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[REVIEW]: hilbertmodgroup: Reduction algorithms and framework for Hilbert Modular Groups #3996

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: !--author-handle-->@fredstro<!--end-author-handle-- (Fredrik Stromberg) Repository: https://github.com/fredstro/hilbertmodgroup Branch with paper.md (empty if default branch): paper_joss Version: 0.1.0 Editor: !--editor-->@danielskatz<!--end-editor-- Reviewers: @tbirkandan, @videlec Archive: 10.5281/zenodo.6422510

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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

@tbirkandan & @videlec, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @tbirkandan

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @videlec

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tbirkandan, @videlec it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.07 s (225.1 files/s, 113385.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           6            503           1936            839
Cython                           4            490           1476            753
Jupyter Notebook                 4              0           1769            234
Markdown                         1              9              0             35
make                             1              4              0             13
-------------------------------------------------------------------------------
SUM:                            16           1006           5181           1874
-------------------------------------------------------------------------------

Statistical information for the repository '494e0acadc817ca17597ad89' was
gathered on 2021/12/15.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Fredrik Stromberg                6          3659            381          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Fredrik Stromberg          3278           89.6          0.1                6.50
whedon commented 2 years ago

PDF failed to compile for issue #3996 with the following error: 

 Can't find any papers to compile :-(
danielskatz commented 2 years ago

@whedon generate pdf from branch paper_joss

whedon commented 2 years ago 
Attempting PDF compilation from custom branch paper_joss. Reticulating splines etc...
danielskatz commented 2 years ago

@whedon check references from branch paper_joss

whedon commented 2 years ago 
Attempting to check references... from custom branch paper_joss
whedon 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:

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

OK DOIs

- 10.1007/s10711-019-00474-w is OK
- 10.1112/S1461157015000121 is OK

MISSING DOIs

- 10.1109/mcse.2010.118 may be a valid DOI for title: Cython: The best of both worlds

INVALID DOIs

- None
danielskatz commented 2 years ago

@tbirkandan and @videlec - Thanks for agreeing to review this submission. This is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. 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.

Please read the first couple of comments in this issue carefully, so that you can accept the invitation from JOSS and be able to check items, and so that you don't get overwhelmed with notifications from other activities in JOSS.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3996 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 reviews to be completed within about 2-4 weeks (though recognize that this may be delayed due to the holidays and that @videlec may be unable to start until Feb 1). Please let me know if either of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

danielskatz commented 2 years ago

@fredstro - note that the possibly missing DOI that whedon suggests appears to be correct. Please feel free to make this change to your .bib file, then use the command @whedon check references from branch paper_joss to check again, and the command @whedon generate pdf from branch paper_joss when the references are right to make a new PDF. Whedon commands need to be the first entry in a new comment.

fredstro commented 2 years ago

@whedon check references from branch paper_joss

whedon commented 2 years ago 
Attempting to check references... from custom branch paper_joss
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s10711-019-00474-w is OK
- 10.1112/S1461157015000121 is OK

MISSING DOIs

- 10.1109/mcse.2010.118 may be a valid DOI for title: Cython: The best of both worlds

INVALID DOIs

- None
fredstro commented 2 years ago

@whedon check references from branch paper_joss

whedon commented 2 years ago 
Attempting to check references... from custom branch paper_joss
whedon commented 2 years ago

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "url" (NAME) [#, "@", #, {:title=>["Cython: The best of both worlds"], :author=>["Behnel, Stefan and Bradshaw, Robert and Citro, Craig and Dalcin, Lisandro and Seljebotn, Dag Sverre and Smith, Kurt"], :journal=>["Computing in Science \& Engineering"], :volume=>"13", :number=>"2", :pages=>["31--39"], :year=>"2011", :publisher=>["IEEE"], :doi=>["10.1109/mcse.2010.118"]}]

fredstro commented 2 years ago

@whedon check references from branch paper_joss

whedon commented 2 years ago 
Attempting to check references... from custom branch paper_joss
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/mcse.2010.118 is OK
- 10.1007/s10711-019-00474-w is OK
- 10.1112/S1461157015000121 is OK

MISSING DOIs

- None

INVALID DOIs

- None
fredstro commented 2 years ago

@whedon generate pdf from branch paper_joss

whedon commented 2 years ago 
Attempting PDF compilation from custom branch paper_joss. Reticulating splines etc...
whedon 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:

tbirkandan commented 2 years ago

I installed and run the package (all doctest and all example notebooks by following arXiv:2111.13274 [math.NT]) with no problem. I just have two comments on the references of the paper (as this is not about the software, I am not opening an issue on the repository):

1) The reference of PARI/GP should be corrected according to https://pari.math.u-bordeaux.fr/faq.html (Please see the answer to the question "Need I formally cite PARI/GP in my paper?") 2) The arXiv number arXiv:2111.13274 [math.NT] can be added to the reference Strömberg, F. (2021). A reduction algorithm for Hilbert modular groups. However, as it is a preprint, I leave the decision to the author.

danielskatz commented 2 years ago

Thanks @tbirkandan

  1. I think adding the arxiv number to the reference is a good idea
  2. You didn't check the performance box in your review - What do you need in order to check that one off?
fredstro commented 2 years ago

@tbirkandan: about the PARI reference, except the text "available from" the bibtex entry is the same as in the faq.html but the reference style used in JOSS does not output it in the right way (in particular the 'note' field is ignored). I assume that you want me to modify the BibTex entry so that the output is in line with the example in the FAQ, i.e: The PARI~Group, PARI/GP version \texttt{2.13.1}, Univ. Bordeaux, 2021, \url{http://pari.math.u-bordeaux.fr/}.

@danielskatz: it seems that the note field is ignored, should I put a link in a url field to the ArXiv article or cite the ArXiv directly? (I was hoping to get it accepted by JNT soon...)

I just pushed a new version with updated references. Please let me know if these are ok.

danielskatz commented 2 years ago

@whedon generate pdf from branch paper_joss

@fredstro - note that you can do this too to check the PDF when you make changes in the .md or .bib files

whedon commented 2 years ago 
Attempting PDF compilation from custom branch paper_joss. Reticulating splines etc...
whedon 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:

danielskatz commented 2 years ago

And note that the JOSS examples show some ways to get things to work

danielskatz commented 2 years ago

finally, I note that for the ref with the arxiv preprint - this looks fine in terms of the arxiv part, but you could change Hilbert to {H}ilbert in the title to protect that case.

fredstro commented 2 years ago

Sorry, I did check using the docker container but I missed Hilbert... I have corrected it now

danielskatz commented 2 years ago

@whedon generate pdf from branch paper_joss

whedon commented 2 years ago 
Attempting PDF compilation from custom branch paper_joss. Reticulating splines etc...
whedon 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:

tbirkandan commented 2 years ago

@danielskatz and @fredstro - I checked the remaining "performance" and "references" boxes. My final suggestion is to publish the final form of the paper in JOSS.

danielskatz commented 2 years ago

Thanks @tbirkandan - let's see what @videlec finds in the second review

whedon commented 2 years ago

:wave: @videlec, please update us on how your review is going (this is an automated reminder).

videlec commented 2 years ago

I opened 4 issues regarding the basic setup configuration of the project (fredstro/hilbertmodgroup#1, fredstro/hilbertmodgroup#2, fredstro/hilbertmodgroup#3, fredstro/hilbertmodgroup#4). I am starting my reading of the source code now.

videlec commented 2 years ago

@fredstro : if you need help to implement any one of the issue feel free to ping me in the corresponding issue discussions.

danielskatz commented 2 years ago

👋 @fredstro - Any comments on the review suggestions so far?

fredstro commented 2 years ago

@danielskatz @videlec all good. I just got swamped with teaching/admin work... I have done everything suggested by @videlec except the github actions which I am still working on. (and I have only uploaded it to test.pypi so far)

danielskatz commented 2 years ago

@fredstro - any update?

fredstro commented 2 years ago

I have done everything suggested in the issues so I am just waiting for @videlec to comment on the last issue before I close it.

danielskatz commented 2 years ago

@videlec - Did you see the comment above?

danielskatz commented 2 years ago

👋 @videlec - Did you see the comment above? And in the meantime, are there other items in your checklist that you can check off, or raise issues about if you can't check them off?

Is there anything else I or @fredstro can do to help your progress?

videlec commented 2 years ago

Sorry for the delay. I opened a new issue about the setup configuration (https://github.com/fredstro/hilbertmodgroup/issues/5) which prevented me from installing hilbertmodgroup in my compiled version of sage. I started looking at the code and opened 3 issues (https://github.com/fredstro/hilbertmodgroup/issues/6, https://github.com/fredstro/hilbertmodgroup/issues/7 and https://github.com/fredstro/hilbertmodgroup/issues/8).

danielskatz commented 2 years ago

👋 @fredstro - it looks like there are some issues for you to work on from @videlec - any news on these?

fredstro commented 2 years ago

I’m working on them. Unfortunately one of the issues is a bit complex. I’m suggested to switch off pip’s build isolation and it seems to be a bit tricky without asking users to add the no-build-isolation flag manually to ‘pip install’ but I’m still looking into it

danielskatz commented 2 years ago

👋 @fredstro - any news on this?