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[PRE REVIEW]: Sapsan: Framework for Supernovae Turbulence Modeling with Machine Learning #3146

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @pikarpov-lanl (Platon I. Karpov) Repository: https://github.com/pikarpov-LANL/Sapsan Version: v0.2.5 Editor: @dfm Reviewers: @kburns, @milescranmer Managing EiC: Daniel S. Katz

: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.

Author instructions

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

@pikarpov-lanl 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

PDF failed to compile for issue #3146 with the following error:

Can't find any papers to compile :-(

whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.95 s (74.5 files/s, 8286.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          57           1268           1307           4174
Markdown                         4             78              0            204
Jupyter Notebook                 3              0            492            166
YAML                             5             12              3            161
Dockerfile                       1              5              3             11
make                             1              2              3              5
-------------------------------------------------------------------------------
SUM:                            71           1365           1808           4721
-------------------------------------------------------------------------------

Statistical information for the repository '9e6f9cbac95d3e62f12cc685' was
gathered on 2021/04/05.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
IceKhan13                        1            43              6            0.21
Iskandar Sitdikov               22          3330            396           16.31
Platon I Karpov                 16          3825           2270           26.68
Platon Karpov                   16          1544           1217           12.09
pikarpov                        57          6688           3522           44.70

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
IceKhan13                     6           14.0         16.5                0.00
Iskandar Sitdikov          1493           44.8         12.3                7.97
Platon I Karpov            2814           73.6          4.7               12.08
Platon Karpov              2436          157.8          4.7                6.65
danielskatz commented 3 years ago

👋 @mbobra - are you able to edit this JOSS submission?

danielskatz commented 3 years ago

@whedon invite @mbobra as editor

whedon commented 3 years ago

@mbobra has been invited to edit this submission.

danielskatz commented 3 years ago

@pikarpov-LANL - Given the comment in your README: "currently Sapsan is in alpha, but we are actively working on it and introduce new feature on a daily basis" and given that JOSS is looking for papers that are complete, I suggest this submission be withdrawn until it is more stable and more mature. Does this seem ok to you? If so, I will mark it as withdrawn.

pikarpov-LANL commented 3 years ago

Hi Daniel,

This is an outdated note, left behind before I had any physics-informed methods, analytical tools, and wiki. As it stands, Sapsan is full-featured and ready for general use as outlined in the paper. I have removed that note from README.

Thank you for bringing it to my attention!

Plato

From: Daniel S. Katz @.***> Sent: Monday, April 5, 2021 5:52:19 PM To: openjournals/joss-reviews Cc: Karpov, Platon; Mention Subject: [EXTERNAL] Re: [openjournals/joss-reviews] [PRE REVIEW]: Sapsan: Framework for Supernovae Turbulence Modeling with Machine Learning (#3146)

@pikarpov-LANLhttps://github.com/pikarpov-LANL - Given the comment in your README: "currently Sapsan is in alpha, but we are actively working on it and introduce new feature on a daily basis" and given that JOSS is looking for papers that are complete, I suggest this submission be withdrawn until it is more stable and more mature. Does this seem ok to you? If so, I will mark it as withdrawn.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/3146#issuecomment-813714663, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANYOTSJBGVDC4WWW4XOXQFLTHJELHANCNFSM42M6PW3Q.

danielskatz commented 3 years ago

👋 @dfm - are you able to edit this submission?

danielskatz commented 3 years ago

@whedon invite @dfm as editor

whedon commented 3 years ago

@dfm has been invited to edit this submission.

dfm commented 3 years ago

@whedon assign me as editor

Yes - I'm happy to edit.

@pikarpov-LANL: I'll do a first pass and then start looking for reviewers in the next few days. I'll keep you posted as this progresses and if I have any questions. You should also feel free to ask me any questions as we go.

whedon commented 3 years ago

OK, the editor is @dfm

pikarpov-LANL commented 3 years ago

@dfm great, thank you!

dfm commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
whedon commented 3 years ago

PDF failed to compile for issue #3146 with the following error:

ORCID looks malformed /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:155:in block in check_orcids': Problem with ORCID (to-fill) for Platon I. Karpov (RuntimeError) from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:153:ineach' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:153:in check_orcids' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:90:ininitialize' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in new' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:inset_paper' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:58:in prepare' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in<top (required)>' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in

'

dfm commented 3 years ago

@whedon check references from branch joss

whedon commented 3 years ago 
Attempting to check references... from custom branch joss
dfm commented 3 years ago

@whedon check repository from branch joss

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1103/PhysRevE.93.031301 is OK
- 10.1103/PhysRevFluids.3.074602 is OK
- 10.1103/RevModPhys.91.045002 is OK
- 10.1080/14685240802376389 is OK
- 10.1038/nature12128 is OK
- 10.1126/science.359.6377.725 is OK

MISSING DOIs

- 10.1109/tkde.2017.2720168 may be a valid DOI for title: Theory-guided Data Science: A New Paradigm for Scientific Discovery from Data

INVALID DOIs

- None
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.44 s (161.5 files/s, 17950.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          57           1268           1307           4174
Markdown                         4             77              0            203
Jupyter Notebook                 3              0            492            166
YAML                             5             12              3            161
Dockerfile                       1              5              3             11
make                             1              2              3              5
-------------------------------------------------------------------------------
SUM:                            71           1364           1808           4720
-------------------------------------------------------------------------------

Statistical information for the repository '14fee00b678c84b921e8e16e' was
gathered on 2021/04/08.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
IceKhan13                        1            43              6            0.21
Iskandar Sitdikov               22          3330            396           16.31
Platon I Karpov                 16          3825           2270           26.68
Platon Karpov                   16          1544           1217           12.09
pikarpov                        57          6688           3522           44.70

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
IceKhan13                     6           14.0         16.5                0.00
Iskandar Sitdikov          1493           44.8         12.3                7.97
Platon I Karpov            2814           73.6          4.7               12.08
Platon Karpov              2436          157.8          4.7                6.65
dfm commented 3 years ago

@pikarpov-LANL: Can you make these small changes:

  1. Fix the ORCID in the manuscript
  2. Add the suggested DOI: 10.1109/tkde.2017.2720168
  3. Add an explicit "Statement of need" section to the paper
pikarpov-LANL commented 3 years ago

@dfm

  1. Done
  2. Done
  3. I think that my Introduction served as a Statement of Need, hence I renamed it to the latter. However, if you think it is too lengthy, I will be happy to edit it down. Let me know.

Also, would it be possible to add my personal github account (pikarpov) to this thread? This way I will receive email notifications to my personal email box. Work email is a bit harder and it is only available during work hours. LANL requires us to have a separate account that is distinctly LANL, however, I push to Sapsan from both since it is open-sourced now.

dfm commented 3 years ago

@whedon generate pdf from branch joss

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
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:

dfm commented 3 years ago

@whedon assign @kburns as reviewer

@kburns will be one of our reviewers - thanks Keaton! Once I have confirmation on a second reviewer, I'll get the main review started.

whedon commented 3 years ago

OK, @kburns is now a reviewer

dfm commented 3 years ago

@pikarpov-LANL: would you like me to switch this review to your @pikarpov account altogether or would you rather the submission still be associated with @pikarpov-LANL? Sorry I didn't get back to you about this sooner!

pikarpov-LANL commented 3 years ago

@dfm please keep the submission under @pikarpov-lanl, for the lab's record. However, I will reply faster @pikarpov, since I get notifications straight to my personal email, hence my phone. I cannot do the same with the lab's account.

dfm commented 3 years ago

@whedon add @milescranmer as reviewer

Thanks Miles for agreeing to be our second reviewer! I'll get the review started shortly in a new thread, so we can all head over there for the rest of the process. Please don't hesitate to ask if you have any questions as the review progresses.

whedon commented 3 years ago

OK, @milescranmer is now a reviewer

dfm 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/3199.