[REVIEW]: PyExperimenter: Easily distribute experiments and track results

[editorialbot]

Submitting author: @tornede (Tanja Tornede)
Repository: https://github.com/tornede/py_experimenter
Branch with paper.md (empty if default branch): develop
Version: v1.2.0
Editor: @timtroendle
Reviewers: @ArsamAryandoust, @schnorr
Archive: 10.5281/zenodo.7838280

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/dcf48ed122c5f78cf16057a1897b90c7"><img src="https://joss.theoj.org/papers/dcf48ed122c5f78cf16057a1897b90c7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/dcf48ed122c5f78cf16057a1897b90c7/status.svg)](https://joss.theoj.org/papers/dcf48ed122c5f78cf16057a1897b90c7)

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

@ArsamAryandoust & @schnorr, 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 @timtroendle 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 @ArsamAryandoust

📝 Checklist for @schnorr

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (681.4 files/s, 71183.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            428            284           1830
Markdown                         4             84              0            258
reStructuredText                10            160             74            213
TeX                              1             11              0            189
Jupyter Notebook                 2              0            515            138
YAML                             3              4             13             96
JSON                             3              0              0             91
TOML                             1              3              0             46
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            43            702            894           2896
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1038

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.6536395 is OK
- 10.5281/zenodo.7264816 is OK
- 10.25080/shinma-7f4c6e7-008 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[timtroendle]

@ArsamAryandoust, @schnorr, see above for instructions to review. If anything is unclear, just let me know. Please finish your reviews within six weeks at the very latest. I will add a reminder in two weeks from now for both of you.

[timtroendle]

@editorialbot remind @ArsamAryandoust in two weeks

[editorialbot]

Reminder set for @ArsamAryandoust in two weeks

[timtroendle]

@editorialbot remind @schnorr in two weeks

[editorialbot]

Reminder set for @schnorr in two weeks

[ArsamAryandoust]

Review checklist for @ArsamAryandoust

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/tornede/py_experimenter?
• 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 (@tornede) 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]

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

[editorialbot]

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

[schnorr]

Review checklist for @schnorr

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/tornede/py_experimenter?
• 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 (@tornede) 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?

[timtroendle]

Hi @ArsamAryandoust and @schnorr, can you let us know how the review is going? Half of the review time has elapsed and I'll set another reminder for both of you to let you know when the review time is almost over.

[timtroendle]

@editorialbot remind @schnorr in two weeks

[editorialbot]

Reminder set for @schnorr in two weeks

[timtroendle]

@editorialbot remind @ArsamAryandoust in two weeks

[editorialbot]

Reminder set for @ArsamAryandoust in two weeks

[schnorr]

Hi @timtroendle, I've started my review and hope to finish this week.

[timtroendle]

Great, thanks for letting us know.

[schnorr]

So, just to let you know that I've completed my review. My opinion after regarding the source code, documentation, testing the commands suggested by the authors, etc, is that the PyExperimenter software has good maturity. It also has some people already using it, as can be seen in the Issues tabs for people requesting new functionality. I've only found a minor problem that I've registered as an issue in their repository.

About the Functionality, I think the tool is very useful because usually R or Python packages are focused on generating the experimental project without handling the experiment run. The PyExperimenter let the user define a function that will receive the configuration parameters. The function must then run the experiment itself with those parameters and let PyExperimenter know that everything went okay. So, the functionality provides a way to define the experiment project and also run it (eventually in parallel with the n_jobs parameter). Of course, some R packages especially are much more advanced because they would allow one to define specific screening projects to optimize the number of experiments to be run (avoiding a cartesian product of all configurations - which might be overwhelming). But that is not the focus of this project, which is focused in a specific type of experimental project.

I've checked all the bullet points in the review, running sloccount (for the number of lines ~ about 1k lines), checking the number of committers, and so on. As consequence, I conclude that the software checks all the requirements. So, my general opinion is a go for accept.

Thank you once again for considering my for JOSS @timtroendle !

[editorialbot]

Done! version is now v1.2.0

[timtroendle]

@editorialbot check references

[timtroendle]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.6536395 is OK
- 10.5281/zenodo.7264816 is OK
- 10.25080/shinma-7f4c6e7-008 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[timtroendle]

@tornede, it all looks good to me and I am happy to move forward.

Thanks again @schnorr and @ArsamAryandoust for your reviews!

[timtroendle]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

👋 @openjournals/dsais-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#4138, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.3509134 is OK
- 10.5281/zenodo.6536395 is OK
- 10.5281/zenodo.7264816 is OK
- 10.25080/shinma-7f4c6e7-008 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[tornede]

@timtroendle It looks good to me, too. Do I have to tell it to the editorial bot, or do you do it?

Thanks again everyone :)

[timtroendle]

@tornede, there is nothing you need to do at this point. One of the editors-in-chief will take over from here. :)

[arfon]

@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: Tornede
  given-names: Tanja
  orcid: "https://orcid.org/0000-0001-9954-462X"
- family-names: Tornede
  given-names: Alexander
  orcid: "https://orcid.org/0000-0002-2415-2186"
- family-names: Fehring
  given-names: Lukas
  orcid: "https://orcid.org/0000-0001-8057-4650"
- family-names: Gehring
  given-names: Lukas
- family-names: Graf
  given-names: Helena
  orcid: "https://orcid.org/0000-0001-9447-0609"
- family-names: Hanselle
  given-names: Jonas
  orcid: "https://orcid.org/0000-0002-1231-4985"
- family-names: Mohr
  given-names: Felix
  orcid: "https://orcid.org/0000-0002-9293-2424"
- family-names: Wever
  given-names: Marcel
  orcid: "https://orcid.org/0000-0001-9782-6818"
contact:
- family-names: Tornede
  given-names: Tanja
  orcid: "https://orcid.org/0000-0001-9954-462X"
doi: 10.5281/zenodo.7838280
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Tornede
    given-names: Tanja
    orcid: "https://orcid.org/0000-0001-9954-462X"
  - family-names: Tornede
    given-names: Alexander
    orcid: "https://orcid.org/0000-0002-2415-2186"
  - family-names: Fehring
    given-names: Lukas
    orcid: "https://orcid.org/0000-0001-8057-4650"
  - family-names: Gehring
    given-names: Lukas
  - family-names: Graf
    given-names: Helena
    orcid: "https://orcid.org/0000-0001-9447-0609"
  - family-names: Hanselle
    given-names: Jonas
    orcid: "https://orcid.org/0000-0002-1231-4985"
  - family-names: Mohr
    given-names: Felix
    orcid: "https://orcid.org/0000-0002-9293-2424"
  - family-names: Wever
    given-names: Marcel
    orcid: "https://orcid.org/0000-0001-9782-6818"
  date-published: 2023-04-20
  doi: 10.21105/joss.05149
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5149
  title: "PyExperimenter: Easily distribute experiments and track
    results"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05149"
  volume: 8
title: "PyExperimenter: Easily distribute experiments and track results"

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.05149 joss-papers#4153
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05149
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...

[arfon]

@ArsamAryandoust, @schnorr – many thanks for your reviews here and to @timtroendle for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@tornede – your paper is now accepted and published in JOSS ⚡🚀💥

[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.05149/status.svg)](https://doi.org/10.21105/joss.05149)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05149">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05149/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05149/status.svg
   :target: https://doi.org/10.21105/joss.05149

This is how it will look in your documentation:

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