Closed editorialbot closed 4 months ago
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.09 s (564.8 files/s, 87819.5 lines/s)
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Language files blank comment code
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Python 24 1312 1941 3503
reStructuredText 18 259 409 177
TeX 1 8 0 105
YAML 4 15 12 90
Markdown 1 10 0 31
DOS Batch 1 8 1 26
make 1 4 7 9
TOML 1 0 0 3
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SUM: 51 1616 2370 3944
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 551
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.3847/1538-4357/abb085 is OK
- 10.1103/PhysRevD.96.023522 is OK
- 10.1088/1475-7516/2015/02/045 is OK
- 10.1093/mnras/stab3201 is OK
- 10.1093/mnras/stae171 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:
@gcalderone, @corentinravoux thank you for agreeing to review this submission! Please review the guidelines above: https://github.com/openjournals/joss-reviews/issues/6373#issue-2142638233
Comments and recommendations for changes should ideally be in issues opened on the code repo but comments in this thread are also welcome. When you are finished, please let us know in the comments here.
We are looking for reviews in 3-4 weeks, so let's aim for March 18th at the latest for the first round of comments.
Let me know if you have questions!
@ivastar Thank you, I will try to do my best to provide those comments quickly
I have a COI with this review, I work in the same collaboration than the main author (DESI), and we are co-author of some papers (Karaçaylı et al. 2024, Ravoux et al. 2023). I am contributing and using the picca code mentioned in the paper. However, I think I am able to provide an impartial assessment of this work, as I am open to using alternative continuum fitting algorithm, and I never used QSOnic. I request to waive this COI if this is possible.
Comments on the joss-paper (I used the download version):
https://github.com/openjournals/joss-reviews/issues/6373#issuecomment-1953747932
@corentinravoux The COI can be waived for this specific case. Thank you declaring your relation to the author and this work.
The review process is quite faster than I expected. I summarized my comments in the following issue: https://github.com/p-slash/qsonic/issues/92. There are some comments that are blocking the completion on my checklist. I let time to the main author of QSOnic to address them before I validate all points.
I provided my comments in https://github.com/p-slash/qsonic/issues/93
@p-slash I believe we have both sets of comments now. The ball is in your court. Please review the comments and respond to them here or in the review issues that have been opened. I would appreciate it if you could do this in the next 3-4 weeks.
My other responses can be found at https://github.com/p-slash/qsonic/issues/93#issuecomment-2000103671 and https://github.com/p-slash/qsonic/issues/92#issuecomment-2000114200. The updated documentation can be accessed here: https://qsonic.readthedocs.io/en/paper/index.html.
Thanks @corentinravoux for the feedback. This is the second part of my response.
* For the reference, I would add Armengaud et al. 2017 for the dark matter constraints, and Ravoux et al. 2023 for the measurements.
Added.
* The sentence "The field has devised ..." is unclear. Do you mean recent studies ? And to which "well-known modes" are you referring ?
Paper now says: Recent studies have devised a simple continuum model to homogenize the analysis across quasars so that the errors in the estimated continuum are contained to well-known modes, such as the amplitude and slope of the quasar continuum.
* "a polynomial of ln 𝜆" Maybe I am wrong but i thought that for DESI, it is just "𝜆" ?
We are still fitting for ln lambda for DESI. There was a version of picca that performed the continuum fitting on lambda, but that was eventually removed before EDR analyses took off.
* "a delete-one Jackknife estimate for the covariance matrix used in pipeline noise calibration correction calculation" Here, do you mean the picca equivalent of eta ? This end of sentence might be too technical for the statement of need here.
Paper now says: It saves detailed intermediate data products including best-fit parameters for each quasar and the covariance matrix used in pipeline noise calibration correction ($\eta$ parameter in references [@bourbouxCompletedSDSSIVExtended:2020; @karacayliOptimal1DLy:2024]).
* When you say that QSOnic is built on the same algorithm than picca, do you mean that you used part of the software, or that the principle of the algorithm is the same ? Please clarify that on the text.
Paper now says: QSOnic
is built on the same principle of picca continuum fitting algorithm. Unlike picca
, QSOnic
has robust convergence criteria, provides a generic API for DESI quasar spectra, and saves more intermediate data products. Due to optimized IO routines, MPI parallelization and efficient numerical algorithms, it may be faster than picca
.
Thank you for the fast turn-around on the comments, @p-slash!!!
@gcalderone and @corentinravoux, could you please review the responses and let me know if you believe all points have been addressed? If no, please add additional comments. If yes, please recommend publications.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Thanks @p-slash for the updates! Please find my new comment in the same issue: https://github.com/p-slash/qsonic/issues/93
Thanks @p-slash, you answered all my comments. I have checked all the items of my checklist, and I recommend this package for publication.
I have a minor comment which is very technical and does not interfere at all with the review:
* "a polynomial of ln 𝜆" Maybe I am wrong but i thought that for DESI, it is just "𝜆" ?
We are still fitting for ln lambda for DESI. There was a version of picca that performed the continuum fitting on lambda, but that was eventually removed before EDR analyses took off.
On this aspect, I was sure that it was in lambda in picca, but after double checking it is indeed in log_lambda. I do not understand why this is the case for DESI data which are linearly binned, did you test on QSOnic the difference in term of continuum fitting with different term in the polynomial term (lambda vs log lambda) ?
Thanks. I addressed @gcalderone's comments under the issue.
@corentinravoux, re: ln lambda: Yes, DESI is linearly spaced, but this term is related to the quasar continuum model, so it does not need to be tied to the observational grid. If I remember correctly, ln lambda is the better of the two for the quasar continuum model theoretically, but I do not have a document to point you to. I had the comparison with picca, and the difference was small, but I did not code within qsonic. Furthermore, changing this model then propagates to the distortion matrix calculation. It complicates the entire analysis, so it may be that we simplified it to a single choice in the end.
Thanks @p-slash ! I closed the https://github.com/p-slash/qsonic/issues/93 issue, and recommend acceptance of the paper.
Thank you @gcalderone and @corentinravoux for the comments. @ivastar let me know what the next steps are.
Thank you @gcalderone and @corentinravoux for the detailed review and thank you @p-slash for the quick turn-around on the comments!
I am going to move forward on the pre-publication review. I will read the paper to check for any editorial issues and follow up with comments here.
@editorialbot generate pdf
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.3847/1538-4357/abb085 is OK
- 10.1103/PhysRevD.96.023522 is OK
- 10.1088/1475-7516/2015/02/045 is OK
- 10.1093/mnras/stab3201 is OK
- 10.1093/mnras/stae171 is OK
- 10.1093/mnras/stad3008 is OK
- 10.1093/mnras/stx1870 is OK
- 10.1086/427976 is OK
MISSING DOIs
- No DOI given, and none found for title: picca: Package for Igm Cosmological-Correlations A...
- No DOI given, and none found for title: The DESI Experiment Part I: Science,Targeting, and...
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
The DOI for the DESI Experiment Part I paper is https://doi.org/10.48550/arXiv.1611.00036
picca
should just be cited with the du Max Bourboux paper as per the instructions on the repo:
https://doi.org/10.48550/arXiv.2007.08995
Some editorial comments in https://github.com/p-slash/qsonic/pull/96
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
@p-slash once the editorial changes are complete, please review the tasks above.
picca
should just be cited with the du Max Bourboux paper as per the instructions on the repo:
@ivastar could you clarify this comment? Do you want me to remove Karaçaylı et al. (2024) citations or add this citation instead of a link to the repo? Note that this paper is already cited.
@ivastar could you clarify this comment? Do you want me to remove Karaçaylı et al. (2024) citations or add this citation instead of a link to the repo? Note that this paper is already cited.
I think use the paper citation instead of the link to the repo. Just trying to resolve the "missing DOI" issues.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.3847/1538-4357/abb085 is OK
- 10.1103/PhysRevD.96.023522 is OK
- 10.1088/1475-7516/2015/02/045 is OK
- 10.1093/mnras/stab3201 is OK
- 10.1093/mnras/stae171 is OK
- 10.1093/mnras/stad3008 is OK
- 10.48550/arXiv.1611.00036 is OK
- 10.1093/mnras/stx1870 is OK
- 10.1086/427976 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@ivastar could you clarify this comment? Do you want me to remove Karaçaylı et al. (2024) citations or add this citation instead of a link to the repo? Note that this paper is already cited.
I think use the paper citation instead of the link to the repo. Just trying to resolve the "missing DOI" issues.
Ok. The problem was an unused entry in the bib file, not the link to the repo. No more missing DOIs now
@p-slash great! Please create an archive and share the version and DOI here.
Thanks! I tagged version v1.0.0. Zenodo link: https://zenodo.org/records/11105006 DOI: 10.5281/zenodo.11105006
@editorialbot set 10.5281/zenodo.11105006 as archive
Done! archive is now 10.5281/zenodo.11105006
@editorialbot set v1.0.0 as version
Done! version is now v1.0.0
@editorialbot generate pdf
@editorialbot check references
:warning: An error happened when generating the pdf.
@editorialbot generate pdf
:warning: An error happened when generating the pdf.
@editorialbot set main as branch
Done! branch is now main
Submitting author: !--author-handle-->@p-slash<!--end-author-handle-- (Naim Göksel Karaçaylı) Repository: https://github.com/p-slash/qsonic Branch with paper.md (empty if default branch): main Version: v1.0.0 Editor: !--editor-->@ivastar<!--end-editor-- Reviewers: @gcalderone, @corentinravoux Archive: 10.5281/zenodo.11105006
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@gcalderone & @corentinravoux, 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:
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