Closed editorialbot closed 11 months 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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Software report:
github.com/AlDanial/cloc v 1.88 T=0.16 s (752.3 files/s, 230036.6 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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C++ 12 1440 1092 6711
Python 25 1756 3137 4879
CSS 4 453 161 2033
Cython 9 366 468 1125
YAML 14 206 212 803
C/C++ Header 11 372 2243 757
Markdown 11 241 0 524
Jupyter Notebook 7 0 3961 451
reStructuredText 8 277 272 305
TeX 2 22 0 247
make 2 129 91 217
JavaScript 4 56 103 215
Bourne Shell 4 64 112 169
INI 2 56 0 148
TOML 1 13 2 92
HTML 2 3 32 68
-------------------------------------------------------------------------------
SUM: 118 5454 11886 18744
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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
- 10.1093/mnras/sty3249 is OK
- 10.1093/mnras/stx2333 is OK
- 10.1103/PhysRevD.95.063508 is OK
- 10.48550/arXiv.1611.00036 is OK
- 10.48550/arXiv.1110.3193 is OK
- 10.1007/s41114-017-0010-3 is OK
- 10.1016/s0370-1573(02)00135-7 is OK
- 10.1103/PhysRevD.74.023522 is OK
- 10.1093/mnras/stx721 is OK
- 10.1103/PhysRevD.103.083533 is OK
- 10.1086/307220 is OK
- 10.1103/PhysRevD.92.083532 is OK
- 10.1093/mnras/sty1063 is OK
- 10.1093/pasj/58.1.93 is OK
- 10.1093/mnras/stw2576 is OK
- 10.1201/9780367806934 is OK
- 10.3847/1538-3881/aadae0 is OK
- 10.1093/mnras/stw1229 is OK
- 10.1086/427087 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1086/174036 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Wordcount for paper.md
is 1615
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Dear @MikeSWang,
In general I think that this package is amazing! It has lots of useful functionality and it is easy to install and use. I can certainly see myself using this in future projects!
I had four minor comments:
Super minor: there seems to be an example folder in the repo but it is empty?
This package is wonderful, congratulations! My apologies for the slow review.
Thanks @wcoulton for your valuable feedback!
I just came back from a conference and will be travelling again soon, but I will incorporate your suggestions especially with regard to number 2 (you're right about it; I have just opened a new feature request https://github.com/MikeSWang/Triumvirate/issues/22).
A quick response to the last comment: the examples
folder is a placeholder, and I meant to collect users' scripts for different use cases like a 'gallery', which may not be formal enough to be included in the official documentation :)
Dear @MikeSWang,
In general I think that this package is amazing! It has lots of useful functionality and it is easy to install and use. I can certainly see myself using this in future projects!
I had four minor comments:
- I think it would be useful to add a little more description to the returns of the functions in the documentation. A few function outputs are just described as "results – Measurement results". The actual returned dictionary has a few parts and it could be useful to either describe that there or link to the examples where the output is explained in detail.
- Unless I have misunderstood, it seems necessary to repeatedly run the program, iteratively updating idx_bin, to compute all the elements in the full 2D bispectrum. For my applications, and I suspect that of some other users, the full bispectrum would often be of interest. Perhaps a function could be added that returns this?
- Perhaps in the background material you could add a sentence or two more summarizing the window functions?
- In your supporting paper, I think it may be useful to add a reference to, and discussion of, some other codes that have some similar functionality. The first one that jumps first to mind is: https://github.com/oliverphilcox/Spectra-Without-Windows
Super minor: there seems to be an example folder in the repo but it is empty?
This package is wonderful, congratulations! My apologies for the slow review.
@alfonso-veropalumbo thank you for going through the checklist! If you have any comments in addition to those previously listed, please add them here. If not, let me and the authors know that they can move to responding to the review.
Dear @MikeSWang
First of all, thank you for your patience. I'm sorry for this delayed answer.
I've had the chance to test Triumvirate, and I've particularly appreciated the ease of use, the completeness of the documentation and the high performance in dealing with this task. Moreover, the advantage of Triumvirate is that it allows computation of the anisotropic three-point correlation function (3PCF), fully exploiting the information encoded in the higher orders moment of the galaxy density field. This aspect constitutes a new feature (apart from Triumvirate predecessor, Hitomi) and a critical advancement of the clustering field.
I have minor suggestions related to the paper:
1) quantify performances in the paper. 3PCF computation is generally thought to be (and for large samples, it is) an expensive procedure, and it could be helpful to report the performances of this specific task. 2) improve the comparison with other codes on the market (e.g. https://arxiv.org/abs/2105.08722). On this point, I have a doubt about the description of nbodykit made in the draft. Looking at the documentation (https://nbodykit.readthedocs.io/en/latest/api/_autosummary/nbodykit.algorithms.threeptcf.html#nbodykit.algorithms.threeptcf.SimulationBox3PCF) nbodykit implements the Slepian 2015 procedure, which is not assigning spherical harmonics to the mesh grid. This procedure computes the spherical harmonics on a pair-to-pair basis. As a result, it should be more accurate but significantly slower.
Apart from these minor comments, thank you again for this work, which is important for the clustering community. I hope packages like this will help people approach this field, which will gain more and more importance for clustering analyses in cosmology.
Sorry again for the delayed comments. I'm available in case further clarifications are needed.
Thank you @alfonso-veropalumbo for the detailed review! @MikeSWang the ball is in your court. Please let us all know when you've had a chance to address the comments.
Thank you all for the updates! I'm back from travelling and will address these comments in the coming weeks.
A quick question about comment 1 from @alfonso-veropalumbo: we have included some performance metrics for the bispectrum, so I guess you are asking about the 3PCF in configuration space in particular?
And a quick reply to comment 2: nbodykit
's 3PCF algorithm does use the actual lines of sight, and in the paper we were thinking about its 2-point algorithms... Given it would be better to compare with its 3PCF, I will clarify this in the text.
Friendly reminder to get to these updates soon please @MikeSWang. @alfonso-veropalumbo – I think the author asked you a question here too...
A quick question about comment 1 from @alfonso-veropalumbo: we have included some performance metrics for the bispectrum, so I guess you are asking about the 3PCF in configuration space in particular?
Hi @arfon thanks for the reminder. Indeed as I am writing now I am working on resubmitting the new draft and making a new release, aiming for the coming week. Apologies summer travel and other things have delayed my response. I have also added other optimisations to the code not asked for by the reviewer, hence the new version release has taken longer.
I actually have a question about updating the draft @arfon @ivastar. It will be available in a new commit in my own repo, but how do I get the JOSS editorial bot to compile it here?
@editorialbot generate pdf
Anyone here can do this ☝️ @MikeSWang
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Friendly reminder to get to these updates soon please @MikeSWang. @alfonso-veropalumbo – I think the author asked you a question here too...
A quick question about comment 1 from @alfonso-veropalumbo: we have included some performance metrics for the bispectrum, so I guess you are asking about the 3PCF in configuration space in particular?
Yes, sure, I think it could be useful. Computational time is the main issue, computationally speaking, for configuration space estimators (and particularly for 3PCF).
@editorialbot commands
Hello @MikeSWang, here are the things you can ask me to do:
# List all available commands
@editorialbot commands
# Get a list of all editors's GitHub handles
@editorialbot list editors
# Check the references of the paper for missing DOIs
@editorialbot check references
# Perform checks on the repository
@editorialbot check repository
# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist
# Set a value for branch
@editorialbot set joss-paper as branch
# Generates the pdf paper
@editorialbot generate pdf
# Generates a LaTeX preprint file
@editorialbot generate preprint
# Get a link to the complete list of reviewers
@editorialbot list reviewers
@editorialbot check references @editorialbot check repository
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1093/mnras/sty3249 is OK
- 10.1093/mnras/stx2333 is OK
- 10.1103/PhysRevD.95.063508 is OK
- 10.48550/arXiv.1611.00036 is OK
- 10.48550/arXiv.1110.3193 is OK
- 10.1007/s41114-017-0010-3 is OK
- 10.1016/s0370-1573(02)00135-7 is OK
- 10.1103/PhysRevD.74.023522 is OK
- 10.1093/mnras/stx721 is OK
- 10.1103/PhysRevD.103.083533 is OK
- 10.1086/307220 is OK
- 10.1093/pasj/58.1.93 is OK
- 10.1093/mnras/stw2576 is OK
- 10.1103/PhysRevD.92.083532 is OK
- 10.1093/mnras/stv2119 is OK
- 10.1093/mnras/sty1063 is OK
- 10.1093/mnrasl/slv133 is OK
- 10.1103/physrevd.104.123529 is OK
- 10.1201/9780367806934 is OK
- 10.3847/1538-3881/aadae0 is OK
- 10.1093/mnras/stw1229 is OK
- 10.1086/427087 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1086/174036 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1093/mnras/sty3249 is OK
- 10.1093/mnras/stx2333 is OK
- 10.1103/PhysRevD.95.063508 is OK
- 10.48550/arXiv.1611.00036 is OK
- 10.48550/arXiv.1110.3193 is OK
- 10.1007/s41114-017-0010-3 is OK
- 10.1016/s0370-1573(02)00135-7 is OK
- 10.1103/PhysRevD.74.023522 is OK
- 10.1093/mnras/stx721 is OK
- 10.1103/PhysRevD.103.083533 is OK
- 10.1086/307220 is OK
- 10.1093/pasj/58.1.93 is OK
- 10.1093/mnras/stw2576 is OK
- 10.1103/PhysRevD.92.083532 is OK
- 10.1093/mnras/stv2119 is OK
- 10.1093/mnras/sty1063 is OK
- 10.1093/mnrasl/slv133 is OK
- 10.1103/physrevd.104.123529 is OK
- 10.1201/9780367806934 is OK
- 10.3847/1538-3881/aadae0 is OK
- 10.1093/mnras/stw1229 is OK
- 10.1086/427087 is OK
- 10.3847/1538-4357/ac7c74 is OK
- 10.1086/174036 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot check repository
Software report:
github.com/AlDanial/cloc v 1.88 T=0.23 s (539.2 files/s, 171570.0 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
C++ 12 1658 1115 8095
Python 27 1798 3238 5115
CSS 4 453 161 2033
Cython 11 391 517 1201
YAML 14 216 304 817
C/C++ Header 11 388 2304 799
Markdown 11 291 0 637
reStructuredText 9 355 290 441
Jupyter Notebook 7 0 4088 439
TeX 2 26 0 284
make 2 137 100 256
JavaScript 4 56 103 215
INI 2 60 0 201
Bourne Shell 4 64 112 169
TOML 1 13 2 92
HTML 2 3 32 68
-------------------------------------------------------------------------------
SUM: 123 5909 12366 20862
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 2080
Dear editor @ivastar and reviewers @wcoulton & @alfonso-veropalumbo,
Many thanks for your feedback and patience. I am happy to announce that
are now both available.
To address your questions in turn:
@wcoulton
@alfonso-veropalumbo
In the meantime, there have been other bug fixes, additional features, performance enhancement, code maintenance and documentation improvements since the reviewed release.
Let me know if you have any questions and many thanks again!
On behalf of all authors, @MikeSWang
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@MikeSWang thank you for making the changes recommended by the reviewer!
@wcoulton & @alfonso-veropalumbo, please review the changes and if you are satisfied with the code and manuscript, please comment that you accept the submission for publication.
Otherwise, comment further on the relevant issues or in this thread to recommend further changes.
@wcoulton & @alfonso-veropalumbo, pinging this thread again. I would appreciate it if you could sign off on the changes so we can move to publication.
This all looks good to me and I am happy to recommend that the submission for publication. Great work!!
Everything looks good to me! Green light from my side for publication. Thank you very much for your work!
Thank you @wcoulton, @alfonso-veropalumbo and @ivastar for your work and feedback too!
@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
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
I can confirm the following:
Additional Author Tasks After Review is Complete
- [x] Double check authors and affiliations (including ORCIDs)
- [x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper. ---> Version 0.3.0
- [x] Archive the release on Zenodo/figshare/etc and post the DOI here. ---> 10.5281/zenodo.10072128
- [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
- [x] Make sure that the license listed for the archive is the same as the software license.
Thanks @MikeSWang! I am doing a quick read through the paper to make sure the text and references are ok.
@MikeSWang a couple of small corrections:
Thanks @ivastar for the suggestions! I have made these edits and updated the paper in the repo.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot set 10.5281/zenodo.10072128 as archive
Done! archive is now 10.5281/zenodo.10072128
@editorialbot set v0.3.0 as version
Done! version is now v0.3.0
@editorialbot generate pdf
Submitting author: !--author-handle-->@MikeSWang<!--end-author-handle-- (Mike Shengbo Wang) Repository: https://github.com/MikeSWang/Triumvirate Branch with paper.md (empty if default branch): Version: v0.3.0 Editor: !--editor-->@ivastar<!--end-editor-- Reviewers: @alfonso-veropalumbo, @wcoulton Archive: 10.5281/zenodo.10072128
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
@alfonso-veropalumbo & @wcoulton, 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 @ivastar 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 @wcoulton
📝 Checklist for @alfonso-veropalumbo