[REVIEW]: EXP: a Python/C++ package for basis function expansion methods in galactic dynamics

[editorialbot]

Submitting author: @michael-petersen (Michael Petersen)
Repository: https://github.com/EXP-code/EXP
Branch with paper.md (empty if default branch):
Version: v7.7.99
Editor: @dfm
Reviewers: @schuhmaj, @pmocz
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/869a8ce345b8756b1235b1b32986794f/status.svg)](https://joss.theoj.org/papers/869a8ce345b8756b1235b1b32986794f)

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

@schuhmaj, 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 @dfm 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 @schuhmaj

📝 Checklist for @pmocz

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.51 s (1357.7 files/s, 440942.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                            346          28410          15821         103143
C/C++ Header                   259           9115           9838          24907
CUDA                            15           2467           1802           8525
Fortran 77                       3             22           1646           4173
C                               21            736           1526           4073
CSS                              4            466            196           2964
XML                              3              5              7           1593
CMake                           19            308            200           1319
TeX                              2             95             16            810
HTML                             4             53             16            730
Markdown                         9            187              0            723
Python                           8            204            252            434
YAML                             3             21             58            120
Bourne Shell                     1              3              0             10
C Shell                          1              6              4              7
JSON                             1              0              0              7
-------------------------------------------------------------------------------
SUM:                           699          42098          31382         153538
-------------------------------------------------------------------------------

Commit count by author:

  4667	Martin D. Weinberg
   937	weinberg
   223	mdw
    66	Martin Weinberg
    41	michael-petersen
    28	michael_petersen
    20	jhchoi
    16	Adrian Price-Whelan
    11	Robert Blackwell
    10	r-j-arnold
     2	Becky Arnold
     1	(no author)
     1	Martin Weinberg [[email protected]]
     1	Michael
     1	arora125

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1504

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

✅ OK DOIs

- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201832865 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.21105/joss.00388 is OK
- 10.1093/mnras/stad2591 is OK
- 10.1093/mnras/staa3997 is OK
- 10.1093/mnras/stab3639 is OK
- 10.1093/mnras/stad485 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1086/300669 is OK
- 10.1109/MCSE.2007.53 is OK
- 10.3233/978-1-61499-649-1-87 is OK
- 10.3847/1538-4357/ac0b44 is OK
- 10.1086/168845 is OK
- 10.1086/171025 is OK
- 10.1086/304888 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Galactic Dynamics: Second Edition
- No DOI given, and none found for title: Hierarchical data format version 5
- No DOI given, and none found for title: pybind11 – Seamless operability between C++11 and ...
- No DOI given, and none found for title: Analysis of time series structure: SSA and related...
- No DOI given, and none found for title: Eigen v3
- No DOI given, and none found for title: CUDA, release: 10.2.89
- No DOI given, and none found for title: MPI: A Message-Passing Interface Standard Version ...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[dfm]

@schuhmaj — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate!

👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7302 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 the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible!

[editorialbot]

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

[schuhmaj]

Review checklist for @schuhmaj

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/EXP-code/EXP?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@michael-petersen) 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?

[dfm]

@editorialbot add @pmocz as reviewer

Thanks @pmocz for agreeing to be the second reviewer for this submission!!

@pmocz — Please take a look at the comments higher in this thread for more information about the review process, and don't hesitate to ask if you have any questions. Thanks again!

[editorialbot]

@pmocz added to the reviewers list!

[pmocz]

Review checklist for @pmocz

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/EXP-code/EXP?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@michael-petersen) 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?

[pmocz]

Looking good! I had trouble installing it from scratch just because I had missing libraries. The docker script works well. When I try the first tutorial example, I get an error:

Cell In[3], line 25
      9 config="""
     10 ---
     11 id: sphereSL
   (...)
     20 ...
     21 """
     23 # Construct the basis instances
     24 #
---> 25 basis = pyEXP.basis.Basis.factory(config)

RuntimeError: SphericalSL requires a specified cachename in your YAML config
for consistency with previous invocations and existing coefficient
sets.  Please add explicitly add 'cachename: name' to your config
with new 'name' for creating a basis or an existing 'name' for
reading a previously generated basis cache

which goes away if I specify a name in the config

[pmocz]

Don't know if this is helpful, but a visualization or graphic of when inputs and outputs look like somewhere in the intro docs would be helpful to quickly communicate what your code is doing

Saving figures as .svg instead of .png will also make them look more crisp on the web

[pmocz]

The Contributing guides says: cite the EXP published papers. These should be included in the github repo CITATIONS.bib file (I understand the JOSS paper will be one of them)

[dfm]

@schuhmaj — I wanted to check in with you here too. I see that you've started on your checklist, but please let us know if you run into any blockers. Thanks!

[schuhmaj]

@schuhmaj — I wanted to check in with you here too. I see that you've started on your checklist, but please let us know if you run into any blockers. Thanks!

Hey, I am sorry; I was a bit on hold due to some more urgent tasks in the last few weeks. I try to catch up here this week 👍

[dfm]

@schuhmaj — Any updates on this? Please take a look. Thanks!

[schuhmaj]

Hi - I concluded my review and I fully recommend accepting this submission into JOSS. The software is amazing. There are only two small improvements which need to be undertaken upfront so that I can checkmark the last two items from the list.

• [JOSS REVIEW] Add comparison to commonly used N-Body Codes into the Paper EXP-code/EXP#97
  • The paper does currently not compare its implementation to other well-known packages in the area, but restricts itself to presenting only dependencies.
  • Given that such a comparison exists in a referenced paper by the same authors, this should be low-effort to add
• [JOSS REVIEW] Document Dependencies Versions EXP-code/EXP#96
  • The dependencies' versions are not documented to a satisfactory level. I had a compile error witheigen 3.3.7 on one of my three testing systems, only resolvable switching to eigen 3.4 (which is not the default on Ubuntu 20.04)
  • Resolvable by either specifying the concrete versions or by embracing the CMake build system more to make the installation fully automatic (relates to [JOSS REVIEW] Improve Install Instructions/ Process EXP-code/EXP#94)

The two other opened issues are strong recommendations, but no blockers in the context of this review.

[michael-petersen]

Thanks all for the reviews! We will address these this week and get back to you.