[REVIEW]: CADET-Core 5.0: High-Performance Solver for Advanced Biotechnology Process Modeling

[editorialbot]

Submitting author: @lieres (Eric von Lieres)
Repository: https://github.com/cadet/CADET-Core
Branch with paper.md (empty if default branch): paper/JOSS_2024
Version: V5.0.1
Editor: @jedbrown
Reviewers: @bdice, @goxberry
Archive: Pending

Status

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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

@bdice & @goxberry, 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 @jedbrown 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 @goxberry

[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.1016/j.compchemeng.2023.108340 is OK
- 10.3390/pr8010065 is OK
- 10.1016/j.compchemeng.2018.02.025 is OK
- 10.1016/j.ces.2015.08.050 is OK
- 10.1016/j.compchemeng.2010.03.008 is OK
- 10.1016/j.compchemeng.2024.108612 is OK
- 10.2139/ssrn.4957804 is OK
- 10.1016/j.chroma.2024.464772 is OK
- 10.1016/j.chroma.2024.465512 is OK
- 10.1002/btpr.3483 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.60 s (1136.3 files/s, 457904.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                            167          16432          14906          64457
C/C++ Header                   222          15884          32621          52754
JSON                            38              0              0          18169
C                               34           5316           5796          17165
reStructuredText               115           3635           1479           6038
Bourne Shell                     5            779            817           5317
CMake                           30            683           1170           3654
Markdown                        39           1108              0           2735
Text                             6            442              0           1636
m4                               7             93             47            883
TeX                              3             73             13            725
YAML                             5             21             22            291
Python                           3             68             62            184
make                             5             15              7             47
HTML                             2              0              0             31
MATLAB                           1             11              0             28
CSS                              1              3              3              6
SVG                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                           684          44563          56943         174123
-------------------------------------------------------------------------------

Commit count by author:

   601	Samuel Leweke
    66	Jan Breuer
    50	Johannes Schmölder
    15	Eric von Lieres
    12	Lanzrath, Hannah
    11	Jayghosh Rao
    11	Ronald Jäpel
    11	r.jaepel
     7	Jazib Hassan
     4	Hannah Lanzrath
     3	William Heymann
     2	Antonia Berger
     2	Flynn Zhang
     2	WFlynnZ
     2	franzperdido
     2	ronald.jaepel
     1	Jonathan Rocher
     1	Salah Azzouzi
     1	a.berger
     1	jbreue16

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1100

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[jedbrown]

Hi, @bdice @goxberry! 👋 Welcome to JOSS and thanks for agreeing to review! The comments from @editorialbot above outline the review process, which takes place in this thread (possibly with issues filed in the CADET-Core repository). I'll be watching this thread if you have any questions.

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 this issue 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 a month or two. Please let me know if you require some more time. 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 (@jedbrown) if you have any questions/concerns.

[editorialbot]

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

[goxberry]

Review checklist for @goxberry

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/cadet/CADET-Core?
• 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 (@lieres) 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?

[goxberry]

Added cadet/CADET-Core#371 for issue tracking.

To summarize the issues in the link, I'm currently blocked on the remaining tasks because I can't install CADET-Core on macOS via the installation instructions. I can build it from source on macOS and I can run the automated unit tests, but the documented examples require Python packages (CADET-Process or CADET-Python) that link to CADET-Core and I'd rather not have to figure out how to install those from source as well. I may try later to provision a Linux VM for review, but given that the project documentation indicates support for macOS, my preference would be for the project's authors to pursue at least one of the following options:

• update their conda package to support arm64 macOS platforms
• add an example that doesn't require CADET-Python or CADET-Process to run, with some code to visualize the output (e.g., using Python with some common data science packages like h5py and matplotlib)