Closed editorialbot closed 6 months ago
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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1080/01621459.1962.10482147 is OK
- 10.1093/biomet/asx076 is OK
- 10.18637/jss.v101.i01 is OK
- 10.2466/pr0.95.2.449-458 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.88 T=0.21 s (119.7 files/s, 13481.5 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 14 398 393 1375
reStructuredText 2 83 15 164
make 1 28 6 143
YAML 4 10 0 80
TeX 1 5 0 44
Markdown 1 13 0 43
JSON 1 0 0 11
INI 1 0 0 4
-------------------------------------------------------------------------------
SUM: 25 537 414 1864
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 638
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
pip install combine_pvalues_discrete
works on Colab.scipy.stats.combine_pvalues
.
Followup: I've verified some of the claims more directly. Using scipy.stats.monte_carlo_test
, I wrote my own version of Fisher's approach to combining p-values. This is similar to what the author shows in Checking the result. So I haven't done a line-by-line review of all functionality, but the basic functionality is definitely there. combine_pvalues_discrete
implements this approach in a:atol
, rtol
are important and often neglected) and computes the p-value from counts (see "Permutation P-values should never be zero").requirements.txt
file.scipy.stats.combine_pvalues
, is only valid for p-values from continuous tests, and the paper cites this. It also cites the R poolr
package. However, to more fully satisfy this criterion, the paper could mention other meta-analysis packages in Python (e.g. PythonMeta, PyMARE, statsmodels.stats.meta_analysis) and/or other languages (e.g. R's metap
).@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Good: All functions/methods are documented including example inputs and outputs
OK: Core API functionality is documented
Bad (not acceptable): API is undocumented
because I agree this is good practice. I also asked if lines could be wrapped in the docstrings to make them easier to read in a terminal. Right now there lines up to over 400 characters wide.
Hi, @Wrzlprmft could you please update us on your status in addressing issues raised by @mdhaber?
Hi, @steppi could you please update us on the progress of your review? I see there are some checkboxies unchecked. Is it because there are still in progress or there is some issue with them?
Hi, @Wrzlprmft could you please update us on your status in addressing issues raised by @mdhaber?
In my understanding, there is nothing for me to address at the moment. I addressed @mdhaber’s last comments here (and the commits referenced therein). Since my last reply was mostly asserting his understandings, I didn’t expect a response and assumed no further clarification or changes were needed.
Yes, my comments were addressed, and I only planned to do a more detailed check of the reference section.
Hi, @steppi could you please update us on the progress of your review? I see there are some checkboxies unchecked. Is it because there are still in progress or there is some issue with them?
Sorry @vissarion, since agreeing to review this I ended up being busier than expected but things are settling down. I will be able to complete my review within two weeks. The unchecked boxes are for things that are still in progress.
I completed my checklist. References look good except for "metap" probably isn't intended to be capitalized in the rendered document.
References look good except for "metap" probably isn't intended to be capitalized in the rendered document.
Fixed. While I disagree with lowercasing proper names, this is reproducing the lack of capitalisation of the cited source.
@mdhaber do you recommend to accept this paper?
Hi @steppi, do you have any news from this review?
Sorry for the delay. I’ll get it done this week.
@mdhaber do you recommend to accept this paper?
Yes
I've completed my review and recommend this paper for publication. I would like to see the updates I suggested made to the documentation but don't think this is a blocker.
@Wrzlprmft it seems that both reviewers recommend acceptance! Could you please address the issue of the documentation raised by @steppi ?
When a submission is ready to be accepted, we ask that the authors issue a new tagged release of the software (if changed), and archive it (see this guide). Please do this and post the version number and archive DOI here.
@vissarion, @Wrzlprmft has addressed the issues, or in one case provided his rationale for deviating from standard practice.
@Wrzlprmft it seems that both reviewers recommend acceptance!
So it does.
Thanks to the reviewers (@mdhaber and @steppi) for their diligent criticism and constructive comments.
When a submission is ready to be accepted, we ask that the authors issue a new tagged release of the software (if changed), and archive it (see this guide). Please do this and post the version number and archive DOI here.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@Wrzlprmft please edit the zenodo record so that the title, author names and affiliation are the same as in paper.
Hopefully done. I added the paper title as an alternative title. Please tell me if it should be the main title.
@Wrzlprmft please change the main title of zenodo to "A Python module to combine 𝑝 values arising from1 discrete tests." i.e. as in JOSS paper so that the DOI looks correct and has the same title as in your paper.
@Wrzlprmft please change the main title of zenodo to "A Python module to combine 𝑝 values arising from1 discrete tests." i.e. as in JOSS paper so that the DOI looks correct and has the same title as in your paper.
Done (except for the stray “1” which I presume to be an error).
@editorialbot set 10.5281/zenodo.8338798 as archive
Done! archive is now 10.5281/zenodo.8338798
@editorialbot set 1.2.2 as version
Done! version is now 1.2.2
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1080/01621459.1962.10482147 is OK
- 10.1093/biomet/asx076 is OK
- 10.18637/jss.v101.i01 is OK
- 10.2466/pr0.95.2.449-458 is OK
- 10.2202/1544-6115.1585 is OK
- 10.5281/zenodo.4266738 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:
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1080/01621459.1962.10482147 is OK
- 10.1093/biomet/asx076 is OK
- 10.18637/jss.v101.i01 is OK
- 10.2466/pr0.95.2.449-458 is OK
- 10.2202/1544-6115.1585 is OK
- 10.5281/zenodo.4266738 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/dsais-eics, this paper is ready to be accepted and published.
Check final proof :point_right::page_facing_up: Download article
If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5038, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
@editorialbot accept
Doing it live! Attempting automated processing of paper acceptance...
Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.
If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.
You can copy the contents for your CITATION.cff file here:
``` cff-version: "1.2.0" authors: - family-names: Ansmann given-names: Gerrit orcid: "https://orcid.org/0000-0002-5472-7067" doi: 10.5281/zenodo.8338798 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Ansmann given-names: Gerrit orcid: "https://orcid.org/0000-0002-5472-7067" date-published: 2024-02-29 doi: 10.21105/joss.06096 issn: 2475-9066 issue: 94 journal: Journal of Open Source Software publisher: name: Open Journals start: 6096 title: A Python module to combine p values arising from discrete tests. type: article url: "https://joss.theoj.org/papers/10.21105/joss.06096" volume: 9 title: A Python module to combine $p$ values arising from discrete tests. ```
If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.
🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨
Here's what you must now do:
Any issues? Notify your editorial technical team...
🎉 Everything looks fine to me. Thanks to everybody involved.
However, I cannot close this issue (or find the editorial technical team to contact about this) as instructed. It seems like @vissarion or @arfon has to do this.
@steppi, @mdhaber – many thanks for your reviews here and to @vissarion for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨
@Wrzlprmft – your paper is now accepted and published in JOSS :zap::rocket::boom:
:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:
If you would like to include a link to your paper from your README use the following code snippets:
Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06096/status.svg)](https://doi.org/10.21105/joss.06096)
HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06096">
<img src="https://joss.theoj.org/papers/10.21105/joss.06096/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06096/status.svg
:target: https://doi.org/10.21105/joss.06096
This is how it will look in your documentation:
We need your help!
The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
Submitting author: !--author-handle-->@Wrzlprmft<!--end-author-handle-- (Gerrit Ansmann) Repository: https://github.com/BPSB/combine-p-values-discrete Branch with paper.md (empty if default branch): Version: 1.2.2 Editor: !--editor-->@vissarion<!--end-editor-- Reviewers: @steppi, @mdhaber Archive: 10.5281/zenodo.8338798
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
@steppi & @mdhaber, 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 @vissarion 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 @mdhaber
📝 Checklist for @steppi