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Published 20 hours ago • verified publisher icon pyOpenSci

climate_indices (drought monitoring, SPI, SPEI, etc.)

Open monocongo opened this issue 2 years ago • 6 comments

Submitting Author: James Adams (@monocongo) All current maintainers: (@monocongo) Package Name: climate_indices One-Line Description of Package: A suite of climate indices developed for drought.gov at NOAA, useful for drought monitoring. Repository Link: https://github.com/monocongo/climate_indices Version submitted: Please use the master branch or latest from PyPI Editor: TBD
Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD
Version accepted: TBD Date accepted (month/day/year): TBD

Code of Conduct & Commitment to Maintain Package

Description

  • Include a brief paragraph describing what your package does: This package computes commonly used drought indices such as SPI, SPEI, and PET. The individual indices can be computed via an API where precipitation and temperature values are passed in as numpy arrays, and there is a command line option that allows the usage of NetCDF files as input/output format. These were developed while I worked as part of the drought.gov team (NIDIS/NOAA).

Scope

  • Please indicate which category or categories. Check out our package scope page to learn more about our scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry):

    • [ ] Data retrieval
    • [ ] Data extraction
    • [x] Data processing/munging
    • [ ] Data deposition
    • [ ] Data validation and testing
    • [ ] Data visualization[^1]
    • [ ] Workflow automation
    • [ ] Citation management and bibliometrics
    • [ ] Scientific software wrappers
    • [ ] Database interoperability

Domain Specific & Community Partnerships

- [x] Geospatial
- [ ] Education
- [ ] Pangeo

Community Partnerships

If your package is associated with an existing community please check below:

[^1]: Please fill out a pre-submission inquiry before submitting a data visualization package.

  • For all submissions, explain how the and why the package falls under the categories you indicated above. In your explanation, please address the following points (briefly, 1-2 sentences for each):

    • Who is the target audience and what are scientific applications of this package?
      Audience: Climate scientists, hydrologists Application: Climate monitoring and analysis

    • Are there other Python packages that accomplish the same thing? If so, how does yours differ? climx In my opinion, climx is a more solid offering overall, and they have a team of professionals maintaining it. Ours seems to be more performant and focused on fewer but more complex drought indices, and in the end, we should merge so as to not duplicate/waste efforts, I just haven't had the time to fold this into their codebase and guide our users in their direction. From what I can tell our package gets more use in the community based on the number of stars. My main concern is that it follows "best practices", and I can mostly handle the software side of that, but I am not a scientist and need help validating that this code is solid from a scientific perspective. Also, the code here was the code used to produce the various monthly indices provided by NOAA, and my initial goal was to make that as transparent as possible via an open-source approach.

    • 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:

Technical checks

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  • [x] does not violate the Terms of Service of any service it interacts with.
  • [x] uses an OSI approved license.
  • [x] contains a README with instructions for installing the development version.
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  • [x] has a test suite.
  • [x] has a continuous integration setup, such as GitHub Actions CircleCI, and/or others.

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monocongo avatar May 12 '23 19:05 monocongo

Welcome to pyOpenSci @monocongo and thank you for your submission!

Good news: climate_indices passes most of the initial checks, and we think we have already found an editor for this review.

There's just a couple things missing I need you to add:

  • [ ] I don't find API documentation -- if that's correct, can you please add it? (e.g. with autodoc)
  • [ ] Can you please add install instructions to the README? Just a pip install climate-indices is fine

Please let me know when you've added those and we can proceed with the review. Appreciate it!

Editor in Chief checks

Hi there! Thank you for submitting your package for pyOpenSci review. Below are the basic checks that your package needs to pass to begin our review. If some of these are missing, we will ask you to work on them before the review process begins.

Please check our Python packaging guide for more information on the elements below.

  • [x] Installation The package can be installed from a community repository such as PyPI (preferred), and/or a community channel on conda (e.g. conda-forge, bioconda).
    • [x] The package imports properly into a standard Python environment import package-name.
      • importing finishes without an error but nothing was imported; climate_indices/__init__.py does not import anything from the package
      • I tested that the script process_climate_indices got installed; it gave me the argparse options as expected, so this suggests that installation does work
  • [x] Fit The package meets criteria for fit and overlap.
  • [ ] Documentation The package has sufficient online documentation to allow us to evaluate package function and scope without installing the package. This includes:
    • [x] User-facing documentation that overviews how to install and start using the package.
    • [x] Short tutorials that help a user understand how to use the package and what it can do for them.
    • [ ] API documentation (documentation for your code's functions, classes, methods and attributes): this includes clearly written docstrings with variables defined using a standard docstring format. We suggest using the Numpy docstring format.
  • [ ] Core GitHub repository Files
    • [ ] README The package has a README.md file with clear explanation of what the package does, instructions on how to install it, and a link to development instructions.
    • [x] Contributing File The package has a CONTRIBUTING.md file that details how to install and contribute to the package.
    • [x] Code of Conduct The package has a Code of Conduct file.
    • [x] License The package has an OSI approved license. NOTE: We prefer that you have development instructions in your documentation too.
  • [x] Issue Submission Documentation All of the information is filled out in the YAML header of the issue (located at the top of the issue template).
  • [x] Automated tests Package has a testing suite and is tested via GitHub actions or another Continuous Integration service.
  • [x] Repository The repository link resolves correctly.
  • [x] Package overlap The package doesn't entirely overlap with the functionality of other packages that have already been submitted to pyOpenSci.
  • [ ] 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)?
  • [x] Initial onboarding survey was filled out We appreciate each maintainer of the package filling out this survey individually. :raised_hands: Thank you authors in advance for setting aside five to ten minutes to do this. It truly helps our organization. :raised_hands:

Editor comments

NickleDave avatar May 16 '23 22:05 NickleDave

Thank you for this initial review @NickleDave . I will further document the code with docstrings and generate API docs via autodoc.

monocongo avatar May 22 '23 14:05 monocongo

Perfect, thank you @monocongo!

Just let us know once you add those and the install instructions in the README.

Looking forward to getting you a review!

NickleDave avatar May 22 '23 15:05 NickleDave

Hi @monocongo just want to check back where you're at with API docs and adding install instructions to the README.

If it's okay with you, I'll open an issue on the climate_indices repo with these to-do items that references this issue. That way we can better track changes made as part of the review process, and we can also follow the link back here to know where you're at with it

We do have an editor that can start the review, but if you aren't able to get to the API docs soon, I totally understand, believe me. If I open the issue on climate_indices that will also help us know when you're ready

NickleDave avatar Jun 14 '23 21:06 NickleDave

Yes, David. Thanks! I will be on PTO at the end of this month and hopefully, I will get to that as well as some other issues during that time.

I appreciate the work you all are doing, this ain't easy.

--James

On Wed, Jun 14, 2023 at 5:16 PM David Nicholson @.***> wrote:

Hi @monocongo https://github.com/monocongo just want to check back where you're at with API docs and adding install instructions to the README.

If it's okay with you, I'll open an issue on the climate_indices repo with these to-do items that references this issue, just so we can track changes made as part of the process, and so we can follow the link here to know where you're at with it

We do have an editor that can start the review, but if you aren't able to get to the API docs soon, I totally understand, believe me. If I open the issue on climate_indices that will also help us know when you're ready

— Reply to this email directly, view it on GitHub https://github.com/pyOpenSci/software-submission/issues/111#issuecomment-1591996074, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKEIHRYFJO6FEL6RYHF3W3XLIS3PANCNFSM6AAAAAAX756SLI . You are receiving this because you were mentioned.Message ID: @.***>

monocongo avatar Jun 15 '23 21:06 monocongo

Great, thanks for letting us know @monocongo. I will raise that issue later today so we can track.

🙌 we appreciate the work you're doing too! And on your PTO even 🙂

NickleDave avatar Jun 16 '23 13:06 NickleDave

hi everyone 👋🏻 i'm going through old issues and closing ones that have been open with no movement for over a year. If you have any questions please let me know.

Also you are always welcome to restart this review in the future if you'd like to!! I hope everyone here is well!

lwasser avatar Oct 03 '24 00:10 lwasser