Open editorialbot opened 2 years ago
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Checking the BibTeX entries failed with the following error:
No paper file path
Software report:
github.com/AlDanial/cloc v 1.88 T=0.17 s (629.4 files/s, 102055.1 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 65 2795 2286 10220
reStructuredText 29 271 228 574
YAML 5 19 2 129
TOML 1 8 4 110
make 1 5 6 14
Jupyter Notebook 1 0 171 12
Markdown 1 3 0 6
SVG 1 0 0 1
-------------------------------------------------------------------------------
SUM: 104 3101 2697 11066
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Failed to discover a Statement of need
section in paper
:warning: An error happened when generating the pdf. Paper file not found.
@editorialbot set paper as branch
Done! branch is now paper
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
:wave: @nlhepler – how are you getting along with your review here?
@arfon We moved the repository from theislab/anndata to https://github.com/scverse/anndata. Could you update the metadata here?
@arfon apologies for the delay. I aim to have it done today, certainly no later than tomorrow.
Let me try to generate an up-to-date version that includes our response to @rcannood:
@editorialbot generate pdf
editorialbot commands need to be the first entry in a new comment.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@falexwolf, I see that @rcannood has opened scverse/anndata#769, would you prefer I piggy-back my comments there or open a separate issue?
Thanks for checking! It'd be great if you added your comments to the existing thread! It's more efficient if we address both of your comments in ideally one additional pass on the paper (or as many it takes until your happy)! 😅
:wave: folks. Just checking how things are going here? @nlhepler, @rcannood – it looks like you're well on your way to completing your reviews, have you had a chance to provide all of your feedback to @falexwolf?
:wave: Hi @arfon, the conversation is mostly happening in scverse/anndata#769 -- we're still going back and forth
Yes, all reviews are there! Isaac was on a several-week-long conference and holiday trip.
He just got back last week and we want to get back to reviews this Monday.
:wave: folks. Just checking in again here – @nlhepler, @rcannood – are your reviews mostly complete?
I made my suggestions in https://github.com/scverse/anndata/issues/769, waiting for the authors to get back to us.
Thanks @rcannood.
@falexwolf – when do you think you might be able to respond to @rcannood's feedback?
@arfon, we responded to most of it.
@ivirshup, when do you think you can address the outstanding items?
@luizirber @falexwolf @ivirshup can you provide any updates on the above ☝️
My problem is that the remaining edits can only be performed by the first author. @ivirshup, could you provide an estimate?
Quick update, I emailed @ivirshup earlier today to see when they might be able to provide updates.
Did @ivirshup get back to you?
Alternatively, we could omit statements regarding performance from the manuscript. WDYT?
I'd be OK with that! But I still hope this gets finalized in the form we foresaw after all the work that got put in by many people.
@falexwolf @arfon did you hear back from @ivirshup ? It would be good to move on here.
I couldn't get through. Just tried to ping @ivirshup through the repo now.
@falexwolf @ivirshup any updates to report? This review is taking very long due to inaction on the part of the authors. If this remains the case we will have no other option than to reject/retract this submission. Please can you respond in full to all reviewer comments and post a detailed update here at your earliest convenience. I will put a deadline of August 18th on this. If the review can continue and the authors are onboard to help make edits in a timely matter we can continue. If not we will proceed to reject.
It's very understandable that you'd retract the submission. I'm sorry for the effort we caused. At least, it seems the basic idea of having a paper for anndata wasn't wrong and the preprint is cited with 75 citations according to https://badge.dimensions.ai/details/id/pub.1144066001.
The blocker consists in a few technical points that only the first author (@ivirshup) can answer.
All other points have a response in the thread we have with the reviewers (https://github.com/scverse/anndata/issues/769). I'll happily move them here should @ivirshup make the response complete.
Though I think having the joint collaboration of the authors to tackle the remaining issues in scverse/anndata#769 would be the best outcome, I don't think it's the only solution.
In an attempt to get this submission finally accepted, let me provide a recap of the only remaining blocking item in my review at scverse/anndata#769:
IMO, I think these are the following options for resolving the matter:
Hopefully this helps in figuring out a solution to the remaining issues.
Thank you, @rcannood - your contributions are beyond anything that could be expected from any reviewer.
I'm happy to implement Option 2 if this is something reviewers and editors can accept. Option 3, I guess, equates to an acceptance of the current revision. Option 1 is what I can't do because it's highly technical and @ivirshup has been working on this for years (and is still working on it with the team, I believe).
Hey @falexwolf ! Sorry for not responding earlier, it wasn't clear to me that you were posing a question.
Options 1 to 3 are all viable solutions for me :) :+1:
@luizirber can you check in with this review to ensure we keep up the pace, thanks.
@Kevin-Mattheus-Moerman @luizirber Can I just check the [ ] Performance
checkbox and quietly get this over with?
While I think the benchmarks themselves would be super interesting; at this stage I feel like I'm doing the scientific community a disservice for not allowing the AnnData paper to be published, since the performance of AnnData is not really the main point of the package or the accompanying manuscript.
@rcannood given what you describe that may be acceptable. I'll let @luizirber decide as he is the handling editor.
Sounds good! :+1: Any updates on this?
@luizirber this thread needs your attention. 👋
@Kevin-Mattheus-Moerman: @luizirber seems to be unresponsive. Do you have other ways of reaching out to @luizirber ?
sorry for the unresponsiveness :disappointed:
@Kevin-Mattheus-Moerman @luizirber Can I just check the
[ ] Performance
checkbox and quietly get this over with?While I think the benchmarks themselves would be super interesting; at this stage I feel like I'm doing the scientific community a disservice for not allowing the AnnData paper to be published, since the performance of AnnData is not really the main point of the package or the accompanying manuscript.
I agree. Not that performance is not important, but option 2 ("If that is not possible, the performance claims made in the paper could be removed or watered down, as the paper is still valuable even without making any claims related to performance.") seems the best to proceed because the main focus is the usability and the use cases enabled by the library.
Alright, in that case I'll leave it in the hands of @falexwolf and colleagues to make changes to the paper.
@luizirber Could you run @editorialbot set https://github.com/scverse/anndata as repository
?
Will do it this week! :)
@editorialbot set https://github.com/scverse/anndata as repository
Submitting author: !--author-handle-->@falexwolf<!--end-author-handle-- (F. Alexander Wolf) Repository: https://github.com/scverse/anndata Branch with paper.md (empty if default branch): paper Version: 0.10.9 Editor: !--editor-->@luizirber<!--end-editor-- Reviewers: @nlhepler, @rcannood Archive: 10.5281/zenodo.13643180
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
@nlhepler & @rcannood, 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 @luizirber 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 @nlhepler
📝 Checklist for @rcannood