[REVIEW]: AstroImages.jl

whedon commented 1 year ago

Submitting author: !--author-handle-->@sefffal@pitsianis<!--end-editor-- Reviewers: @oschulz, @lucaferranti Archive: Pending

Status

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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:

Make sure you're logged in to your GitHub account
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

[x] 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

[x] I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] 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?
[x] 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)?
[x] Page limit: Is the page limit for extended abstracts respected by the submitted document?

Content

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

Review checklist for @lucaferranti

Conflict of interest
[x] 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

[x] I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

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

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] 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?

lucaferranti commented 1 year ago

@whedon generate pdf

whedon commented 1 year ago

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

 Can't find any papers to compile :-(

lucaferranti commented 1 year ago

@whedon generate pdf from branch paper

whedon commented 1 year ago

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

whedon commented 1 year ago

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

lucaferranti commented 1 year ago

@sefffal should I generate the pdf from the branch paper or paper2? Can you take a quick look at the latest generated pdf and confirm whether from a content perspective it's up to date and ready for review?

lucaferranti commented 1 year ago

@whedon check references

sefffal commented 1 year ago

@sefffal should I generate the pdf from the branch paper or paper2? Can you take a quick look at the latest generated pdf and confirm whether from a content perspective it's up to date and ready for review?

Excellent, thank you for your review! The paper proof is up to date content wise but is still missing the author and journal info. I tried my best to find the issue but for some reason whedon is not updating the linked PDF.

sefffal commented 9 months ago

Bump on this. I would really appreciate if someone can find out why the PDF for this isn’t updating (it’s stale). Alternatively could we make an exception and do this manually?

lucaferranti commented 9 months ago

@sefffal , the editorial team got some fresh blood and we are among other things upgrading the bot from the old whedon to editorial-bot which should make latex workflow easier. This should happen within the end of the month, but I can nevertheless also look into the specific issue of this and try to get this fixed before.

Meanwhile, I've actually almost finished the review from paper side and will post the comments soon (only minor comments), so this should go forward, apologies for the loong delay

sefffal commented 9 months ago

Ok excellent, thank you so much for the update!

matbesancon commented 9 months ago

@whedon assign @pitsianis as editor

lucaferranti commented 9 months ago

@whedon generate pdf from branch paper

whedon commented 9 months ago

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

whedon commented 9 months ago

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

lucaferranti commented 9 months ago

@sefffal, at least compilation runs without errors, but there's still the issue of authors not being inserted.

As a quick check, may I ask you to try the following?

Save the content of your paper, metadata in paper.yml and references in ref.bib
Overwrite the paper folder with a fresh template from https://github.com/JuliaCon/JuliaConSubmission.jl
Replace the new paper.yml and ref.bib with your own and reinser the paper body into paper.tex

If this work, then we can all be happy. If it doesnt, then I'll try to narrow down the issue further.

sefffal commented 9 months ago

Okay thanks @lucaferranti, I’ll give that a shot in the next day. Much appreciated!

sefffal commented 9 months ago

As a first test, I have reset the the paper folder (paper branch) to the exact contents of the template. I'll try to build this and see if it works.

If that works, I'll add back in our paper content.

sefffal commented 9 months ago

@whedon generate pdf from branch paper

whedon commented 9 months ago

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

whedon commented 9 months ago

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

sefffal commented 9 months ago

@whedon generate pdf from branch paper

whedon commented 9 months ago

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

whedon commented 9 months ago

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

sefffal commented 9 months ago

@whedon generate pdf from branch paper

whedon commented 9 months ago

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

whedon commented 9 months ago

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 14
  Citation `fitsstandard' on page 1 undefined on input line 22
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 14
  Citation `fitsstandard' on page 1 undefined on input line 22
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 14
  Citation `fitsstandard' on page 1 undefined on input line 22
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 commented 9 months ago

@whedon generate pdf from branch paper

whedon commented 9 months ago

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

whedon commented 9 months ago

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 14
  Citation `fitsstandard' on page 1 undefined on input line 22
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 14
  Citation `fitsstandard' on page 1 undefined on input line 22
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 14
  Citation `fitsstandard' on page 1 undefined on input line 22
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 commented 9 months ago

So after these tests, there's no issues with paper.yml. The issues start after I swapped out the body of the paper template and ref.bib.

Building locally, the references are picked up as intended.

sefffal commented 9 months ago

@whedon generate pdf from branch paper

whedon commented 9 months ago

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

whedon commented 9 months ago

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"'
------------
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"'
------------
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"'
------------
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 commented 9 months ago

For this test above, I removed all uses of \cite. Looks like that wasn't the issue, and there is something deeper. I will fully revert paper.tex and add paragraphs one by one...

sefffal commented 9 months ago

@whedon generate pdf from branch paper

whedon commented 9 months ago

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

whedon commented 9 months ago

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

sefffal commented 9 months ago

@whedon generate pdf from branch paper

whedon commented 9 months ago

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

whedon commented 9 months ago

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

sefffal commented 9 months ago

@whedon generate pdf from branch paper

whedon commented 9 months ago

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

sefffal commented 9 months ago

@whedon generate pdf from branch paper

whedon commented 9 months ago

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

lucaferranti commented 9 months ago

@whedon generate pdf from branch paper

whedon commented 9 months ago

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

lucaferranti commented 9 months ago

looks like we broke whedon?

pitsianis commented 8 months ago

@whedon assign @pitsianis as editor

pitsianis commented 8 months ago

@whedon commands

JuliaCon / proceedings-review