Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[PRE REVIEW]: CompactObject: An open-source Python package for full-scope neutron star equation of state inference #7487

Closed
editorialbot opened this issue Nov 15, 2024 · 39 comments
Assignees
Labels
pre-review Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences

Comments

@editorialbot
Copy link
Collaborator

editorialbot commented Nov 15, 2024

Submitting author: @ChunHuangPhy (Chun Huang)
Repository: https://github.com/ChunHuangPhy/CompactObject
Branch with paper.md (empty if default branch):
Version: v1.9.9
Editor: @warrickball
Reviewers: @kelslund, @rhaas80
Managing EiC: Warrick Ball

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/767dfa84e527ba5fca907401e51cd371"><img src="https://joss.theoj.org/papers/767dfa84e527ba5fca907401e51cd371/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/767dfa84e527ba5fca907401e51cd371/status.svg)](https://joss.theoj.org/papers/767dfa84e527ba5fca907401e51cd371)

Author instructions

Thanks for submitting your paper to JOSS @ChunHuangPhy. Currently, there isn't a JOSS editor assigned to your paper.

@ChunHuangPhy if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
@editorialbot editorialbot added pre-review Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences labels Nov 15, 2024
@editorialbot
Copy link
Collaborator Author

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

Software report:

github.com/AlDanial/cloc v 1.90  T=0.15 s (978.7 files/s, 316789.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      16           2435           2505           9216
Python                          42           1673           2064           3957
Jupyter Notebook                29              0          10196           3564
CSV                              3              0              0           3451
SVG                              1              0              0           2671
HTML                            12            272             36           2334
CSS                              4            187             35            756
reStructuredText                30            363            250            447
TeX                              1             22              0            347
Markdown                         2             71              0            218
YAML                             2              4              6             67
TOML                             1              2              0             35
DOS Batch                        1              8              1             26
make                             2              8             14             18
-------------------------------------------------------------------------------
SUM:                           146           5045          15107          27107
-------------------------------------------------------------------------------

Commit count by author:

   341	ChunHuangPhy
   105	9
    30	osborn62
    29	João Cartaxo
    16	Nicole Osborn
     9	zhoutz
     8	nwhitsett
     7	Shashwat Sourav
     6	Xuezhi Liu
     5	Tuhin Malik
     5	obs-oertel
     4	crystalywl
     3	ZhihengWA
     3	fizban007
     2	DELL
     2	dxy21
     1	John John Groger
     1	jgroger

@editorialbot
Copy link
Collaborator Author

Paper file info:

📄 Wordcount for paper.md is 1341

✅ The paper includes a Statement of need section

@editorialbot
Copy link
Collaborator Author

License info:

🟡 License found: Other (Check here for OSI approval)

@editorialbot
Copy link
Collaborator Author

@warrickball
Copy link

@ChunHuangPhy — Thanks for your submission! All the suitable JOSS editors are currently working at capacity so I'm going to "waitlist" this review until an editor with the relevant expertise is available to take it on.

I also noticed that our system hasn't automatically recognised your MIT License. I'm not quite sure why not but it might be because your specific text differs from the standard version. Specifically, I think these lines

Copyright (c)[2024 Chun Huang, João Cartaxo, Tuhin Malik, Wenli Yuan,
Shashwat Sourav, Xuezhi Liu, Tianzhe Zhou, John Groger, Zhiheng Wang, Nicole Osborn, Nathan Whitsett]

might need to be

Copyright (c) 2024 Chun Huang, João Cartaxo, Tuhin Malik, Wenli Yuan,
Shashwat Sourav, Xuezhi Liu, Tianzhe Zhou, John Groger, Zhiheng Wang, Nicole Osborn, Nathan Whitsett

and you might even need to put all the authors back on one line. Have a look at other MIT Licensed code you might know of or browse past JOSS articles to see what might be the issue here, then run @editorialbot check repository to rerun our checks.

Also, the paper is failing to build at least because of a YAML error in the metadata, which is also flagged by the GitHub UI if you view the file there. Specifically, I think the tags should be indented by two spaces, not four.

If you think you've fixed this, you can try rebuilding the paper with @editorialbot generate pdf.

@warrickball warrickball added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Nov 15, 2024
@ChunHuangPhy
Copy link

@editorialbot check repository

@editorialbot
Copy link
Collaborator Author

Software report:

github.com/AlDanial/cloc v 1.90  T=0.15 s (966.3 files/s, 312850.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      16           2435           2505           9216
Python                          42           1673           2064           3957
Jupyter Notebook                29              0          10196           3564
CSV                              3              0              0           3451
SVG                              1              0              0           2671
HTML                            12            272             36           2334
CSS                              4            187             35            756
reStructuredText                30            367            250            451
TeX                              1             22              0            347
Markdown                         2             71              0            218
YAML                             2              4              6             67
TOML                             1              2              0             35
DOS Batch                        1              8              1             26
make                             2              8             14             18
-------------------------------------------------------------------------------
SUM:                           146           5049          15107          27111
-------------------------------------------------------------------------------

Commit count by author:

   343	ChunHuangPhy
   105	9
    30	osborn62
    29	João Cartaxo
    16	Nicole Osborn
     9	zhoutz
     8	nwhitsett
     7	Shashwat Sourav
     6	Xuezhi Liu
     5	Tuhin Malik
     5	obs-oertel
     4	crystalywl
     3	ZhihengWA
     3	fizban007
     2	DELL
     2	dxy21
     1	John John Groger
     1	jgroger

@editorialbot
Copy link
Collaborator Author

Paper file info:

📄 Wordcount for paper.md is 1341

✅ The paper includes a Statement of need section

@editorialbot
Copy link
Collaborator Author

License info:

🟡 License found: Other (Check here for OSI approval)

@ChunHuangPhy
Copy link

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

@ChunHuangPhy
Copy link

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

@warrickball
Copy link

warrickball commented Nov 16, 2024

I appreciate your efforts here @ChunHuangPhy. I'll try to debug why the paper doesn't compile.

In the meantime, does someone in @openjournals/dev know why the pipeline isn't detecting the MIT License? Is it because the authors are spread over a line break? Aside from quotation-mark styles, the text looks exactly correct.

@ChunHuangPhy
Copy link

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

@ChunHuangPhy
Copy link

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

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

@editorialbot
Copy link
Collaborator Author

Five most similar historical JOSS papers:

CosmicProfiles: A Python package for radial profiling of finitely sampled dark matter halos and galaxies
Submitting author: @tibordome
Handling editor: @adonath (Active)
Reviewers: @benediktdiemer, @phil-mansfield
Similarity score: 0.7341

X-PSI: A Python package for neutron star X-ray pulse simulation and inference
Submitting author: @drannawatts
Handling editor: @adonath (Active)
Reviewers: @JohannesBuchner, @matteobachetti
Similarity score: 0.7307

CoReCon: an open, community-powered collection of Reionization constraints
Submitting author: @EGaraldi
Handling editor: @eloisabentivegna (Retired)
Reviewers: @iliantiliev, @afialkov, @Stefan-Heimersheim
Similarity score: 0.7301

Paicos: A Python package for analysis of (cosmological) simulations performed with Arepo
Submitting author: @tberlok
Handling editor: @JBorrow (Active)
Reviewers: @ttricco, @kyleaoman
Similarity score: 0.7241

Foam: A Python package for forward asteroseismic modelling of gravity modes
Submitting author: @MichielsenM
Handling editor: @warrickball (Active)
Reviewers: @AnkitBarik, @ashleychontos
Similarity score: 0.7238

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

@ChunHuangPhy
Copy link

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

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

@editorialbot
Copy link
Collaborator Author

Five most similar historical JOSS papers:

CosmicProfiles: A Python package for radial profiling of finitely sampled dark matter halos and galaxies
Submitting author: @tibordome
Handling editor: @adonath (Active)
Reviewers: @benediktdiemer, @phil-mansfield
Similarity score: 0.7313

X-PSI: A Python package for neutron star X-ray pulse simulation and inference
Submitting author: @drannawatts
Handling editor: @adonath (Active)
Reviewers: @JohannesBuchner, @matteobachetti
Similarity score: 0.7274

CoReCon: an open, community-powered collection of Reionization constraints
Submitting author: @EGaraldi
Handling editor: @eloisabentivegna (Retired)
Reviewers: @iliantiliev, @afialkov, @Stefan-Heimersheim
Similarity score: 0.7265

CWInPy: A Python package for inference with continuous gravitational-wave signals from pulsars
Submitting author: @mattpitkin
Handling editor: @dfm (Active)
Reviewers: @GregoryAshton, @ColmTalbot
Similarity score: 0.7199

The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained
Submitting author: @AxelBrandenburg
Handling editor: @arfon (Active)
Reviewers: @zingale, @rtfisher
Similarity score: 0.7195

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

@xuanxu
Copy link
Member

xuanxu commented Nov 19, 2024

does someone in @openjournals/dev know why the pipeline isn't detecting the MIT License?

The license detection is based on comparing the license file with the 'official' templates. My guess is that the line for authors here is so long, and the MIT license is so short, that it makes the text differ from the template a big enough percentage so it is marked as 'Other'.

@ChunHuangPhy
Copy link

Do we need to change the MIT license to make it pass the test?

@xuanxu
Copy link
Member

xuanxu commented Nov 19, 2024

Do we need to change the MIT license to make it pass the test?

No need. The bot check is just a tool to help editors, reading the license file I think is clear it's a valid MIT license.

@ChunHuangPhy
Copy link

Great, thanks!

@warrickball
Copy link

Hi again @ChunHuangPhy, and sorry for the long wait. I'll take this on as an editor and start looking for (at least) two reviewers. If you have anyone you'd like to suggest, let me know here. You may wish to have a look at authors of previous JOSS papers and in our reviewer database. Note that we do have a conflict of interest policy.

I'll start looking largely by these routes in the meantime.

@ChunHuangPhy
Copy link

Thanks! I will wait for the reviews.

@warrickball
Copy link

@editorialbot assign me as editor

@editorialbot
Copy link
Collaborator Author

Assigned! @warrickball is now the editor

@warrickball warrickball removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Feb 5, 2025
@warrickball
Copy link

@editorialbot add @kelslund as reviewer

@editorialbot
Copy link
Collaborator Author

@kelslund added to the reviewers list!

@warrickball
Copy link

@editorialbot add @rhaas80 as reviewer

@editorialbot
Copy link
Collaborator Author

@rhaas80 added to the reviewers list!

@warrickball
Copy link

Hi @ChunHuangPhy, I've identified two reviewers and am ready to start the review.

For transparency, note that both reviewers have indicated potential conflicts of interest that I've acknowledged and am happy to waive. @kelslund is on a conference organising committee that's vice-chaired by one of the authors and @rhaas80 co-authored a large review article in 2024 with another. I don't believe these conflicts will influence their reviews but I'll wait a few days to start the review in case you wish to comment.

@ChunHuangPhy
Copy link

Thanks for your efforts, I happy to start the review process, and have no more comments to add on.

@warrickball
Copy link

@editorialbot start review

@editorialbot
Copy link
Collaborator Author

OK, I've started the review over in #7759.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
pre-review Track: 1 (AASS) Astronomy, Astrophysics, and Space Sciences
Projects
None yet
Development

No branches or pull requests

4 participants