[REVIEW]: AstroImages.jl

whedon commented 1 year ago

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

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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

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

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✨ 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?

whedon commented 1 year ago

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 :tada:.

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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 😿

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whedon commented 1 year ago

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

 Can't find any papers to compile :-(

whedon commented 1 year ago

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 commented 1 year ago

@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 commented 1 year ago

The paper draft is still missing an author list.

carstenbauer commented 1 year ago

@sefffal ☝️

lucaferranti commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

whedon commented 1 year ago

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

sefffal commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

sefffal commented 1 year ago

@whedon commands

whedon commented 1 year ago

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 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

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 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:

sefffal commented 1 year ago

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 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:

sefffal 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:

sefffal 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:

sefffal commented 1 year ago

@whedon generate pdf from branch paper2

whedon commented 1 year ago

Attempting PDF compilation from custom branch paper2. 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:

sefffal 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:

sefffal commented 1 year ago

@whedon generate pdf from branch paper2

whedon commented 1 year ago

Attempting PDF compilation from custom branch paper2. 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:

sefffal commented 1 year ago

@whedon generate pdf from branch paper2

whedon commented 1 year ago

Attempting PDF compilation from custom branch paper2. 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:

sefffal commented 1 year ago

@whedon generate pdf from branch paper2

whedon commented 1 year ago

Attempting PDF compilation from custom branch paper2. 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:

oschulz commented 1 year ago

Authors are still missing. :-)

sefffal commented 1 year ago

@oschulz @carstenbauer I can confirm that the PDF generated by whedon does not reflect the contents of the repository. I even tried manually inserting the authors and title instead of letting whedon insert it with the ruby script. Changing the text also has no effect.

I tried to echo the latex log but I'm not sure where that goes.

Unfortunately I am now truly out of ideas on how to debug this without digging into the whedon infrastructure itself.

oschulz commented 1 year ago

@carstenbauer can I ignore the authors stuff in the review?

lucaferranti commented 1 year ago

apologies for the long radio silence, I've now finally managed to review from the software side and I have only few minor nitpicks

[ ] The pages Polarization and Spectral Axes in the manual are empty
[ ] While the organization docs has a short Contributing section in the homepage, for the purpose of submission it would be good to add a short minimalistic contributing guidelines also for the package readme.

(this is an extra improvement suggestion, not needed for this submission). One thing I noticed while trying the examples in the docs is that it was downloading manually some images. Have you considered doing something like TestImages.jl but for astro images? (maybe call it AstroTestImages.jl) That could offer a nicer interface for users to play with popular(?) astro images e.g. while going through the documentation.

JuliaCon / proceedings-review