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[PRE REVIEW]: pyMARS: automatically reducing chemical kinetic models in Python #1523

Closed whedon closed 5 years ago

whedon commented 5 years ago

Submitting author: @kyleniemeyer (Kyle E Niemeyer) Repository: https://github.com/Niemeyer-Research-Group/pyMARS Version: v1.0.0 Editor: @katyhuff Reviewers: @fcontino

Author instructions

Thanks for submitting your paper to JOSS @kyleniemeyer. Currently, there isn't an JOSS editor assigned to your paper.

@kyleniemeyer if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
whedon commented 5 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@whedon commands

What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

arfon commented 5 years ago

:wave: @katyhuff - would you be willing to edit this submission for JOSS?

katyhuff commented 5 years ago

Oh darn. I was going to suggest @kyleniemeyer as the editor... But I see he's the author.

Sure, I'll do it. @kyleniemeyer , do you have reviewer suggestions (obviously, folks who have no COI reviewing your paper).

katyhuff commented 5 years ago

@whedon assign @katyhuff as editor

whedon commented 5 years ago

OK, the editor is @katyhuff

kyleniemeyer commented 5 years ago

Thanks @katyhuff! Here are some suggestions.

No conflicts from my domain:

From the JOSS pool:

katyhuff commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

katyhuff commented 5 years ago

@jcsutherland: Prof. James Sutherland, are you able to and interested in taking on this review?

katyhuff commented 5 years ago

@fcontino : Prof. Francesco Contino, are you able to and interested in taking on this review?

katyhuff commented 5 years ago

@zbeekman : Zaak Beekman are you able to and interested in taking on this review?

zbeekman commented 5 years ago

I'm interested but a bit short on time these days. I just finished on JOSS review (f90nml), and my portion of another is still in progress but nearly done.

Also, I don't know if this would be a COI, but my employer, ParaTools Inc., has a commercial product, KPP Accelerated (KPPA), that may have some overlap of pyMARS, and, might be a competitive alternative. (I say might, because I have not yet dug into the specifics of pyMARS' capabilities, and I'm only familiar with some of KPPA's.) It is also a python based tool, although its main purpose is to generate fast C code that can interface with Fortran, C, etc. and run on accelerators like GPUs. I'm not sure if KPPA does any model reduction, or just graph-partitioning/matrix-ordering etc. optimizations.

All things being equal, this may not be considered a COI on JOSS' end, but it's possible that it would be my employer's end. If you cannot come up with two other reviewers, then please let me know and I can ask if reviewing this would be OK.

katyhuff commented 5 years ago

Thanks @zbeekman . We'll wait and see what the others say.

fcontino commented 5 years ago

Sure and with great pleasure. I'll need some time thought because I have many other review tasks on my plate right now. What would be an acceptable deadline?

Thank you for involving me in this.

Best regards,

Francesco

On Mon, Jun 24, 2019 at 11:23 PM Katy Huff notifications@github.com wrote:

@fcontino https://github.com/fcontino : Prof. Francesco Contino, are you able to and interested in taking on this review?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1523?email_source=notifications&email_token=AAG3J77UPSYMG5YQXOV2ZT3P4E3MXA5CNFSM4H3CI27KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYOIVUY#issuecomment-505187027, or mute the thread https://github.com/notifications/unsubscribe-auth/AAG3J75N3NE4DUH6TUR4FLLP4E3MXANCNFSM4H3CI27A .

--

(Call for papers special issue of Frontiers journal on alternative fuels https://www.frontiersin.org/research-topics/10590/fundamental-characterization-and-performance-of-alternative-fuels )

Francesco Contino

Department of Mechanical Engineering

Combustion and Robust optimization (BURN http://burn-research.be/)

Thermo and Fluid dynamics (FLOW)

Brussels Faculty of Engineering (BRUFACE http://bruface.eu/)

Vrije Universiteit Brussel (VUB http://www.vub.ac.be/)

jcsutherland commented 5 years ago

I'm happy to provide a review, but it will take me at least a week.

James C. Sutherland Professor of Chemical Engineering The University of Utah 50 S. Central Campus Dr, 3290 MEB Salt Lake City, UT 84112-9203 +1-801-585-1246 sutherland https://sutherland.che.utah.edu/.che.utah.edu https://sutherland.che.utah.edu

On Mon, Jun 24, 2019 at 3:21 PM Katy Huff notifications@github.com wrote:

@jcsutherland https://github.com/jcsutherland: Prof. James Sutherland, are you able to and interested in taking on this review?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1523?email_source=notifications&email_token=ACAKDAPR4UW2FU3RC4YTP33P4E3FJA5CNFSM4H3CI27KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYOIQJA#issuecomment-505186340, or mute the thread https://github.com/notifications/unsubscribe-auth/ACAKDAO46N2ZR7JJ763LEALP4E3FJANCNFSM4H3CI27A .

jcsutherland commented 5 years ago

A newb question: where do I put my review? And does the review checklist get pre-populated somewhere?

zbeekman commented 5 years ago

@jcsutherland once the editor (@katyhuff) selects the reviewers via whedon commands, it will open a new review issue, with more instructions. So sit tight until that happens.

@katyhuff it looks like you have two reviewers now. Please LMK if you need me for anything, but I'm unsubscribing for now :wave:. @ mention me if you want to get my attention.

katyhuff commented 5 years ago

That's right. I just had a busy week since my last comment on this topic. I'll assign reviewers and start the review now.

katyhuff commented 5 years ago

@whedon assign @jcsutherland as reviewer

whedon commented 5 years ago

OK, the reviewer is @jcsutherland

katyhuff commented 5 years ago

@whedon assign @fcontino as reviewer

whedon commented 5 years ago

OK, the reviewer is @fcontino

katyhuff commented 5 years ago

@fcontino : We would like reviews to be completed in two weeks if possible. I hope that will be an acceptable deadline for you. Notably, the paper is quite short and since @kyleniemeyer knows the requirements for a JOSS submission quite well, we hope it won't take more than a few hours once you begin.

katyhuff commented 5 years ago

@whedon start review

whedon commented 5 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1543. Feel free to close this issue now!

katyhuff commented 5 years ago

Ok folks, let's move over to #1543 where you will find guidance and a checklist regarding the review process.