[REVIEW]: OpenPelt: Python Framework for Thermoelectric Temperature Control System Development

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@gdetor@rkurchin<!--end-editor-- Reviewers: @tpurcell90, @danaraujocr Archive: 10.5281/zenodo.6514903

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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) 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

@tpurcell90 & @danaraujocr, 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 @rkurchin 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 @tpurcell90

📝 Checklist for @danaraujocr

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (273.2 files/s, 26939.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          15            218            294            967
Markdown                         2             59              0            277
TeX                              1              7              0             81
Bourne Shell                     1              3              0             43
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            20            288            298           1386
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/S0003-2670(03)00676-7 is OK
- 10.1049/el:20062442 is OK
- 10.1145/1731022.1731030 is OK
- 10.1109/IMTC.2000.848895 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1016/j.applthermaleng.2004.03.001 is INVALID
- 10.1007/978-3-642-23099-8 is INVALID

editorialbot commented 2 years ago

Wordcount for paper.md is 1206

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

tpurcell90 commented 2 years ago

Review checklist for @tpurcell90

Conflict of interest

[x] 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

[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 https://github.com/thejackal360/OpenPelt-Public?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@gdetor) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

tpurcell90 commented 2 years ago

@gdetor and @thejackal360 would you rather all comments be made here or in issues on the repository?

tpurcell90 commented 2 years ago

The paper is generally well written, but there are issues with the documentation that make the using the code difficult for a new user

1) The installation instructions presented in the README only works if one has the right version of gcc (I think it has to be 8.2.1+ because of GLIBC_2.29). This is because instead of providing the source code for the modified version of ngspiceas a submodule or an external code, the repository includes libngspice.so which was compiled with gcc-9.4. This is a major limiting factor for installing the code, and I think that the ngspice library's source code should be provided, including instructions on how to compile it. Ideally this would be done automatically with pip, but that would be non-trivial to set up.

2) The README has a few typos in it, including links to the private repository for OpenPelt.

3) While the tests are automated, they are done with a seperate bash script that overrides LD_LIBRARY_PATH to include the provided libngspice.so file. If you have to compile ngspice from source this breaks the script. I'd recommend converting the existing testing protocol to use pytest

4) The provided examples and API are not enough for a newcomer to understand how to use the code. I'd include a description of the physical model that is being modeled in the examples. Improvements to the python API would also be helpful as it is currently incomplete.

I opened issues on the repository for these problems

thejackal360 commented 2 years ago

Thank you for your feedback! We've resolved all the issues on the OpenPelt repo.

tpurcell90 commented 2 years ago

There are still a few functions in controller.py and all of neural_network.py that are undocumented

gdetor commented 2 years ago

@tpurcell90 Thank you for pointing out that issue. We fixed that.

rkurchin commented 2 years ago

@tpurcell90, many thanks for starting your review so promptly! @danaraujocr, please don't hesitate to ask if you need any clarifications on how the process works.

danaraujocr commented 2 years ago

Review checklist for @danaraujocr

Conflict of interest

[x] 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

[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 https://github.com/thejackal360/OpenPelt-Public?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@gdetor) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

tpurcell90 commented 2 years ago

All my comments have been addressed.

rkurchin commented 2 years ago

👋 Hi @danaraujocr, just checking in on how your review is going!

danaraujocr commented 2 years ago

Hi Rachel,

Sorry about the delay. Had an issue with my computer and just solved it. Will continue the work later today.

danaraujocr commented 2 years ago

@gdetor and @thejackal360 The paper is well written, but the installation doc are still not perfectly clear. I ran a new ubuntu 20.04 installation on a virtual machine to check if the installation would run exactly as described but it didn't for minor reasons. The few things I would suggest adding/changing are: 1 - in the build_nspice.sh file a YACC command is called and those were not available in the build I used. Easily solvable. I commented on the issue opened by @tpurcell90 adding this complication. 2 - In the instructions to add the lbngspice environment variable the text suggests that one needs to copy/paste the snippet into .bashrc and what is in it is a command that does that for you. that might be confusing for some users. 3 - In the snippet that contains the code below : $ cd OpenPelt/ $ ./build_ngspice.sh $ pip3 (or pip) install . I think you should only keep the last line, as the two previous lines have probably already been executed. (especially the shell script)

Other than those minor things, nothing else to add.

gdetor commented 2 years ago

@danaraujocr Thank you for your comments/suggestions. We updated the README file including all your suggestions.

danaraujocr commented 2 years ago

@rkurchin no other commentaries to make.

rkurchin commented 2 years ago

Thanks everyone! Authors, I'll do an editorial pass over the manuscript and send any comments shortly. In the meantime, the next steps for you are:

Merge any and all changes from this review into your main branch and issue a new version tag. (If you want to merge in the paper, you may, but it is not required that the actual manuscript live into the repo in perpetuity since JOSS will host it and you can simply add a badge link or whatever you like. But the actual changes to software and docs do need to be merged!)
Create a DOI for the contents of the repo at the same commit corresponding to that version tag, e.g. using figshare or Zenodo. Please make sure that the metadata (version number, title, author list, etc.) match those of your manuscript.
Post a comment here with the version number and DOI.

rkurchin commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/j.applthermaleng.2004.03.001 is OK
- 10.1016/S0003-2670(03)00676-7 is OK
- 10.1049/el:20062442 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1145/1731022.1731030 is OK
- 10.1109/IMTC.2000.848895 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rkurchin commented 2 years ago

Some small editorial comments:

There's a weirdly-formatted citation at the end of the first paragraph in the Statement of Need, where one typesets in square brackets and the other not (broad note on citation formatting, to cite multiple sources at once, you can do e.g. [@doe99; @smith2000; @smith2004]) to get them all in one set of parentheses)
line 29: hyphenate "several-minute" (compound adjective)
45: hyphenate "open-source" (ditto)
I suggest surrounding code with ` to get monospace typesetting, e.g. for mentions oftec_plant` et al.
line 71: should be "...unlikely to be very many..."
74: suggest rephrasing to "...they are solved using iterative methods for systems of differential equations." (removes duplication of "solve" in same sentence)

gdetor commented 2 years ago

@rkurchin Thank you for the suggestions/comments. We have incorporated all your suggestions to the text. Soon we will provide the DOI and the tag.

thejackal360 commented 2 years ago

@editorialbot set beta as version

editorialbot commented 2 years ago

I'm sorry @thejackal360, I'm afraid I can't do that. That's something only editors are allowed to do.

thejackal360 commented 2 years ago

Version Number: beta DOI: 10.5281/zenodo.6514903

Are we able to change the version to "beta" for the submission? JOSS won't let us use "@editorialbot set beta as version" since we are not editors.

rkurchin commented 2 years ago

@editorialbot set beta as version

editorialbot commented 2 years ago

Done! version is now beta

rkurchin commented 2 years ago

@editorialbot set 10.5281/zenodo.6514903 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6514903

rkurchin commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rkurchin commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/j.applthermaleng.2004.03.001 is OK
- 10.1016/S0003-2670(03)00676-7 is OK
- 10.1049/el:20062442 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1145/1731022.1731030 is OK
- 10.1109/IMTC.2000.848895 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3191

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3191, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer commented 2 years ago

Hi @gdetor, I'm the AEIC on duty this week doing some final checks.

It looks like one reference is missing a DOI: Degrave et al. 2022. (Not sure why the automated check missed this.) Can you add this?

gdetor commented 2 years ago

@kyleniemeyer Thank you for pointing that out. We added the missing DOI.

kyleniemeyer commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kyleniemeyer commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3195
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04306
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 2 years ago

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

Many thanks to @tpurcell90 and @danaraujocr for reviewing this, and @rkurchin for editing it.

editorialbot commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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reStructuredText:
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   :target: https://doi.org/10.21105/joss.04306

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