editorialbot commented 4 months ago

Submitting author: !--author-handle-->@giswqs@cheginit<!--end-editor-- Reviewers: @alexgleith, @platipodium Archive: 10.5281/zenodo.13368024

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/41071553539ff10aad4c69727f1063e9"><img src="https://joss.theoj.org/papers/41071553539ff10aad4c69727f1063e9/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/41071553539ff10aad4c69727f1063e9/status.svg)](https://joss.theoj.org/papers/41071553539ff10aad4c69727f1063e9)

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

@alexgleith & @platipodium, 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 @cheginit 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 @platipodium

📝 Checklist for @alexgleith

editorialbot commented 4 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:

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editorialbot commented 4 months ago

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

OK DOIs

- 10.21105/joss.03414 is OK
- 10.21105/joss.01450 is OK
- 10.1016/j.rse.2020.112154 is OK
- 10.3390/rs15153765 is OK
- 10.5281/zenodo.583693 is OK
- 10.1117/12.2537146 is OK
- 10.1109/IGARSS47720.2021.9554217 is OK
- 10.1016/S0034-4257(98)00064-9 is OK
- 10.3390/s19204471 is OK
- 10.1117/1.3361375 is OK
- 10.1029/2019wr026058 is OK
- 10.1109/MGRS.2013.2244672 is OK
- 10.5281/zenodo.10728098 is OK
- 10.1007/s00267-017-0880-x is OK
- 10.2112/JCOASTRES-D-10-00103.1 is OK
- 10.1109/TGRS.2003.812907 is OK
- 10.3389/fenvs.2021.649528 is OK
- 10.1016/j.rse.2019.04.023 is OK
- 10.1016/j.rse.2020.111898 is OK
- 10.1016/j.marpolbul.2007.02.003 is OK
- 10.1007/s00027-012-0278-z is OK
- 10.1890/1051-0761(2001)011[0981:HCATMO]2.0.CO;2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 4 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1297.0 files/s, 201954.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            777           1242           2460
Markdown                        18            317              0            666
Jupyter Notebook                15              0           3050            486
YAML                            12             30             24            406
TeX                              1             22              0            390
TOML                             1             17              0             67
HTML                             1              2              0              9
-------------------------------------------------------------------------------
SUM:                            64           1165           4316           4484
-------------------------------------------------------------------------------

Commit count by author:

    84  Qiusheng Wu
     3  Bingqing Liu
     3  pre-commit-ci[bot]
     2  dependabot[bot]
     1  Guillermo E. Ponce-Campos
     1  arfy slowy

editorialbot commented 4 months ago

Paper file info:

📄 Wordcount for paper.md is 679

✅ The paper includes a Statement of need section

editorialbot commented 4 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

platipodium commented 4 months ago

Review checklist for @platipodium

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/opengeos/HyperCoast?
[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 (@giswqs) 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 4 months ago

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

cheginit commented 4 months ago

👋🏼 @giswqs, @alexgleith, and @platipodium, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step, as mentioned in the first comment of this issue, is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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 openjournals/joss-reviews#XXXX 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 reviews to be completed within about 2-4 weeks. Please notify me if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please don't hesitate to ping me (@cheginit) if you have any questions/concerns.

giswqs commented 4 months ago

@cheginit Thank you for handling our submission.

@alexgleith @platipodium Thank you for agreeing to reviewing our submission. We look forward to your feedback and will try our best to resolve any questions or concerns you may have.

Thank you.

platipodium commented 4 months ago

@cheginit what do you think of the 2 pages references versus 1-2 pages of text? Is it ok or should the authors try to balance more and reduce refs?

danielskatz commented 4 months ago

As a comment from a track editor, JOSS generally does not want to limit references, unless they are not relevant to the work.

cheginit commented 4 months ago

@danielskatz Thanks for chiming in, appreciate it!

platipodium commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

cheginit commented 3 months ago

👋🏼 @alexgleith, just a friendly reminder for this review.

platipodium commented 3 months ago

@cheginit the label TeX should be removed from this issue

cheginit commented 3 months ago

@platipodium Thanks for paying attention to this. These labels are automatically generated based on the "Software report", since there are Tex files in the repo, the label is added.

cheginit commented 3 months ago

👋🏼 @alexgleith and @platipodium, just a friendly reminder for this review.

alexgleith commented 3 months ago

Ok no worries!

Edit: whoops, still learning how to marshall the bots haha

danielskatz commented 3 months ago

👋 @alexgleith - you likely have to do that again - @editorialbot commands need to be the first thing in a comment, and editing probably doesn't work

alexgleith commented 3 months ago

Review checklist for @alexgleith

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/opengeos/HyperCoast?
[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 (@giswqs) 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?

alexgleith commented 3 months ago

Some very minor comments on code quality:

There are some unused imports, like numpy in desis.py and others that are probably imported for the context function (not the right word), but should be annotated, like import hvplot.xarray # noqa F401. These are little, but my linter highlights them, and it's cleaner to fix it.
In the main hypercoast.py file, there are * imports, which are not recommended from .aviris import *
spectral is used, but isn't in the dependencies list
I'll make a PR with some example code cleanups.

Some opinions from me:

I don't like that EMIT data has been stored in GitHub, like this: https://github.com/opengeos/datasets/releases/tag/netcdf. I would much prefer that the notebooks point to the data direct at NASA.
Following on from the first point, wrapping up the EarthData access into the download_nasa_data function, which calls leafmap.nasa_data_download, which then calls earthaccess.download is two abstractions too far! It does make it simple, though. I have an example over here that uses NASA's STAC API to find EMIT granules and load them, and it's still pretty complex, but what is good is that it uses the open standard STAC to discover granules.
It's great that the function emit_xarray has been adapted to make wavelength a dimension!
I can't see how this method, in the emit.ipynb notebook is working, or if it works. I tried changing the numbers and nothing changed: m.add("spectral", xlim=(400, 1400))
The function m.spectral_to_df() structures the dataframe in an unexpected way. I think exporting something with a geometry, or with lon/lat columns and 285 more spectral columns would make more sense, even if the structure is a bit clumsy.

On the review points, I'd like a couple of changes please:

~For installation, please make sure all dependencies are listed in the pyproject.toml file (spectral was not, and neither was pyvista)~. Edit: resolved by removing unused code.
~For community guidelines, please include a contributing file.~ Edit: my mistake, there's a contributing file in the docs folder.

giswqs commented 3 months ago

@alexgleith Thank you very much for the feedback. I will be addressing your comments in another PR.

For installation, please make sure all dependencies are listed in the pyproject.toml file (spectral was not, and neither was pyvista)

Regarding the dependencies, pyvista has already been listed as an optional dependency in pyproject.toml. ~~spectral is not a dependency of the package. We did not use it anywhere in the source code.~~ https://github.com/opengeos/HyperCoast/blob/07888c48f9edc207cb4ec855986f52bb56f408fb/pyproject.toml#L39

giswqs commented 3 months ago

My mistakes. The spectral package is used by the write_envi function inherited from the nasa/EMIT-Data-Resources repo. However, the function is not used in our source code. I will remove it from the source code.

alexgleith commented 3 months ago

pyvista has already been listed as an optional dependency

Ah, sorry, I missed that.

platipodium commented 3 months ago

@platipodium Thanks for paying attention to this. These labels are automatically generated based on the "Software report", since there are Tex files in the repo, the label is added.

Automatic does not mean correct :=). this is not a tex project, so it is misleading. But we could file a bug with JOSS itself?

giswqs commented 3 months ago

@alexgleith Thank you for reviewing. All your comments have been addressed. Thank you.

@platipodium Thank you for reviewing. All your comments for far have been addressed. Please let me know if you have any additional comments. Thank you.

giswqs commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

platipodium commented 3 months ago

@cheginit I have concluded my review. I recommend publishing the software. I commend the authors on their overall good software practices!

cheginit commented 3 months ago

👋🏼 @platipodium and @alexgleith, thank you both for your time and effort to review this submission and providing constructive comments for its improvement.

cheginit commented 3 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 pull request)
[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
[x] Recommend acceptance with @editorialbot recommend-accept

cheginit commented 3 months ago

@giswqs, thank you for diligently addressing the comments raised by the reviewer.

I have some comments on the paper:

[x] Line 25: Please use German Aerospace Center (DLR)
[x] Line 30: Pleas use earthaccess instead of earthaccess.
[x] Line 59: Please clarify why HyperSpy is not tailored for coastal applications. My understanding is that HyperSpy is somewhat similar to xarray. So, I find this sentence vague.
[x] Please use a consistent format for paper titles in References. Some references, e.g., the first one, have title case style, and others, like the fourth one, only the first letter is capitalized. Please pick one style and apply to all reference.
[x] References on lines 93 and 134 are missing journal name.

giswqs commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

giswqs commented 3 months ago

@cheginit Thank you for the feedback. All your comments have been addressed in https://github.com/opengeos/HyperCoast/pull/129.

Latest release: v0.7.8 Zenodo DOI: https://doi.org/10.5281/zenodo.13368024

cheginit commented 3 months ago

@editorialbot set v0.7.8 as version

editorialbot commented 3 months ago

Done! version is now v0.7.8

cheginit commented 3 months ago

@editorialbot set 10.5281/zenodo.13368024 as archive

editorialbot commented 3 months ago

Done! archive is now 10.5281/zenodo.13368024

cheginit commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago

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

✅ OK DOIs

- 10.21105/joss.03414 is OK
- 10.21105/joss.01450 is OK
- 10.5281/zenodo.583693 is OK
- 10.1117/12.2537146 is OK
- 10.1109/IGARSS47720.2021.9554217 is OK
- 10.1016/S0034-4257(98)00064-9 is OK
- 10.3390/s19204471 is OK
- 10.1117/1.3361375 is OK
- 10.1029/2019wr026058 is OK
- 10.1109/MGRS.2013.2244672 is OK
- 10.5281/zenodo.10728098 is OK
- 10.1007/s00267-017-0880-x is OK
- 10.2112/JCOASTRES-D-10-00103.1 is OK
- 10.1109/TGRS.2003.812907 is OK
- 10.3389/fenvs.2021.649528 is OK
- 10.1016/j.rse.2019.04.023 is OK
- 10.1016/j.rse.2020.111898 is OK
- 10.1016/j.marpolbul.2007.02.003 is OK
- 10.1007/s00027-012-0278-z is OK
- 10.1890/1051-0761(2001)011[0981:HCATMO]2.0.CO;2 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

cheginit commented 3 months ago

@giswqs Thanks for quickly addressing the comments, we're almost there! Please use the same title for the Zenodo archive as of this submission, i.e., "HyperCoast: A Python Package for Visualizing and Analyzing Hyperspectral Data in Coastal Environments".

giswqs commented 3 months ago

@cheginit The title has been updated. Thank you!

cheginit commented 3 months ago

@giswqs Awesome! I will now hand over the submission to EiC for the final checks before acceptance. Thanks for working with the reviewers and me to address the comments, in a timely manner.

cheginit commented 3 months ago

@editorialbot recommend-accept

editorialbot commented 3 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 months ago

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

✅ OK DOIs

- 10.21105/joss.03414 is OK
- 10.21105/joss.01450 is OK
- 10.5281/zenodo.583693 is OK
- 10.1117/12.2537146 is OK
- 10.1109/IGARSS47720.2021.9554217 is OK
- 10.1016/S0034-4257(98)00064-9 is OK
- 10.3390/s19204471 is OK
- 10.1117/1.3361375 is OK
- 10.1029/2019wr026058 is OK
- 10.1109/MGRS.2013.2244672 is OK
- 10.5281/zenodo.10728098 is OK
- 10.1007/s00267-017-0880-x is OK
- 10.2112/JCOASTRES-D-10-00103.1 is OK
- 10.1109/TGRS.2003.812907 is OK
- 10.3389/fenvs.2021.649528 is OK
- 10.1016/j.rse.2019.04.023 is OK
- 10.1016/j.rse.2020.111898 is OK
- 10.1016/j.marpolbul.2007.02.003 is OK
- 10.1007/s00027-012-0278-z is OK
- 10.1890/1051-0761(2001)011[0981:HCATMO]2.0.CO;2 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 3 months ago

:wave: @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5810, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

giswqs commented 3 months ago

@cheginit Fantastic! Thank you very much for handling the submission. Your timely reminders and feedback are greatly appreciated.

openjournals / joss-reviews

[REVIEW]: HyperCoast: A Python Package for Visualizing and Analyzing Hyperspectral Data in Coastal Environments #7025

Status

Reviewer instructions & questions

Checklists

Review checklist for @platipodium

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @alexgleith

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