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[PRE REVIEW]: nnde: A Python package for solving differential equations using neural networks #3309

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @elwinter (Eric Winter) Repository: https://github.com/elwinter/nnde Version: 0.0.7 Editor: @diehlpk Reviewers: @taless474, @hayesall Managing EiC: Arfon Smith

: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.

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Markdown: [![status](https://joss.theoj.org/papers/928f78def0b6f73aecf73326fd390aeb/status.svg)](https://joss.theoj.org/papers/928f78def0b6f73aecf73326fd390aeb)

Author instructions

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

@elwinter if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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 3 years ago

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:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.11 s (813.9 files/s, 83836.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          86           2297           2105           4778
Markdown                         2             27              0             47
make                             1              3              0              8
JSON                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            90           2327           2105           4839
-------------------------------------------------------------------------------

Statistical information for the repository 'd69281d3a87121bdbe2d8c8b' was
gathered on 2021/05/23.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Eric Winter                    191         18127           8947          100.00

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
Eric Winter                9180           50.6          5.8               13.41
whedon commented 3 years ago

PDF failed to compile for issue #3309 with the following error: 

 pandoc: paper.bib: openBinaryFile: does not exist (No such file or directory)
Looks like we failed to compile the PDF
arfon commented 3 years ago

:wave: @elwinter – thanks for your submission to JOSS. It looks like you're missing the BibTeX file to go with the paper.md file here?

elwinter commented 3 years ago

DOH! Will upload it when i get home.

I hope all is well with you Arfon. I left ST in December for APL.

Eric

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From: Arfon Smith @.> Sent: Sunday, May 23, 2021 11:05:41 AM To: openjournals/joss-reviews @.> Cc: Eric Winter @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: nnde: A Python package for solving differential equations using neural networks (#3309)

👋 @elwinterhttps://github.com/elwinter – thanks for your submission to JOSS. It looks like you're missing the BibTeX file to go with the paper.md file here?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/3309#issuecomment-846577525, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABSFWC2CVQ2UHL7P5KIACF3TPEKULANCNFSM45LZJJXA.

arfon commented 3 years ago

I hope all is well with you Arfon. I left ST in December for APL.

:wave: all good here thanks! Congrats on the new role, I hope APL is treating you well!

elwinter commented 3 years ago

Hi Arfon. I added the paper.bib file to the nnde repo. Sorry about that.

Take care, Eric

On Mon, May 24, 2021 at 4:30 AM Arfon Smith @.***> wrote:

I hope all is well with you Arfon. I left ST in December for APL.

👋 all good here thanks! Congrats on the new role, I hope APL is treating you well!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3309#issuecomment-846877264, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSFWC6FAPEWULZU6QIRNNDTPIFC7ANCNFSM45LZJJXA .

arfon commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arfon commented 3 years ago

@elwinter – thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

danielskatz commented 3 years ago

👋 @diehlpk - would you be able to edit this submission?

danielskatz commented 3 years ago

@whedon invite @diehlpk as editor

whedon commented 3 years ago

@diehlpk has been invited to edit this submission.

diehlpk commented 3 years ago

@danielskatz Sure, I can take the submission.

diehlpk commented 3 years ago

@whedon assign @diehlpk as editor

whedon commented 3 years ago

OK, the editor is @diehlpk

diehlpk commented 3 years ago

@elwinter Can you please recommend some reviewers?

elwinter commented 3 years ago

Hmm, i thought I had picked one from the list. I'll check tonight and send the name to you.

Thanks Eric

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From: Patrick Diehl @.> Sent: Tuesday, June 15, 2021 2:29:15 PM To: openjournals/joss-reviews @.> Cc: Eric Winter @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: nnde: A Python package for solving differential equations using neural networks (#3309)

@elwinterhttps://github.com/elwinter Can you please recommend some reviewers?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/3309#issuecomment-861736156, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABSFWC3LSDMDRDIYY4BDJGDTS6LXXANCNFSM45LZJJXA.

diehlpk commented 3 years ago

Hey @taless474 would you be interested to review this paper?

taless474 commented 3 years ago

Sure, I will do that.

diehlpk commented 3 years ago

@whedon assign @taless474 as reviewer

whedon commented 3 years ago

OK, @taless474 is now a reviewer

diehlpk commented 3 years ago

Hey @rougier @betatim @pragyansmita @stsievert @road2stat @nilesh-patil would you be interested in reviewing this paper?

stsievert commented 3 years ago

Sorry, I don't have the bandwidth right now. After a brief glance, I would encourage the author to look carefully at the JOSS review criteria, especially the documentation section.

elwinter commented 3 years ago

Ok, I'll review it again, thanks. Eric

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From: Scott Sievert @.> Sent: Wednesday, June 16, 2021 1:14:18 PM To: openjournals/joss-reviews @.> Cc: Eric Winter @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: nnde: A Python package for solving differential equations using neural networks (#3309)

Sorry, I don't have the bandwidth right now. After a brief glance, I would encourage the author to look carefully at the JOSS review criteriahttps://joss.readthedocs.io/en/latest/review_criteria.html, especially the documentation sectionhttps://joss.readthedocs.io/en/latest/review_criteria.html#documentation.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/3309#issuecomment-862560812, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABSFWCYLE6W34EXBK5LQD23TTDLWVANCNFSM45LZJJXA.

diehlpk commented 3 years ago

Hey, @AvianaGlobal @a-r-j @chekoduadarsh @diegoonna @coljac @davismcc would you be interested in reviewing this paper?

diehlpk commented 3 years ago

Hey @johntfoster would you be interested to review this paper?

a-r-j commented 3 years ago

Hi @diehlpk, afraid I don't have the bandwidth right now either. Apologies!

coljac commented 3 years ago

@diehlpk : Apologies, I usually try and squeeze in reviews when asked, but I have to decline this one.

davismcc commented 3 years ago

Apologies, this application (solving differential equations) is too far outside my expertise to be confident evaluating it.

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From: Colin Jacobs @.> Sent: Tuesday, June 22, 2021 9:42:58 AM To: openjournals/joss-reviews @.> Cc: Davis McCarthy @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: nnde: A Python package for solving differential equations using neural networks (#3309)

@diehlpkhttps://github.com/diehlpk : Apologies, I usually try and squeeze in reviews when asked, but I have to decline this one.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/3309#issuecomment-865415391, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAMXMGUZ3YA4XZ5VI7PC2H3TT7FAFANCNFSM45LZJJXA.

diehlpk commented 3 years ago

@elwinter Do you have some reviewers in mind?

diehlpk commented 3 years ago

Hey @tianxzhu @paragkulkarni11 @GalenStocking @nhejazi @dvysardana @glemaitre @Scivision @rasbt would you be interested to review this paper?

nhejazi commented 3 years ago

Thank you for considering me, but I am unable to provide a timely review at present.

diehlpk commented 3 years ago

@elwinter Do you have some reviewers in mind?

@elwinter Do you have reviewers in mind? I would appreciate getting some names from you?

diehlpk commented 3 years ago

Hey @smith42 @hayesall @anki-xyz @vasudev-sharma @88d52bdba0366127fffca9dfa93895 @magedhelmy1 would you be interested in reviewing this paper?

elwinter commented 3 years ago

Hi Patrick. Sorry for the delayed reply. I had suggested one reviewer from the JOSS list when I submitted the paper, but I see in my email archive that you are not having much luck getting a reviewer from your usual team. The only person on your team I could suggest is Arfon, but we know each other from working together at STScI, so that would not be appropriate, unless the reviews are blind. But even then, there’s a good chance he’d know it’s me, so Arfon should not be a candidate. Should I go through the list of your reviewers from the web site again? Or do you need to find an external reviewer at this point?

Take care

Eric

From: Patrick Diehl @.> Sent: Tuesday, July 6, 2021 5:07 PM To: openjournals/joss-reviews @.> Cc: Eric Winter @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: nnde: A Python package for solving differential equations using neural networks (#3309)

@elwinter https://github.com/elwinter Do you have some reviewers in mind?

@elwinter https://github.com/elwinter Do you have reviewers in mind? I would appreciated to get some names from you?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3309#issuecomment-875081672 , or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSFWC6MKC7O57QUGMQHQ3TTWNV6PANCNFSM45LZJJXA . https://github.com/notifications/beacon/ABSFWC26FRGIPEAQH5JPRGLTWNV6PA5CNFSM45LZJJXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOGQUK7SA.gif

diehlpk commented 3 years ago

Hi Patrick. Sorry for the delayed reply. I had suggested one reviewer from the JOSS list when I submitted the paper, but I see in my email archive that you are not having much luck getting a reviewer from your usual team. The only person on your team I could suggest is Arfon, but we know each other from working together at STScI, so that would not be appropriate, unless the reviews are blind. But even then, there’s a good chance he’d know it’s me, so Arfon should not be a candidate. Should I go through the list of your reviewers from the web site again? Or do you need to find an external reviewer at this point? Take care Eric From: Patrick Diehl @.> Sent: Tuesday, July 6, 2021 5:07 PM To: openjournals/joss-reviews @.> Cc: Eric Winter @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: nnde: A Python package for solving differential equations using neural networks (#3309) @elwinter https://github.com/elwinter Do you have some reviewers in mind? @elwinter https://github.com/elwinter Do you have reviewers in mind? I would appreciated to get some names from you? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3309 (comment)> , or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSFWC6MKC7O57QUGMQHQ3TTWNV6PANCNFSM45LZJJXA . https://github.com/notifications/beacon/ABSFWC26FRGIPEAQH5JPRGLTWNV6PA5CNFSM45LZJJXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOGQUK7SA.gif

Yeah, I think I asked some of the reviewers in the JOSS list. I can wait for some time and ask the next round. I was thinking you have can recommend some external ones.m since you work on this topic.

elwinter commented 3 years ago

Hmm, OK. I’ll see what I (or my advisor) can come up with.

Take care

Eric

From: Patrick Diehl @.> Sent: Thursday, July 8, 2021 11:48 AM To: openjournals/joss-reviews @.> Cc: Eric Winter @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: nnde: A Python package for solving differential equations using neural networks (#3309)

Hi Patrick. Sorry for the delayed reply. I had suggested one reviewer from the JOSS list when I submitted the paper, but I see in my email archive that you are not having much luck getting a reviewer from your usual team. The only person on your team I could suggest is Arfon, but we know each other from working together at STScI, so that would not be appropriate, unless the reviews are blind. But even then, there’s a good chance he’d know it’s me, so Arfon should not be a candidate. Should I go through the list of your reviewers from the web site again? Or do you need to find an external reviewer at this point? Take care Eric From: Patrick Diehl @.> Sent: Tuesday, July 6, 2021 5:07 PM To: openjournals/joss-reviews @.> Cc: Eric Winter @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: nnde: A Python package for solving differential equations using neural networks (#3309 https://github.com/openjournals/joss-reviews/issues/3309 ) @elwinter https://github.com/elwinter https://github.com/elwinter Do you have some reviewers in mind? @elwinter https://github.com/elwinter https://github.com/elwinter Do you have reviewers in mind? I would appreciated to get some names from you? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3309 (comment) https://github.com/openjournals/joss-reviews/issues/3309#issuecomment-875081672 > , or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSFWC6MKC7O57QUGMQHQ3TTWNV6PANCNFSM45LZJJXA . https://github.com/notifications/beacon/ABSFWC26FRGIPEAQH5JPRGLTWNV6PA5CNFSM45LZJJXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOGQUK7SA.gif

Yeah, I think I asked some of the reviewers in the JOSS list. I can wait for some time and ask the next round. I was thinking you have can recommend some external ones.m since you work on this topic.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3309#issuecomment-876549158 , or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSFWC77LPMACPB6W4WU3YDTWXCCFANCNFSM45LZJJXA . https://github.com/notifications/beacon/ABSFWCZ76ZZCAOUAWKZSDKDTWXCCFA5CNFSM45LZJJXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOGQ7RIJQ.gif

hayesall commented 3 years ago

Hey @diehlpk I can help review.

diehlpk commented 3 years ago

@whedon add @hayesall as reviewer

diehlpk commented 3 years ago

@whedon add @hayesall as reviewer

whedon commented 3 years ago

OK, @hayesall is now a reviewer

diehlpk commented 3 years ago

@whedon start review

whedon commented 3 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3465.

diehlpk commented 3 years ago

@elwinter Luckily, I found enough reviewers and I started the review.

elwinter commented 3 years ago

Wonderful, thanks!

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From: Patrick Diehl @.> Sent: Friday, July 9, 2021 9:58:20 AM To: openjournals/joss-reviews @.> Cc: Eric Winter @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: nnde: A Python package for solving differential equations using neural networks (#3309)

@elwinterhttps://github.com/elwinter Luckily, I found enough reviewers and I started the review.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/3309#issuecomment-877209561, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABSFWC34D56MCQ65QHI3753TW357ZANCNFSM45LZJJXA.