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[REVIEW]: ASGarD: Adaptive Sparse Grid Discretization #4378

Closed editorialbot closed 1 year ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@quantumsteve<!--end-author-handle-- (Steven Hahn) Repository: https://github.com/project-asgard/asgard Branch with paper.md (empty if default branch): paper Version: v0.4.0 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @joglekara, @drobnyjt, @cticenhour Archive: Pending

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HTML: <a href="https://joss.theoj.org/papers/dbc8b3d352b73a460d8cc57f1de1debf"><img src="https://joss.theoj.org/papers/dbc8b3d352b73a460d8cc57f1de1debf/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/dbc8b3d352b73a460d8cc57f1de1debf/status.svg)](https://joss.theoj.org/papers/dbc8b3d352b73a460d8cc57f1de1debf)

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

@joglekara & @drobnyjt & @cticenhour, 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:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon 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 @joglekara

📝 Checklist for @cticenhour

editorialbot commented 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
editorialbot commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.35 s (324.7 files/s, 103997.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             54           3280           1517          18976
C/C++ Header                    41           1539           1530           7843
CMake                            7            173            248            998
YAML                             3              7             11            197
Markdown                         6             66              0            189
MATLAB                           2             41             21            177
Bourne Shell                     1              2              0              7
diff                             1              0              8              5
-------------------------------------------------------------------------------
SUM:                           115           5108           3335          28392
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
arfon commented 2 years ago

@editorialbot set paper as branch

editorialbot commented 2 years ago

Done! branch is now paper

arfon commented 2 years ago

@editorialbot check repository

editorialbot commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.45 s (258.3 files/s, 127260.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                    42           4443           2605          24659
C++                             54           3234           1517          18830
CMake                            7            179            275           1034
Markdown                         7             75              0            266
MATLAB                           2             41             21            177
YAML                             3              7             11            174
TeX                              1              6              0             80
Bourne Shell                     1              2              0              7
-------------------------------------------------------------------------------
SUM:                           117           7987           4429          45227
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 852

editorialbot commented 2 years ago

Failed to discover a Statement of need section in paper

arfon commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arfon commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.jcp.2017.10.009 is OK
- 10.1063/1.4776712 is OK
- 10.1063/1.3167820 is OK

MISSING DOIs

- 10.1088/1361-6544/ac337f may be a valid DOI for title: Algorithms for Solving High Dimensional PDEs: From Nonlinear Monte Carlo to Machine Learning

INVALID DOIs

- https://doi.org/10.1016/j.jco.2010.04.001 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cpc.2020.107412 is INVALID because of 'https://doi.org/' prefix
arfon commented 2 years ago

@joglekara, @drobnyjt, @cticenhour – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing: 

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/4378 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

joglekara commented 2 years ago

Review checklist for @joglekara

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

arfon commented 2 years ago

:wave: folks just checking in here to see how things are going. @drobnyjt, @cticenhour – it looks like you've not started your reviews yet? As a reminder, you need to type the following to get started:

@editorialbot generate my checklist
cticenhour commented 2 years ago

Review checklist for @cticenhour

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

arfon commented 2 years ago

Just checking in on this review as it has been a while since there has been any movement. @joglekara – it looks like you were having some issues building the package on your (M1) architecture. Did you manage to get past this yet?

@cticenhour – it looks like you've generated your checklist but haven't gotten much further than that. Could you updates us here on when you think you might be able to complete your review by?

Many thanks!

cticenhour commented 2 years ago

@arfon Thanks for checking in - I had started the process, but failed to check off boxes here as I went along. I recently worked through getting the basic installation working on my M1 architecture - identified a couple issues with an optional dependency that I'll be passing along to the development team likely today or tomorrow.

I think I'll be able to get moving on going through the documentation this week, with a paper review either the end of this week or next week. Hoping to finally get this initial review knocked out by the end of next week.

joglekara commented 2 years ago

@arfon , thanks for checking in. Yes I'm following up with them re: M1. @cticenhour provided a nice report on the conda build process. I'm working through the Accelerate + Homebrew build.

arfon commented 2 years ago

Hi folks, just checking in again here. How are you getting along with responding to reviewer feedback @joglekara ?

joglekara commented 2 years ago

Thanks for checking in. I opened a couple of issues asking for example usage and a summary / statement of need and forgot to cross-link them.

https://github.com/project-asgard/asgard/issues/429 https://github.com/project-asgard/asgard/issues/430

danielskatz commented 1 year ago

👋 @joglekara - what's the next step to make progress on this?

joglekara commented 1 year ago

Hey @danielskatz , see https://github.com/openjournals/joss-reviews/issues/4378#issuecomment-1250159180 .

In general, the repo needs some more documentation and examples. To be specific, there are a couple of issues I wrote that will help me keep going through the checklist.

danielskatz commented 1 year ago

👋 @quantumsteve - How are you doing on the issues mentioned by @joglekara?

danielskatz commented 1 year ago

👋 @quantumsteve - Again, how are you doing on the issues mentioned by @joglekara?

danielskatz commented 1 year ago

👋 @quantumsteve - Again, how are you doing on the issues mentioned by @joglekara?

danielskatz commented 1 year ago

I've emailed @quantumsteve about this. If there's no action in the next couple if weeks, we'll reject this submission

arfon commented 1 year ago

I've emailed @quantumsteve about this. If there's no action in the next couple if weeks, we'll reject this submission

OK, sounds reasonable. This seems to have gone completely stale. Thanks for e-mailing the author here @danielskatz

quantumsteve commented 1 year ago

Hi, sorry for the delayed response. We addressed the issues the reviewer's found when building ASGarD. We intend to add an examples page and update the paper soon.

arfon commented 1 year ago

OK thank you for the update. What's your ETA for completing these changes?

arfon commented 1 year ago

:wave: happy new year @quantumsteve. Just checking in here on when you anticipate being able to make these changes?

arfon commented 1 year ago

Friendly bump here again @quantumsteve. We'd like to have a committed date from you here to make these changes.

arfon commented 1 year ago

@quantumsteve – it's been many months now since any substantial updates were made by you to this submission. If we don't get a firm date for addressing reviewer feedback in the next couple of weeks, we will reject this submission.

arfon commented 1 year ago

@editorialbot reject

Thanks for your efforts here @joglekara, @drobnyjt, @cticenhour but unfortunately we're going to reject this submission due to author inactivity.

editorialbot commented 1 year ago

Paper rejected.