[REVIEW]: HARDy: Handling Arbitrary Recognition of Data in Python

[whedon]

Submitting author: @MariaPoliti (Maria Politi)
Repository: https://github.com/EISy-as-Py/hardy
Branch with paper.md (empty if default branch):
Version: v1.0.1
Editor: @gkthiruvathukal
Reviewers: @andrewtarzia, @alberto-battistel
Archive: 10.5281/zenodo.6339767

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6bcfb38bd849bb22b02615607236a98d"><img src="https://joss.theoj.org/papers/6bcfb38bd849bb22b02615607236a98d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6bcfb38bd849bb22b02615607236a98d/status.svg)](https://joss.theoj.org/papers/6bcfb38bd849bb22b02615607236a98d)

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

@andrewtarzia & @alberto-battistel, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @gkthiruvathukal 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 ✨

Review checklist for @andrewtarzia

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@MariaPoliti) 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

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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @alberto-battistel

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@MariaPoliti) 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

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: Does the paper have a section titled 'Statement of Need' that clearly states 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. @andrewtarzia, @alberto-battistel it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ 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

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1378

[whedon]

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

OK DOIs

- 10.1021/acs.chemmater.9b03043.s001 is OK
- 10.1002/aenm.201900555 is OK
- 10.1109/dsaa.2015.7344858 is OK
- 10.24963/ijcai.2017/352 is OK
- 10.1107/s1600576720000552 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.11 s (611.6 files/s, 120428.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30            845           1884           2675
Markdown                        10            186              0            560
YAML                            11            112            136            481
Jupyter Notebook                 4              0           5756            133
reStructuredText                 9             81             90            118
TeX                              1              7              0             73
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            67           1243           7874           4075
-------------------------------------------------------------------------------


Statistical information for the repository '653737375ea3b5c6c4ffd45d' was
gathered on 2021/10/16.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Abdul Moeez                      1            51             62            0.14
David Hurt                      55          3545           1093            5.76
Maria Politi                    89         19618           4301           29.71
MariaPoliti                      7           222            425            0.80
Moeez                            2             2              2            0.00
amoeezuw                       136         26172          25012           63.58

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Abdul Moeez                  19           37.3         15.6               21.05
David Hurt                  969           27.3         15.2               15.79
Maria Politi               2725           13.9         14.2                7.08
amoeezuw                   1696            6.5         12.4               13.03

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[andrewtarzia]

I have read the manuscript and very excited to review and test out this software!

Created some issues about getting started and installation, which has not been smooth for me - although I acknowledge that it could be because I have not used TensorFlow before and I am not used to its installation:
EISy-as-Py/hardy#9
EISy-as-Py/hardy#10
EISy-as-Py/hardy#11

Comments on the manuscript:

• The figures are a little unclear. Some explanation of Fig 1 would be great.
• Explanation of the left most column in Fig 2 and the distinction between symbols in Figure 3 are necessary.

[whedon]

👋 @alberto-battistel, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @andrewtarzia, please update us on how your review is going (this is an automated reminder).

[andrewtarzia]

I have read the manuscript and very excited to review and test out this software!

Created some issues about getting started and installation, which has not been smooth for me - although I acknowledge that it could be because I have not used TensorFlow before and I am not used to its installation: EISy-as-Py/hardy#9 EISy-as-Py/hardy#10 EISy-as-Py/hardy#11

Comments on the manuscript:

• The figures are a little unclear. Some explanation of Fig 1 would be great.
• Explanation of the left-most column in Fig 2 and the distinction between symbols in Figure 3 are necessary.

The above has mostly been answered. Still awaiting a way to test parts of Hardy that do not require the costly training that I cannot perform (issue 11). At this point, it is still unclear how to use Hardy after training a model that can make the classifications.

The checklist above highlights what is missing.

[andrewtarzia]

I have completed my review and recommend acceptance of this software paper, the work is potentially very useful, although some checklist items above remain unticked for me, which I highlight here:

• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

Google colab notebooks have been developed throughout this review process to answer issues I have sent that show the analysis and use of models from hardy. These guides should be formalised and made easy to find from the README and docs.

• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

This goes with the issue above, I think the documentation is scattered in different forms (examples, documentation and READMEs) and is difficult to grasp. Additionally, many functions/methods lack complete documentation (e.g., data_wrapper in run_hardy.py)

• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?

The writing is good and the manuscript quality is overall good, just some minor comments I highlighted earlier:

• The figures are a little unclear. Some explanation of Fig 1 would be great.
• Explanation of the left most column in Fig 2 and the distinction between symbols in Figure 3 are necessary.

[MariaPoliti]

@andrewtarzia Thank you so much for the feedback and the review you provided for this paper. The remaining points on your checklist have been addressed:

• A new version of the manuscript has been uploaded on the repository with new figures and captions.
• Jupyter Notebooks/Google Collab notebooks have been uplaoded in the doc/examples/ folder in the repository. These cover a variety of use cases and functionalities of the software.
• The documentation has been consolidated in the aformentioned folder and should now be more accessible and easy to find.

@gkthiruvathukal adn @alberto-battistel : Is there any update for this publication? When can we expect the review to be completed?

Thank you again all for your work and your feedback on this software!

[gkthiruvathukal]

@MariaPoliti I am just returning from my "out of office", so I should be able to follow up shortly (hopefully within 24-48 hours). Thanks for the gentle nudge!

[gkthiruvathukal]

@andrewtarzia Thanks for your feedback.
@MariaPoliti Thanks for addressing @andrewtarzia's feedback.

@alberto-battistel Have you been able to review this submission? I don't see any input on the checklist or comments. We need input from you to complete this review.

Thanks to everyone for your patience. I was out of office until the 4th but also became department chairperson at my university. So it took me a few days to catch up.

[alberto-battistel]

Hello @MariaPoliti,
I apologize for my very slow response.

I am trying installing the package. I tried all proposed methods, but they all fail.

Installation via conda
Installing the package via conda as suggested, but it failed. I opened an Issue with the description, see https://github.com/EISy-as-Py/hardy/issues/13#issue-1114920637.

Installation via GitHub repository
I also tried following the GitHub repository, but is also failed. I opened another Issues with the details:
https://github.com/EISy-as-Py/hardy/issues/14#issue-1114946713

Installation using evironment.yml
Following https://hardy.readthedocs.io/en/latest/installation.html#installation-using-evironment-yml-recommended I tried the recommended way, but it also failed.
I opened another Issue with the details: https://github.com/EISy-as-Py/hardy/issues/15#issue-1115195845

[alberto-battistel]

Dear @MariaPoliti <https://github.com/MariaPoliti>, I have read the manuscript. I used the version it was send by .@wedon in the very beginning. See in the attachment for a couple of comments I have for the text. In  hardy/joss-paper/paper.md I see the .md file, but the captions for the figures are missing. This was a point to improve mentioned by @andrewtarzia <https://github.com/andrewtarzia>. If you have a new version of the manuscript I will be happy to go through it directly. General comments on the manuscript The manuscript is well-written and clear, but some details and explanations are missing. 1. Figure 1 should be explained more in detail. 2. Figure 2 should also be explained more in detail. In particular, the Small Angle Scattering (SAS) data should be better described. 3. It is not clear what is the RGB representation of the data. I am going to flash a drive with a standard Ubuntu system and try the installation one more time.

…

On 16.01.22 16:38, George K. Thiruvathukal wrote: @andrewtarzia <https://github.com/andrewtarzia> Thanks for your feedback. @MariaPoliti <https://github.com/MariaPoliti> Thanks for addressing @andrewtarzia <https://github.com/andrewtarzia>'s feedback. @alberto-battistel <https://github.com/alberto-battistel> Have you been able to review this submission? I don't see any input on the checklist or comments. We need input from you to complete this review. Thanks to everyone for your patience. I was out of office until the 4th but also became department chairperson at my university. So it took me a few days to catch up. — Reply to this email directly, view it on GitHub <#3829 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACNDTJ26N6WDYSRHEJTFWV3UWLQ6RANCNFSM5GDZOXKQ>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[MariaPoliti]

@whedon generate pdf

@alberto-battistel @andrewtarzia As mentioned in a previous message, the documentation has been updated and additional examples have been added- see doc/examples folder.
If the documentation is not to a satisfactory level, we can add more examples/explanations.

@alberto-battistel the manuscript version on the repository is the final one. It seems like the captions are nto shown when opening the .md file on GitHub directly. If whedon does not generate a new version, you can generate it directly on this link: https://whedon.theoj.org/ by just pasting the repository's URL [ https://github.com/EISy-as-Py/hardy ].

Let us know if anything can be improved or need further attention.

Thank you all again for the feedback provided

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[alberto-battistel]

Thank you, it is everything fine.
On my side the article is as accepted.
I am going to close or give the last comments to the issues I opened.

Best,
Alberto

[MariaPoliti]

@gkthiruvathukal @andrewtarzia : Is there any update for this publication? When can we expect the review to be completed?

Thank you again all for your work and your feedback on this software!

[andrewtarzia]

I'll do it in the next few days. I wasn't sure it was ready yet, sorry!

[gkthiruvathukal]

@MariaPoliti I think we're almost ready to go.

Can you scroll up to the checklist of items remaining to be addressed by @andrewtarzia? It looks like you addressed all of these comments, but I did not see any follow up from @andrewtarzia. It may not be needed but I would like you to confirm that you addressed all of the points there.

Once I have said confirmation, I can proceed with final checks and to recommend acceptance.

[andrewtarzia]

Sorry about the delay. Having looked through the docs, examples and manuscript again, I am happy with it and recommend publication.

@gkthiruvathukal

[MariaPoliti]

@alberto-battistel There seems to be one task not checked off from your list. I believe we have addressed it, but I am just double checking with you.

@gkthiruvathukal What are the next steps after the review is completed? When can we expect for a final decision to be made about this publication?

Thank you agian all for your great feedback and your reviews

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[gkthiruvathukal]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1021/acs.chemmater.9b03043.s001 is OK
- 10.1002/aenm.201900555 is OK
- 10.1109/dsaa.2015.7344858 is OK
- 10.24963/ijcai.2017/352 is OK
- 10.1107/s1600576720000552 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3037

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3037, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[gkthiruvathukal]

@MariaPoliti Thank you for your patience.
@andrewtarzia and @alberto-battistel Thank you for your great help on reviewing this submission.

I have recommended acceptance and look forward to seeing this work published in JOSS.

[alberto-battistel]

Thanks, @alberto-battistel. @MariaPoliti, let me know when you have a chance to act on the above checklist of final steps.

I ticked the missing point. Is there anything else?

[Kevin-Mattheus-Moerman]

@MariaPoliti I have proofread your paper and it seems in order, but please do consider the following comment;

• Use a capital letter for names like python see for instance python-based in the text which should read python-based, please check throughout.

If you make changes to the paper please update it here using @editorialbot generate pdf. Thanks.

[MariaPoliti]

@editorialbot generate pdf

[MariaPoliti]

@Kevin-Mattheus-Moerman Thank you for pointing out the issues with capitalization. I have fixed those I could find in the manuscript and generated a new .pdf using the command you indicated.

[kyleniemeyer]

@editorialbot generate pdf

[kyleniemeyer]

👋 Hi @MariaPoliti! Good to "see" you here!

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kyleniemeyer]

@MariaPoliti I made a few more minor formatting edits in this PR, can you merge it? EISy-as-Py/hardy#17

[MariaPoliti]

@kyleniemeyer it is good to "see" you too here! Thank you for the help with the paper formatting!

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kyleniemeyer]

This looks all good now, ready to publish!

[kyleniemeyer]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 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.03829 joss-papers#3050
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03829
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...

[kyleniemeyer]

Congratulations @MariaPoliti on your article's publication in JOSS!

Many thanks to @andrewtarzia and @alberto-battistel for reviewing this, and @gkthiruvathukal for editing it.

[editorialbot]

🎉🎉🎉 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.03829/status.svg)](https://doi.org/10.21105/joss.03829)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03829">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03829/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03829/status.svg
   :target: https://doi.org/10.21105/joss.03829

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss