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[REVIEW]: PyCUTEst: an open source Python package of optimization test problems
Submitting author: @jfowkes (Jaroslav Fowkes) Repository: https://github.com/jfowkes/pycutest Branch with paper.md (empty if default branch): Version: 1.2 Editor: @diehlpk Reviewers: @stsievert, @jonjoncardoso Archive: Pending
Status
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HTML: <a href="https://joss.theoj.org/papers/d1664af7c708cd78b5478beaa27878e6"><img src="https://joss.theoj.org/papers/d1664af7c708cd78b5478beaa27878e6/status.svg"></a>
Markdown: [](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:
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diehlpk know.
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Checklists
📝 Checklist for @jonjoncardoso
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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
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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
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Review checklist for @stsievert
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/jfowkes/pycutest?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [x] (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?
- [x] 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
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] (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
- [x] (added) 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] (added) 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?
Sorry @diehlpk; my deadline just passed. I will complete my review before Monday June 20.
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.
I could volunteer to review this one if needed
@jonjoncardoso that would be great, I will invite you soon.
@diehlpk fyi I am finally getting around to reviewing this after a (too long) delay.
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 https://github.com/openjournals/joss-reviews/issues/4377#issuecomment-1118435375. 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)
@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?
@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.
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.
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Review checklist for @jonjoncardoso
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/jfowkes/pycutest?
- [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 (@jfowkes) 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, who the target audience is, and its relation to other work?
- [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?
'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.
Ah I see, thank you. I will investigate. It looks like these are old leftover tests that should be removed.
@diehlpk @jonjoncardoso @stsievert we have now made all the requested changes, could you please re-review?
Please see the PR jfowkes/pycutest#23 for the full changelist (in particular I have removed the ancient test files from the examples/ directory and added and documented another useful usage example solve_arglale.py).
Thanks @jfowkes. I had put off reviewing as I noticed you were addressing previous comments. I will send in my review later this week.