[REVIEW]: Pyccel: a Python-to-X transpiler for scientific high-performance computing #4991

editorialbot · 2022-12-03T20:36:52Z

Submitting author: @yguclu (Yaman Güçlü)
Repository: https://github.com/pyccel/pyccel/
Branch with paper.md (empty if default branch): joss-paper
Version: v1.7.2
Editor: @danielskatz
Reviewers: @aholmes, @IgorBaratta, @boegel
Archive: 10.5281/zenodo.7711108

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8b565b8f36e1d0cccb3c749ff22857e3"><img src="https://joss.theoj.org/papers/8b565b8f36e1d0cccb3c749ff22857e3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8b565b8f36e1d0cccb3c749ff22857e3/status.svg)](https://joss.theoj.org/papers/8b565b8f36e1d0cccb3c749ff22857e3)

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

@aholmes & @IgorBaratta & @boegel, 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 @danielskatz 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 @aholmes

📝 Checklist for @boegel

📝 Checklist for @IgorBaratta

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-12-03T20:36:54Z

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:

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editorialbot · 2022-12-03T20:36:58Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.80 s (951.5 files/s, 119099.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         616          15362          12849          52658
Markdown                        22           1089              0           3348
CMake                           31            495            567           1811
C                                6            170            273           1398
reStructuredText                56           1339           1230           1108
YAML                            19             82             70            761
C/C++ Header                     5             50            147            260
TeX                              2             23             26            209
Fortran 90                       2             99             30            186
DOS Batch                        2              8              1             43
INI                              1              0              0             11
TOML                             1              0              0             10
make                             1              4              6             10
Bourne Shell                     1              3             13              5
-------------------------------------------------------------------------------
SUM:                           765          18724          15212          61818
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-12-03T20:37:01Z

Wordcount for paper.md is 1192

editorialbot · 2022-12-03T20:37:14Z

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

OK DOIs

- 10.1109/MCSE.2010.118 is OK
- 10.1088/1749-4680/8/1/014001 is OK
- 10.1145/1565824.1565827 is OK
- 10.1145/1238844.1238856 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.ascom.2014.12.001 is INVALID because of 'https://doi.org/' prefix

editorialbot · 2022-12-03T20:38:21Z

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

danielskatz · 2022-12-03T20:39:29Z

👋 @yguclu please fix the incorrectly formatted DOI that editorialbot found. After you make the change to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

danielskatz · 2022-12-03T20:39:35Z

👋 @aholmes, @IgorBaratta, and @boegel - 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.

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. There are also links to the JOSS reviewer guidelines.

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#4991 so that a link is created to this 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 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

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

boegel · 2022-12-03T21:12:55Z

Review checklist for @boegel

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/pyccel/pyccel/?
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 (@yguclu) 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?

aholmes · 2022-12-04T19:19:19Z

Review checklist for @aholmes

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/pyccel/pyccel/?
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 (@yguclu) 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?

JOSS submission [requires](https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort) "... that software should be feature-complete (i.e., no half-baked solutions), packaged appropriately according to common community standards for the programming language being used." I identified that, upon installing the defined dependencies (in setup.cfg) with `pip install -e .`, `pytest` was not runnable. The dependencies for `pytest` are listed in [README.md](https://github.com/pyccel/pyccel/blob/8ca23f07fa9aed4ed1974c7b7d6f427bcce7f7df/README.md#requirements), however, this requires manual management of development dependencies to maintain. Therefore, this PR adds the test dependencies to setup.cfg as "optional," which allows them to be installed with `pip install -e .[test]` - thus leaving the "production" dependencies as they are. In addition, the "pytest-xdist," "astunparse," and "tblib" dependencies that are not explicitly mentioned under "Requirements" have been added to setup.cfg. Documentation on how to install these dependencies has been updated. Related: openjournals/joss-reviews#4991

EmilyBourne · 2022-12-05T07:58:51Z

@editorialbot check references

editorialbot · 2022-12-05T07:59:07Z

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

OK DOIs

- 10.1109/MCSE.2010.118 is OK
- 10.1088/1749-4680/8/1/014001 is OK
- 10.1016/j.ascom.2014.12.001 is OK
- 10.1145/1565824.1565827 is OK
- 10.1145/1238844.1238856 is OK

MISSING DOIs

- None

INVALID DOIs

- None

EmilyBourne · 2022-12-05T08:00:18Z

@editorialbot generate pdf

editorialbot · 2022-12-05T08:01:45Z

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

IgorBaratta · 2022-12-05T10:08:11Z

Review checklist for @IgorBaratta

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/pyccel/pyccel/?
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 (@yguclu) 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?

In pyccel#5, benchmarks were moved to the tests/ directory from the benchmark_code/ directory. This change updates that path. This error is received on attempting to run the benchmarks: ```sh $ python benchmarks/run_benchmarks.py --verbose =========================================== Ackermann =========================================== Traceback (most recent call last): File "/home/aholmes/repos/pyccel-benchmarks/benchmarks/run_benchmarks.py", line 209, in <module> shutil.copyfile(test_file, os.path.join(new_folder, basename)) File "/usr/lib/python3.10/shutil.py", line 254, in copyfile with open(src, 'rb') as fsrc: FileNotFoundError: [Errno 2] No such file or directory: '/home/aholmes/repos/pyccel-benchmarks/benchmarks/benchmark_code/ackermann_mod.py' ``` Related: http://openjournals/joss-reviews#4991

EmilyBourne · 2023-03-09T07:44:56Z

The tagged version is v1.7.2

yguclu · 2023-03-09T08:18:45Z

The tagged version is v1.7.2

Indeed. The latest Pyccel version on PyPI is now 1.7.3, but the benchmarks in the article were run with version 1.7.2. Hence we stick to 1.7.2.

EmilyBourne · 2023-03-09T08:30:09Z

Make a tagged release of your software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
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.

EmilyBourne · 2023-03-09T08:37:17Z

The DOI of the archived version is : https://doi.org/10.5281/zenodo.7711108

EmilyBourne · 2023-03-09T08:45:34Z

@danielskatz Our checklist is now complete. Thank you for your help with the review process. And thanks to the reviewers for their time and helpful interactions.

danielskatz · 2023-03-09T12:15:27Z

@editorialbot set v1.7.2 as version

editorialbot · 2023-03-09T12:15:29Z

Done! version is now v1.7.2

danielskatz · 2023-03-09T12:15:47Z

@editorialbot set 10.5281/zenodo.7711108 as archive

editorialbot · 2023-03-09T12:15:50Z

Done! Archive is now 10.5281/zenodo.7711108

danielskatz · 2023-03-09T12:16:36Z

@editorialbot recommend-accept

this will generate the final proof that I will then check over and perhaps get back to you about

editorialbot · 2023-03-09T12:16:38Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-03-09T12:17:12Z

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

OK DOIs

- 10.1109/MCSE.2010.118 is OK
- 10.1088/1749-4680/8/1/014001 is OK
- 10.1016/j.ascom.2014.12.001 is OK
- 10.1145/1565824.1565827 is OK
- 10.1145/1238844.1238856 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-03-09T12:18:26Z

👋 @openjournals/csism-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#4039, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-03-09T12:29:51Z

@yguclu and @EmilyBourne - I've suggested some minor changes in pyccel/pyccel#1341 - please merge this, or let me know what you disagree with, then we can proceed to publication.

danielskatz · 2023-03-09T12:42:32Z

@editorialbot recommend-accept

hopefully final check

editorialbot · 2023-03-09T12:42:33Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-03-09T12:43:17Z

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

OK DOIs

- 10.1109/MCSE.2010.118 is OK
- 10.1088/1749-4680/8/1/014001 is OK
- 10.1016/j.ascom.2014.12.001 is OK
- 10.1145/1565824.1565827 is OK
- 10.1145/1238844.1238856 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-03-09T12:44:13Z

👋 @openjournals/csism-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#4040, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-03-09T12:46:42Z

@editorialbot accept

editorialbot · 2023-03-09T12:46:44Z

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

editorialbot · 2023-03-09T12:49:08Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-03-09T12:49:09Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-03-09T12:49:10Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.04991 joss-papers#4041
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04991
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2023-03-09T12:55:05Z

Congratulations to @yguclu (Yaman Güçlü), @EmilyBourne, and co-authors!!

And thanks to @aholmes, @IgorBaratta, and @boegel for reviewing!
We couldn't do this without you

editorialbot · 2023-03-09T12:55:07Z

🎉🎉🎉 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.04991/status.svg)](https://doi.org/10.21105/joss.04991)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04991">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04991/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04991/status.svg
   :target: https://doi.org/10.21105/joss.04991

This is how it will look in your documentation:

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yguclu · 2023-03-09T13:56:11Z

Thank you @danielskatz, @aholmes, @IgorBaratta and @boegel!! The review process has been well organized and insightful. I have really appreciated your input, which has allowed us to improve Pyccel!

editorialbot added CMake Python review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Dec 3, 2022

editorialbot assigned danielskatz Dec 3, 2022

editorialbot mentioned this issue Dec 3, 2022

[PRE REVIEW]: Pyccel: a Python-to-X transpiler for scientific high-performance computing #4986

Closed

aholmes mentioned this issue Dec 4, 2022

[JOSS] Contribution and authorship pyccel/pyccel#1243

Closed

This was referenced Dec 5, 2022

[JOSS] Reproducibility - consider locking dependency versions pyccel/pyccel#1249

Closed

[JOSS] Reproducibility - Resolve issue with looking for benchmark tests in the wrong path. pyccel/pyccel-benchmarks#7

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 9, 2023

editorialbot added accepted published Papers published in JOSS labels Mar 9, 2023

danielskatz closed this as completed Mar 9, 2023

[REVIEW]: Pyccel: a Python-to-X transpiler for scientific high-performance computing #4991

[REVIEW]: Pyccel: a Python-to-X transpiler for scientific high-performance computing #4991

Comments

editorialbot commented Dec 3, 2022 • edited Loading

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Reviewer instructions & questions

Checklists

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Review checklist for @boegel

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

aholmes commented Dec 4, 2022 • edited Loading

Review checklist for @aholmes

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

EmilyBourne commented Dec 5, 2022

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IgorBaratta commented Dec 5, 2022 • edited Loading

Review checklist for @IgorBaratta

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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yguclu commented Mar 9, 2023

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