Closed editorialbot closed 1 month ago
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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5281/zenodo.7385533 is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.5281/zenodo.7976754 is OK
- 10.5281/zenodo.7836668 is OK
- 10.5281/zenodo.2677911 is OK
- 10.5281/zenodo.7740140 is OK
- 10.5281/zenodo.10804357 is OK
MISSING DOIs
- 10.32614/cran.package.admmdensestsubmatrix may be a valid DOI for title: admmDensestSubmatrix: Alternating Direction Method...
- 10.32614/cran.package.fselector may be a valid DOI for title: FSelector: Selecting Attributes
- 10.32614/cran.package.varrank may be a valid DOI for title: varrank: Heuristics Tools Based on Mutual Informat...
INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.90 T=0.02 s (1537.0 files/s, 197948.6 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
R 19 374 444 1104
Rmd 1 161 540 439
Markdown 4 54 0 177
CSV 1 0 0 162
TeX 2 10 0 119
YAML 1 0 4 18
-------------------------------------------------------------------------------
SUM: 28 599 988 2019
-------------------------------------------------------------------------------
Commit count by author:
121 Anna Graff
77 Marc Lischka
21 marclischka
11 Taras Zakharko
9 Work
5 reinhardfurrer
2 Balthasar Bickel
Paper file info:
📄 Wordcount for paper.md
is 1319
✅ The paper includes a Statement of need
section
License info:
🟡 License found: GNU Affero General Public License v3.0
(Check here for OSI approval)
@elenlefoll this is the review issue. Please let me know if you have any questions.
I will keep looking for one or more additional reviewers.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
:wave: @yjunechoe @stefanocoretta @dosc91 would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html
@osorensen Happy to review!
Wonderful @yjunechoe!
@editorialbot add @yjunechoe as reviewer
@yjunechoe added to the reviewers list!
@yjunechoe, I have added you as a reviewer, and you are welcome to start your review whenever you like, but it would be great if you could do so within the next three weeks. You find instructions at the top of this thread, and are welcome to reach out to me if you have any questions.
Hi @osorensen ! Happy to review too if you need a second
@editorialbot add @stefanocoretta as reviewer
@stefanocoretta added to the reviewers list!
Thanks @stefanocoretta. You see the instructions at the top of this thread. Please reach out to me if you have any questions.
Just curious - @annagraff do you/coauthors have plans to eventually submit the package to CRAN as well? I have some suggestions which are beyond the standards of JOSS (i.e., not acceptance-blocking) but may be helpful to get the package past the initial submission check by CRAN.
Hello @yjunechoe - this would be our intention, yes!
@osorensen I raised this as a checklist comment for the software paper but I now feel a bit uncertain - could you clarify whether demonstrating package design/features via code blocks is allowed for JOSS papers? In the review criteria, I see:
Note the paper should not include software documentation such as API (Application Programming Interface) functionality, as this should be outlined in the software documentation.
The paper in this submission contains example code, but is not quite documentation of the API, so I'm having trouble evaluating the current case.
@osorensen I raised this as a checklist comment for the software paper but I now feel a bit uncertain - could you clarify whether demonstrating package design/features via code blocks is allowed for JOSS papers? In the review criteria, I see:
Note the paper should not include software documentation such as API (Application Programming Interface) functionality, as this should be outlined in the software documentation.
The paper in this submission contains example code, but is not quite documentation of the API, so I'm having trouble evaluating the current case.
Thanks for raising the issue @yjunechoe. Looking at the paper, I feel this is more detailed code than usual JOSS paper. I hence agree with you that this belongs in README and/or vignettes, and that the paper instead should focus on the high-level architecture of the software.
@elenlefoll this is the review issue. Please let me know if you have any questions.
I will keep looking for one or more additional reviewers.
I have completed the review check list. Is there anything else that I need to do?
Thanks for your review, @elenlefoll. There is nothing more you need to do know. We appreciate your work.
@stefanocoretta can you please update us on how it's going with your review?
@stefanocoretta can you please update us on how it's going with your review?
Very sorry for the delay! It was very busy at work with dissertations.
Hi @stefanocoretta, do I understand correctly that your review is already complete with no new issues? If this is the case, I will proceed to soon push the changes made to address issues raised by @elenlefoll and @yjunechoe.
Just to expedite the process: I've read through the revisions in the draft PR and I'm really happy with all the changes I see, so I've checked off all boxes for my review. I think the submission can move forward to the next step.
One small follow-up suggestion to authors: it'd be nice if the README could also print the output of some of the code being ran (vs. having every line be an assignment to a variable).
@annagraff, it seems like all reviews are completed then. I'll read through the paper soon, and let you know if I have any further comments.
@editorialbot generate pdf
@editorialbot check references
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
✅ OK DOIs
- 10.5281/zenodo.7385533 is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.5281/zenodo.7976754 is OK
- 10.5281/zenodo.7836668 is OK
- 10.5281/zenodo.2677911 is OK
- 10.5281/zenodo.7740140 is OK
- 10.5281/zenodo.10804357 is OK
🟡 SKIP DOIs
- None
❌ MISSING DOIs
- 10.32614/cran.package.admmdensestsubmatrix may be a valid DOI for title: admmDensestSubmatrix: Alternating Direction Method...
- 10.32614/cran.package.fselector may be a valid DOI for title: FSelector: Selecting Attributes
- 10.32614/cran.package.varrank may be a valid DOI for title: varrank: Heuristics Tools Based on Mutual Informat...
❌ INVALID DOIs
- None
@osorensen: I still need to merge the changes to the paper to main, which I will do once Stefano confirms there are are no further issues from his end
@annagraff, you don't really have to wait for that, since completing the checklist implies that the review is completed, as far as JOSS is concerned.
@annagraff, any progress on merging the changes into main?
Sorry for the delay, I have just merged them now!
On 26 Aug 2024, at 21:24, Øystein Sørensen @.***> wrote:
@annagraff https://github.com/annagraff, any progress on merging the changes into main?
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7024#issuecomment-2310913959, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKEXNOPM5YBITBXWBLDCLF3ZTN6IBAVCNFSM6AAAAABLKHMGZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJQHEYTGOJVHE. You are receiving this because you were mentioned.
@editorialbot generate pdf
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
✅ OK DOIs
- 10.5281/zenodo.7385533 is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.5281/zenodo.7976754 is OK
- 10.5281/zenodo.7836668 is OK
- 10.5281/zenodo.2677911 is OK
- 10.5281/zenodo.7740140 is OK
- 10.5281/zenodo.10804357 is OK
🟡 SKIP DOIs
- None
❌ MISSING DOIs
- 10.32614/cran.package.admmdensestsubmatrix may be a valid DOI for title: admmDensestSubmatrix: Alternating Direction Method...
- 10.32614/cran.package.fselector may be a valid DOI for title: FSelector: Selecting Attributes
- 10.32614/cran.package.varrank may be a valid DOI for title: varrank: Heuristics Tools Based on Mutual Informat...
❌ INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Reference check summary (note 'MISSING' DOIs are suggestions that need verification): ✅ OK DOIs - 10.5281/zenodo.7385533 is OK - 10.1093/bioinformatics/bty633 is OK - 10.5281/zenodo.7976754 is OK - 10.5281/zenodo.7836668 is OK - 10.5281/zenodo.2677911 is OK - 10.5281/zenodo.7740140 is OK - 10.5281/zenodo.10804357 is OK 🟡 SKIP DOIs - None ❌ MISSING DOIs - 10.32614/cran.package.admmdensestsubmatrix may be a valid DOI for title: admmDensestSubmatrix: Alternating Direction Method... - 10.32614/cran.package.fselector may be a valid DOI for title: FSelector: Selecting Attributes - 10.32614/cran.package.varrank may be a valid DOI for title: varrank: Heuristics Tools Based on Mutual Informat... ❌ INVALID DOIs - None
@annagraff, I've now read through the paper, and everything looks good. However, could you please add the suggested DOIs to the R packages that you are citing, and then let me know when this is done?
Hi @osorensen https://github.com/osorensen, I have added the DOIs. Thank you very much!
On 28 Aug 2024, at 13:52, Øystein Sørensen @.***> wrote:
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
✅ OK DOIs
- 10.5281/zenodo.7385533 is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.5281/zenodo.7976754 is OK
- 10.5281/zenodo.7836668 is OK
- 10.5281/zenodo.2677911 is OK
- 10.5281/zenodo.7740140 is OK
- 10.5281/zenodo.10804357 is OK
🟡 SKIP DOIs
- None
❌ MISSING DOIs
- 10.32614/cran.package.admmdensestsubmatrix may be a valid DOI for title: admmDensestSubmatrix: Alternating Direction Method...
- 10.32614/cran.package.fselector may be a valid DOI for title: FSelector: Selecting Attributes
- 10.32614/cran.package.varrank may be a valid DOI for title: varrank: Heuristics Tools Based on Mutual Informat...
❌ INVALID DOIs
- None @annagraff https://github.com/annagraff, I've now read through the paper, and everything looks good. However, could you please add the suggested DOIs to the R packages that you are citing, and then let me know when this is done?
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7024#issuecomment-2315118252, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKEXNOPBHX6NXBFVPI7YIXDZTW2ZNAVCNFSM6AAAAABLKHMGZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJVGEYTQMRVGI. You are receiving this because you were mentioned.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
✅ OK DOIs
- 10.5281/zenodo.7385533 is OK
- 10.32614/cran.package.admmdensestsubmatrix is OK
- 10.32614/cran.package.fselector is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.5281/zenodo.7976754 is OK
- 10.5281/zenodo.7836668 is OK
- 10.5281/zenodo.2677911 is OK
- 10.5281/zenodo.7740140 is OK
- 10.5281/zenodo.10804357 is OK
- 10.32614/cran.package.varrank is OK
🟡 SKIP DOIs
- None
❌ MISSING DOIs
- None
❌ INVALID DOIs
- None
@annagraff, at this point could you:
I can then move forward with recommending acceptance.
@osorensen https://github.com/osorensen:
On 28 Aug 2024, at 16:04, Øystein Sørensen @.***> wrote:
@annagraff https://github.com/annagraff, at this point could you:
Make a tagged release of your software, and list the version tag of the archived version here. Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository) Check the archival deposit (e.g., in Zenodo) 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. Please list the DOI of the archived version here. I can then move forward with recommending acceptance.
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7024#issuecomment-2315414033, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKEXNOMOR3XUWGVOCDD6A7DZTXKFTAVCNFSM6AAAAABLKHMGZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJVGQYTIMBTGM. You are receiving this because you were mentioned.
@editorialbot set 1.0.0 as version
Submitting author: !--author-handle-->@annagraff<!--end-author-handle-- (Anna Graff) Repository: https://github.com/annagraff/densify Branch with paper.md (empty if default branch): main Version: 1.0.0 Editor: !--editor-->@osorensen<!--end-editor-- Reviewers: @elenlefoll, @yjunechoe, @stefanocoretta Archive: 10.5281/zenodo.13384828
Status
Status badge code:
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
@elenlefoll, 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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @osorensen 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 @elenlefoll
📝 Checklist for @yjunechoe
📝 Checklist for @stefanocoretta