[REVIEW]: PyCUTEst: an open source Python package of optimization test problems #4377

editorialbot · 2022-05-05T03:14:51Z

Submitting author: @jfowkes (Jaroslav Fowkes)
Repository: https://github.com/jfowkes/pycutest
Branch with paper.md (empty if default branch):
Version: v1.4
Editor: @diehlpk
Reviewers: @stsievert, @jonjoncardoso
Archive: 10.5281/zenodo.7244291

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/d1664af7c708cd78b5478beaa27878e6/status.svg)](https://joss.theoj.org/papers/d1664af7c708cd78b5478beaa27878e6)

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

@GuillaumeDerval & @stsievert, 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 @diehlpk 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 @stsievert

📝 Checklist for @jonjoncardoso

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

editorialbot · 2022-05-05T03:14:52Z

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editorialbot · 2022-05-05T03:14:54Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.23 s (481.5 files/s, 132003.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      13           2405           2470           9222
HTML                            31            576             87           4439
SVG                              1              0              0           2671
Python                          23            867           3121           1640
CSS                              4            191             35            759
reStructuredText                29            234            137            419
Bourne Shell                     1             16             16            284
YAML                             3              9              4            100
TeX                              1              7              0             63
Markdown                         1             17              0             57
INI                              1              1              0             17
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                           109           4327           5876          19681
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-05-05T03:14:54Z

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

OK DOIs

- 10.1145/200979.201043 is OK
- 10.1145/962437.962439 is OK
- 10.1007/s10589-014-9687-3 is OK
- 10.5281/zenodo.1188851 is OK
- 10.1137/15M1020575 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-05-05T03:14:55Z

Wordcount for paper.md is 669

editorialbot · 2022-05-05T03:16:09Z

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

stsievert · 2022-05-05T11:18:06Z

Review checklist for @stsievert

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/jfowkes/pycutest?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
(explained in #4377 (comment)) Contribution and authorship: Has the submitting author (@jfowkes) 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](https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
(there are no performance claims; checking off as instructed) 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

(added) 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).
(added) 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 and who the target audience is?
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?

diehlpk · 2022-05-20T14:36:53Z

Hi @GuillaumeDerval, @stsievert how is your review going?

diehlpk · 2022-06-15T15:02:41Z

@jfowkes can you please recommend new reviewers?

stsievert · 2022-06-16T01:47:12Z

Sorry @diehlpk; my deadline just passed. I will complete my review before Monday June 20.

diehlpk · 2022-06-16T16:45:07Z

Sorry @diehlpk; my deadline just passed. I will complete my review before Monday June 20.

Thanks for the heads up. Looking forward to your review.

jonjoncardoso · 2022-06-20T14:25:17Z

I could volunteer to review this one if needed

diehlpk · 2022-06-20T16:03:52Z

I could volunteer to review this one if needed

@jonjoncardoso that would be great, I will invite you soon.

diehlpk · 2022-06-20T16:04:13Z

@editorialbot add @jonjoncardoso as reviewer

editorialbot · 2022-06-20T16:04:14Z

@jonjoncardoso added to the reviewers list!

diehlpk · 2022-06-20T16:04:56Z

@GuillaumeDerval are you still available to review this paper?

stsievert · 2022-06-20T18:12:32Z

@diehlpk fyi I am finally getting around to reviewing this after a (too long) delay.

stsievert · 2022-06-20T20:55:59Z

I think this paper is nearly ready for acceptance into JOSS, however, I do not think it is ready now, as-is. Correspondingly, I have checked most of the boxes in #4377 (comment). I found two clearly blocking issues:

I did not find any guidelines for third parties wishing to contribute, report and find support.
Who's Arpad Burmen, and why is he listed as an author? He's listed as a first author, but doesn't have any commits to this project.

I had significant difficulty installing this software on macOS 10.14 to complete this review; I had to put PyCUTEst in it's own Dockerfile and complete my review there. I think the install docs could use some improvement/modification. Here's my Dockerfile:

The Dockerfile I used to install PyCUTEst

FROM continuumio/miniconda3
# docker build -t pyc .  # build the container
# docker run -dt pyc  # launch the container
# docker exec -it f651b5e17dec /bin/bash  # log in to the container

WORKDIR /pycutest
RUN apt update
RUN apt install -y build-essential git gfortran
RUN git clone https://github.com/ralna/ARCHDefs ./archdefs
RUN git clone https://github.com/ralna/SIFDecode ./sifdecode
RUN git clone https://github.com/ralna/CUTEst ./cutest
RUN git clone https://bitbucket.org/optrove/sif ./mastsif

ENV ARCHDEFS /pycutest/archdefs/
ENV SIFDECODE /pycutest/sifdecode/
ENV MASTSIF /pycutest/mastsif/
ENV CUTEST /pycutest/cutest/
ENV MYARCH "pc64.lnx.gfo"
ENTRYPOINT ./archdefs/install_optrove && tail -f /dev/null

I recommend adding this as an install option to the docs. Other issues/style nits include the following (in no particular order):

I'm not sure I'd say the documentation homepage "clearly state[s]" the problem of interest, certainly not as clear as the paper.
Types are missing on the API documentation (e.g., what's a "Lagrange multiplies" in CUTEstProblem.hess, and what's the shape of it? Is the "input vector" a NumPy ndarray, or can it be a PyTorch Tensor?)
The testing section of the documentation is not complete, or misnamed.
I tried to install with pip. It didn't work, I got a RuntimeError: "Could not find CUTEST installation - have CUTEST and MYARCH environment variables been set correctly?"
- I first installed with pip, then I tried homebrew (which hung), then I (successfully) tried the Dockerfile above.
There are multiple files in examples/ with no clear purpose. e.g.,
- allintic.py only defines functions. What's the purpose?
- param_warning_test.py raises a RuntimeError "SIFDECODE error: Failed setting HNS to 4". (which looks expected, and is caught in the tests).
- I get errors on test_cutest_full.py, test_dimensions.py and test_cutest_ls.py, I think because new breaking versions have been released (no attribute getinfo).
- test_available_params_print.py doesn't do much (only prints available parameters).
- (note: successful/proper examples include run_demo_problem.py, solve_rosenbrock.py)

diehlpk · 2022-06-25T00:21:12Z

@jfowkes please have a look at the comments above.

jfowkes · 2022-06-27T07:22:20Z

@stsievert thank you very much for taking the time to review our submission, much appreciated. In response to the two blocking issues you raised:

We will of course add guidelines for contributors to the readme and docs, apologies for the omission, we missed that this was a requirement.
As stated at the start of the readme and docs, Arpad Burmen wrote the original PyCUTEr of which PyCUTEst is an evolution. He is responsible for writing the majority of c_interface.py (as acknowledged in the code headers) and is thus a major contributor. Arpad Burmen has no commits to the project as his PyCUTEr was never under version control and dates back to 2011 (please see his PyCUTEr website).

I'm sorry to hear that you had difficulties installing on macOS but version 10.14 is rather outdated now and no longer supported by homebrew. Our CI tests PyCUTEst installation with homebrew on the latest macOS as well as Linux (see our Github Actions). We are of course happy to add your dockerfile as an alternative installation option to the docs.

Regarding the other issues you raised:

We agree the homepage could state the problem of interest more clearly, we will update it to more closely align with the problem statement in the paper.
We agree that the API documentation should have types, we will add these.
We agree that the testing section of the documentation is misnamed, this is a holdover from when we used a setup.py entry-point for tests.
As the docs state, CUTEst is required for installation (we are a python fronted for it)
Regarding the issues with the tests, we will carefully look into these: it is possible that new breaking versions have been released in the past few months (all of the tests were passing on our CI as of our last release). We really should have a scheduled GitHub Action that regularly runs our CI tests, we will add this in due course.

@diehlpk what is the procedure going forward? Do we make the requested changes and then come back here for a re-review?

diehlpk · 2022-06-27T12:00:11Z

@jfowkes yes, you do all the requested changes and ping the reviewer here on GitHub.

If you need clarification, you will ask him here as well.

stsievert · 2022-06-29T01:52:12Z

Regarding the issues with the tests, we will carefully look into these: it is possible that new breaking versions have been released in the past few months (all of the tests were passing on our CI as of our last release). We really should have a scheduled GitHub Action that regularly runs our CI tests, we will add this in due course.

'scuse me, I mean that some files in the examples/ directory raise errors (e.g., examples/test_cutest_full.py). All these files were added 4 years ago. The fact that two useful examples (e.g., examples/solve_rosenbrock.py) still run successfully is rather impressive.

jonjoncardoso · 2022-07-01T15:39:17Z

@editorialbot commands

diehlpk · 2022-10-23T20:24:58Z

@jfowkes

I have some minor editorial comments on the paper:

With over 12,000 downloads we firmly believe , please add something like at the time this paper was written or by 2022 to make it clear when this amount was measured.
PyCUTEst has had over 12,000 downloads, and we believe is well on please see above.

Please address these timely, so we can publish the paper next week.

After you addressed these comments, please do the following:

Generate a new release including all changes done during the review and post the number here.
Please upload that release to Zenodo or FigShare and post the DOI here. Note that the title and authors of the archive have to be consitent with the paper.

jfowkes · 2022-10-24T09:21:06Z

@editorialbot generate pdf

editorialbot · 2022-10-24T09:22:36Z

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

jfowkes · 2022-10-24T15:34:11Z

@diehlpk thank you, I have addressed the minor editorial comments in the paper.

We have also released a new version (Version 1.4) with all the changes.

This has been uploaded to Zenodo under the following DOI:
10.5281/zenodo.7244291

diehlpk · 2022-10-24T20:19:28Z

@editorialbot set 10.5281/zenodo.7244291 as archive

editorialbot · 2022-10-24T20:19:30Z

Done! Archive is now 10.5281/zenodo.7244291

diehlpk · 2022-10-24T20:20:29Z

@editorialbot set v1.4 as version

editorialbot · 2022-10-24T20:20:30Z

Done! version is now v1.4

diehlpk · 2022-10-24T20:20:48Z

@editorialbot recommend-accept

editorialbot · 2022-10-24T20:20:49Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-10-24T20:20:58Z

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

OK DOIs

- 10.1145/200979.201043 is OK
- 10.1145/962437.962439 is OK
- 10.1007/s10589-014-9687-3 is OK
- 10.5281/zenodo.1188851 is OK
- 10.1137/15M1020575 is OK

MISSING DOIs

- None

INVALID DOIs

- None

diehlpk · 2022-10-24T20:22:10Z

@jfowkes Thanks, I can now recommend the paper for publication.

editorialbot · 2022-10-24T20:22:43Z

👋 @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#3643, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2022-10-25T12:02:46Z

@jfowkes - I'm the track editor who will accept and publish this paper. I have a few minor changes that I've suggested in jfowkes/pycutest#35 - please merge this or let me know what you disagree with, then we can complete the process.

jfowkes · 2022-10-25T12:07:02Z

@danielskatz thank you very much, I have merged your minor changes.

danielskatz · 2022-10-25T12:25:01Z

@editorialbot recommend-accept

editorialbot · 2022-10-25T12:25:02Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-10-25T12:25:31Z

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

OK DOIs

- 10.1145/200979.201043 is OK
- 10.1145/962437.962439 is OK
- 10.1007/s10589-014-9687-3 is OK
- 10.5281/zenodo.1188851 is OK
- 10.1137/15M1020575 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-10-25T12:27:04Z

👋 @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#3644, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2022-10-25T12:30:01Z

@editorialbot accept

editorialbot · 2022-10-25T12:30:03Z

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

editorialbot · 2022-10-25T12:34:18Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-10-25T12:34:19Z

🚨🚨🚨 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.04377 joss-papers#3645
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04377
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2022-10-25T12:40:08Z

Congratulations to @jfowkes (Jaroslav Fowkes) and co-authors!!

And thanks to @stsievert and @jonjoncardoso for reviewing, to @diehlpk for editing!

We couldn't do this without you

editorialbot · 2022-10-25T12:40:10Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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editorialbot added Python review Shell TeX labels May 5, 2022

editorialbot assigned diehlpk May 5, 2022

editorialbot mentioned this issue May 5, 2022

[PRE REVIEW]: PyCUTEst: an open source Python package of optimization test problems #4271

Closed

editorialbot assigned jonjoncardoso Jun 20, 2022

jfowkes mentioned this issue Jun 28, 2022

Update docs and CI tests jfowkes/pycutest#23

Merged

7 tasks

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 24, 2022

editorialbot added accepted published Papers published in JOSS labels Oct 25, 2022

danielskatz closed this as completed Oct 25, 2022

editorialbot mentioned this issue Aug 23, 2024

[PRE REVIEW]: PySLSQP: A transparent Python package for the SLSQP optimization algorithm modernized with utilities for visualization and post-processing #7138

Closed

[REVIEW]: PyCUTEst: an open source Python package of optimization test problems #4377

[REVIEW]: PyCUTEst: an open source Python package of optimization test problems #4377

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Review checklist for @stsievert

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Software paper

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