[PRE REVIEW]: DORiE: A discontinuous Galerkin solver for soil water flow and passive solute transport based on DUNE

whedon commented 4 years ago

Submitting author: @peanutfun (Lukas Riedel) Repository: https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie Version: v2.0 Editor: @meg-simula Reviewers: @gassmoeller, @pratikvn Managing EiC: Kristen Thyng

:warning: JOSS reduced service mode :warning:

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

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whedon commented 4 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 4 years ago

PDF failed to compile for issue #2195 with the following error:

Can't find any papers to compile :-(

whedon commented 4 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.46 s (599.1 files/s, 82286.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                    96           3132           6419          12302
C++                             23            705            436           3392
Python                          51            612            653           1949
reStructuredText                22            813            714           1616
XML                              5            148             16           1014
Markdown                        17            359              0           1009
CMake                           37            178            363            806
YAML                            19             71             34            675
GLSL                             4              0            143            139
CSS                              1             12              0             62
-------------------------------------------------------------------------------
SUM:                           275           6030           8778          22964
-------------------------------------------------------------------------------

Statistical information for the repository '2195' was gathered on 2020/05/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Dion Häfner                     44         21870          10746           17.28
Lukas Riedel                   446         33015          29191           32.96
Santiago                       122          7213           8655            8.41
Santiago Ospina                257         39854          27048           35.45
Santiago Ospina De L             8           258            304            0.30
Santiago Ospina De L            71          5378           5199            5.60

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
Dion Häfner                3503           16.0         20.9               16.27
Lukas Riedel              11796           35.7         14.9               20.63
Santiago                   1156           16.0         15.8               15.22
Santiago Ospina           11141           28.0         15.7               16.85
Santiago Ospina De L       1985           36.9         13.4               26.50

kthyng commented 4 years ago

Hi @peanutfun! Do you have a JOSS paper somewhere in your repo, or maybe another repo? Our bot can't find it.

kthyng commented 4 years ago

Hi @meg-simula! Would you be able to edit this submission?

meg-simula commented 4 years ago

Yes, can do. (But public holiday here until Monday, will follow up then.)

danielskatz commented 4 years ago

@whedon assign @meg-simula as editor

whedon commented 4 years ago

OK, the editor is @meg-simula

peanutfun commented 4 years ago

@whedon generate pdf from branch joss-paper

whedon commented 4 years ago

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon commented 4 years ago

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

peanutfun commented 4 years ago

Hello everybody and thanks for having us! The paper is located in the joss-paper branch of the repository in order to quickly update it during the review process. I just had it compiled from there.

peanutfun commented 4 years ago

As potential reviewers and I would like to suggest rreinecke, mikaem, gassmoeller, dvalters, and pratikvn

meg-simula commented 4 years ago

Thank you for the submission @peanutfun, I look forward to taking a closer look at DORiE. List of potential reviewers also much appreciated.

Before we move this along, please note that the JOSS guidelines stipulate a paper length of 250-1000 words:

https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain

As far as I can tell, the current DORiE paper is substantially longer than this. Could you please revise? Perhaps some of the text could enter in the DORiE documentation?

peanutfun commented 4 years ago

Hi @meg-simula! 👋 You are correct. Excluding formulae, the current manuscript comprises some 3000 words, with ca. 1300 words in the longest section "Discontinuous Galerkin Discretization".

To the best of our knowledge, applying the described discretization method to the physical problem and providing the software implementing it is a novelty. We therefore included the mentioned section in the paper, as potential readers might have a strong interest not only in the software, but also the numerical methods. Currently, the documentation is hosted online but in general, users will have to build it locally after a lengthy installation process which might be a major hurdle to some (see README.md#manual-installation). Additionally, the paper will potentially receive a more thorough review than the documentation. We thus would still prefer keeping this section in the paper. However, we could declare it an "Appendix" section of the paper and move it to its end, if that is possible.

Apart from this section, I see few opportunities for shortening the paper substantially:

Dropping "Summary" would leave readers without overview of the software and the paper.
Removing "Physics of Simulated Processes" might leave non-specialists wondering what the software actually computes.
"Research and Use Cases" demonstrates that the software is operational and has been applied successfully.
Each of the "Showcases" demonstrates a major feature of the software.

What do you think? Would exceeding the word limit be acceptable in our case?

meg-simula commented 4 years ago

I completely understand your reasoning @peanutfun. If the discretization is novel, I would suggest that you consider submitting a manuscript describing those bits (and perhaps other material) to a suitable venue. JOSS papers are only expected to contain a limited set of metadata (see example below), a Statement of Need, Summary, Acknowledgements, and References sections. You can look at an example accepted paper at the aforementioned link.

peanutfun commented 4 years ago

@whedon generate pdf from branch joss-paper

whedon commented 4 years ago

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon commented 4 years ago

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

peanutfun commented 4 years ago

@whedon generate pdf from branch joss-paper

whedon commented 4 years ago

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

whedon commented 4 years ago

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

peanutfun commented 4 years ago

Fair enough, @meg-simula! We were hoping to put all this information on the software in one publication, but I understand that the numerics exceed the scope of a JOSS paper.

We drastically pruned the originally submitted paper to a word count of 1090, including the figure captions (see the latest version compiled by @whedon). The paper now contains a summary, a background section giving the statement of need, a feature overview, a section on past research, a shortened showcase section and acknowledgements.

Also, sorry for the noise in this thread! I had @whedon compile the latest version and immediately noticed a typo 🙈

meg-simula commented 4 years ago

Great, thanks @peanutfun. This looks very much ready for review. I'll reach out to reviewers and get back to you.

meg-simula commented 4 years ago

@rreinecke, @mikaem, @gassmoeller, @dvalters, @pratikvn @: Would you like to review this submission for JOSS? Feel free to take a look at our reviewer guidelines here:

https://joss.readthedocs.io/en/latest/reviewer_guidelines.html .