[REVIEW]: StoSpa2: A C++ software package for stochastic simulations of spatially extended systems

whedon commented 4 years ago

Submitting author: @BartoszBartmanski (Bartosz Bartmanski) Repository: https://github.com/BartoszBartmanski/StoSpa2 Version: 2.0.29 Editor: @pdebuyl Reviewers: @CFGrote, @mbkumar Archive: 10.5281/zenodo.3901670

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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

@CFGrote and @mbkumar , please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @CFGrote

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 repository url?
[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 (@BartoszBartmanski) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @mbkumar

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 repository url?
[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 (@BartoszBartmanski) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @CFGrote it looks like you're currently assigned to review this paper :tada:.

: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.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1371/journal.pcbi.1004923 is OK
- 10.1063/1.4975167 is OK
- 10.1371/journal.pcbi.1005387 is OK
- 10.1007/s40571-015-0082-3 is OK
- 10.1063/1.4816377 is OK

MISSING DOIs

- https://doi.org/10.1137/070705039 may be missing for title: The reaction-diffusion master equation as an asymptotic approximation of diffusion to a small target

INVALID DOIs

- None

whedon commented 4 years ago

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

pdebuyl commented 4 years ago

@whedon add @mbkumar as reviewer

whedon commented 4 years ago

OK, @mbkumar is now a reviewer

pdebuyl commented 4 years ago

@CFGrote , @mbkumar , make sure to accept the invitation to the reviewers group and to have a look at the reviewer guidelines.

The review process will happen in this issue page, so questions to the author or to me can be added as comments here.

pdebuyl commented 4 years ago

@mbkumar please write the comments on the manuscript here, so that the review page keeps trace of it. The issues in the software repository are more suited for direct software problems (bugs, missing dependencies, for instance).

mbkumar commented 4 years ago

Section on the status of the field is missing.

BartoszBartmanski commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

BartoszBartmanski commented 4 years ago

Apologies for not including that section. I just updated paper.md with an additional section about competing software packages

mbkumar commented 4 years ago

Completed the review and my recommendation is publish as it is.

The manuscript is well written and the software was coded well with best practices.

@pdebuyl Could you please send me an email acknowledging the completion of review for my record?

CFGrote commented 4 years ago

@whedon check repository

whedon commented 4 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.19 s (254.1 files/s, 121196.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                     8           3287           1366          13960
SVG                              1              0             16           1014
Markdown                         3            100             10            446
Python                          11            133             87            396
C++                              7             95             26            276
Jupyter Notebook                 1              0            651            259
YAML                             2             38             13            173
TeX                              1             10              0            130
reStructuredText                 4             90             24            123
CMake                            7             32             19             83
Bourne Shell                     2              7              4             26
TOML                             1              0              0              2
-------------------------------------------------------------------------------
SUM:                            48           3792           2216          16888
-------------------------------------------------------------------------------

Statistical information for the repository '2293' was gathered on 2020/06/15.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
bartosz.bartmanski              43         21078            642          100.00

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
bartosz.bartmanski        20436           97.0          0.4                8.79

CFGrote commented 4 years ago

Can't run the example. See https://github.com/BartoszBartmanski/StoSpa2/issues/8 .

CFGrote commented 4 years ago

The target audience is not clearly mentioned (neither in README nor in the documentation).

CFGrote commented 4 years ago

I suggest to add short sections on how to contribute and how to seek support (i.e. link to gh issues) to the README.

CFGrote commented 4 years ago

Some references in the manuscript are not correctly rendered in the autogenerated pdf but this may be a conversion problem. Please check the page number in Osborne et al 2017) and Isaacson 2009.

CFGrote commented 4 years ago

Installation instructions: Only after reading the manuscript, I understood that it is not required to compile the c++ code if one is only using the python interface. This should maybe be stated more clearly in the online installation instructions in README and docs.

pdebuyl commented 4 years ago

@mbkumar Thank you for the review (email sent).

BartoszBartmanski commented 4 years ago

@CFGrote thank you for these comments. I just pushed two commits to the repository for StoSpa2, which hopefully address all of the above mentioned points.

BartoszBartmanski commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

BartoszBartmanski commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

pdebuyl commented 4 years ago

@BartoszBartmanski Some references still don't appear correctly, as you can only use one bib reference per square brackets. Can you fix that?

BartoszBartmanski commented 4 years ago

Sorry, I did not realise that it was one reference per square brackets. I just updated the repository with those changes. Thank you for clarifying that.

@whedon generate pdf

danielskatz commented 4 years ago

Hi 1 - you can have multiple references inside one set of square brackets, but they need to separated with ;s, not ,s - they may also not support a space after the ; but I am not sure. Try [@a;@b] for example. 2 - commands to whedon need to be the very start of a comment

pdebuyl commented 4 years ago

Thank you @danielskatz

Sorry @BartoszBartmanski , it is indeed better to have the grouped citations as originally intended.

BartoszBartmanski commented 4 years ago

Thank you @danielskatz for both suggestions

@pdebuyl I just updated the citations in the repository. Let's see whether it's fixed

BartoszBartmanski commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

BartoszBartmanski commented 4 years ago

@pdebuyl That seems to have fixed that issue

CFGrote commented 4 years ago

still missing the target audience in the docs/readme.

CFGrote commented 4 years ago

Indentation in the README is off at "## Example"

BartoszBartmanski commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

BartoszBartmanski commented 4 years ago

@CFGrote Thank you for spotting Examples section misalignment. A typo in the README caused this section title to be interpreted as a code block. I also added target audience to both the README and the docs in the most recent commit.

CFGrote commented 4 years ago

@BartoszBartmanski, very good. I'm happy with the repo now and recommend publication as is.

CFGrote commented 4 years ago

@whedon commands

whedon commented 4 years ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

CFGrote commented 4 years ago

@pdebuyl I'm done with the review, my recommendation is: publish as is. Thanks for the experience, this was my first JOSS review.

pdebuyl commented 4 years ago

@CFGrote thank you for the review and the feedback!

I will take care of the paper for publication after going through the editor's checklist.

pdebuyl commented 4 years ago

@whedon generate pdf

pdebuyl commented 4 years ago

@whedon check references

whedon commented 4 years ago

PDF failed to compile for issue #2293 with the following error:

sh: 0: getcwd() failed: No such file or directory pandoc: 10.21105.joss.02293.pdf: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.1371/journal.pcbi.1005387 is OK

MISSING DOIs

- https://doi.org/10.1186/1752-0509-6-76 may be missing for title: URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries
- https://doi.org/10.1093/bioinformatics/bts584 may be missing for title: MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit
- https://doi.org/10.1371/journal.pcbi.1004923 may be missing for title: Stochastic simulation of biomolecular networks in dynamic environments
- https://doi.org/10.1063/1.4975167 may be missing for title: Reaction rates for reaction-diffusion kinetics on unstructured meshes
- https://doi.org/10.1007/s40571-015-0082-3 may be missing for title: Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results
- https://doi.org/10.1137/070705039 may be missing for title: The reaction-diffusion master equation as an asymptotic approximation of diffusion to a small target
- https://doi.org/10.1063/1.4816377 may be missing for title: A convergent reaction-diffusion master equation

INVALID DOIs

- None

pdebuyl commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

pdebuyl commented 4 years ago

@BartoszBartmanski can you add the doi for all references in the bib file?

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