[PRE REVIEW]: Nyx: A Massively Parallel AMR Code for Computational Cosmology

[whedon]

Submitting author: @jmsexton03 (Jean M. Sexton) Repository: https://github.com/AMReX-Astro/Nyx Version: 21.02.1 Editor: @dfm Reviewers: @c-white, @bwoshea Managing EiC: Arfon Smith

:warning: JOSS reduced service mode :warning:

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Editor instructions

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[whedon]

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

:warning: JOSS reduced service mode :warning:

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

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[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/mnras/stz984 is OK
- 10.21105/joss.01370 is OK
- 10.1088/1742-6596/1225/1/012005 is OK
- 10.1088/0004-637X/715/2/1221 is OK
- 10.1016/0021-9991(84)90143-8 is OK
- 10.1016/0021-9991(90)90233-Q is OK

MISSING DOIs

- 10.1088/0004-637x/765/1/39 may be a valid DOI for title: Nyx: A Massively Parallel AMR Code for Computational Cosmology
- 10.21105/joss.01757 may be a valid DOI for title: MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver

INVALID DOIs

- https://doi.org/10.1016/j.jcp.2007.07.035 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jpdc.2014.07.003 is INVALID because of 'https://doi.org/' prefix

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.66 s (363.6 files/s, 62989.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C++                              84           3952           2607          17841
C/C++ Header                     33           1192           1009           5343
reStructuredText                 28            947            396           2578
CMake                            26            176            128            651
Python                            6            222            249            638
make                             23            217             91            559
Markdown                          6            102              0            460
Fortran 90                        4             93             72            405
TeX                               3             32              5            302
YAML                              8             27             11            295
INI                               1             30              0            288
Bourne Shell                     13             60            132            152
Bourne Again Shell                3             25             67             44
JSON                              1              0              0              3
--------------------------------------------------------------------------------
SUM:                            239           7075           4767          29559
--------------------------------------------------------------------------------

Statistical information for the repository '4e0ecd20b81f5752131252cb' was
gathered on 2021/02/13.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Andrew Myers                    40           580           1039            1.03
Ann Almgren                    301         27441          21525           31.17
Arnur Nigmetov                   6           840            285            0.72
Brian Friesen                   54           464            342            0.51
Cyrus Harrison                   1            45            205            0.16
Dmitriy Morozov                  5           144              1            0.09
Frederick Davies                 3           265             35            0.19
Gunther H. Weber                 2           148             42            0.12
Hannah Ross                      6           173            140            0.20
Jean M. Sexton                 497         26958          18071           28.66
Jean Sexton                     81          4655           2089            4.29
Matt Larsen                      1             0              3            0.00
Michael Zingale                  4            98              6            0.07
Michele Rosso                    2             1              3            0.00
Peter McCorquodale               4            35             10            0.03
Weiqun Zhang                    44          1589           2568            2.65
Wolfram Schmidt                 11          2826            906            2.38
Yinghe Lu                        3            41             34            0.05
Zarija                           3            18          11597            7.39
Zarija Lukic                    31         18944            198           12.18
hr203                            1           989            312            0.83
jbb                              6            74             61            0.09
jmsexton03                       1           604             34            0.41
mic84                            3            43             20            0.04
petermcLBL                      27          1673           2133            2.42
vince                           46          2410            621            1.93
zarija                           8          1178           2598            2.40

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
Andrew Myers                381           65.7         32.7                3.94
Ann Almgren               13565           49.4          6.3               11.25
Arnur Nigmetov              598           71.2         17.8               11.04
Brian Friesen                24            5.2         41.2                0.00
Cyrus Harrison               39           86.7         11.4               46.15
Dmitriy Morozov             142           98.6         33.2               16.20
Frederick Davies            256           96.6         12.8               10.94
Gunther H. Weber              2            1.4         48.8                0.00
Jean M. Sexton             7070           26.2         10.5               12.11
Michael Zingale              81           82.7         50.1                3.70
Michele Rosso                38         3800.0          1.4                0.00
Weiqun Zhang                625           39.3         39.7                1.28
Wolfram Schmidt             973           34.4         45.2               14.59
Zarija                     1370         7611.1          7.2               10.88
jbb                          31           41.9          6.2               16.13
petermcLBL                  327           19.5         44.9               13.76
vince                       346           14.4         22.4                4.91

[whedon]

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

[Kevin-Mattheus-Moerman]

@whedon invite @eloisabentivegna as editor

[whedon]

@eloisabentivegna has been invited to edit this submission.

[Kevin-Mattheus-Moerman]

@eloisabentivegna I realize you are handling quite a few submissions already! This submission does seem like your cup of tea but if you cannot handle it I understand.

[Kevin-Mattheus-Moerman]

Alternatively @dfm @xuanxu are you able to edit this work? Thanks

[xuanxu]

@Kevin-Mattheus-Moerman right now I don't have enough time to take another one, sorry.

[jmsexton03]

I was asked to suggest people without tagging them: Alice Harpolea (harpolea) or Erik Schnetter (eschnett)

[dfm]

@whedon assign me as editor

I'm happy to edit!

[whedon]

OK, the editor is @dfm

[eloisabentivegna]

@eloisabentivegna I realize you are handling quite a few submissions already! This submission does seem like your cup of tea but if you cannot handle it I understand.

@Kevin-Mattheus-Moerman, you are right, this was fully within my domain. I have my hands full at the moment though -- glad you could find another editor!

[dfm]

@whedon assign @c-white as reviewer

Thanks Chris! We should have a second reviewer lined up shortly and we'll get the review started.

[whedon]

OK, @c-white is now a reviewer

[dfm]

@whedon add @bwoshea as reviewer

Brian will be our second reviewer. Thanks @bwoshea!

I'll get the review started in a new thread and we can all head over there to get started. There will be a lot of information automatically added to that thread, but please don't hesitate to ask me if you have any questions as the review proceeds!

[whedon]

OK, @bwoshea is now a reviewer

[dfm]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3068.