[REVIEW]: AstroImages.jl

[whedon]

Submitting author: @sefffal (William R. Thompson)
Repository: https://github.com/JuliaAstro/AstroImages.jl.git
Branch with paper.md (empty if default branch): paper2
Version:
Editor: @pitsianis
Reviewers: @oschulz, @lucaferranti
Archive: Pending

Status

Status badge code:

HTML: <a href="https://proceedings.juliacon.org/papers/f7d8d2eed40f067a7f7f2a562b4536f4"><img src="https://proceedings.juliacon.org/papers/f7d8d2eed40f067a7f7f2a562b4536f4/status.svg"></a>
Markdown: [![status](https://proceedings.juliacon.org/papers/f7d8d2eed40f067a7f7f2a562b4536f4/status.svg)](https://proceedings.juliacon.org/papers/f7d8d2eed40f067a7f7f2a562b4536f4)

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

@oschulz & @lucaferranti, 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 @carstenbauer 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 @oschulz

Conflict of interest

• As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Authorship: Has the submitting author (@sefffal) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Paper format

• Authors: Does the paper.tex file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
• Page limit: Is the page limit for extended abstracts respected by the submitted document?

Content

• Context: is the scientific context motivating the work correctly presented?
• Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
• Results: are the results presented and compared to approaches with similar goals?

Review checklist for @lucaferranti

Conflict of interest

• As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Authorship: Has the submitting author (@sefffal) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Paper format

• Authors: Does the paper.tex file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
• Page limit: Is the page limit for extended abstracts respected by the submitted document?

Content

• Context: is the scientific context motivating the work correctly presented?
• Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
• Results: are the results presented and compared to approaches with similar goals?

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/JuliaCon/proceedings-review) 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:

1. Set yourself as 'Not watching' https://github.com/JuliaCon/proceedings-review:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

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

@whedon generate pdf

[whedon]

PDF failed to compile for issue #126 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (794.5 files/s, 101392.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           19            635            526           3481
Markdown                        20            328              0           1117
YAML                             7             14             25            169
TOML                             2              5              0             67
CSS                              1              4              0              6
JSON                             1              0              0              4
-------------------------------------------------------------------------------
SUM:                            50            986            551           4844
-------------------------------------------------------------------------------


Statistical information for the repository '554d6f29db2e65dd5b68cdb9' was
gathered on 2023/03/20.
No commited files with the specified extensions were found.

[carstenbauer]

@oschulz, @lucaferranti
Please take a look at the paper here: https://github.com/JuliaAstro/AstroImages.jl/blob/paper/paper/paper.pdf
It would be great to get your reviews in within the next two weeks. Please let me know if you need more time. Thanks in advance!

[oschulz]

The paper draft is still missing an author list.

[carstenbauer]

@sefffal ☝️

[lucaferranti]

I can start reviewing the software side, but for the paper, I'd prefer to be able to compile the pdf on demand with wheedon and have the latest version available. The manually added pdf gets easily outdated

[sefffal]

Hi all, thanks for continuing with the review. It’s still not clear to me why the pdf won’t compile with wheedon and will need outside help to fix the issue.

The author list consists of myself and @giordano. The metadata file should be correct so hopefully when the above issue is solved the author list will be inserted correctly into the PDF.

[whedon]

👋 @lucaferranti, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @oschulz, please update us on how your review is going (this is an automated reminder).

[sefffal]

Is there someone who could help me resolve the issues compiling the PDF? Again, it works locally for me. The author list is only missing since that is supposed to be inserted into the compilation process automatically which is not part of the local compile process.

[carstenbauer]

Hey @sefffal, unfortunately, the editorial staff is currently dramatically overwhelmed - In fact, some of us, including myself, will be stepping down as editor soon. For this reason, I'm afraid, the only way to move on with this is if you manage to fix the compilation issue yourself. I'm sorry for the inconvenience that causes. We would certainly want to help you but it's currently not feasible.

[sefffal]

Thanks @carstenbauer , I appreciate all the hard work the editorial staff must do.
I'll see what I can do to debug things.

[sefffal]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[sefffal]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #126 with the following error:

 Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Rule 'pdflatex': Rules & subrules not known to be previously run:
   pdflatex
Rule 'pdflatex': The following rules & subrules became out-of-date:
      'pdflatex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: List of undefined refs and citations:
  Citation `bezanson2017julia' on page 1 undefined on input line 17
  Citation `fitsstandard' on page 1 undefined on input line 25
Latexmk: Summary of warnings:
  Latex failed to resolve 2 citation(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.aux'
------------
Run number 2 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: List of undefined refs and citations:
  Citation `bezanson2017julia' on page 1 undefined on input line 17
  Citation `fitsstandard' on page 1 undefined on input line 25
Latexmk: Summary of warnings:
  Latex failed to resolve 2 citation(s)
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'paper.out'
------------
Run number 3 of rule 'pdflatex'
------------
------------
Running 'pdflatex  -recorder  "paper.tex"'
------------
Latexmk: List of undefined refs and citations:
  Citation `bezanson2017julia' on page 1 undefined on input line 17
  Citation `fitsstandard' on page 1 undefined on input line 25
Latexmk: Summary of warnings:
  Latex failed to resolve 2 citation(s)
Failure to make 'paper.pdf'
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'paper.log' for details
Looks like we failed to compile the PDF

[sefffal]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[sefffal]

Hmm strange, in order to debug the failure I added a post build command to latexmkrc to echo paper.log. And now it succeeded in generating a proof?

[sefffal]

@whedon generate pdf from branch paper

[pitsianis]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[lucaferranti]

@arfon @xuanxu could you help figuring out why whedon does not produce the pdf (nor informs about an error) are the logs of the action available somewhere?

[xuanxu]

The problem is caused by the presence of more than one paper.md/.tex file

[pitsianis]

@xuanxu thank you! It would be good the generate pdf from command to provide a link to the compilation (error) logs, even though the link would get invalidated after a little while so that we do not have to bother you that often :-) Alternatively, provide the compilation environment and scripts so a motivated user can replicate the latexmk command independently.

@sefffal please make the suggested correction.

[arfon]

@xuanxu thank you! It would be good the generate pdf from command to provide a link to the compilation (error) logs, even though the link would get invalidated after a little while so that we do not have to bother you that often :-) Alternatively, provide the compilation environment and scripts so a motivated user can replicate the latexmk command independently.

@pitsianis – in the future this will be addressed as JuliaCon moves off @whedon and onto the new EditorialBot.

[sefffal]

Thanks all for helping to identify the problem. Could you clarify it a bit more for me though, in branch paper I have a folder called paper with paper.tex. The only other .tex files come from the template, and there are no .md files.

[sefffal]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[sefffal]

Bump on this; I would still love to see this proceeding go through.

[oschulz]

Do we have a final PDF now?

[lucaferranti]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf. Paper file not found.

[lucaferranti]

@editorialbot generate pdf from branch paper

[editorialbot]

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

@editorialbot commands

[lucaferranti]

@editorialbot commands

[editorialbot]

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

# List all available commands
@editorialbot commands

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

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

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

# Reject paper
@editorialbot reject

# Withdraw paper
@editorialbot withdraw

# Invite an editor to edit a submission (sending them an email)
@editorialbot invite @(.*) as editor

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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

# Generates the pdf paper
@editorialbot generate pdf

# Accept and publish the paper
@editorialbot accept

# Update data on an accepted/published paper
@editorialbot reaccept

# Generates a LaTeX preprint file
@editorialbot generate preprint

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

[lucaferranti]

@editorialbot set paper as branch

[editorialbot]

Done! branch is now paper

[lucaferranti]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[lucaferranti]

@sefffal pdf generation works 🎉 . I wasn't sure which branch to use paper or paper2, can you take a look at the paper and let me know?

[sefffal]

Thanks @lucaferranti that's excellent news! I will check things over and comment when I've confirmed it's showing the right content.

[sefffal]

@editorialbot set paper2 as branch

[editorialbot]

Done! branch is now paper2

[sefffal]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.