[REVIEW]: fractopo: A Python package for fracture network analysis

[editorialbot]

Submitting author: @nialov (Nikolas Ovaskainen)
Repository: https://github.com/nialov/fractopo
Branch with paper.md (empty if default branch):
Version: v0.5.3
Editor: @elbeejay
Reviewers: @dglaeser, @lachlangrose
Archive: 10.5281/zenodo.7915808

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4802347c7e5918ebc751e82340773796"><img src="https://joss.theoj.org/papers/4802347c7e5918ebc751e82340773796/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4802347c7e5918ebc751e82340773796/status.svg)](https://joss.theoj.org/papers/4802347c7e5918ebc751e82340773796)

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

@dglaeser & @lachlangrose, 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 @elbeejay 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 @lachlangrose

📝 Checklist for @dglaeser

[editorialbot]

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.00 s (145.1 files/s, 343505.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            26              0              0         312997
Python                          60           2642           4509          12285
TeX                              2            334              0           5720
YAML                            14             21            100            692
reStructuredText                29            469            503            686
Markdown                         3            188              0            338
Nix                              2             39             96            265
TOML                             1             19             10            150
Jupyter Notebook                 3              0            994            141
SVG                              1              0              0             21
Bourne Shell                     2              4              0              9
Lua                              1              0              0              5
XML                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                           145           3716           6212         333311
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 847

[editorialbot]

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

OK DOIs

- 10.1130/GES01595.1 is OK
- 10.1016/j.jsg.2021.104304 is OK
- 10.1029/2000WR000180 is OK
- 10.1016/j.earscirev.2019.103055 is OK
- 10.1371/journal.pone.0085777 is OK
- 10.1016/j.jsg.2015.01.005 is OK
- 10.1029/1999RG000074 is OK
- 10.21105/joss.03021 is OK
- 10.1016/j.jsg.2022.104528 is OK
- 10.5281/zenodo.7262879 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[elbeejay]

Thanks again @dglaeser and @lachlangrose for agreeing to review fractopo. Instructions about how to generate your reviewer checklist as well as how to conduct a JOSS review are provided in the above comments, but please feel free to reach out to me if you have any questions. I'll be asking the bot to send out reminders about the review in 3 weeks time; note that we are currently asking our reviewers to complete their reviews within 6 weeks.

[elbeejay]

@editorialbot remind @dglaeser in three weeks

[editorialbot]

Reminder set for @dglaeser in three weeks

[elbeejay]

@editorialbot remind @lachlangrose in three weeks

[editorialbot]

Reminder set for @lachlangrose in three weeks

[lachlangrose]

Review checklist for @lachlangrose

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 https://github.com/nialov/fractopo?
• 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 (@nialov) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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, who the target audience is, and its relation to other work?
• 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?

[dglaeser]

Review checklist for @dglaeser

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 https://github.com/nialov/fractopo?
• 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 (@nialov) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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, who the target audience is, and its relation to other work?
• 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?

[editorialbot]

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

[editorialbot]

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

[dglaeser]

I'll try to finish my review until the end of next week, I hope that's fine!

[elbeejay]

That sounds great, thanks for the update @dglaeser.

[elbeejay]

Hi @nialov, @dglaeser, and @lachlangrose

I wanted to check-in here and ask how the review process is going. Both @dglaeser and @lachlangrose have opened up issues in the repository - @nialov how is the resolution to those items going?

@dglaeser and @lachlangrose have you finished your initial reviews of the software?

Thanks all,
Jay

[dglaeser]

@elbeejay, I opened a few (rather minor) issues:

• Minor issues in the readme nialov/fractopo#29
• Link validation errors in README nialov/fractopo#31
• Add context to validation error docs nialov/fractopo#32
• [Docs] links to the tutorials all seem to point to the same location nialov/fractopo#33
• [CLI][tracevalidate] save validation results into a sub-dir of pwd? nialov/fractopo#34
• [CLI][tracevalidate] default value for allow-fix nialov/fractopo#35
• [CLI][tracevalidate] make area a named argument? nialov/fractopo#36
• [paper] proposition for summary nialov/fractopo#38

and as PR:

• [docs][notebook1] minor rephrasing of snap_thresh nialov/fractopo#37

I will have one more pass over the paper tomorrow and tick off the final marks and/or post remarks about the paper.

[elbeejay]

That sounds fantastic, thanks @dglaeser

[nialov]

@elbeejay All issue reports so far have been very helpful in making fractopo a better package both in terms of code and documentation! I have already fixed issues by both dglaeser and lachlangrose in pull requests and will continue to do so in the next few weeks. Thank you for the reviews so far!

[dglaeser]

@elbeejay, I added some more points to my previous comment with the related issues/prs. I just left one tickbox open in my review, for which an open issue exists. My points raised are actually rather minor and also partly subjective. Thanks @nialov for this very nice package.

[nialov]

Hey, @elbeejay,

I have implemented the suggested fixes along with a few rephrasings to finalize the manuscript in nialov/fractopo#47.

* [ ]  (please consider) Re-releasing the package on PyPi and conda so that there are versions in the package managers that correspond to what is going to be the JOSS-publication version

During the start of the review I had to choose the version/tag to submit for the review (v0.5.2). Can I release an updated version (i.e. v0.5.3) and use it as the referenced version for the JOSS publication i.e. change it? (Just making sure)

[elbeejay]

Hi @nialov - yes that would be great.

[nialov]

All done @elbeejay

Once you have completed any revisions and finalized the manuscript text, please do the following:

* [ ]  Make a tagged release of your software, and list the version tag of the archived version here.

Version tag is v0.5.3.

* [ ]  Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository) (in this case please update the archived version)

* [ ]  Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.

* [ ]  Please list the DOI of the archived version here.

DOI is https://doi.org/10.5281/zenodo.7915808

* [ ]  (please consider) Re-releasing the package on PyPi and conda so that there are versions in the package managers that correspond to what is going to be the JOSS-publication version

PyPi package has been released. Conda will follow shortly as the feedstock workflow finishes: https://github.com/conda-forge/fractopo-feedstock

[elbeejay]

@editorialbot set v0.5.3 as version

[editorialbot]

Done! version is now v0.5.3

[elbeejay]

@editorialbot set 10.5281/zenodo.7915808 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.7915808

[elbeejay]

Awesome, thanks for doing all that @nialov. I'm now going to request that we accept this for publication. At some point in the next week or so, an editor-in-chief will do one final review and the final publishing step.

[elbeejay]

@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

- 10.1130/GES01595.1 is OK
- 10.1016/j.jsg.2021.104304 is OK
- 10.1029/2000WR000180 is OK
- 10.1016/j.earscirev.2019.103055 is OK
- 10.1371/journal.pone.0085777 is OK
- 10.1016/j.jsg.2015.01.005 is OK
- 10.1029/1999RG000074 is OK
- 10.21105/joss.03021 is OK
- 10.1016/j.jsg.2022.104528 is OK
- 10.5281/zenodo.7262879 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4215, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[nialov]

Thanks @elbeejay and thank you to the reviewers @lachlangrose and @dglaeser! All criticism was excellent and just the kind of inspection I believed my submission and package needed.

[kthyng]

Hi @nialov! Here is my to do list for wrapping up publication.

• Check that version was updated
• Check that software archive exists, has been input to JOSS, and title and author list look good
• Check paper

[kthyng]

Ok everything looks good!

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Ovaskainen
  given-names: Nikolas
  orcid: "https://orcid.org/0000-0003-1562-0280"
doi: 10.5281/zenodo.7915808
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Ovaskainen
    given-names: Nikolas
    orcid: "https://orcid.org/0000-0003-1562-0280"
  date-published: 2023-05-15
  doi: 10.21105/joss.05300
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5300
  title: "fractopo: A Python package for fracture network analysis"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05300"
  volume: 8
title: "fractopo: A Python package for fracture network analysis"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot 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.05300 joss-papers#4227
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05300
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...

[kthyng]

Congratulations on your new publication @nialov! Many thanks to editor @elbeejay and reviewers @dglaeser and @lachlangrose for your time, hard work, and expertise!!

[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.05300/status.svg)](https://doi.org/10.21105/joss.05300)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05300">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05300/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05300/status.svg
   :target: https://doi.org/10.21105/joss.05300

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://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[kthyng]

@nialov You might consider volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join

Thanks!

[nialov]

Yay and thanks @kthyng !