[REVIEW]: parafields: A generator for distributed, stationary Gaussian processes

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@dokempf@diehlpk<!--end-editor-- Reviewers: @shahmoradi, @gchure Archive: 10.5281/zenodo.10355636

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@max-little & @shahmoradi, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diehlpk know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @shahmoradi

📝 Checklist for @gchure

editorialbot commented 1 year ago

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

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

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (806.5 files/s, 135174.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             4              0              0           2680
Python                          13            288            371            917
CMake                            4            142             50            853
YAML                             7             54             26            287
Markdown                         3             45              0            161
C++                              1             18              9            148
TeX                              1              2              0            133
Jupyter Notebook                 4              0            820            126
C/C++ Header                     3             22             30             77
TOML                             1              9             21             65
reStructuredText                 3              5             13              3
-------------------------------------------------------------------------------
SUM:                            44            585           1340           5450
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 816

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/j.advwatres.2016.12.006 is OK
- 10.1137/s1064827592240555 is OK
- 10.1137/17m1149730 is OK
- 10.1109/MCSE.2021.3083216 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1016/j.camwa.2020.06.007 is OK
- 10.5281/zenodo.2565368 is OK
- 10.2307/1390903 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

diehlpk commented 1 year ago

@editorialbot remind @max-little in 2 weeks

editorialbot commented 1 year ago

Reminder set for @max-little in 2 weeks

diehlpk commented 1 year ago

@editorialbot remind @shahmoradi in 2 weeks

editorialbot commented 1 year ago

Reminder set for @shahmoradi in 2 weeks

editorialbot commented 1 year ago

:wave: @max-little, please update us on how your review is going (this is an automated reminder).

editorialbot commented 1 year ago

:wave: @shahmoradi, please update us on how your review is going (this is an automated reminder).

diehlpk commented 1 year ago

@editorialbot remind @max-little in 1 weeks

editorialbot commented 1 year ago

Reminder set for @max-little in 1 weeks

diehlpk commented 1 year ago

@editorialbot remind @shahmoradi in 1 weeks

editorialbot commented 1 year ago

Reminder set for @shahmoradi in 1 weeks

shahmoradi commented 1 year ago

Review checklist for @shahmoradi

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/parafields/parafields?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@dokempf) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

editorialbot commented 1 year ago

:wave: @max-little, please update us on how your review is going (this is an automated reminder).

editorialbot commented 1 year ago

:wave: @shahmoradi, please update us on how your review is going (this is an automated reminder).

diehlpk commented 1 year ago

Hi @max-little and @shahmoradi how is your review going?

diehlpk commented 1 year ago

Hi @max-little and @shahmoradi how is your review going?

diehlpk commented 1 year ago

Hi @max-little are you still available for the review?

diehlpk commented 1 year ago

Hi @shahmoradi are you still available for the review?

diehlpk commented 1 year ago

Hi @max-little I have not heard from you for a while, I will remove you as a reviewer and will add you again once I hear from you.

diehlpk commented 1 year ago

@editorialbot remove @max-little as reviewer

editorialbot commented 1 year ago

@max-little removed from the reviewers list!

diehlpk commented 1 year ago

Hi @shahmoradi I have not heard from you for a while, I will remove you as a reviewer and will add you again once I hear from you.

diehlpk commented 1 year ago

@editorialbot @shahmoradi as reviewer

editorialbot commented 1 year ago

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

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diehlpk commented 1 year ago

@editorialbot remove @shahmoradi as reviewer

editorialbot commented 1 year ago

@shahmoradi removed from the reviewers list!

diehlpk commented 1 year ago

Hi @dokempf it seems both reviewers disappeared. I will look for new once today. Do you have any recommendations?

diehlpk commented 1 year ago

Hi @OsAmaro do you have the time review this paper?

diehlpk commented 1 year ago

Hi @y-yao do you have time to review this paper?

diehlpk commented 1 year ago

Hi @GregoryAshton do you have time to review this paper?

shahmoradi commented 1 year ago

Sorry for missing this assignment. I have been assigned multiple JOSS review tasks, making it super-confusing to determine what is complete and what needs completion with all other daily life events. I realize my name was removed as a reviewer. Nevertheless, since I made the promise once, I'd happily help with the review if needed over the weekend.

diehlpk commented 1 year ago

@shahmoradi I am happy to add you again.

diehlpk commented 1 year ago

@editorialbot add @shahmoradi as reviewer

editorialbot commented 1 year ago

@shahmoradi added to the reviewers list!

y-yao commented 1 year ago

Hi @y-yao do you have time to review this paper?

I will pass this time as this is outside of my area of expertise. Thanks for the invite.

GregoryAshton commented 1 year ago

Hi @GregoryAshton do you have time to review this paper?

Hi @diehlpk I'm sorry but mid-semester teaching is too much at the moment to take on extra review. My apologies.

shahmoradi commented 1 year ago

Thank you for your efforts to create this library. I am sure the Python community will find this package helpful. Everything about this project and JOSS submission looks good, except the following comments I have for the authors:

The installation page should likely go before the usage page in the documentation website.
Adding a complete MPI-parallel example in the documentation would be helpful.
Instructions for running the unit tests (serial/parallel) would be very helpful (I am sure many, like me, do not know or remember how to run tests off the top of their heads).
A similar argument, but less severely, applies to docs generation. The instructions are particularly important and vital for future contributors.
Can the authors check if "Community guidelines: 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support" exist in the repository and if so, point me to those docs?
Are there any alternative options available in the literature that the authors could cite in "State of the field: Do the authors describe how this software compares to other commonly-used packages?"

OsAmaro commented 1 year ago

Hi @OsAmaro do you have the time review this paper?

Hi. Unfortunately, this topic is a bit outside of my area of expertise. I'll have to pass this time. Thanks for the invite anyways

diehlpk commented 1 year ago

Thank you for your efforts to create this library. I am sure the Python community will find this package helpful. Everything about this project and JOSS submission looks good, except the following comments I have for the authors:

1. The **installation** page should likely go before the **usage** page in the documentation website.

2. Adding a complete MPI-parallel example in the documentation would be helpful.

3. Instructions for running the unit tests (serial/parallel) would be very helpful (I am sure many, like me, do not know or remember how to run tests off the top of their heads).

4. A similar argument, but less severely, applies to docs generation. The instructions are particularly important and vital for future contributors.

5. Can the authors check if "Community guidelines: 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support" exist in the repository and if so, point me to those docs?

6. Are there any alternative options available in the literature that the authors could cite in "State of the field: Do the authors describe how this software compares to other commonly-used packages?"

@dokempf please take a look at these comments.

dokempf commented 1 year ago

@shahmoradi Thanks a lot for your comments, much appreciated.

1. The **installation** page should likely go before the **usage** page in the documentation website.

Done in main.

2. Adding a complete MPI-parallel example in the documentation would be helpful.

I have moved the MPI documentation from a Jupyter notebook (that cannot really be run in parallel) to the Sphinx documentation. Added additional bit especially about the differences between sequential and parallel use (same API, different shapes of the results of evaluate)

3. Instructions for running the unit tests (serial/parallel) would be very helpful (I am sure many, like me, do not know or remember how to run tests off the top of their heads).

Done in main.

4. A similar argument, but less severely, applies to docs generation. The instructions are particularly important and vital for future contributors.

Done in main.

5. Can the authors check if "Community guidelines: 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support" exist in the repository and if so, point me to those docs?

Done in main. They are in the README which is also used to render the introduction section of the Readthedocs page.

6. Are there any alternative options available in the literature that the authors could cite in "State of the field: Do the authors describe how this software compares to other commonly-used packages?"

We added a paragraph about related (software) work to the paper draft.

dokempf commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

dokempf commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

diehlpk commented 1 year ago

@shahmoradi can you please have a look at the changes?

diehlpk commented 1 year ago

Hi @gchure do you have time to review this paper?

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