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Stingray Submission #201
Description
Submitting Author: @matteobachetti
All current maintainers: @dhuppenkothen, @mgullik, @jdswinbank, @matteolucchini1
Package Name: Stingray
One-Line Description of Package: A spectral-timing software package for astrophysical X-ray (and other) data
Repository Link: https://github.com/stingraysoftware/stingray
Version submitted: 2.1
EiC: @cmarmo
Editor: @hamogu
Reviewer 1: @taldcroft
Reviewer 2: @masonng-astro
Archive:
JOSS DOI: 10.21105/joss.07389
Version accepted: 2.1
Date accepted (month/day/year): 10/01/2024
Code of Conduct & Commitment to Maintain Package
- I agree to abide by pyOpenSci's Code of Conduct during the review process and in maintaining my package after should it be accepted.
- I have read and will commit to package maintenance after the review as per the pyOpenSci Policies Guidelines.
Description
- Include a brief paragraph describing what your package does:
Stingray is a Python library for "spectral timing", i.e. time-series analysis techniques that can be used to study how variability changes or correlates between different energy bands/wavelengths. It is Astropy-affiliated, and with an ever growing user base now comprising hundreds of researchers around the globe.
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
- Data processing/munging
- Data deposition
- Data validation and testing
- Data visualization1
- Workflow automation
- Citation management and bibliometrics
- Scientific software wrappers
- Database interoperability
Domain Specific
- Geospatial
- Education
Community Partnerships
If your package is associated with an
existing community please check below:
- Astropy:My package adheres to Astropy community standards
- Pangeo: My package adheres to the Pangeo standards listed in the pyOpenSci peer review guidebook
- For all submissions, explain how 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):
This package is mostly focused on the analysis of new data from high-energy missions. We added data validation and testing because it can be used as a quick look tool to point out possible anomalies in observations (e.g. solar or other background flares).
- Who is the target audience and what are scientific applications of this package?
The target audience is principally researchers and students of X-ray and multi-wavelength astronomy.
This package fills a void for a free and open source (spectral-)timing package for X-ray astronomy. XRONOS, formerly maintained by HEASARC, is currently unmaintained, and the analysis of high-energy timeseries is done mostly with proprietary software or mission-specific packages. We provide a Python package that eases the learning curve for newcomers, also thanks to extensive tutorials based on Jupyter notebooks, and provides experts with a powerful, robust library for their analysis. We provide software to analyze astronomical time series and do a number of things, including periodicity searches, time lag calculations, covariance spectra, power spectral modeling.
- Are there other Python packages that accomplish the same thing? If so, how does yours differ?
Our package is arguably the most well-known Python package for X-ray spectral timing.
- If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or
@tagthe editor you contacted:
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.
- uses an OSI approved license.
- [ x contains a README with instructions for installing the development version.
- includes documentation with examples for all functions.
- contains a tutorial with examples of its essential functions and uses.
- has a test suite.
- has continuous integration setup, such as GitHub Actions CircleCI, and/or others.
Publication Options
- Do you wish to automatically submit to the Journal of Open Source Software? If so:
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.mdmatching JOSS's requirements with a high-level description in the package root or ininst/. We have a previous JOSS paper describing the package. Is it acceptable to have a new paper, including the many improvements made in the last five years? - The package is deposited in a long-term repository with the DOI:
Note: JOSS accepts our review as theirs. You will NOT need to go through another full review. JOSS will only review your paper.md file. Be sure to link to this pyOpenSci issue when a JOSS issue is opened for your package. Also be sure to tell the JOSS editor that this is a pyOpenSci reviewed package once you reach this step.
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.
Confirm each of the following by checking the box.
- I have read the author guide.
- I expect to maintain this package for at least 2 years and can help find a replacement for the maintainer (team) if needed.
Please fill out our survey
- Last but not least please fill out our pre-review survey. This helps us track
submission and improve our peer review process. We will also ask our reviewers
and editors to fill this out.
P.S. Have feedback/comments about our review process? Leave a comment here
Editor and Review Templates
The editor template can be found here.
The review template can be found here.
Footnotes
-
Please fill out a pre-submission inquiry before submitting a data visualization package. ↩
Metadata
Metadata
Assignees
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- Status
Activity
cmarmo commentedon Jul 1, 2024
Editor in Chief checks
Hi there! I'm Chiara and I am taking care of the Editor in chief role for the next three months.
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.
import package.README.mdfile with clear explanation of what the package does, instructions on how to install it, and a link to development instructions.CONTRIBUTING.mdfile that details how to install and contribute to the package.CODE_OF_CONDUCT.mdfile.NOTE: We prefer that you have development instructions in your documentation too.
YAMLheader of the issue (located at the top of the issue template).We appreciate each maintainer of the package filling out this survey individually. 🙌
Thank you authors in advance for setting aside five to ten minutes to do this. It truly helps our organization. 🙌
Editor comments
Stingray is in excellent form! 💪
Congratulations!
I am going to check the availability of our Astropy editors and we will be back to you shortly.
cmarmo commentedon Jul 2, 2024
Hello @matteobachetti I am pleased to announce that @hamogu will take care of your submission as editor.
Thank you Moritz!
I'm wishing to all of you a nice review process! :)
hamogu commentedon Jul 2, 2024
Editor response to review:
Editor comments
👋 Hi @taldcroft and @masonng-astro! Thank you for volunteering to review
for pyOpenSci!
Please fill out our pre-review survey
Before beginning your review, please fill out our pre-review survey. This helps us improve all aspects of our review and better understand our community. No personal data will be shared from this survey - it will only be used in an aggregated format by our Executive Director to improve our processes and programs.
The following resources will help you complete your review:
here as a comment, once your review is complete.
Please get in touch with any questions or concerns! Your review is due:
Reviewers: Tom Aldcroft and Mason Ng
Due date: Sept 6th, 2024
24 remaining items
hamogu commentedon Sep 28, 2024
@masonng-astro Could you have a look if your concerns have been resolved or if you can provide a more detailed look at why it fails? It seems that @matteobachetti tried to reproduce your failure, but failed to do so. Of course, we don't want to accept a failing package, but it's also hard to figure out what went wrong. 😕
Once you think it's ready to be accepted, please edit the post with your review and tick the box on "I recommend approving this package." and leave. short message here (GH will inform me when you post a new comment, but not when you edit an existing one).
masonng-astro commentedon Oct 1, 2024
Sorry for my late response - I did eventually manage to hunt down the issue and it boiled down to a weird esoteric mix of architectures in my Anaconda installation which I never encountered until now! Apologies for holding up the review. I'll go ahead and approve now. I did check everything else and all is good on my end!
hamogu commentedon Oct 1, 2024
🎉 Stingray has been approved by pyOpenSci! Thank you @matteobachetti for submitting stingray and many thanks to @taldcroft and @masonng-astro for reviewing this package! 😸
Author Wrap Up Tasks
There are a few things left to do to wrap up this submission:
[](https://github.com/pyOpenSci/software-review/issues/issue-number).It looks like you would like to submit this package to JOSS. Here are the next steps:
🎉 Congratulations! You are now published with both JOSS and pyOpenSci! 🎉
Editor Final Checks
Please complete the final steps to wrap up this review. Editor, please do the following:
6/pyOS-approved6 🚀🚀🚀.6/pyOS-approvedlabel). Once accepted add the label9/joss-approvedto the issue. Skip this check if the package is not submitted to JOSS.If you have any feedback for us about the review process please feel free to share it here. We are always looking to improve our process and documentation in the peer-review-guide.
hamogu commentedon Oct 1, 2024
@matteobachetti We at pyOpenSci would love to highlight stingray in a blog post similar to what these packages have done: pandera, movingpandas (We have an md template that you could use as a guide when creating your post.)
but I know that you've written a lot about Stingray before, and this is certainly not a requirement!
I also want to invite all three of you to the PyOpenSci slack - there is a very active community that discusses best practices in packaging, testing , and administration of Python packages. Personally, I found a lot of those discussions very insightful and useful, thought I myself have never contributed by posting - I just use it as a resource to look at. If you'd like to join, let me know which email address I should invite!
matteobachetti commentedon Oct 1, 2024
@hamogu I opened a PR with the badge, and filled in the form. Later on I will open the JOSS issue. Thanks a lot!
matteobachetti commentedon Oct 1, 2024
I think it's a good idea, I have some matters to deal with in the next few weeks but I'll try to do it. Thanks!
Sent in private message!
hamogu commentedon Nov 13, 2024
I see that there is a JOSS DOI now, so I've updated all the information and will close this issue. Thanks everyone!