[REVIEW]: autoStreamTree: Genomic variant data fitted to geospatial networks

editorialbot commented 9 months ago

Submitting author: !--author-handle-->@tkchafin@crvernon<!--end-editor-- Reviewers: @xin-huang, @abhishektiwari Archive: 10.5281/zenodo.10866066

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/233409855e9d2064941a4f68f6921d38/status.svg)](https://joss.theoj.org/papers/233409855e9d2064941a4f68f6921d38)

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

@xin-huang & @abhishektiwari, 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 @crvernon 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 @xin-huang

📝 Checklist for @abhishektiwari

editorialbot commented 9 months ago

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editorialbot commented 9 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (427.1 files/s, 94912.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          20            860           1174           3117
Markdown                         2            138              0            444
TeX                              1             15              0            145
YAML                             3             12              0             93
Bourne Shell                     1              0              1              1
-------------------------------------------------------------------------------
SUM:                            27           1025           1175           3800
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 9 months ago

Wordcount for paper.md is 1435

editorialbot commented 9 months ago

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

OK DOIs

- 10.1111/j.1461-0248.2006.01007.x is OK
- 10.1111/j.1558-5646.1967.tb03411.x is OK
- 10.1111/ddi.13160 is OK
- 10.1007/BF01386390 is OK
- 10.1093/bioinformatics/btn129 is OK
- 10.1139/F08-171 is OK
- 10.1038/s41597-019-0300-6 is OK
- 10.1111/ele.12084 is OK
- 10.1061/(ASCE)0733-9429(1990)116:7(946) is OK
- 10.1111/evo.12883 is OK
- 10.21105/joss.03021 is OK
- 10.2307/2408641 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 9 months ago

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

crvernon commented 9 months ago

👋 @tkchafin , @xin-huang , and @abhishektiwari - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6160 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

xin-huang commented 9 months ago

Review checklist for @xin-huang

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/tkchafin/autostreamtree?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@tkchafin) 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?

abhishektiwari commented 9 months ago

Review checklist for @abhishektiwari

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/tkchafin/autostreamtree?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@tkchafin) 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?

crvernon commented 8 months ago

👋 @tkchafin , @xin-huang , and @abhishektiwari

Just touching base to see how this review is going? Post a short update here when you have a moment if you will.

Thanks!

xin-huang commented 8 months ago

The authors have developed a valuable tool for the study of landscape genetics utilizing population genomic data. Given the increasing availability of genomic and geospatial data, this tool stands to aid researchers in understanding how evolutionary or ecological processes influence the spatial patterns of genetic variation. I have raised specific concerns regarding the documentation and the software paper through the opening of two issues https://github.com/tkchafin/autostreamtree/issues/5 and https://github.com/tkchafin/autostreamtree/issues/6. Additionally, it is imperative that the authors make the data and codes available for replicating the analyses and performance comparisons presented in their paper, as this is a requirement of the journal.

crvernon commented 8 months ago

:wave: @tkchafin , @xin-huang , and @abhishektiwari

I will be unavailable from Jan. 17-29. Please keep up the great work while I am out and I will be happy to address any questions you have when I come back!

Thanks!

abhishektiwari commented 8 months ago

thanks @crvernon. I will make sure my feedback/comments are in by mid-next week.

tkchafin commented 8 months ago

@editorialbot generate pdf

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

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

tkchafin commented 8 months ago

@editorialbot generate pdf

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:

tkchafin commented 8 months ago

@editorialbot generate pdf

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:

abhishektiwari commented 7 months ago

@tkchafin See my initial feedback

Installation

At this point I am unable to test the package due to installation issues. I tried installing on Mac, Ubuntu 22.04, Docker images (condaforge/miniforge3:latest ) but no luck. Can you please share guidance on issue here?

Data & Scripts

I see you added reference to data and scripts associated with this work but DOI format seems wrong. Can you update the DOI URL format for archive (https://doi.org/10.17605/OSF.IO/4UXFJ).

abhishektiwari commented 7 months ago

@tkchafin Thanks for adding Docker images for the autoStreamTree. I was able to quickly validate the functionality and examples.

Suggested improvement (non-blocking)

I think it will be great if you can move the autoStreamTree package doc from pandoc generated PDF to Read the docs. Given docstrings already exists in package files, it will be relatively small change to enable Read the docs and I strongly recommend it. It will improve readability of the package API documentation.
autoStreamTree is offered as CLI which is great to interact and interface with modular data pipeline tools like Nextflow. This seems right approach in my opinion. That said, given a large number of arguments as input, autoStreamTree can benefit by improving the CLI interface. Something like Python click will make this params implementation more simpler, extendable, and unit testable. In current structure, I am not sure if all permutation/combination of inputs are testable. Again, author has done a great job adding enough automated test to detect regression so I am less fussy about this improvement.

tkchafin commented 7 months ago

@abhishektiwari Thanks for the suggestions, I've moved the documentation to a navigable HTML hosted in GitHub Pages, since this was easy to integrate into the existing CI workflow. This should now be re-built and kept up to date on each commit: https://tkchafin.github.io/autostreamtree/. For now I'll put switching to click as an enhancement as it might be a while before I can get to it, but if it simplifies getting higher test coverage it sounds like a good move

tkchafin commented 6 months ago

Sorry these revisions took a while! In trying to comply with the suggestion in #6 to make the analysis behind Figure 1 reproducible, I discovered that the R code I had uploaded was calling some custom externally sourced functions that I couldn't find, so I wrote new code for the analysis and plotting. This was also a good chance to make the feature selection more robust (as this was somewhat arbitrary before), as well as to show how to string all of the analysis steps together with autostreamtree as an automated workflow. The new data repository should be self-contained, and has a NextFlow pipeline implementing the analyses used in the case study. Links should all be updated now in the README and paper, so after that is regenerated I think I've addressed all of the issues brought up so far.

tkchafin commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

tkchafin commented 6 months ago

@editorialbot generate pdf

tkchafin commented 6 months ago

(updated runtimes in MS)

editorialbot commented 6 months ago

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

crvernon commented 6 months ago

:wave: @xin-huang and @abhishektiwari

Could you provide a short update here pertaining to how things are going on this review? Thanks!

xin-huang commented 6 months ago

Hello @crvernon

@tkchafin has addressed all my concerns. I have no further comments.

abhishektiwari commented 6 months ago

Same here - all questions were answered by authors so no hold from my side.

crvernon commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago

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

OK DOIs

- 10.1111/j.1461-0248.2006.01007.x is OK
- 10.1111/j.1558-5646.1967.tb03411.x is OK
- 10.1111/ddi.13160 is OK
- 10.1093/bioinformatics/btr330 is OK
- 10.1007/BF01386390 is OK
- 10.1093/bioinformatics/btn129 is OK
- 10.1139/F08-171 is OK
- 10.1038/s41597-019-0300-6 is OK
- 10.1111/ele.12084 is OK
- 10.1061/(ASCE)0733-9429(1990)116:7(946) is OK
- 10.1111/evo.12883 is OK
- 10.21105/joss.03021 is OK
- 10.2307/2408641 is OK

MISSING DOIs

- No DOI given, and none found for title: Package ‘adespatial’
- No DOI given, and none found for title: Exploring network structure, dynamics, and functio...
- No DOI given, and none found for title: Diversification across a dynamic landscape: Phylog...
- No DOI given, and none found for title: Scikit-learn: Machine learning in Python

INVALID DOIs

- None

crvernon commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

crvernon commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

crvernon commented 6 months ago

:wave: Great job on this @tkchafin !

The following are changes that I need you to address in the paper:

[x] LINE 83: Since we are an international journal, please state the country designation after the "Colorado River"
[x] LINE 96: Only use single parenthesis around "r"
[x] Figure 1 caption: Are you missing a "the" in "...highlighted according to [the] most closely..."?
[x] LINE 116: spacing should be consistent, either include or not, for "...environmental/ spatial..." before and after the "/"
[x] LINE 131: your hyperlink to the DOI link is missing something and thus is not formatting correctly.
[x] LINE 164: your "*" are not translating and "R" in the genus should be capitalized as well as the "N" and "A" in North America

The paper is a bit long for what we usually accept in JOSS, but I do like the framing so let's see if we can work with it the way it is. Once you address the above, we will move on to the next stages of getting you published! Thanks!

tkchafin commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

tkchafin commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

tkchafin commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

tkchafin commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

tkchafin commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

tkchafin commented 6 months ago

Sorry for the multiple attempts. Just realized I could have the pdf compiled in GH Actions...

tkchafin commented 6 months ago

@editorialbot generate pdf

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