[REVIEW]: XLUR: A land use regression wizard for ArcGIS Pro

[whedon]

Submitting author: @anmolter (Anna Mölter)
Repository: https://github.com/anmolter/XLUR
Version: v1.0.1
Editor: @hugoledoux
Reviewer: @Athelena, @fortinma
Archive: 10.5281/zenodo.3889604

Status

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Review checklist for @Athelena

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@anmolter) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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 @fortinma

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@anmolter) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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]

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

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[whedon]

Reference check summary:

OK DOIs

- 10.1016/j.atmosenv.2013.02.037 is OK
- 10.1021/es301948k is OK
- 10.1002/2012jd019399 is OK
- 10.1016/j.scitotenv.2010.08.027 is OK
- 10.1016/j.scitotenv.2010.10.005 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.envres.2016.07.005 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/S0022-0981(03)00359-9 is INVALID because of 'https://doi.org/' prefix

[whedon]

👉 Check article proof 📄 👈

[arfon]

@anmolter - this PR should fix your DOIs: anmolter/XLUR#1

[anmolter]

@arfon Thanks, I've merged it.

[arfon]

@whedon re-invite @fortinma as reviewer

[whedon]

OK, the reviewer has been re-invited.

@fortinma please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[anmolter]

@arfon @hugoledoux There was an article published in Frontiers of Environmental Science & Engineering last months (https://doi.org/10.1007/s11783-020-1221-5) about a GIS tool called 'PyLUR'. There's no link in the article to the tool, so I can't compare the code to mine, but reading the article I think there are definite differences, e.g. the published tool can't produce hybrid models, it doesn't have a wizard style interface etc. However, I will need to rename my tool to avoid any confusion with the other PyLUR. Obviously, this won't change the source code just the documentation.

[anmolter]

@arfon @hugoledoux Will renaming the repository cause any issues?

[arfon]

@arfon @hugoledoux Will renaming the repository cause any issues?

No, this should be fine. Just let us know the new repository address and the updated name for the package (you can update the paper.md yourself).

[anmolter]

@arfon @hugoledoux I've renamed the package and repository 'XLUR'. The address is: https://github.com/anmolter/XLUR . I've also updated paper.md and I've gone through the documentation and changed the name.

[arfon]

Thanks @anmolter, I've updated the repository address here too.

[fortinma]

Hi @anmolter. I am stuck. I managed the install, but when I start the tutorial i get the following errors for pandas library, which is installed. See the screen cap for details.

Any help in moving forward?

[anmolter]

Hi @fortinma , I think you may have a newer version of pandas installed, where they changed pandas.tools. plotting to pandas.plotting. I've added try except code with both versions. Is it working now?

[fortinma]

Thanks, @anmolter. It's working now.

[fortinma]

hi again, @anmolter. The ApplyLUR script has the same issue with Pandas Unfortunately. See screencap.

[anmolter]

Hi @fortinma, sorry, I forgot that it is in both tools. I have fixed it now. Which version of ArcPro are you using?

[fortinma]

Thanks, @anmolter. I just updated to ArcGIS Pro 2.5.0, which seems to be the latest -- for today at least.

[anmolter]

@fortinma Nice! The university I work for has disabled the automatic updates in ArcPro, so I'm stuck on version 2.2.4 😒

[Athelena]

I have tried twice but I can't get it to run. I get stuck in an endless loop at the following step where it never stops running

I also see this message:

[anmolter]

Hi @Athelena, could you close the wizard by clicking the x in the top right corner (don't click cancel, because that will probably delete the outputs), then go to your outputs folder and open the GOTCHA text file and let me know what that says?

[Athelena]

2020-05-04 13:23:25.407 ERROR build - exception_hook: Uncaught exception Traceback (most recent call last): File "<string>", line 1, in <module> AttributeError: 'ToolValidator' object has no attribute 'isLicensed' 2020-05-04 13:23:26.085 ERROR build - exception_hook: Uncaught exception Traceback (most recent call last): File "<string>", line 1, in <module> AttributeError: 'ToolValidator' object has no attribute 'isLicensed' 2020-05-04 13:27:34.045 ERROR build - exception_hook: Uncaught exception Traceback (most recent call last): File "<string>", line 1, in <module> AttributeError: 'ToolValidator' object has no attribute 'isLicensed' 2020-05-04 13:27:34.541 ERROR build - exception_hook: Uncaught exception Traceback (most recent call last): File "<string>", line 1, in <module> AttributeError: 'ToolValidator' object has no attribute 'isLicensed' 2020-05-04 13:31:23.324 ERROR build - exception_hook: Uncaught exception Traceback (most recent call last): File "<string>", line 1, in <module> AttributeError: 'ToolValidator' object has no attribute 'isLicensed' 2020-05-04 13:31:23.789 ERROR build - exception_hook: Uncaught exception Traceback (most recent call last): File "<string>", line 1, in <module> AttributeError: 'ToolValidator' object has no attribute 'isLicensed' 2020-05-04 13:39:29.410 ERROR build - exception_hook: Uncaught exception Traceback (most recent call last): File "\\Mac\Home\Downloads\XLUR-master\XLUR\Code\build.py", line 5853, in onNext arcpy.sa.ExtractValuesToPoints(out_fds+"\\sites",out_fgdb+"\\"+pG_name,out_fgdb+"\\"+pG_name+"_sites","","VALUE_ONLY") #join cell values to points File "c:\users\alabetski\appdata\local\programs\arcgis\pro\Resources\arcpy\arcpy\sa\Functions.py", line 1645, in ExtractValuesToPoints add_attributes) File "c:\users\alabetski\appdata\local\programs\arcgis\pro\Resources\arcpy\arcpy\sa\Utils.py", line 53, in swapper result = wrapper(*args, **kwargs) File "c:\users\alabetski\appdata\local\programs\arcgis\pro\Resources\arcpy\arcpy\sa\Functions.py", line 1638, in Wrapper add_attributes) File "c:\users\alabetski\appdata\local\programs\arcgis\pro\Resources\arcpy\arcpy\geoprocessing\_base.py", line 511, in <lambda> return lambda *args: val(*gp_fixargs(args, True)) arcgisscripting.ExecuteError: Failed to execute. Parameters are not valid. ERROR 000824: The tool is not licensed. Failed to execute (ExtractValuesToPoints).

[anmolter]

@Athelena It looks like you don't have a license for Spatial Analyst. Could you check your Licensing information? Here's a link for more info: https://pro.arcgis.com/en/pro-app/help/analysis/spatial-analyst/basics/enabling-the-spatial-analyst-extension.htm

[Athelena]

Oh yes, I see that now. I don't have a license for it, I've asked our IT department about it, I'll see if I can get it.

[anmolter]

Done. The new DOI is 10.5281/zenodo.3889604

[hugoledoux]

@whedon set 10.5281/zenodo.3889604 as archive

[whedon]

OK. 10.5281/zenodo.3889604 is the archive.

[hugoledoux]

@whedon set v1.0.1 as version

[whedon]

OK. v1.0.1 is the version.

[hugoledoux]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1016/j.atmosenv.2013.02.037 is OK
- 10.1016/j.envres.2016.07.005 is OK
- 10.1021/es301948k is OK
- 10.1002/2012jd019399 is OK
- 10.1016/S0022-0981(03)00359-9 is OK
- 10.1016/j.atmosenv.2020.117535 is OK
- 10.1007/s11783-020-1221-5 is OK
- 10.1016/j.scitotenv.2010.08.027 is OK
- 10.1016/j.scitotenv.2010.10.005 is OK
- 10.1016/j.envsoft.2018.03.030 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1488

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1488, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[hugoledoux]

Congratulations @anmolter your paper/code is now accepted! Your paper will handled and published in the near future.

Thanks to @Athelena and @fortinma for the reviews and feedback!

[hugoledoux]

@whedon accept deposit=true

[whedon]

I'm sorry @hugoledoux, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

[anmolter]

🎉 Thanks @hugoledoux @Athelena @fortinma for your help!

[labarba]

@anmolter -- please edit the metadata of your Zenodo deposit (title and author fields) to match the JOSS paper.

In the paper, I found this problematic sentence:

Unlike XLUR, RLUR and PyLUR it does not use the ESCAPE methodology…

It is unclear what the subject of the sentence is: "it does not use..." makes the subject "it" but before that you have three names of software, and we don't know which of these is the one that does not use the ESCAPE methodology. Please fix.

Also, it is kind of verbose to have "Journal article" as an added string with every cited publication. Please remove that.

[anmolter]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[anmolter]

@labarba I've made the changes. Zenodo reset everything to default when I did a new release, but I've edited the metadata now, so everything should be correct.

[labarba]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02177 joss-papers#1489
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02177
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[labarba]

Congratulations, @anmolter, your JOSS paper is published! 🚀

Huge thanks to our editor: @hugoledoux, and the reviewers: @Athelena, @fortinma — we couldn't do this without you 🙏

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02177/status.svg)](https://doi.org/10.21105/joss.02177)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.02177/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.02177

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