[REVIEW]: pySRURGS - a python package for symbolic regression by uniform random global search

whedon commented 5 years ago

Submitting author: @pySRURGS (Sohrab Towfighi) Repository: https://github.com/pySRURGS/pySRURGS Version: 0.1 Editor: @mbobra Reviewer: @henrik227, @SirSharpest Archive: 10.5281/zenodo.3442594

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Reviewer instructions & questions

@henrik227 & @SirSharpest, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @henrik227

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: 0.1
[x] Authorship: Has the submitting author (@pySRURGS) 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 @SirSharpest

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: 0.1
[x] Authorship: Has the submitting author (@pySRURGS) 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 commented 5 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @henrik227, @SirSharpest it looks like you're currently assigned to review this paper :tada:.

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whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

mbobra commented 5 years ago

👋Thank you so much @henrik227 and @SirSharpest for agreeing to review this submission! The review checklist is above. Please let me know if there is anything else you need!

sohrabtowfighi commented 5 years ago

Hi, I have rewritten the test script test.py to better meet criteria described herein.

sohrabtowfighi commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

hbarthels commented 5 years ago

@sohrabtowfighi Regarding the authorship: Are you also using the @pySRURGS account, or is this someone else?

sohrabtowfighi commented 5 years ago

@henrik227, I am also using the @pySRURGS account. There is no other author.

pySRURGS commented 5 years ago

I added API documentation to https://pysrurgs.github.io/pySRURGS/ which is linked from the main pySRURGS github page under the API section.

pySRURGS commented 5 years ago

I have integrated the coveralls package for test-suite coverage reporting - currently at 89%.

sohrabtowfighi commented 5 years ago

I have added an -exhaustive flag which performs brute-force exhaustive search instead of uniform random global search

pySRURGS commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

pySRURGS commented 5 years ago

I have added the -deterministic flag and made other changes to address @SirSharpest' comments.

sohrabtowfighi commented 5 years ago

After acknowledging Dr. Luther Tychonievich, I added a wayback machine archive link to the blog post where Dr. Tychonievich details the algorithm mapping integers to binary trees.

mbobra commented 5 years ago

@SirSharpest are you still working on your review? Please let me know!

AoifeHughes commented 5 years ago

Yes - sorry for delay. I am happy with the changes made.

sohrabtowfighi commented 5 years ago

@SirSharpest do the changes meet the checkbox criteria for the review?

AoifeHughes commented 5 years ago

Yes, all updated now

pySRURGS commented 5 years ago

Ok great thanks. @mbobra please let me know how to proceed when you get the chance.

sohrabtowfighi commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

sohrabtowfighi commented 5 years ago

I removed the word 'actually' from the paper.

whedon commented 5 years ago

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

mbobra commented 5 years ago

@sohrabtowfighi We're almost there! Could you please go ahead and create a new release that incorporates all of these fixes? And can you please archive your release on Zenodo to obtain a DOI and then put the Zenodo badge in your README.md file? After that I think we're done 🎉

mbobra commented 5 years ago

Thank you for your reviews, @henrik227 and @SirSharpest! We really appreciate it 👏

pySRURGS commented 5 years ago

Done. Thanks! https://zenodo.org/badge/latestdoi/200314164

mbobra commented 5 years ago

@whedon set 10.5281/zenodo.3442594 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3442594 is the archive.

mbobra commented 5 years ago

@whedon set 0.1 as version

whedon commented 5 years ago

OK. 0.1 is the version.

mbobra commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1186/s13040-018-0164-x is OK
- 10.1145/2464576.2482691 is OK

MISSING DOIs

- https://doi.org/10.1016/0303-2647(94)90062-0 may be missing for title: Genetic Programming: On the Programming of Computers by Means of Natural Selection
- https://doi.org/10.1016/0012-365x(71)90023-9 may be missing for title: Enumerating Trees
- https://doi.org/10.1287/moor.6.1.19 may be missing for title: Minimization by Random Search Techniques

INVALID DOIs

- None

mbobra commented 5 years ago

@pySRURGS Can you please make sure all the references in the paper.bib file include DOIs? Thanks!

sohrabtowfighi commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

sohrabtowfighi commented 5 years ago

@mbobra I have fixed references. The work of Tychonievich has no DOI.

sohrabtowfighi commented 5 years ago

Wait found issue and need to regenerate pdf.

sohrabtowfighi commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

sohrabtowfighi commented 5 years ago

@mbobra ok done

mbobra commented 5 years ago

@whedon check references

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1007/BF00175355 is OK
- 10.1186/s13040-018-0164-x is OK
- 10.1145/2464576.2482691 is OK
- 10.1287/moor.6.1.19 is OK

MISSING DOIs

- https://doi.org/10.1016/0012-365x(71)90023-9 may be missing for title: Enumerating Trees

INVALID DOIs

- None

openjournals / joss-reviews