[PRE REVIEW]: NodePy: A package for the analysis of numerical ODE solvers

[whedon]

Submitting author: @ketch (David Ketcheson) Repository: https://github.com/ketch/nodepy Version: 0.9 Editor: @VivianePons Reviewers: @fruzsinaagocs, @wingtorres Managing EiC: Lorena A Barba

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Author instructions

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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]

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]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=1.81 s (39.3 files/s, 49504.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          35           1725           3312          79278
reStructuredText                16            237            151            556
TeX                              2             86              0            554
Jupyter Notebook                 8              0           2774            212
Markdown                         4             52              0            201
make                             1             22              4            113
HTML                             1              5              0             63
JSON                             1              0              0             34
YAML                             2              7              1             28
Bourne Shell                     1              0              0              2
-------------------------------------------------------------------------------
SUM:                            71           2134           6242          81041
-------------------------------------------------------------------------------

Statistical information for the repository '2485' was gathered on 2020/07/18.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Alex Fikl                        2           250            204            0.41
Colin Macdonald                  1             1              1            0.00
David Ketcheson                295         59906          35385           85.70
Hendrik Ranocha                 36          1158            401            1.40
JohnSell620                      2            11             24            0.03
Kevin Siswandi                   1            26             10            0.03
Matteo Parsani                  23           757            282            0.93
Mikael Mortensen                 4            21             32            0.05
Sidafa Conde                     2           116             11            0.11
Umairbin Waheed                  1           104              0            0.09
Yiannis Hadjimichael             1            48              0            0.04
ketch                            5          8343           3723           10.85
umairbinwaheed                  21           342             31            0.34

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
Alex Fikl                   240           96.0         50.2                1.67
Colin Macdonald               1          100.0        119.0                0.00
David Ketcheson           80664          134.7         92.6                0.80
Hendrik Ranocha             907           78.3          4.3                8.38
JohnSell620                   8           72.7         25.3               25.00
Kevin Siswandi                5           19.2          2.5                0.00
Matteo Parsani              471           62.2        104.1               23.14
Mikael Mortensen             12           57.1         33.1                0.00
Sidafa Conde                 75           64.7         64.8                4.00
Yiannis Hadjimichael         36           75.0         91.7               11.11
ketch                      1721           20.6         22.3               15.80
umairbinwaheed              175           51.2         90.3                5.71

[whedon]

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

[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1016/0378-4754(87)90083-8 may be missing for title: Solving ordinary differential equations I: Nonstiff Problems
- https://doi.org/10.1137/07070485x may be missing for title: Highly Efficient Strong Stability Preserving Runge-Kutta Methods with Low-Storage Implementations
- https://doi.org/10.1016/j.jcp.2009.11.006 may be missing for title: Runge–Kutta methods with minimum storage implementations
- https://doi.org/10.1137/100818674 may be missing for title: Step Sizes for Strong Stability Preservation with Downwind-Biased Operators
- https://doi.org/10.1137/130936245 may be missing for title: Internal error propagation in explicit Runge–Kutta methods
- https://doi.org/10.2140/camcos.2014.9.175 may be missing for title: A comparison of high order explicit Runge-Kutta, extrapolation, and deferred correction methods in serial and parallel
- https://doi.org/10.1109/mcse.2011.37 may be missing for title: The NumPy array: a structure for efficient numerical computation
- https://doi.org/10.1109/mcse.2007.55 may be missing for title: Matplotlib: A 2D graphics environment
- https://doi.org/10.1016/j.rinam.2019.100004 may be missing for title: Some notes on summation by parts time integration methods
- https://doi.org/10.1002/fld.4773 may be missing for title: More efficient time integration for Fourier pseudospectral DNS of incompressible turbulence

INVALID DOIs

- None

[labarba]

👋 @ketch -- have a look at whedon's report above... we're going to need DOIs added to all references that have them. Go ahead and make those edits, then run the command @whedon generate pdf here, as a single-line comment.

[labarba]

@whedon invite @VivianePons as editor

[whedon]

@VivianePons has been invited to edit this submission.

[ketch]

@whedon generate pdf

[whedon]

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

[ketch]

I've added DOIs for everything that has them. Note that one of the DOIs suggested by the bot actually corresponds to a book review rather than the book, so I didn't add it.

[ketch]

Some suggested referees:

• Lisandro Dalcin (dalcinl)
• Mikael Mortensen (mikaem)
• fruzsinaagocs (from volunteer list)
• wingtorres (from volunteer list)

[VivianePons]

@whedon add @VivianePons as editor

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[VivianePons]

@whedon assign @VivianePons as editor

[whedon]

OK, the editor is @VivianePons

[VivianePons]

@whedon assign @fruzsinaagocs as reviewer

[whedon]

OK, @fruzsinaagocs is now a reviewer

[VivianePons]

@whedon add @wingtorres as reviewer

[whedon]

OK, @wingtorres is now a reviewer

[VivianePons]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2515.