Joss-reviews: [PRE REVIEW]: pyOptSparse: A Python framework for large-scale constrained nonlinear optimization of sparse systems
Submitting author: @nwu63 (Neil Wu)
Repository: https://github.com/mdolab/pyoptsparse/
Version: v2.1.3
Editor: @poulson
Reviewers: @jgoldfar, @vissarion, @matbesancon
Managing EiC: Lorena A Barba
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Thanks for submitting your paper to JOSS @nwu63. Currently, there isn't an JOSS editor assigned to your paper.
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All 41 comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.
:warning: JOSS reduced service mode :warning:
Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.
For a list of things I can do to help you, just type:
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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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PDF failed to compile for issue #2490 with the following error:
Can't find any papers to compile :-(
whedon
on 18 Jul 2020
Software report (experimental):
github.com/AlDanial/cloc v 1.84 T=0.68 s (407.6 files/s, 145543.6 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
C++ 51 5855 7238 27893
Python 63 2534 3870 9251
Fortran 77 33 414 4760 7143
C 22 491 697 5411
C/C++ Header 63 2532 9879 4797
SWIG 3 295 525 2508
CSS 3 115 105 792
reStructuredText 26 311 252 673
make 1 24 5 124
JavaScript 1 15 33 112
Fortran 90 2 21 134 106
Markdown 3 29 0 104
HTML 4 10 0 97
YAML 2 7 10 88
Bourne Shell 1 0 0 8
-------------------------------------------------------------------------------
SUM: 278 12653 27508 59107
-------------------------------------------------------------------------------
Statistical information for the repository '2490' was gathered on 2020/07/18.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Andrew Ning 1 77398 0 3.28
Anil Yildirim 1 16 16 0.00
Ben Brelje 1 1 0 0.00
Benjamin Brelje 1 102 31 0.01
Bret Naylor 6 78738 39 3.34
Drayton Munster 3 1454 463 0.08
Eirikur Jonsson 3 51 21 0.00
Frederik Zahle 1 17 6 0.00
Gaetan Kenway 2 502 189 0.03
Graeme Kennedy 2 420 6 0.02
John Jasa 35 621099 503 26.35
Justin Gray 6 142 86 0.01
Kenneth Moore 6 528 26 0.02
Kenneth-T-Moore 5 211 8 0.01
Neil Wu 45 6781 7401 0.60
Nicolas 1 7 5 0.00
Nicolas Bons 14 293304 284 12.44
Ping He 2 2 2 0.00
Rob Falck 11 79088 73 3.36
S Ryan 1 14 4 0.00
Sabet Seraj 2 27 6 0.00
Stephen Ryan 1 17156 0 0.73
Yicong Fu 1 9 0 0.00
elee 2 16531 0 0.70
frza 4 77098 130 3.27
gjkennedy 3 99 219 0.01
gkennedy 8 50922 411 2.18
hschilling 1 98 4 0.00
jjasa 1 79070 0 3.35
johnjasa 11 521 443 0.04
kenneth_moore 1 69 0 0.00
kenway 143 624144 18283 27.23
kmarsteller 2 6 0 0.00
lambe 37 99993 606 4.26
lvzhoujie 2 16373 1 0.69
mader 10 186942 46 7.93
nbons 6 97 27 0.01
nischintu 1 615 0 0.03
swryan 1 144 134 0.01
Below are the number of rows from each author that have survived and are still
intact in the current revision:
Author Rows Stability Age % in comments
Anil Yildirim 9 56.2 14.7 0.00
Benjamin Brelje 102 100.0 6.5 46.08
Bret Naylor 15 0.0 25.1 6.67
Eirikur Jonsson 3 5.9 7.8 33.33
John Jasa 19 0.0 32.0 26.32
Justin Gray 23 16.2 17.8 30.43
Kenneth Moore 463 87.7 19.4 16.20
Neil Wu 5409 79.8 2.2 5.58
Nicolas 5 71.4 7.9 0.00
Ping He 1 50.0 28.6 0.00
Rob Falck 4 0.0 2.6 50.00
Sabet Seraj 27 100.0 1.4 22.22
Yicong Fu 6 66.7 2.4 50.00
eirikurj 30 100.0 4.2 23.33
gkennedy 257 0.5 15.5 10.12
hschilling 96 98.0 1.2 11.46
jjasa 938 1.2 34.8 13.97
johnjasa 327 62.8 9.8 32.72
kenneth_moore 4 5.8 6.0 0.00
kenway 70264 11.3 32.5 27.23
kmarsteller 4 66.7 24.7 0.00
nbons 2214 2282.5 33.7 22.67
nischintu 397 64.6 13.0 24.18
@whedon generate pdf from branch paper
labarba
on 18 Jul 2020
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
👋 @nwu63 — I'm going to send this back for a bit of work on the paper. Currently, it does not follow our guidance in providing a clear _Statement of Need_. See the section What should my paper contain? in our documentation. Tell us why the research world needs your software!
labarba
on 18 Jul 2020
@poulson — the author suggested you as handling editor... could you take a look?
labarba
on 18 Jul 2020
Hi @labarba, sorry about that I didn't realize it had to be a separate section. I've updated the paper and pushed it to the repo, please take a look if you have time. I would also be happy to suggest reviewers if needed.
nwu63
on 18 Jul 2020
@whedon generate pdf from branch paper
labarba
on 19 Jul 2020
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
@whedon invite @poulson as editor
labarba
on 19 Jul 2020
@poulson has been invited to edit this submission.
whedon
on 19 Jul 2020
@whedon set @poulson as editor
poulson
on 19 Jul 2020
I'm sorry human, I don't understand that. You can see what commands I support by typing:
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@whedon commands
poulson
on 19 Jul 2020
Here are some things you can ask me to do:
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@whedon assign @poulson as editor
poulson
on 19 Jul 2020
OK, the editor is @poulson
whedon
on 19 Jul 2020
Hi Mathieu (@matbesancon) :wave: -- This submission on large-scale contrained nonlinear optimization of sparse systems seems like a great fit for your expertise in optimization and python. Would you be able to serve as one of the reviewers?
poulson
on 24 Jul 2020
Hi Vissarion (@vissarion) :wave: -- Given your extensive work on optimization (including high-dimensional volume estimation) and your experience in python, it would be extremely helpful if you would serve as one of the reviewers of this submission on large-scale constrained nonlinear optimization. Would you have the time to do so?
poulson
on 24 Jul 2020
Hi Jonathan (@jgoldfar) :wave: -- Given your expertise in fast computation for PDEs and optimal control, and that you listed python as your preferred language, you seem to be a great fit for reviewing this submission on large-scale constrained nonlinear optimization. Would you be willing to serve as a reviewer for it?
poulson
on 24 Jul 2020
Hi Jack (@poulson), I am interested to do the review. When is the deadline? I will be offline the most of the August.
vissarion
on 24 Jul 2020
Good day Jack. I would be happy to review this package.
- Jack Poulson notifications@github.com [2020-07-24 06:24:03 -0700]:
Hi Jonathan (@jgoldfar) :wave: -- Given your expertise in fast computation for PDEs and optimal control, and that you listed python as your preferred language, you seem to be a great fit for reviewing this submission on large-scale constrained nonlinear optimization. Would you be willing to serve as a reviewer for it?
--
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub:
https://github.com/openjournals/joss-reviews/issues/2490#issuecomment-663536414
jgoldfar
on 24 Jul 2020
Hi @poulson, just wondering if the paper can be moved to the review phase, or if it's waiting for some action from me.
nwu63
on 4 Aug 2020
Hi @vissarion -- I will reach out to more potential reviewers. Ideally we can get three -- we currently have one confirmed. If we don't find at least one more by the end of August I will circle back.
poulson
on 11 Aug 2020
@whedon add @jgoldfar as reviewer
poulson
on 11 Aug 2020
OK, @jgoldfar is now a reviewer
whedon
on 11 Aug 2020
Hi Mathieu (@matbesancon) :wave: -- I thought I would reach out one more time to see if you would be interested in reviewing this submission on large-scale nonlinear optimization.
poulson
on 11 Aug 2020
Hi @poulson, just wondering if the paper can be moved to the review phase, or if it's waiting for some action from me.
This is on me. Thank you for your patience on this!
poulson
on 11 Aug 2020
Hi Severin (@sevberg) :wave: -- Given your expertise in Python and optimization, you would seem to be a great candidate for reviewing this submission on large-scale nonlinear optimization (in Python).
[FWIW: It seems that your username is incorrectly listed in the JOSS reviewer spreadsheet as @dsryberg]
poulson
on 11 Aug 2020
Hi David (@torressa) :wave: -- Given your expertise in Linear Programming and python, you seem like a great candidate for reviewing this submission on large-scale nonlinear optimization in Python.
Please let us know if you have the capacity and interest to review this software and paper.
poulson
on 11 Aug 2020
hi, I would be available to review the paper and project but likely not before september
matbesancon
on 11 Aug 2020
hi, I would be available to review the paper and project but likely not before september
Thank you for the fast response, Mathieu. Both you and Vissarion (@vissarion) have the same constraint and would make a complete set of reviewers if added. I lean towards adding you both as reviewers and kicking off the review under the knowledge that the review won't start until September.
poulson
on 11 Aug 2020
@whedon add @vissarion as reviewer
poulson
on 11 Aug 2020
OK, @vissarion is now a reviewer
whedon
on 11 Aug 2020
@whedon add @matbesancon as reviewer
poulson
on 11 Aug 2020
OK, @matbesancon is now a reviewer
whedon
on 11 Aug 2020
@whedon start review
poulson
on 11 Aug 2020
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2564.
whedon
on 11 Aug 2020
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OK, the editor is @poulson