Joss-reviews: [REVIEW]: pyMannKendall: a python package for non parametric Mann Kendall family of trend tests.

[whedon]

Submitting author: @mmhs013 (Md. Manjurul Hussain)
Repository: https://github.com/mmhs013/pyMannKendall
Version: 1.1
Editor: @mbobra
Reviewer: @dhhagan, @rreinecke
Archive: 10.5281/zenodo.3347253

Status

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Markdown: [![status](http://joss.theoj.org/papers/14903dbd55343be89105112e585d262a/status.svg)](http://joss.theoj.org/papers/14903dbd55343be89105112e585d262a)

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

@dhhagan & @rreinecke, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

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

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

Review checklist for @dhhagan

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

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

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: 1.1
• [x] Authorship: Has the submitting author (@mmhs013) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @rreinecke

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

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

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: 1.1
• [x] Authorship: Has the submitting author (@mmhs013) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

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

:star: Important :star:

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

To fix this do the following two things:

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@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[mbobra]

👋 @dhhagan @rreinecke Thanks for agreeing to review this submission! Whedon generated a checklist for you above. Feel free to ask me any questions -- I'm always happy to help.

[rreinecke]

@mmhs013 I did not have the time to take a closer look at your code but here are already some comments on the overall documentation that you could improve:

• mmhs013/pyMannKendall#1
• mmhs013/pyMannKendall#2
• mmhs013/pyMannKendall#3
• mmhs013/pyMannKendall#4
• mmhs013/pyMannKendall#5
• mmhs013/pyMannKendall#6

[rreinecke]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

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

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

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

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

[rreinecke]

@mmhs013 I had a look at your code now and I think it is nicely documented but without robust unit tests and an thoroughly explained example problem it is not possible for me to judge if the code actually provides the promised functionality. See also mmhs013/pyMannKendall#5 Let me know if you need further input. I will continue my review when this is implemented.

[rreinecke]

@mbobra @mmhs013 FYI I'm not available from 13th till the 20th. I will continue the review after my return. See also my notes for @mmhs013 above.
Cheers

[mmhs013]

@rreinecke thanks for your comments. According to your comments, I am already updated readme file with Installation Instructions, list of dependencies (mmhs013/pyMannKendall#1), project description (mmhs013/pyMannKendall#2) and added new details example ipython notebook file with some plots (mmhs013/pyMannKendall#3) and added DOI in paper bib file (mmhs013/pyMannKendall#6).

The input and output parameters of functions are almost the same, which are described in Function details section in the readme file. I think, the new updates of readme file and example also describe more clearly about functions (mmhs013/pyMannKendall#4).

I write this unit test using pytest for my own purpose because when I update/modify my code, this test compares those functions with some known results. If I unintentionally make some mistakes, which produce the wrong result, This will warn me. I think this is fine for me (mmhs013/pyMannKendall#5).

I don't use the unit test previously. So I am not an expert in this section. I don't clearly understand how can I improve my unit test. Do you have any suggestions for me?

Please check my updates. If you are satisfied with my updates, then close relevant issues. I am waiting for your respond.

[rreinecke]

@whedon check references

[whedon]

Attempting to check references...

[rreinecke]

@mbobra I'm done. I think the submission substantially improved throughout the review and is ready to be accepted after @dhhagan concerns have been addressed.

@mmhs013 I would suggest to you to go through the README and code files with a spellchecker there are still a couple typos and grammar mistakes. ;)

Cheers
Robert

[mmhs013]

Thanks a lot, @rreinecke . My English is poor. :( I will check and update my README and others by a professional writer.

[dhhagan]

@mbobra Just finished up the review - It looks like after the paper is regenerated and the DOI's appear, it is good to go! I agree with @rreinecke that the english could be improved a bit - @mmhs013 Let me know if you would like any help with this and I could probably run through the ReadMe real quick, though I don't want to step on any toes.

[mbobra]

@rreinecke and @dhhagan Thank you so much for reviewing! We really appreciate your time and effort ☀️

@mmhs013 We're almost there! I have a couple comments:

• Do you have access to someone who can read over the docs and give some feedback on improving the English? If not, let me know and we can help you.
• Can you please archive your release on Zenodo to obtain a DOI and then put that in your README.md file?

After these two items I think we're done 🎉

[mmhs013]

@rreinecke, @dhhagan and @mbobra thanks a lot for reviewing my project.

@mbobra, I already checked the README.md file and others with my friend. I think it's been better than before. I also archive my package on Zenodo and add Zenodo DOI in my README.md file.

[mbobra]

@whedon set 10.5281/zenodo.3347253 as archive

[whedon]

OK. 10.5281/zenodo.3347253 is the archive.

[mbobra]

@whedon set 1.1 as version

[whedon]

OK. 1.1 is the version.

[mbobra]

@whedon check references

[whedon]

Attempting to check references...

[mbobra]

@whedon check references

[whedon]

Attempting to check references...

[mbobra]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1556 with the following error:

Error reading bibliography ./paper.bib (line 15, column 3):
unexpected "d"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[mbobra]

@mmhs013 It looks like there is a small error in paper.bib. Could you add a comma at the end of line 14?

[mmhs013]

@mbobra, I already fix this error. Please check it again.

[mbobra]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[mbobra]

@openjournals/joss-eics This paper is ready for acceptance! (I could not get Whedon to check the references but it looks fine in the pdf). Nice work @mmhs013 🎉

[mmhs013]

@mbobra, all references are not visible in pdf!

[whedon]

```Reference check summary:

OK DOIs

• 10.2307/1907187 is OK
• 10.1016/j.atmosres.2016.02.008 is OK
• 10.1029/WR018i001p00107 is OK
• 10.1016/S0022-1694(97)00125-X is OK
• 10.2307/2333424 is OK
• 10.1023/B:WARM.0000043140.61082.60 is OK
• 10.1029/2001WR000861 is OK
• 10.1002/hyp.1095 is OK
• 10.1021/es051650b is OK
• 10.1002/env.507 is OK
• 10.1080/01621459.1968.10480934 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[mmhs013]

@mbobra, when I update my paper for improving English, I accidentally remove some of my reference from paper. So those are not shown in pdf. I am sorry for that. I already fix it. Can you regenerate pdf?

[mbobra]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[mmhs013]

Now, it looks good. Thanks a lot @mbobra for accept my paper. :D

[whedon]

```Reference check summary:

OK DOIs

• 10.2307/1907187 is OK
• 10.1016/j.atmosres.2016.02.008 is OK
• 10.1029/WR018i001p00107 is OK
• 10.1016/S0022-1694(97)00125-X is OK
• 10.2307/2333424 is OK
• 10.1023/B:WARM.0000043140.61082.60 is OK
• 10.1029/2001WR000861 is OK
• 10.1002/hyp.1095 is OK
• 10.1021/es051650b is OK
• 10.1002/env.507 is OK
• 10.1080/01621459.1968.10480934 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

```Reference check summary:

OK DOIs

• 10.2307/1907187 is OK
• 10.1016/j.atmosres.2016.02.008 is OK
• 10.1029/WR018i001p00107 is OK
• 10.1016/S0022-1694(97)00125-X is OK
• 10.2307/2333424 is OK
• 10.1023/B:WARM.0000043140.61082.60 is OK
• 10.1029/2001WR000861 is OK
• 10.1002/hyp.1095 is OK
• 10.1021/es051650b is OK
• 10.1002/env.507 is OK
• 10.1080/01621459.1968.10480934 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[kyleniemeyer]

Hi @mmhs013, one final thing: could you edit the Zenodo archive to make the title match the paper title?

[kyleniemeyer]

Also, @mmhs013 please merge the two pull requests I just submitted, which fix a few things in the paper and references: https://github.com/mmhs013/pyMannKendall/pull/9 and https://github.com/mmhs013/pyMannKendall/pull/10

[mmhs013]

@kyleniemeyer, I already update Zenodo title and also merge your two pull requests. Thanks for you help.

[kyleniemeyer]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/860

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/860, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[kyleniemeyer]

@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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/861
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01556
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[kyleniemeyer]

Congrats @mmhs013 on your paper's publication in JOSS! Thanks to @dhhagan and @rreinecke for reviewing, and @mbobra for editing!

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01556/status.svg)](https://doi.org/10.21105/joss.01556)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01556">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01556/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01556/status.svg
   :target: https://doi.org/10.21105/joss.01556

This is how it will look in your documentation:

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