Closed editorialbot closed 1 year ago
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Software report:
github.com/AlDanial/cloc v 1.88 T=5.24 s (485.0 files/s, 163896.3 lines/s)
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Language files blank comment code
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Cython 124 5953 9618 17108
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Meson 88 397 192 4878
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SUM: 2543 119746 276590 462936
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 866
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.2307/2331554 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1214/aoms/1177729437 is OK
- 1544-6115.1585 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Dear @coatless, Dear @SaranjeetKaur
This is the review thread. Firstly, type
@editorialbot generate my checklist
to generate your own checklist. In that checklist, there are 23 check items. Whenever you complete the corresponding task, you can check off them.
Please write your comments as separate posts and do not modify your checklist descriptions.
The review process is interactive so you can always interact with the authors, reviewers, and the editor. You can also create issues and pull requests in the target repository. Please do mention this thread's URL in the issues so we can keep tracking what is going on out of our world.
Please do not hesitate to ask me about anything, anytime.
Thank you in advance!
@coatless, @SaranjeetKaur - could you please generate your task list and update your status? thank you in advance.
@coatless, @SaranjeetKaur - After three weeks from assigning as reviewers, I am still failed to get at least a life signal from you (Are you fine?). Please generate your task lists to start your review. If you are not available, please ping me, so I can find another reviewers to proceed. Thank you in advance.
@coatless - no worries, thank you for the response
@SaranjeetKaur - We are waiting to hear from you also.
Thank you in advance.
@jbytecode - I am looking at this thread now
Since the paper is about specific contributions to a much larger library (as discussed in https://github.com/openjournals/joss-reviews/issues/5047#issuecomment-1377678757), I thought it might be helpful to point out some relevant files.
License: SciPy's license file is available at https://github.com/scipy/scipy/blob/main/LICENSE.txt.
Contributions: The "blame" of scipy.stats._resampling.py
and scipy.stats.tests.test_resampling.py
reveal some of my contributions to these features over the past two years.
Installation: Installation instructions for the whole library are at https://scipy.org/install/. The list of dependencies is available in the environment.yml file. Please use the latest version of SciPy (1.10.1) for best results.
Documentation: The scipy.stats API reference includes both input/output documentation and examples. More realistic usage examples are available in the scipy.stats tutorials.
Tests: Automated tests are in scipy.stats.tests.test_resampling.py
. Continuous integration test results can be seen in any pull request to SciPy, or tests can be run locally using import scipy.stats; scipy.stats.test(verbose=2)
.
Community Guidlines: Community guidelines are available in the Developer Documentation.
Functionality: One way of verifying the functionality would be to follow the examples in the API reference. For example, the documentation of bootstrap
shows that the true (population) value of the statistic lies within the 90% confidence interval approximately 900 times out of 1000 trials. The documentation of permutation_test
and monte_carlo_test
each compare the p-value produced by the function against the p-value of a comparable hypothesis test function. Many similar examples of real-world use cases are available in the tutorials. Of course, the functionality was also verified when the PRs introducing the functionally were reviewed by SciPy maintainers. The original PRs were:
https://github.com/scipy/scipy/pull/13371
https://github.com/scipy/scipy/pull/13899
https://github.com/scipy/scipy/pull/14576
Additional functionality has been added over the past few years; the relevant PRs can be found by reviewing the "blame" of stats.stats._resampling.py
.
Performance: The paper claims that these methods are "fast" because "the functions take advantage of vectorized user code, avoiding slow Python loops". There is an easy way to verify this. All three functions accept an argument statistic
(callable) and a parameter vectorized
(boolean). All of the examples show how the function can be used with a vectorized statistic; that is, one that accepts an $N$ dimensional array as input and returns the statistic of each slice defined by the parameter axis
. To see that the functions take advantage of vectorized statistics to improve performance, simply replace statistic
with a function that does not have an axis
argument, and ensure that vectorized
is not passed as an argument.
I hope this helps!
@jbytecode would it be appropriate for me to also suggest how some functionality and performance claims might be verified? Done!
@mdhaber - of course, addition to this, you can provide some reproducible test benchmark if exists. thank you.
Thanks @jbytecode I added notes on how one might begin to verify the functionality and performance claims. I'd be happy to provide other examples if it would help!
@coatless, @SaranjeetKaur - Could you please update your status and inform us on how is your review going? Thank you in advance.
Hi @jbytecode - I have reviewed it for general checks and am yet to test the software functionality and documentation part.
@SaranjeetKaur - Thank you for responding and updating your status.
@coatless, @SaranjeetKaur - Could you please update your status and tell us how is your review going? Thank you in advance.
@coatless, @SaranjeetKaur - Is it possible to get a life signal? Could you please update your status? Thank you in advance.
Dear @coatless and @SaranjeetKaur,
I am so sorry if I am bothering you. We are a little bit ahead of normal review times. Moreover, I can only reach the reviewers by email which in turn does not give me a significant result.
Please declare your availability and set a deadline in a few days. If you are not able to review this manuscript let me know, so I'll find new reviewers.
Thank you in advance.
@mdhaber - it might be helpful to add link to the references in the section "Statement of need" (that is, for all the 3 questions, when you are sharing examples which were introduced in the Summary)
Also when you are describing the state of the ecosystem before the release of SciPy 1.9.0 and how it was partially met by tutorials, blog posts, medium.com, and niche packages - share some references here too, if possible.
Thanks @SaranjeetKaur; I've attempted to address your comments in mdhaber/scipy#101. Please let me know if that looks good to you.
@mdhaber - I have reviewed the rendered versions and those look good to me. Thanks for your work!
@jbytecode - Apologies that this has taken longer than I expected! I have completed the review of this work and it looks good to me now. What happens next?
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@SaranjeetKaur - thank you for finishing your review. we are now just waiting @coatless to finish their tasks.
@coatless - could you please update your status? review process of this manuscript is a little bit out of normal time intervals. thank you in advance
@coatless - May I kindly ask you to come back and finalize your review? Thank you in advance.
Hello everyone! I had contacted the esteemed @coatless, who was assigned as a reviewer for this submission, once via email and received a response, fulfilling part of the refereeing process. However, despite sending several emails and calling from here, I have not received a response again. In this situation, I would like to inform that if I do not receive feedback by Friday, May 5th, 2023, I will have to look for a new reviewer.
@turgeonmaxime, @kose-y - Hi again, I had invited you to review this submission, but unfortunately, I did not receive a response from you in a timely manner. Currently, one of our reviewers is unresponsive, and I am in urgent need of finding a replacement. Would one of you be willing to assist in reviewing this submission for JOSS now?
Yes, I am available.
@editorialbot add @kose-y as reviewer
@kose-y added to the reviewers list!
@kose-y - thank you! could you please generate your tasklist by typing
@editorialbot generate my checklist
@editorialbot remove @coatless from reviewers
@coatless removed from the reviewers list!
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Thanks very much @kose-y. I thought I'd point out https://github.com/openjournals/joss-reviews/issues/5092#issuecomment-1445240137, which I wrote to facilitate review.
@kose-y - Just pinging, sorry if I am bothering. How is your review going? Could you please update your status and inform us? Thank you in advance!
I have completed software paper and general checks part, moving on to the software functionality and documentation part.
Dear @kose-y
Could you please update your status?
Thank you in advance.
I will finish it by this weekend.
I have completed the review. Looks good to me for publication.
@kose-y - thank you so much for your contributions
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.2307/2331554 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1214/aoms/1177729437 is OK
- 1544-6115.1585 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Submitting author: !--author-handle-->@mdhaber<!--end-author-handle-- (Matt Haberland) Repository: https://github.com/mdhaber/scipy Branch with paper.md (empty if default branch): joss_resampling Version: v1.10.0-joss-article Editor: !--editor-->@jbytecode<!--end-editor-- Reviewers: @SaranjeetKaur, @kose-y Archive: 10.5281/zenodo.8031631
Status
Status badge code:
Reviewers and authors:
Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
Reviewer instructions & questions
@coatless & @SaranjeetKaur, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jbytecode know.
✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨
Checklists
📝 Checklist for @SaranjeetKaur
📝 Checklist for @kose-y