur]

I could help with a review. Not specifically known in seismology but I am a hydrogeologist and (co-) develop some python packages. Let me know if help is needed :)

[lwasser]

hi @canyon289 and @raoulcollenteur if you have experience developing packages, and are on the geosciences end of things, I think that could work well for this review. @megies please let me know what you think about two people reviewing who are not from the seismology community explicitly? i suspect this might be challenging to find someone without a conflict of interest and such. I know both are technically qualified based upon the comments above!! Thank you all for your responses.

[megies]

@megies please let me know what you think about two people reviewing who are not from the seismology community explicitly?

I don't see a problem with that at all. 👍

[lwasser]

awesome @raoulcollenteur and @canyon289 if you are still willing, I am going to assign you as reviewers for obspy!! Please plan to have your feedback to @megies by Monday Feb 24th.

You can use our review guide as a basis for your review. https://www.pyopensci.org/dev_guide/peer_review/reviewer_guide.html We actually have some reviews that you can look out now (our guide is dated already!!) which include:

• earthpy:
• pandera:

@megies did check they are ok with issues being submitted directly to the obspy repo! so if you'd like you can organize that review with issues providing commentary here and then linking to issues that you open in obspy. how you prefer to work is up to you!

If you have any questions please get in touch here!! Thank you again for volunteering your time to review this package! It is a very widely used package in this domain looking at the package download stats on conda so we are excited to see it submitted here! Have a wonderful weekend!!