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[REVIEW]: PyVISA: the Python instrumentation package #5304

Closed editorialbot closed 1 year ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@hgrecco<!--end-author-handle-- (Hernan Edgardo Grecco) Repository: https://github.com/pyvisa/pyvisa Branch with paper.md (empty if default branch): joss-paper Version: 1.13.0 Editor: !--editor-->@matthewfeickert<!--end-editor-- Reviewers: @aquilesC, @sidihamady Archive: 10.5281/zenodo.7868199

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/66f6e1e25dcbf380aeb88b40a778a10f"><img src="https://joss.theoj.org/papers/66f6e1e25dcbf380aeb88b40a778a10f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/66f6e1e25dcbf380aeb88b40a778a10f/status.svg)](https://joss.theoj.org/papers/66f6e1e25dcbf380aeb88b40a778a10f)

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

@aquilesC & @sidihamady, 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 @matthewfeickert 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 @sidihamady

📝 Checklist for @aquilesC

editorialbot commented 1 year ago

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 commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.20 s (322.7 files/s, 91269.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          39           3665           4572           7136
reStructuredText                20            708            293           1325
Markdown                         1             40              0            218
CSS                              1             63             22            170
DOS Batch                        1             23              1            166
make                             1             24              5            124
TeX                              1              8              0             66
YAML                             1              5              3             20
INI                              1              2              0              9
-------------------------------------------------------------------------------
SUM:                            66           4538           4896           9234
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 1661

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/62.978361 is OK
- 10.1126/science.215.4534.785 is OK

MISSING DOIs

- 10.4135/9781412950657.n33 may be a valid DOI for title: The Cathedral and the Bazaar

INVALID DOIs

- None
sidihamady commented 1 year ago

Review checklist for @sidihamady

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

matthewfeickert commented 1 year ago

@aquilesC, @sidihamady Thanks for agreeing to review this submission! This is the review thread for the paper. All of our communications will happen here from now on. :+1:

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

As you go over the submission, please check any items that you feel have been satisfied (and if you leave notes on each item that's even better). There are also links to the JOSS reviewer guidelines. I find it particularly helpful to also use the JOSS review criteria and review checklist docs as supplement/guides to the reviewer checklist @editorialbot will make for you.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#5304 so that a link is created to this Issue thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 4 weeks. Please let me know if either of you require some more time (that's perfectly okay). We can also use @editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@matthewfeickert) if you have any questions/concerns.

aquilesC commented 1 year ago

Review checklist for @aquilesC

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

aquilesC commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

aquilesC commented 1 year ago

As a very frequent user of PyVISA, I’m glad to see it becoming a paper. The authors have done a great job over many years.

After reviewing the code and paper, I conclude it is ready for publication.

I only found a typo on the manuscript on line 31 it should read receive instead of receives.

sidihamady commented 1 year ago

Even if at the beginning PyVISA was created as a light wrapper for the VISA shared library C functions, its wide adoption, its simplicity of use and the combination with the many scientific packages of Python made it a must. I use it both for teaching and to prototype characterization tools. Its code is particularly well organized, well documented and the examples are fully functional. It works very well with VISA backends from NI and Keysight. It's a bit harder to use non-proprietary backends, but it's feasible. Authors indicate that will include async IO in a next release, which is particularly interesting for instrumentation but challenging to implement in Python and to use. Another task could be to develop a simulator more usable and less limited than PyVISA-sim, since it is difficult to quickly develop and debug without being continuously connected to real instruments. I recommend its publication in JOSS.

matthewfeickert commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

matthewfeickert commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/62.978361 is OK
- 10.1126/science.215.4534.785 is OK

MISSING DOIs

- 10.4135/9781412950657.n33 may be a valid DOI for title: The Cathedral and the Bazaar

INVALID DOIs

- None
hgrecco commented 1 year ago

There is a version published in a journal. Sh

Raymond, E. The cathedral and the bazaar. Know Techn Pol 12, 23–49 (1999). https://doi.org/10.1007/s12130-999-1026-0

but the official site is this:

http://www.catb.org/~esr/writings/cathedral-bazaar/cathedral-bazaar/

I leave it to the editor to decide what is the most suitable.

matthewfeickert commented 1 year ago

MISSING DOIs

  • 10.4135/9781412950657.n33 may be a valid DOI for title: The Cathedral and the Bazaar

This is the DOI for a chapter by the same title by Theresa M. Senft in the book Encyclopedia of New Media, and so is fine to ignore. :+1:

matthewfeickert commented 1 year ago

I leave it to the editor to decide what is the most suitable.

Ah, sorry missed this before posting given some lag in cached pages. :/ Having some DOI associated is preferable, but the rest of the citation is fine. Let me PR this quickly.

(edit: It is late and I'm travelling so as there is no .bibtex version on Springer's page I'll do it tomorrow unless the authors beat me to it)

matthewfeickert commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

matthewfeickert commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/62.978361 is OK
- 10.1126/science.215.4534.785 is OK
- 10.1007/s12130-999-1026-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None
matthewfeickert commented 1 year ago

@hgrecco all that's left to do now before publication is to ensure that there is a long term public archive of the code that was reviewed. In this case the code was v1.13.0 though there has been some development between then and the current HEAD.

We'd suggest depositing the code either with Zenodo or with figshare to get an archive with a DOI. If you use Zenodo there is an (optional) GitHub integration that can create a Zenodo archive for you anytime you make a GitHub release of your code.

Zenodo_DOI_guide

If you'd like to make a new release of PyVISA to trigger the uploader that's fine and we can have @editorialbot update the version listed in the review. You're also welcome to not do that and just upload the state of the repository at v1.13.0. Either way we'll just need you to share the resulting DOI of the archive created in this thread.

Let me know if you have any questions. :+1:

hgrecco commented 1 year ago

@MatthieuDartiailh any preferences on your side?

hgrecco commented 1 year ago

We have agreed with @MatthieuDartiailh to use the latest published version. This has been deposit in Zenodo under DOI

https://doi.org/10.5281/zenodo.7868199

@matthewfeickert let me know if this is ok.

matthewfeickert commented 1 year ago

@editorialbot set 10.5281/zenodo.7868199 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.7868199

matthewfeickert commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/62.978361 is OK
- 10.1126/science.215.4534.785 is OK
- 10.1007/s12130-999-1026-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 1 year ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4179, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 1 year ago

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: Grecco given-names: Hernán E. orcid: "https://orcid.org/0000-0002-1165-4320" - family-names: Dartiailh given-names: Matthieu C. orcid: "https://orcid.org/0000-0001-6451-0577" - family-names: Thalhammer-Thurner given-names: Gregor orcid: "https://orcid.org/0000-0002-3948-8045" - family-names: Bronger given-names: Torsten orcid: "https://orcid.org/0000-0002-5174-6684" - family-names: Bauer given-names: Florian orcid: "https://orcid.org/0009-0004-5271-5363" contact: - family-names: Grecco given-names: Hernán E. orcid: "https://orcid.org/0000-0002-1165-4320" - family-names: Dartiailh given-names: Matthieu C. orcid: "https://orcid.org/0000-0001-6451-0577" doi: 10.5281/zenodo.7868199 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Grecco given-names: Hernán E. orcid: "https://orcid.org/0000-0002-1165-4320" - family-names: Dartiailh given-names: Matthieu C. orcid: "https://orcid.org/0000-0001-6451-0577" - family-names: Thalhammer-Thurner given-names: Gregor orcid: "https://orcid.org/0000-0002-3948-8045" - family-names: Bronger given-names: Torsten orcid: "https://orcid.org/0000-0002-5174-6684" - family-names: Bauer given-names: Florian orcid: "https://orcid.org/0009-0004-5271-5363" date-published: 2023-04-27 doi: 10.21105/joss.05304 issn: 2475-9066 issue: 84 journal: Journal of Open Source Software publisher: name: Open Journals start: 5304 title: "PyVISA: the Python instrumentation package" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05304" volume: 8 title: "PyVISA: the Python instrumentation package" ```

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 commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4180
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05304
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 1 year ago

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

Many thanks to @aquilesC and @sidihamady for reviewing this, and @matthewfeickert for editing.

editorialbot commented 1 year ago

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

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Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05304/status.svg)](https://doi.org/10.21105/joss.05304)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05304">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05304/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05304/status.svg
   :target: https://doi.org/10.21105/joss.05304

This is how it will look in your documentation:

DOI

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matthewfeickert commented 1 year ago

Congratulations @hgrecco on the publication!

hgrecco commented 1 year ago

Thanks for your support during the process.