[REVIEW]: GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size

[whedon]

Submitting author: @marcoalopez (Marco A. Lopez-Sanchez)
Repository: https://github.com/marcoalopez/GrainSizeTools/
Version: v2.0.1
Editor: @lheagy
Reviewer: @lheagy, @jsta
Archive: 10.6084/m9.figshare.1383130.v23

Status

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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) 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

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

1. Make sure you're logged in to your GitHub account
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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @lheagy know.

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

Review checklist for @lheagy

Conflict of interest

• 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

• 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?
• Version: Does the release version given match the GitHub release (v2.0)?
• Authorship: Has the submitting author (@marcoalopez) 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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @jsta

Conflict of interest

• 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

• 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?

No, per this comment the repository url should be https://github.com/marcoalopez/GrainSizeTools. Also the documentation lists three different download mirrors. Is it too much to maintain a sourceforge, figshare, and Github?

• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (v2.0)?
• Authorship: Has the submitting author (@marcoalopez) 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 function of the software can be verified?

There is an extensive set of manual steps described in the documentation to verify software function. All of them run with minimal machine specific modification.

• 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @jsta it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

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:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #863 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in block in find': No such file or directory (Errno::ENOENT) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/lib/whedon/processor.rb:57:in find_paper_paths'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-e0f72c5e8125/bin/whedon:32:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:in dispatch'
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from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

'

[lheagy]

👋 Thanks @khaors and @jsta for being willing to review! In the main issue thread above, there is a checklist for each of you to help guide the review. Please let me know if you have any questions or if I can provide any clarification.

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[lheagy]

👋 Hi @khaors, @jsta, just checking in. When do you think you will have time to get started on the review? If possible, we would appreciate your input within the next two weeks. Thanks!

[jsta]

@lheagy Should the repository url link point to https://marcoalopez.github.io/GrainSizeTools/ or https://github.com/marcoalopez/GrainSizeTools ?

[lheagy]

Hi @jsta: The repository url should point to the repository with the source code: https://github.com/marcoalopez/GrainSizeTools

[jsta]

I have completed an initial review. Overall, this submission looks great. The author has addressed some comments I made in the source repo Issues. Otherwise, the only outstanding reviewer bullet point that I found lacking was:

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

[marcoalopez]

Hi @jsta, thank you for this initial review. Regarding the community guidelines, I mention in the FAQ section https://github.com/marcoalopez/GrainSizeTools/blob/master/DOCS/FAQ.md the following:

Can I report bugs or submit ideas to improve the script?
Sure. If you have issues using the script, found a bug or see an error in the documentation please just let me know by dropping me an email or open an issue here (you can find my email here: https://github.com/marcoalopez ). Feedback from users is always welcome and important to develop a better and reliable script. Lastly, you can also fork the project and develop your own based on the GST script since it is open source and free.

I guess this text has two problems: (1) it is not obvious to find the community guidelines in the FAQ, and (2) maybe it is too short or not very detailed. Any ideas on how to improve this and give it more visibility? Perhaps I could indicate this more explicitly on the main website.

PS. I fixed a typo in the original FAQ text I copied above. However, the meaning of the text remains the same as the original.

[jsta]

Ah, ok. I guess I read the FAQ awhile ago and didn't catch this text. I expected it to be in the README.

[marcoalopez]

Hi @jsta I've already added the community guidelines to the README and the website as suggested.

[marcoalopez]

Hi @lheagy, how can I redirect the repository URL to https://github.com/marcoalopez/GrainSizeTools and meet the required criteria by @jsta?

[lheagy]

Hi @marcoalopez: I have updated the link in the main issue thread above, so all of the links should now point to https://github.com/marcoalopez/GrainSizeTools/

[lheagy]

👋 Hi @khaors, just checking in. When do you think you will have time to get started on this review? Thanks! Please let me know if there is anything I can clarify

[lheagy]

Thanks @jsta for your review!

👋 Hi @khaors, would you be able to get started on the review soon? Thanks!

[marcoalopez]

Hi @lheagy, I have a question. I would like to launch a script update. It would be minor changes that add some new features (from v2.0 to v2.0.1). Could I do this now or should I wait for the review to finish? I'm not sure if the code should be "frozen" during the review process or it can be modified. Thanks!

[lheagy]

Hi @marcoalopez, not a problem, you can launch the update. Please just let me know when you have and I will update the version number on the review.

[marcoalopez]

Hi @lheagy, it's done. Thank you.

[lheagy]

Thanks @marcoalopez. A quick update, I have email @khaors yesterday and am waiting to hear back. We will give him a couple days to respond, and if not, figure out the next steps for proceeding with the submission

[marcoalopez]

Hi @lheagy, Any news about @khaors?

[lheagy]

Hi @marcoalopez: thanks for checking in. I haven't heard anything. I will check with the editorial board on how to proceed and get back to you.

[lheagy]

👋Hi @marcoalopez: I will take a look through your submission this weekend and see if I have any comments following up from @jsta's review and we can go from there. Thanks for your patience!

[marcoalopez]

You're welcome @lheagy, thank you very much for your help!

[lheagy]

Hi @marcoalopez, I generated a few issues with respect to licensing, packaging and installation. Please take a look when you have a chance and let me know if there is anything I can clarify!

• JOSS review: applying the Apache 2.0 license  marcoalopez/GrainSizeTools#6
• JOSS review: packaging and organization marcoalopez/GrainSizeTools#8
• JOSS review: installation marcoalopez/GrainSizeTools#7

[marcoalopez]

Hi @lheagy, I have several questions that I would like to discuss before merging the proposed modifications with the master branch and modifying the script documentation. I have tested the modifications and everything seems to work fine. However, I think they add a bit of difficulty for the non-expert user, as I will try to explain below. In addition, these modifications would imply maintaining two different branches of the script since the changes introduced will produce a module error when running the GrainSizeTools.py file. In other words, the modifications proposed no longer allow to use the script as before.

So far all script users simply download and run it in an IDE and then interact with it (mainly because of the way it was designed and released). When introducing these modifications, people will have to install the script using the console via pip, import the module, and use the dot notation to interact with the functions. I know this is no big deal, but it's more complicated than just calling a small number of functions and getting the results. Keep in mind here that this script is mainly designed for people without previous experience in Python programming language (indeed most users are of this type in my experience), so my first intention is to keep things as simple as possible. Of course, I see other advantages in using PyPI and I would like that the script could be installed in this way. My doubts are that this would require maintaining two branches of the same script and rewriting most of the documentation. Perhaps the last point could be avoided by briefly explaining the dot notation and the structure of the script for more advanced users. In contrast, I haven't found a way to avoid the maintenance of two branches and I'm a bit stuck at this point. Maybe I'm overthinking it.

[lheagy]

Hi @marcoalopez: thanks for your message. It is up to you, and feel free to disregard the pull request if this is not the direction you want to go. My word-of-caution here is that the current packaging doesn't allow GrainSizeTools to easily interoperate with other packages in the python ecosystem. For example, if I wanted to import grainsize tools into a workflow I have in a Jupyter notebook, that is not easily done.

There is a middle-ground you could consider - keep the script at the top level and package the rest of the utilities as a python e.g.

GrainSizeTools (repo-level) /
    setup.py   (installs everything under grain_size_tools)
    GrainSizeToolsScript.py
    grain_size_tools/ 
        tools.py
        ...

The setup.py would install everything under grain_size_tools (and make everything under grain_size_tools pip-installable). The script would the import from grain_size_tools and you can run it in an IDE.

If this is of interest to you, and you have any questions about how you might approach this, I can make some notes and suggestions in the pull request. If not, no worries :)

[marcoalopez]

Hi @lheagy. Although I fully understand your point of view here, I would like not to give such a drastic change to the way users today interact with the script (if this is ok with you). Also because I need time to deeply understand the way packaging and installation work in Python (this is new to me). In the meantime, I added in the documentation a short text indicating how to interact with the script in a Jupyter notebook (see here) and an example of a notebook itself (see here). I also made a little modification in the script so that the figures produced by the calc_grain_size function look better when working with the inline mode.

On the other hand, I would like to address this packaging issue in the near future and be able to release the script in the PyPI repository. I have added a new branch called future_PyPI in which I would like to develop this. Could I merge your pull request into this branch as a starting point? Lastly, is there any way to use from GrainSizeTools_script import * after executing python setup.py install? I ask this because theoretically using this would allow you to interact with the script in the same way as when running the script in an IDE, wouldn't it? If so, is this way of importing discouraged by Python standards?

[lheagy]

Hi @marcoalopez: sorry for my delayed response.

Not a problem, it is totally up to you to decide the direction of the project :) Excellent, I will take a look at your notebooks!

For sure, feel free to merge the pr if you like, you can change where the pr is being merged to by editing it

and changing the branch

Importing * is generally discouraged -- for example if you have

import numpy as np
import matplotlib

import tools

def grain_size_tools_fct():
    .... 

in your GrainSizeTools_script, then importing * will bring in np, matplotlib, .... This is okay, but discouraged because it is a bit convoluted (it is better if the user knows exactly what functionality they are bringing in).

However, if this is a beneficial first step, then as long as you keep in mind the drawbacks, it is not a bad way to progress.

[lheagy]

Hi again @marcoalopez,

The notebook is a nice addition!

I have gone through the rest of the checklist and there is one remaining items (and two minor items) to be addressed. The main item is testing. I didn't see a clear indication of testing (ideally automated testing, but even manually is okay for acceptance). I have summarized comments on testing here:

• JOSS review: testing marcoalopez/GrainSizeTools#10

The other two minor comments are with respect to the paper and the newly added notebook:

• JOSS Review: doi in paper marcoalopez/GrainSizeTools#11
• JOSS review: jupyter notebooks marcoalopez/GrainSizeTools#12

Please let me know if I can provide any clarification. Once these items are addressed, I think we can go-ahead with publication.

[lheagy]

Thanks for all of your work reviewing @jsta, and nice work @marcoalopez! Thanks for iterating with me and I hope you have found the review process beneficial.

@marcoalopez: could you please archive the software on zenodo or similar and post the doi here. From there, we can proceed with publication 🎉

[marcoalopez]

Hi @lheagy, thank you for your support as an editor and the review. I have learned many things in the process. I would like to say that I really think this is the way to go for the publication and revision of the software. So congratulations to the whole JOSS team for this great idea and keep going. I archive the software as it is now in GitHub repository on the following doi (figshare):

https://doi.org/10.6084/m9.figshare.1383130.v23

[lheagy]

@whedon set 10.6084/m9.figshare.1383130.v23 as archive

[whedon]

OK. 10.6084/m9.figshare.1383130.v23 is the archive.

[lheagy]

@arfon, this submission is ready to be published. One quick question for you: do we want the version number in the doi? (e.g. v23)

Congrats on your submission @marcoalopez and many thanks @jsta for your effort reviewing 🎉!

[arfon]

@arfon, this submission is ready to be published. One quick question for you: do we want the version number in the doi? (e.g. v23)

Yeah, I think this is fine.

@lheagy, @jsta - many thanks for your reviews here and to @lheagy for editing too ✨

@marcoalopez - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00863 ⚡ 🚀 💥

[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:

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