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[REVIEW]: GNU Data Language 1.0: a free/libre and open-source drop-in replacement for IDL/PV-WAVE
Submitting author: @pjb7687 (Jeongbin Park) Repository: https://github.com/gnudatalanguage/gdl Branch with paper.md (empty if default branch): Version: 1.0 Editor: @gkthiruvathukal Reviewers: @mgalloy, @mohawk2 Archive: Pending
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: [](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
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:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
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
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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
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gitinspector failed to run statistical information for the repository
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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?
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?
@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.
@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.
@mgalloy and @mohawk2 Thank you for your reviews! It looks like we are ready to move toward acceptance.
@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 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
@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.
@pjb7687 this commit is already published on Zenodo as a weekly release - we can just change its metadata: https://zenodo.org/record/6796032
@slayoo I would prefer to create another one as I hesitate to change the author list of the existing one.
@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?
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
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!