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[PRE REVIEW]: PyLogGrid: A Python package for fluid dynamics on logarithmic lattices #6087

Closed editorialbot closed 4 months ago

editorialbot commented 8 months ago

Submitting author: !--author-handle-->@hippalectryon-0<!--end-author-handle-- (Amaury Barral) Repository: https://github.com/hippalectryon-0/pyloggrid Branch with paper.md (empty if default branch): joss Version: 2.3.0 Editor: !--editor-->@philipcardiff<!--end-editor-- Reviewers: @slaizet, @marlonsmathias, @weiwangstfc Managing EiC: Arfon Smith

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Markdown: [![status](https://joss.theoj.org/papers/002028861bf61a4a81b3edde40db3d63/status.svg)](https://joss.theoj.org/papers/002028861bf61a4a81b3edde40db3d63)

Author instructions

Thanks for submitting your paper to JOSS @hippalectryon-0. Currently, there isn't a JOSS editor assigned to your paper.

@hippalectryon-0 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

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editorialbot commented 8 months ago

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editorialbot commented 8 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.39 s (210.1 files/s, 23656.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Python                          30           1136           1093           3533
Markdown                         9            152              0            388
reStructuredText                16            340            207            347
Jupyter Notebook                 1              0            344            320
YAML                             5             24             30            242
Cython                           1             22              9            218
C                                1             26              0            169
TeX                              1             13              0             96
PowerShell                       2             17             13             81
Bourne Shell                     5             17             15             70
TOML                             1              9              1             69
SVG                              5              1              1             31
make                             2              9              9             29
DOS Batch                        2              8              1             28
-------------------------------------------------------------------------------
SUM:                            81           1774           1723           5621
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 8 months ago

Wordcount for paper.md is 499

editorialbot commented 8 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1146/annurev.fluid.35.101101.161122 is OK
- 10.1103/PhysRevLett.77.5369 is OK
- 10.48550/arXiv.2006.00047 is OK
- 10.1017/jfm.2023.204 is OK
- 10.3390/atmos14111690 is OK

MISSING DOIs

- 10.1103/physreve.107.065106 may be a valid DOI for title: Reversible Navier-Stokes equation on logarithmic lattices
- 10.1016/j.jcp.2014.09.038 may be a valid DOI for title: Exponential time-differencing with embedded Runge–Kutta adaptive step control

INVALID DOIs

- https://doi.org/10.1016/0167-2789(85)90002-8 is INVALID because of 'https://doi.org/' prefix
editorialbot commented 8 months ago

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

editorialbot commented 8 months ago

Five most similar historical JOSS papers:

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lattice_mc: A Python Lattice-Gas Monte Carlo Module Submitting author: @bjmorgan Handling editor: @labarba (Retired) Reviewers: @asmit3 Similarity score: 0.8046

PyAMG: Algebraic Multigrid Solvers in Python Submitting author: @lukeolson Handling editor: @jedbrown (Active) Reviewers: @mayrmt, @mattmartineau Similarity score: 0.8038

pyro: a framework for hydrodynamics explorations and prototyping Submitting author: @harpolea Handling editor: @labarba (Retired) Reviewers: @mikaem, @ngoldbaum Similarity score: 0.8034

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

kyleniemeyer commented 6 months ago

Hi @hippalectryon-0, sorry for the delay in updates here. We are waiting for an editor to become available to handle your submission, which should hopefully happen soon.

philipcardiff commented 6 months ago

@editorialbot assign me as editor

editorialbot commented 6 months ago

Assigned! @philipcardiff is now the editor

philipcardiff commented 6 months ago

Hello @hippalectryon-0, do you have any suggestions for appropriate reviewers? Maybe even from the list of similar historical JOSS papers?

philipcardiff commented 6 months ago

FYI, I invited Ciro S. Campolina to review this submission via email (and am awaiting a reply), since you refer to their LogLatt library.

hippalectryon-0 commented 6 months ago

@philipcardiff Other than C. Campolina, I don't really have relevant reviewers from my field to suggest, as most aren't really in the numerical side of things. Looking quickly are other JOSS fluid dynamics paper, no reviewers really ring a bell, so I'm not sure that I can make a very relevant suggestion. Just in case, here are a few reviewers that reviewed somewhat similar (?) fluid dynamics papers (I removed the "@" to not ping them all): ashwinvis, NoraLoose, ranocha, eviatarbach, DamienIrving

philipcardiff commented 5 months ago

Hi @hippalectryon-0,

Would you mind addressing the following points on the documentation (https://pyloggrid.readthedocs.io/en/latest/benchmark.html#vs-grid-size):

Also, when I go to the main repository (https://github.com/hippalectryon-0/pyloggrid), the README file says this is not the main repository and it may not always be up to date; this is strange since the review is presumably meant to be on the main repository. At a minimum, please provide a link to the documentation in the README.

I am still searching for suitable reviewers.

philipcardiff commented 5 months ago

For the tutorial at https://pyloggrid.readthedocs.io/en/latest/tutorial/tutorial_first_simu.html#running-the-simulation, can you add more details on the problem definition? e.g.

This would also help me find appropriate reviewers as I would better understand what type of problems PyLogGrid can solve.

Thanks.

philipcardiff commented 5 months ago

HI @slaizet,

Would you be interested in reviewing the submission “PyLogGrid: A Python package for fluid dynamics on logarithmic lattice”, which we received at JOSS? The link for the submission is https://github.com/openjournals/joss-reviews/issues/6087 , and the repository is at https://github.com/hippalectryon-0/pyloggrid.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

philipcardiff commented 5 months ago

Hi @friedenhe,

Would you be interested in reviewing the submission “PyLogGrid: A Python package for fluid dynamics on logarithmic lattice”, which we received at JOSS? The link for the submission is https://github.com/openjournals/joss-reviews/issues/6087 , and the repository is at https://github.com/hippalectryon-0/pyloggrid.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected

slaizet commented 5 months ago

Happy to review this submission!

philipcardiff commented 5 months ago

Happy to review this submission!

Great, thank you.

philipcardiff commented 5 months ago

@editorialbot add @slaizet as reviewer

editorialbot commented 5 months ago

@slaizet added to the reviewers list!

hippalectryon-0 commented 5 months ago

@philipcardiff

Would you mind addressing the following points on the documentation (https://pyloggrid.readthedocs.io/en/latest/benchmark.html#vs-grid-size): (...)

I've pushed a new version, with the fixed typo and missing images. To view it, select the joss branch in the docs, or go directly to https://pyloggrid.readthedocs.io/en/joss/index.html.

Also, when I go to the main repository (https://github.com/hippalectryon-0/pyloggrid), the README file says this is not the main repository and it may not always be up to date; this is strange since the review is presumably meant to be on the main repository.

As explained elsewhere, the repository where the development takes place is a privately-hosted GitLab for administrative reasons, and the Github is simply a mirror to make it accessible to everyone.

At a minimum, please provide a link to the documentation in the README.

Added

PS: thanks for all your work :) PS 2: I'll add some documentation soon on the kind of simulations pyloggrid is suited for, as you requested in another comment; i'll ping you when it's done.

philipcardiff commented 5 months ago

By email, C. Campolina let me know that he is available to review this submission; however, this would appear to be against the JOSS Conflict of Interest Policy as you have recently co-authored a preprint together.

I will continue to search for another reviewer. Thanks for your patience.

friedenhe commented 5 months ago

@philipcardiff Thanks very much for the invitation. However, I am at my maximum bandwidth now, and I am afraid that I won't be able to review this paper.

philipcardiff commented 5 months ago

@philipcardiff Thanks very much for the invitation. However, I am at my maximum bandwidth now, and I am afraid that I won't be able to review this paper.

No problem, thanks for letting me know.

philipcardiff commented 5 months ago

Hi @p-costa,

Would you be interested in reviewing the submission “PyLogGrid: A Python package for fluid dynamics on logarithmic lattice”, which we received at JOSS? The link for the submission is https://github.com/openjournals/joss-reviews/issues/6087 , and the repository is at https://github.com/hippalectryon-0/pyloggrid.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected

p-costa commented 5 months ago

Thanks @philipcardiff for the invite! Unfortunately I don't have time to review this nice submission, as I am on parental leave.

philipcardiff commented 5 months ago

Thanks @philipcardiff for the invite! Unfortunately I don't have time to review this nice submission, as I am on parental leave.

No problem; thanks for your quick reply!

philipcardiff commented 5 months ago

HI @GongZheng-Justin, Would you be interested in reviewing the submission “PyLogGrid: A Python package for fluid dynamics on logarithmic lattice”, which we received at JOSS? The link for the submission is https://github.com/openjournals/joss-reviews/issues/6087 , and the repository is at https://github.com/hippalectryon-0/pyloggrid.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

philipcardiff commented 5 months ago

HI @davecats, Would you be interested in reviewing the submission “PyLogGrid: A Python package for fluid dynamics on logarithmic lattice”, which we received at JOSS? The link for the submission is https://github.com/openjournals/joss-reviews/issues/6087 , and the repository is at https://github.com/hippalectryon-0/pyloggrid.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

slaizet commented 5 months ago

Hi @hippalectryon-0,

I tried to follow your instructions to clone the code but I got an error message:

git clone git@github.com:hippalectryon-0/pyloggrid.git
Cloning into 'pyloggrid'...
The authenticity of host 'github.com (2a0c:5bc0:40:2fff::8c52:7903)' can't be established.
ECDSA key fingerprint is XXX.
Are you sure you want to continue connecting (yes/no/[fingerprint])? yes
Warning: Permanently added 'github.com,2a0c:5bc0:40:2fff::8c52:7903' (ECDSA) to the list of known hosts.
git@github.com: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

Can you double check that the instructions are correct?

Cheers,

Sylvain

hippalectryon-0 commented 5 months ago

@slaizet Can you try git clone https://github.com/hippalectryon-0/pyloggrid.git instead ?

(note that you'll then need to run cd pyloggrid && git checkout joss to switch to the joss branch)

slaizet commented 5 months ago

All good now with the new instructions (you might want to update your doc). Thanks!

hippalectryon-0 commented 5 months ago

For the tutorial at https://pyloggrid.readthedocs.io/en/latest/tutorial/tutorial_first_simu.html#running-the-simulation, can you add more details on the problem definition? e.g.

* Geometry

* Material properties

* Loading/boundary conditions

* Initial conditions

This would also help me find appropriate reviewers as I would better understand what type of problems PyLogGrid can solve.

Thanks.

As requested I've added some more information in the tutorial. I've also updated the docs to reflect the issue @slaizet faced.

(if you still see the old docs, 1) check that you're on the joss branch of the docs 2) clear your browser cache)

slaizet commented 5 months ago

Hi @hippalectryon-0,

I am trying to run my "first simulation" following the instructions here: https://pyloggrid.readthedocs.io/en/latest/tutorial/tutorial_first_simu.html

First of all, you should specify all the Python libraries required to run NS3D.py. Secondly, I get an error message when trying to run the code with python:

File "NS3D.py", line 22
    def get_forcing(grid: Grid) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
                        ^
SyntaxError: invalid syntax

I get a different error when trying to run the code with python3:

Traceback (most recent call last):
  File "NS3D.py", line 14, in <module>
    from pyloggrid.Libs.datasci import randcomplex_like, randcomplex_seeded_by_array
  File "/home/slaizet/reviewJOSS/pyloggrid/log-grid/Simulations/../pyloggrid/Libs/datasci.py", line 33, in <module>
    def mean(data: np.ndarray, ts: Optional[np.ndarray] = None, log: bool = False, start: float = 0, end: float = 1) -> tuple[np.ndarray, np.ndarray | None]:
TypeError: unsupported operand type(s) for |: 'type' and 'NoneType'

I can confirm that I am in the joss branch:

On branch joss
Your branch is up-to-date with 'origin/joss'.

Am I missing something?

Cheers,

Sylvain

philipcardiff commented 5 months ago

Hello @weiwangstfc, Would you be interested in reviewing the submission “PyLogGrid: A Python package for fluid dynamics on logarithmic lattice”, which we received at JOSS? The link for the submission is https://github.com/openjournals/joss-reviews/issues/6087 , and the repository is at https://github.com/hippalectryon-0/pyloggrid.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

philipcardiff commented 5 months ago

Hi @marlonsmathias, Would you be interested in reviewing the submission “PyLogGrid: A Python package for fluid dynamics on logarithmic lattice”, which we received at JOSS? The link for the submission is https://github.com/openjournals/joss-reviews/issues/6087 , and the repository is at https://github.com/hippalectryon-0/pyloggrid.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

marlonsmathias commented 5 months ago

Hello @philipcardiff , yes, I am interested in reviewing the submission. I have not reviewed for JOSS yet, so I will take a look at the documentation.

philipcardiff commented 4 months ago

Hello @philipcardiff , yes, I am interested in reviewing the submission. I have not reviewed for JOSS yet, so I will take a look at the documentation.

Thanks, @marlonsmathias.

philipcardiff commented 4 months ago

@editorialbot add @marlonsmathias as reviewer

editorialbot commented 4 months ago

@marlonsmathias added to the reviewers list!

philipcardiff commented 4 months ago

@editorialbot start review

editorialbot commented 4 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6439.

philipcardiff commented 4 months ago

Hi all, we can continue the review over on the review issue https://github.com/openjournals/joss-reviews/issues/6439.

weiwangstfc commented 4 months ago

Hi Philip,

I can review the mentioned submission if you are still looking for reviewers.

Thanks. Regards, Wei

From: Philip Cardiff @.> Sent: Friday, March 1, 2024 15:27 To: openjournals/joss-reviews @.> Cc: Wang, Wei (STFC,DL,SC) @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: PyLogGrid: A Python package for fluid dynamics on logarithmic lattices (Issue #6087)

Hello @weiwangstfchttps://github.com/weiwangstfc, Would you be interested in reviewing the submission “PyLogGrid: A Python package for fluid dynamics on logarithmic lattice”, which we received at JOSS? The link for the submission is #6087https://github.com/openjournals/joss-reviews/issues/6087 , and the repository is at https://github.com/hippalectryon-0/pyloggrid.

If you are unfamiliar with JOSS, the review process is unique: it takes place in a GitHub issue, is open, and encourages author-reviewer-editor conversations. You can have a look at our review criteria (https://joss.readthedocs.io/en/latest/review_criteria.html) and review checklist (https://joss.readthedocs.io/en/latest/review_checklist.html) to get an idea of what is expected.

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/6087#issuecomment-1973387233, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARMNZ247CJNMQ6CV32UNUKDYWCM7VAVCNFSM6AAAAAA7Y2LER2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZTGM4DOMRTGM. You are receiving this because you were mentioned.Message ID: @.***>

philipcardiff commented 4 months ago

Hi Philip, I can review the mentioned submission if you are still looking for reviewers. Thanks. Regards, Wei …

Great, thanks Wei.

philipcardiff commented 4 months ago

@editorialbot add @weiwangstfc as reviewer

editorialbot commented 4 months ago

@weiwangstfc added to the reviewers list!

hippalectryon-0 commented 4 months ago

@slaizet Apologies for the late answer, I missed the notification.

First of all, you should specify all the Python libraries required to run NS3D.py. Secondly, I get an error message when trying to run the code with python:

Could you confirm that you have successfully ran setup.sh as indicated here ? Your error indicates that you're using a python version which is too old. The setup takes care of installing the right python version, the virtual environment, and all the required packages.