editorialbot commented 11 months ago

Submitting author: !--author-handle-->@jbferet@marcosvital<!--end-editor-- Reviewers: @earth-chris, @nehakn, @ashiklom Archive: 10.5281/zenodo.10480410

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d469ff5d6ba84a1deeeaf4bbd353c5d0"><img src="https://joss.theoj.org/papers/d469ff5d6ba84a1deeeaf4bbd353c5d0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d469ff5d6ba84a1deeeaf4bbd353c5d0/status.svg)](https://joss.theoj.org/papers/d469ff5d6ba84a1deeeaf4bbd353c5d0)

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

@earth-chris & @nehakn & @ashiklom, 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 @marcosvital 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 @earth-chris

📝 Checklist for @nehakn

📝 Checklist for @ashiklom

editorialbot commented 11 months 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:

@editorialbot commands

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

@editorialbot generate pdf

editorialbot commented 11 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (1347.5 files/s, 233394.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               10            103            574           1154
Markdown                         4            210              0            796
Rmd                              6            199            600            320
TeX                              1              6              0            105
YAML                             3             13              6             71
-------------------------------------------------------------------------------
SUM:                            24            531           1180           2446
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 11 months ago

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

OK DOIs

- 10.1364/JOSA.60.000542 is OK
- 10.1016/j.rse.2008.02.012 is OK
- 10.1016/j.rse.2017.03.004 is OK
- 10.1016/j.rse.2018.11.002 is OK
- 10.1016/j.rse.2020.112173 is OK
- 10.1016/0034-4257(90)90100-Z is OK
- 10.1016/j.rse.2020.112176 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 11 months ago

Wordcount for paper.md is 1983

editorialbot commented 11 months ago

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

marcosvital commented 11 months ago

Dear @earth-chris, @nehakn and @ashiklom, thank you again for accepting review this submission for JOSS. The reviewing process is checklist based, and instructions were already posted above by the editorial bot - but let me know if you need any assistance, ok? Also, you can tag @jbferet if you have specific questions about the manuscript.

@jbferet, you can tag your co-author GitHub accounts if you want, so they will be able to follow this issue and answer to questions as well.

earth-chris commented 11 months ago

Review checklist for @earth-chris

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/jbferet/prospect?
[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 (@jbferet) 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?

nehakn commented 11 months ago

Review checklist for @nehakn

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/jbferet/prospect?
[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 (@jbferet) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] 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)?
[ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[ ] 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?
[ ] 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?

ashiklom commented 11 months ago

Review checklist for @ashiklom

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/jbferet/prospect?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- ...but, see https://github.com/jbferet/prospect/issues/3. Consider a non-copyleft license to facilitate use in enterprise contexts (such as at NASA!).
[X] Contribution and authorship: Has the submitting author (@jbferet) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- @jbferet is the primary developer and maintainer, based on commit history, but both authors have contributed to the code. No other known contributors, so the author list is appropriate.
[X] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
- First commit is in 2020, with steady contributions since then.
- Seamless integration of multiple PROSPECT versions and the ability to perform PROSPECT inversion and generate look-up tables is a significant value-add onto the core PROSPECT model.
[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.
- Custom data used for demonstrating the inversion are available in a separate public GitLab repository (https://gitlab.com/jbferet/myshareddata)
- PROSPECT absorption coefficients (needed by the model) are included in the package, but plain-text versions are not (https://github.com/jbferet/prospect/issues/4). Not a requirement, just a suggestion.
[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.
- No original results.
- Code in manuscript and examples runs without problems.
[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?
- ...but see https://github.com/jbferet/prospect/issues/5. Some libraries should be Suggests, not Imports, to simplify the installation.
[X] Functionality: Have the functional claims of the software been confirmed?
- [X] Forward-modeling with different versions of PROSPECT.
- [X] Generating look-up tables
- [X] Inversion.
[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.)
- No performance claims.
- Suggested minor performance improvement: https://github.com/jbferet/prospect/issues/6

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?
- Stated (briefly) in the README heading.
[X] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- Dependency management follows R package best practices.
[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?
- Tests of package functionality are scripts in the examples folder, but these have to be run manually.
- Suggest adding formal unit tests to the package. https://github.com/jbferet/prospect/issues/7
[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
- Missing. See https://github.com/jbferet/prospect/issues/8.

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?
- I suggest briefly mentioning the implementation history of PROSPECT. https://github.com/jbferet/prospect/issues/9
[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?

ashiklom commented 11 months ago

@jbferet I have completed my review. Overall, a very solid piece of work!

The most important things that are missing for JOSS are automated tests and community guidelines. Everything else is fine as is, though I made some minor recommendations in various GitHub issues (all linked above).

jbferet commented 11 months ago

@ashiklom thanks a lot for your review and insightful comments. I will work on addressing these suggestions in the coming days. best regards, Jean-Baptiste

kthyng commented 10 months ago

@ashiklom and @jbferet A note — automated testing is not required by JOSS, but some means of testing that the code is running correctly is.

With that in mind, @jbferet how are your edits coming along?

@earth-chris, @nehakn How are your reviews coming?

earth-chris commented 10 months ago

hi @jbferet, I've concluded my review. Here's my recommended manuscript input. I have left a couple of boxes unchecked but I think there is a short pathway to resolving my current issues.

First is that the install instructions are incomplete. There are external dependencies that need to be installed (V8) that are not documented, which I had to debug. I've chimed in with an additional comment on ashiklom's issue.

Second is that the examples provided in the web documentation don't all run as-is. Primarily, the very first code block doesn't run. There's also an opportunity to port the more recent code blocks from the manuscript to the web docs, which would provide more comprehensive documentation. I've described that in more detail in this issue.

I would like to +1 ashiklom's review, and believe this software will be much improved after addressing those key issues. Many of them are nice-to-haves (like automated testing), and the only blockers to me are the install issues and the broken code in the web docs.

nehakn commented 10 months ago

@jbferet I have completed my review. Automated tests are not described and the software is not compared with the state of the art.

kthyng commented 9 months ago

@jbferet I haven't seen you for awhile. Are you still here?

jbferet commented 9 months ago

@kthyng yes I am! Sorry for the poor communication, I have been working on corrections and updates of my package, following reviews from @ashiklom , @earth-chris and @nehakn . I just pushed an updated version of the package and paper. I will now exchange with @ashiklom and @earth-chris for specific suggestions they made in their detailed review listed in the issues of the package. thanks!

jbferet commented 9 months ago

@editorialbot commands

editorialbot commented 9 months ago

Hello @jbferet, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

jbferet commented 9 months ago

@editorialbot check repository

editorialbot commented 9 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1020.7 files/s, 130930.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               16            111            705           1157
Markdown                         6            187              0            576
Rmd                              6            216            682            255
TeX                              1             14              0            190
YAML                             4             21              9            110
-------------------------------------------------------------------------------
SUM:                            33            549           1396           2288
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 9 months ago

Wordcount for paper.md is 1946

jbferet commented 9 months ago

@editorialbot generate pdf

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:

jbferet commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

OK DOIs

- 10.1364/JOSA.60.000542 is OK
- 10.1016/j.rse.2007.09.005 is OK
- 10.1016/j.rse.2008.02.012 is OK
- 10.1016/j.rse.2017.03.004 is OK
- 10.1016/j.rse.2018.11.002 is OK
- 10.1016/j.rse.2020.112173 is OK
- 10.1016/0034-4257(90)90100-Z is OK
- 10.1016/j.rse.2016.02.029 is OK
- 10.1109/TGRS.2011.2109390 is OK
- 10.1016/j.rse.2020.112176 is OK
- 10.1016/j.rse.2006.12.013 is OK
- 10.1109/TGRS.2007.895844 is OK

MISSING DOIs

- None

INVALID DOIs

- doi:10.1016/j.rse.2008.01.026 is INVALID (failed connection)

jbferet commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

OK DOIs

- 10.1364/JOSA.60.000542 is OK
- 10.1016/j.rse.2007.09.005 is OK
- 10.1016/j.rse.2008.02.012 is OK
- 10.1016/j.rse.2017.03.004 is OK
- 10.1016/j.rse.2018.11.002 is OK
- 10.1016/j.rse.2020.112173 is OK
- 10.1016/0034-4257(90)90100-Z is OK
- 10.1016/j.rse.2016.02.029 is OK
- 10.1109/TGRS.2011.2109390 is OK
- 10.1016/j.rse.2020.112176 is OK
- 10.1016/j.rse.2006.12.013 is OK
- 10.1109/TGRS.2007.895844 is OK

MISSING DOIs

- None

INVALID DOIs

- doi:10.1016/j.rse.2008.01.026 is INVALID (failed connection)

jbferet commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

OK DOIs

- 10.1364/JOSA.60.000542 is OK
- 10.1016/j.rse.2007.09.005 is OK
- 10.1016/j.rse.2008.02.012 is OK
- 10.1016/j.rse.2017.03.004 is OK
- 10.1016/j.rse.2018.11.002 is OK
- 10.1016/j.rse.2020.112173 is OK
- 10.1016/0034-4257(90)90100-Z is OK
- 10.1016/j.rse.2008.01.026 is OK
- 10.1016/j.rse.2016.02.029 is OK
- 10.1109/TGRS.2011.2109390 is OK
- 10.1016/j.rse.2020.112176 is OK
- 10.1016/j.rse.2006.12.013 is OK
- 10.1109/TGRS.2007.895844 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbferet commented 9 months ago

Dear @kthyng, @ashiklom , @earth-chris and @nehakn , After a few commits and new versions 1.5.0 and 1.5.1 of the package, all issues are now solved and missing elements or modifications suggested in your reviews have been implemented. The latest version of the package is functional. I went through the online documentation, and tried my best to improve the manuscript. Automated tests were also added to the package.

Thank you for all these excellent suggestions. Let us know if you are ok with our answers to the issues opened in the github repository, and we will close them if ok for you, or work more on it if needed!

best regards

earth-chris commented 9 months ago

@jbferet I have concluded my review of the updated material and all the outstanding issues have been addressed from my perspective 🎉

ashiklom commented 9 months ago

@jbferet Seconded! All my comments have been addressed, and I think this is ready to be published. Great work!

kthyng commented 9 months ago

@earth-chris and @ashiklom Wonderful! Would you please make sure all the issues you opened have been addressed adequately and check off remaining boxes (unless there is something to bring up)?

earth-chris commented 9 months ago

yes, my checklist is complete and all issues are resolved in the prospect repository

ashiklom commented 9 months ago

Likewise -- checklist completed and all my issues closed.

kthyng commented 9 months ago

Ok great! Next steps.

kthyng commented 9 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[ ] Double check authors and affiliations (including ORCIDs)
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
[ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[ ] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[ ] Recommend acceptance with @editorialbot recommend-accept

kthyng commented 9 months ago

@jbferet please go through the "additional author tasks..." above and do those steps (copy-paste the list as needed).

jbferet commented 9 months ago

DOI for release on zenodo: https://doi.org/10.5281/zenodo.10480410

jbferet commented 9 months ago

@kthyng all items from the list are checked, everything should be ok on my side. The DOI for the zenodo release is in the previous message. Thank you!

kthyng commented 9 months ago

@jbferet and what version did you want associated with this JOSS review?

kthyng commented 9 months ago

@editorialbot set 10.5281/zenodo.10480410 as archive

editorialbot commented 9 months ago

Done! archive is now 10.5281/zenodo.10480410

kthyng commented 9 months ago

@editorialbot generate pdf

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:

jbferet commented 9 months ago

@jbferet and what version did you want associated with this JOSS review?

@kthyng prospect version 1.6.0 is the version including all changes related to the JOSS review. Is there an action on my side in addition to specify it?

kthyng commented 9 months ago

@jbferet paper comments:

remove "[]" from around inline citations, this needs to be fixed many places, starting at line 29. See example paper for more information: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography
weird line break on line 50 — seems like this should be one sentence combined with the following line.
line 65 has two sets of [] apparently
line 67 add space
add code formatting line 124 though installation instructions should be in the docs and in the readme, not in the paper

Please correct all these items and given the number of mistakes found at this point, please go through and do a thorough reading to check for more.

kthyng commented 9 months ago

@editorialbot set 1.6.0 as version

editorialbot commented 9 months ago

Done! version is now 1.6.0

kthyng commented 9 months ago

@editorialbot check references

openjournals / joss-reviews

[REVIEW]: prospect: an R package to link leaf optical properties with their chemical and structural properties with the leaf model PROSPECT #6027

Status

Reviewer instructions & questions

Checklists

Review checklist for @earth-chris

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @nehakn

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @ashiklom

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance