Closed editorialbot closed 12 months ago
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
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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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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1117/12.2552037 is OK
- 10.1117/12.2525978 is OK
- 10.1117/1.jmm.19.2.024001 is OK
- 10.5802/smai-jcm.24 is OK
- 10.1016/j.ress.2007.04.002 is OK
- 10.3390/metrology3010001 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.88 T=0.14 s (293.4 files/s, 50377.8 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Python 15 836 1781 2155
Markdown 9 234 0 654
reStructuredText 9 252 517 185
YAML 3 12 14 88
TeX 1 0 0 77
DOS Batch 1 8 1 26
make 1 4 7 9
TOML 1 0 0 7
-------------------------------------------------------------------------------
SUM: 40 1346 2320 3201
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 697
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
My review is at https://gitlab.com/pythia-uq/pythia/-/issues/1
Perfect thanks, I'll look into it.
@timokoch could you please update us on your review progress?
There is a checklist that you have to generate and check out. Please let me know if you are running into any problems.
@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 added some issues and suggestions at https://gitlab.com/pythia-uq/pythia/-/issues and https://gitlab.com/pythia-uq/pythia/-/merge_requests. In general the shape of the package looks good and follows many best practices. The unit test suite is passing locally for me, is integrated in the CI and looks comprehensive enough. I opened issue for specifics where the documentation is not complete. The application tutorial seems to be currently not reproducible because the data is missing and the code is incomplete. The tutorials are also not tested in the CI and don't seem to be included as scripts. The number of tutorials is relatively small. It demonstrates only the basic set of operations I would expect from a PCE package (create basis, train, predict), (apart from the tutorial on how to optimize the sparsity of the PCE which is very well appreciated!). It would be helpful to document any original techniques. Moreover, the work is currently not sufficiently placed in the context of related works (both software packages and methodology/feature-wise), so I currently can't asses whether the submission satisfies the substantial scholarly effort point (it would help to explicitly point us to what is the main contribution in the author's opinion in the paper/code documentation. For example, with chaospy
there is a well-documented, mature, popular competitor Python package and it is not described in sufficient detail what the advantages of this submissions are in comparison (cf. https://gitlab.com/pythia-uq/pythia/-/issues/1).
π @vissarion - I'm having trouble seeing the status of this submission/review, and what the next step is. Can you tell me where you think things are?
Hi @danielskatz,
We are waiting for the author @Nando-Hegemann to reply to reviewer's comments. In particular, https://github.com/openjournals/joss-reviews/issues/5489#issuecomment-1604717335 by @timokoch and https://gitlab.com/pythia-uq/pythia/-/issues/1 by @ziyiyin97
@Nando-Hegemann how is this progressing?
I started resolving the issues and adding the suggested changes. It is very busy right now, so I assume it'll take two more weeks to finish everything, if that is ok.
Thanks for the reply @Nando-Hegemann! It is OK.
FYI: I'm almost done with the review. On Monday I'll look into similar/related projects to include some general context for the package in the paper and then I'm through with all the comments.
I'm done addressing all the issues and pushed the results.
Thanks @Nando-Hegemann!
@timokoch @ziyiyin97 are you OK with those changes? Do you have any more comments or new issues?
@vissarion @Nando-Hegemann I think you have done a great job in addressing the comments and issues raised. I especially like that all examples are also tested in the CI pipeline now. I think the work is now also sufficiently put into the context of other works and the added value is made clear.
I checked all the boxes on the checklist. From my side, this would be ready to be published.
Thanks @timokoch!
@ziyiyin97 could you please share your feedback too?
I've also checked all the boxes on the checklist! Well-done @Nando-Hegemann to address all the comments!
One (might-be-nitpicky) comment is that I would appreciate a reference after "Typically, the multiindex set is either assembled directly or iteratively based on an $\ell_q
$-bound of the multiindices." to introduce multiindex set and how people usually handle it.
I recommend acceptance overall on my side.
@Nando-Farchmin when a submission is ready to be accepted, we ask that the authors issue a new tagged release of the software (if changed), and archive it (see this guide). Please do this and post the version number and archive DOI here.
Thanks a lot for all the helpful tips for both the code and the paper!
I just uploaded the latest release version to Zenodo:
This is the link https://zenodo.org/record/8329011 please use the same title as in the paper.
Sorry, here is the corrected one:
@editorialbot set 10.5281/zenodo.8329459 as archive
Done! archive is now 10.5281/zenodo.8329459
@editorialbot set v4.0.3 as version
Done! version is now v4.0.3
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1117/12.2526082 is OK
- 10.1117/12.2552037 is OK
- 10.1016/j.cma.2013.11.015 is OK
- 10.1137/21m1461988 is OK
- 10.1615/int.j.uncertaintyquantification.2022039164 is OK
- 10.1117/12.2525978 is OK
- 10.1117/1.jmm.19.2.024001 is OK
- 10.5802/smai-jcm.24 is OK
- 10.5442/ND000005 is OK
- 10.1016/j.ress.2007.04.002 is OK
- 10.3390/metrology3010001 is OK
- 10.1137/s1064827501387826 is OK
- 10.1016/j.softx.2020.100450 is OK
- 10.1016/j.jocs.2015.08.008 is OK
- 10.1007/978-3-319-12385-1_64 is OK
- 10.48550/ARXIV.2106.13639 is OK
- 10.1214/009053604000000067 is OK
- 10.1137/20m1315774 is OK
MISSING DOIs
- 10.1088/0266-5611/28/4/045003 may be a valid DOI for title: Sparse deterministic approximation of Bayesian inverse problems
INVALID DOIs
- None
@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! I created an issue in the repository https://gitlab.com/pythia-uq/pythia/-/issues/15 with some suggestions regarding references.
Done!
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1117/12.2526082 is OK
- 10.1117/12.2552037 is OK
- 10.1016/j.cma.2013.11.015 is OK
- 10.1137/21m1461988 is OK
- 10.1615/int.j.uncertaintyquantification.2022039164 is OK
- 10.1117/12.2525978 is OK
- 10.1117/1.jmm.19.2.024001 is OK
- 10.5802/smai-jcm.24 is OK
- 10.5442/ND000005 is OK
- 10.1088/0266-5611/28/4/045003 is OK
- 10.1016/j.ress.2007.04.002 is OK
- 10.3390/metrology3010001 is OK
- 10.1137/s1064827501387826 is OK
- 10.1016/j.softx.2020.100450 is OK
- 10.1016/j.jocs.2015.08.008 is OK
- 10.1007/978-3-319-12385-1_64 is OK
- 10.48550/ARXIV.2106.13639 is OK
- 10.1214/009053604000000067 is OK
- 10.1111/j.2517-6161.1996.tb02080.x is OK
- 10.1137/20m1315774 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1117/12.2526082 is OK
- 10.1117/12.2552037 is OK
- 10.1016/j.cma.2013.11.015 is OK
- 10.1137/21m1461988 is OK
- 10.1615/int.j.uncertaintyquantification.2022039164 is OK
- 10.1117/12.2525978 is OK
- 10.1117/1.jmm.19.2.024001 is OK
- 10.5802/smai-jcm.24 is OK
- 10.5442/ND000005 is OK
- 10.1088/0266-5611/28/4/045003 is OK
- 10.1016/j.ress.2007.04.002 is OK
- 10.3390/metrology3010001 is OK
- 10.1137/s1064827501387826 is OK
- 10.1016/j.softx.2020.100450 is OK
- 10.1016/j.jocs.2015.08.008 is OK
- 10.1007/978-3-319-12385-1_64 is OK
- 10.48550/ARXIV.2106.13639 is OK
- 10.1214/009053604000000067 is OK
- 10.1111/j.2517-6161.1996.tb02080.x is OK
- 10.1137/20m1315774 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/csism-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/4570, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
@Nando-Farchmin - I'm the track editor, and I'll handle the remaining steps, which will start with me proofreading the submission, then I'll get back to you with what else is needed.
@Nando-Hegemann - can you change line 48 of paper.md to
In contrast to similar model classes such as neural networks, it is possible to exploit the mathematical structure of the polynomial chaos expansion to compute moments (e.g., mean and variance), marginals, global parameter sensitivities [@sudret:2008], and arbitrary derivatives of the surrogate analytically without any computational overhead.
This is just adding two commas. Otherwise, this looks good to me, and once you make this change, we can proceed.
Thanks @danielskatz , I add your suggestion and pushed the change.
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1117/12.2526082 is OK
- 10.1117/12.2552037 is OK
- 10.1016/j.cma.2013.11.015 is OK
- 10.1137/21m1461988 is OK
- 10.1615/int.j.uncertaintyquantification.2022039164 is OK
- 10.1117/12.2525978 is OK
- 10.1117/1.jmm.19.2.024001 is OK
- 10.5802/smai-jcm.24 is OK
- 10.5442/ND000005 is OK
- 10.1088/0266-5611/28/4/045003 is OK
- 10.1016/j.ress.2007.04.002 is OK
- 10.3390/metrology3010001 is OK
- 10.1137/s1064827501387826 is OK
- 10.1016/j.softx.2020.100450 is OK
- 10.1016/j.jocs.2015.08.008 is OK
- 10.1007/978-3-319-12385-1_64 is OK
- 10.48550/ARXIV.2106.13639 is OK
- 10.1214/009053604000000067 is OK
- 10.1111/j.2517-6161.1996.tb02080.x is OK
- 10.1137/20m1315774 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/csism-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/4575, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
Submitting author: !--author-handle-->@Nando-Farchmin<!--end-author-handle-- (Nando Farchmin) Repository: https://gitlab.com/pythia-uq/pythia Branch with paper.md (empty if default branch): paper/joss Version: v4.0.3 Editor: !--editor-->@vissarion<!--end-editor-- Reviewers: @ziyiyin97, @timokoch Archive: 10.5281/zenodo.8329459
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
@ziyiyin97 & @timokoch, 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 @vissarion know.
β¨ 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 β¨
Checklists
π Checklist for @ziyiyin97
π Checklist for @timokoch