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[REVIEW]: epyc: Computational experiment management in Python #3764

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: !--author-handle-->@simoninireland<!--end-author-handle-- (Simon Dobson) Repository: https://github.com/simoninireland/epyc Branch with paper.md (empty if default branch): Version: v1.6.2 Editor: !--editor-->@ajstewartlang<!--end-editor-- Reviewers: @zbeekman, @lorenzo-rovigatti, @amritagos Archive: 10.5281/zenodo.6460760

:warning: JOSS reduced service mode :warning:

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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

@zbeekman & @lorenzo-rovigatti, 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 @ajstewartlang 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 @zbeekman

✨ 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 @lorenzo-rovigatti

✨ 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 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @zbeekman, @lorenzo-rovigatti 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 😿

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whedon commented 3 years ago

Wordcount for paper.md is 932

whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.21 s (454.3 files/s, 137147.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          32           1598           2614           4360
reStructuredText                55           1209            971           1429
make                             2             53             63            219
Jupyter Notebook                 1              0          15440            172
Markdown                         1             24              0            129
TeX                              1              5              0             54
YAML                             1              1              0             29
INI                              1              1              0              5
-------------------------------------------------------------------------------
SUM:                            94           2891          19088           6397
-------------------------------------------------------------------------------

Statistical information for the repository 'c61df284504eea1b5c4eb9af' was
gathered on 2021/09/25.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Simon Dobson                   202         13072           4989           86.84
simoninireland                  26          1442           1296           13.16

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
Simon Dobson               8572           65.6         19.1               17.09
whedon commented 3 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 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1103/physreve.103.062308 may be a valid DOI for title: Two-pathogen model with competition on clustered networks
- 10.1016/j.jtbi.2020.110381 may be a valid DOI for title: Modelling the effects of environmental heterogeneity within the lung on the tuberculosis lifecycle

INVALID DOIs

- None
zbeekman commented 3 years ago

@whedon re-invite @zbeekman as reviewer

whedon commented 3 years ago

I'm sorry @zbeekman, I'm afraid I can't do that. That's something only editors are allowed to do.

zbeekman commented 3 years ago

Sorry, I think I neglected to accept the GitHub joss invitation in a timely fashion and now it’s expired. Could an editor (@ajstewartlang @arfon etc) please re-invite me so I can edit the issue?

I think the command is:

@whedon re-invite @zbeekman as reviewer

thanks

danielskatz commented 3 years ago

@whedon re-invite @zbeekman as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@zbeekman please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

whedon commented 3 years ago

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

whedon commented 3 years ago

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

zbeekman commented 3 years ago

going well, should be wrapped up by the end of the week

lorenzo-rovigatti commented 3 years ago

I have opened a few issues which should be fixed soon. I think that we will be able to wrap things up in the next few days.

zbeekman commented 3 years ago

I wanted to give an update as to my progress with the review, which is that there has not been any since I last checked in: I've been dealing with a family crisis/emergency and unfortunately it has been placing extreme demands on my time and attention. I wish I could say that it is fully resolved--however there is a fairly high likelihood that the current stability of the situation is only temporary. I really want to continue to be a reviewer but it might not be fair to the submitting author to have to wait on me. I will not forget about this and I will attempt to work on it as I can but, it may be in JOSS' and the submitting author's best interest to find an additional/replacement reviewer since it is possible that I may not be able to complete my review in a timely fashion.

ajstewartlang commented 3 years ago

Thanks for the update @zbeekman. Sorry to hear about the emergency. We're only at 27 days since the review started so there is no time pressure at the moment. What I'll do is line up another reviewer - that way we'll definitely have a minimum of 2 reviews of this submission - if you do get a chance to complete yours over the next few weeks, that's great - but don't worry about it if you can't.

lorenzo-rovigatti commented 2 years ago

I'm pretty much done with my review. There are a couple of issues that are still open but as soon as those are solved I'll be happy to recommend publication.

zbeekman commented 2 years ago

@whedon generate pdf

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:

zbeekman commented 2 years ago

@ajstewartlang or @danielskatz I have questions about citations in the bibliography:

  1. Are DOIs preferred over ISBNs?
  2. Do all references need a DOI?

Relevant to https://github.com/simoninireland/epyc/issues/11

danielskatz commented 2 years ago

DOIs are preferred and required for references that have them.

danielskatz commented 2 years ago

@whedon check references

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

OK DOIs

- None

MISSING DOIs

- 10.1103/physreve.103.062308 may be a valid DOI for title: Two-pathogen model with competition on clustered networks
- 10.1016/j.jtbi.2020.110381 may be a valid DOI for title: Modelling the effects of environmental heterogeneity within the lung on the tuberculosis lifecycle

INVALID DOIs

- None
zbeekman commented 2 years ago

@danielskatz the paper already includes DOIs for both of those references, I'm not sure why @whedon is saying they're missing. Maybe there's a formatting/capitalization issue?

Additionally, the bibliography provides both an ISBN and DOI for Bailey, R. A. (2009). Design of comparative experiments but pandoc/the preview system are showing the ISBN rather than the DOI in the draft.

danielskatz commented 2 years ago

The bib file should be updated to store dois in doi = {} fields, not url fields. these should be of the form doi = {a.b/...} without the full URL listing

zbeekman commented 2 years ago

@simoninireland the paper looks great! I opened two issues on the project/paper repository. The first is to address/fix the reference DOI display. The second is that there is an unclosed parenthetical clause at the end of the "Differences with other tools" section. Once those are resolved I can check off all the boxes for the paper.

I'm now moving on to examine the documentation and verify the installation and functionality now. I apologize once again that I haven't gotten through my review sooner. I can't seem to catch a break in my personal/family life: We had to say goodbye to our beloved family dog this week. (After a few busy days of taking him to the veterinary hospital, scheduling appointments & picking up medications as his condition worsened.) Thanks so much for your patience and for the interesting tool and paper--it's helped distract me a bit from my recent loss.

ajstewartlang commented 2 years ago

I've just been going through this submission - it looks like there is just one open issue outstanding. Is it in a position to be closed? @zbeekman and @lorenzo-rovigatti might you soon be in a position to tick off the last few points in the checklist?

lorenzo-rovigatti commented 2 years ago

Hey! It's mostly there for me. There is the small issue about testing (which is what the repo's issue is about) and then the paper is good to go as soon as I am concerned.

ajstewartlang commented 2 years ago

:wave: @zbeekman - hope you're doing ok - have you had a chance to move onto testing the installation and functionality yet?

ajstewartlang commented 2 years ago

@zbeekman It would be helpful if you could check off the final points in your checklist soon. Please reach out if you are having any issues.

ajstewartlang commented 2 years ago

@whedon add @amritagos as reviewer

whedon commented 2 years ago

OK, @amritagos is now a reviewer

amritagos commented 2 years ago

@ajstewartlang sorry for being so late with this review...I can't seem to edit the checklist...

ajstewartlang commented 2 years ago

@amritagos thanks for letting me know - I may need to re-invite you - I'll do that now...

editorialbot commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

editorialbot commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

ajstewartlang commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @ajstewartlang, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author or reviewer to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for archive
@editorialbot set 10.21105/zenodo.12345 as archive

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Flag submission with questionable scope
@editorialbot query scope

# Get a link to the complete list of reviewers
@editorialbot list reviewers

# Open the review issue
@editorialbot start review
ajstewartlang commented 2 years ago

@editorialbot add @amritagos as reviewer

editorialbot commented 2 years ago

@amritagos is already included in the reviewers list

ajstewartlang commented 2 years ago

@amritagos can you try running the command below please? If it works, it will re-generate your checklist for you and you should then be able to edit the checklist.

@editorialbot generate my checklist

amritagos commented 2 years ago

Review checklist for @amritagos

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

amritagos commented 2 years ago

@ajstewartlang thank you so much! I'm working on it.

amritagos commented 2 years ago

The package is nicely documented, and is suitable for running repeated computer experiments without resorting to overly complex workflows. The manuscript is well-written and clearly demonstrates the need for epyc. I've opened one minor issue, but I'm happy to recommend this for publication.

ajstewartlang commented 2 years ago

@simoninireland could you perhaps merge this PR and add the references mentioned by @amritagos here please? Then I'm happy to click the accept button. Thanks for your patience with this and many many thanks to @lorenzo-rovigatti and @amritagos for their time reviewing this great submission!

simoninireland commented 2 years ago

Done.

ajstewartlang 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:

ajstewartlang 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

- 10.1103/PhysRevE.104.024303 is OK
- 10.1103/PhysRevE.103.062308 is OK
- 10.1101/2019.12.12.871269 is OK
- 10.1017/CBO9780511611483 is OK

MISSING DOIs

- None

INVALID DOIs

- None