[REVIEW]: GNU Data Language 1.0: a free/libre and open-source drop-in replacement for IDL/PV-WAVE

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@pjb7687@gkthiruvathukal<!--end-editor-- Reviewers: @mgalloy, @mohawk2 Archive: 10.5281/zenodo.7275468

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b84d8eef2986bcafdb402f60733d56c2"><img src="https://joss.theoj.org/papers/b84d8eef2986bcafdb402f60733d56c2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b84d8eef2986bcafdb402f60733d56c2/status.svg)](https://joss.theoj.org/papers/b84d8eef2986bcafdb402f60733d56c2)

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

@mgalloy & @mohawk2, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @gkthiruvathukal 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 ✨

Checklists

📝 Checklist for @mgalloy

📝 Checklist for @mohawk2

editorialbot commented 2 years ago

Hello humans, 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:

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

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=1.43 s (767.7 files/s, 251887.3 lines/s)
-----------------------------------------------------------------------------------
Language                         files          blank        comment           code
-----------------------------------------------------------------------------------
C++                                207          21907          21433         149809
IDL                                615           4700          28762          42937
C/C++ Header                       206           6307           7994          32036
C                                   10           4922           8775          12048
ANTLR Grammar                        7            972           1118           7025
make                                 1           1362            484           2716
CMake                               28            255            546           1855
Bourne Shell                         1             50             21            515
XML                                  2              0              0            354
YAML                                 3              7              7            345
Markdown                             2             57              0            320
Python                               4             69            128            215
TeX                                  1             14              0            145
HTML                                 2              0            108             95
Prolog                               5             16              0             75
Fortran 90                           1             10              0             28
Bourne Again Shell                   1              1              1             13
diff                                 2              1             15              7
Windows Resource File                1              0              0              1
-----------------------------------------------------------------------------------
SUM:                              1099          40650          69392         250539
-----------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1579

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.48550/arXiv.1101.0679 is OK
- 10.48550/arXiv.1909.02371 is OK
- 10.1038/s41598-021-92923-4 is OK
- 10.1126/sciadv.aax2742 is OK
- 10.1038/s41467-022-29254-z is OK
- 10.1038/s41598-022-08854-1 is OK
- 10.1038/s41586-021-04101-1 is OK
- 10.1016/j.devcel.2021.10.006 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

mgalloy commented 2 years ago

Review checklist for @mgalloy

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/gnudatalanguage/gdl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@pjb7687) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality of the software can be verified?
[x] 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

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

mohawk2 commented 2 years ago

Review checklist for @mohawk2

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/gnudatalanguage/gdl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@pjb7687) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality of the software can be verified?
[x] 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

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

mohawk2 commented 2 years ago

@gkthiruvathukal @pjb7687 I have completed my review as reflected by all the boxes being checked above, and believe the paper and software are good to go.

I did decide to finesse this point a bit:

Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems)

...in that the various papers citing usage of GDL (and the unit tests, etc) definitely meet this, so all is well - but I feel that adding a short snippet of real-world code in the generally excellent project README.md would be a good idea.

mgalloy commented 2 years ago

@gkthiruvathukal I have completed my review and believe the paper is ready for publication.

I agree some direct examples of GDL usage and output in the README.md would be nice, but not required with all the other code examples in the unit tests, the .pro files in the library, and references to IDL examples.

gkthiruvathukal commented 2 years ago

@mgalloy and @mohawk2 Thank you for your reviews! It looks like we are ready to move toward acceptance.

slayoo commented 2 years ago

@gkthiruvathukal, let me ask for the status of this review, thanks.

gkthiruvathukal commented 2 years ago

@slayoo I think we are ready for the next steps!

Please do the following:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo
[ ] Check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
[ ] List the Zenodo DOI of the archived version here.

Let me know when these are done!

pjb7687 commented 2 years ago

@slayoo May I ask if I would do that, or you are already doing it? Thanks!

slayoo commented 1 year ago

@pjb7687 Apparently, we have already automation in place at Zenodo for archival of every release, so this is automatically done. The question is which version to reference in the paper? This can be "1.0.0", the last one, or perhaps a fresh one? Making a fresh one has the advantage that beforehand we can create the .zenodo.json file (like here: https://github.com/nipy/nipype/blob/master/.zenodo.json) which will instruct Zenodo how to populate the paper metadata. One problem is that CI fails as of today :( https://github.com/gnudatalanguage/gdl/actions/runs/3317371821

pjb7687 commented 1 year ago

@slayoo I think it makes more sense to me to deposit the version when we submitted the paper to JOSS, as this is the version of GDL that is actually described in the manuscript. We submitted it to JOSS on Jun 22, and I believe this one (https://github.com/gnudatalanguage/gdl/actions/runs/2613108929) is the closest working build. I would like to ask if you agree with it, if so I would deposit it to Zenodo with the manuscript.

slayoo commented 1 year ago

@pjb7687 this commit is already published on Zenodo as a weekly release - we can just change its metadata: https://zenodo.org/record/6796032

pjb7687 commented 1 year ago

@slayoo I would prefer to create another one as I hesitate to change the author list of the existing one.

slayoo commented 1 year ago

@pjb7687 it's up to you, of course, but I wonder if having two Zenodo archives for the very same commit hash with differing "author lists" is not even more misleading?

pjb7687 commented 1 year ago

Hi all,

I made a tagged release 'v1.0.0-JOSS', based on commit 9416a4b998 (which is the last commit relevant to the JOSS manuscript). Here you can find the tag: https://github.com/gnudatalanguage/gdl/tree/v1.0.0-JOSS
The archive is published at Zenodo.
- Link: https://zenodo.org/record/7275468#.Y2NJfnbP07c
I believe I have entered the metadata correctly but it would be nice if @slayoo would confirm it.
The DOI of the Zenodo release is: 10.5281/zenodo.7275468

Best, Jeongbin

slayoo commented 1 year ago

Thank you, @pjb7687! I've checked the metadata against the paper.md (https://github.com/gnudatalanguage/gdl/blob/master/paper/paper.md) and clicked on all ORCID links - all seems to match.

@gkthiruvathukal, please do proceed, thanks!

slayoo commented 1 year ago

@gkthiruvathukal, please let us know how we can proceed here? Thanks

slayoo commented 1 year ago

@arfon, let me kindly ask how could we proceed here? Thanks

danielskatz commented 1 year ago

@slayoo - I'll help move this forward

danielskatz commented 1 year ago

@editorialbot set v1.0.0-JOSS as version

editorialbot commented 1 year ago

Done! version is now v1.0.0-JOSS

danielskatz commented 1 year ago

@editorialbot set 10.5281/zenodo.7275468 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7275468

danielskatz commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.48550/arXiv.1101.0679 is OK
- 10.48550/arXiv.1909.02371 is OK
- 10.1038/s41598-021-92923-4 is OK
- 10.1126/sciadv.aax2742 is OK
- 10.1038/s41467-022-29254-z is OK
- 10.1038/s41598-022-08854-1 is OK
- 10.1038/s41586-021-04101-1 is OK
- 10.1016/j.devcel.2021.10.006 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3831, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

@pjb7687 - I'm another track editor, helping out since the track editor here is out currently. I've proofread the paper, and have made a bunch of small suggestions in https://github.com/gnudatalanguage/gdl/pull/1443 - please merge this, or let me know what you disagree with, then we can proceed.

pjb7687 commented 1 year ago

@danielskatz Just now I've merged the PR. Thank you so much!

danielskatz commented 1 year ago

@editorialbot recommend-accept

@pjb7687 - once this command finishes, please check the new PDF to make sure everything still looks ok and let me know. I'll do the same, then we can proceed to acceptance and publication

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.48550/arXiv.1101.0679 is OK
- 10.48550/arXiv.1909.02371 is OK
- 10.1038/s41598-021-92923-4 is OK
- 10.1126/sciadv.aax2742 is OK
- 10.1038/s41467-022-29254-z is OK
- 10.1038/s41598-022-08854-1 is OK
- 10.1038/s41586-021-04101-1 is OK
- 10.1016/j.devcel.2021.10.006 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3832, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

pjb7687 commented 1 year ago

@danielskatz I reviewed the text again and it looks good to me.

danielskatz commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3833
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04633
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 1 year ago

@pjb7687 - the DOI isn't resolving for me yet, so I'm going to keep this open for now - I think this is related to maintenance on Crossref which should be complete and catch up in a few hours

pjb7687 commented 1 year ago

@danielskatz The DOI seems to work now, but the iframe shows me 404 instead of the pdf.

danielskatz commented 1 year ago

Let's wait a couple of hours, then I can try something else to fix this if it doesn't resolve itself.

slayoo commented 1 year ago

Thank you @danielskatz! Thank you @gkthiruvathukal, @mgalloy and @mohawk2!

danielskatz commented 1 year ago

@editorialbot reaccept

editorialbot commented 1 year ago

Rebuilding paper!

editorialbot commented 1 year ago

🌈 Paper updated!

New PDF and metadata files :point_right: https://github.com/openjournals/joss-papers/pull/3834

openjournals / joss-reviews