[REVIEW]: GCIdentifier.jl: A Julia package for identifying molecular fragments from SMILES

[editorialbot]

Submitting author: @pw0908 (Pierre Walker) Repository: https://github.com/ClapeyronThermo/GCIdentifier.jl Branch with paper.md (empty if default branch): main Version: v0.2.0 Editor: @zhubonan Reviewers: @Arrondissement5etDemi, @mjohnson541, @moyner Archive: Pending

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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

@Arrondissement5etDemi & @mjohnson541 & @moyner, 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 @zhubonan 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 @Arrondissement5etDemi

📝 Checklist for @moyner

📝 Checklist for @Arrondissement5etDemi

📝 Checklist for @moyner

📝 Checklist for @mjohnson541

[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.1021/ie00067a018 is OK
- 10.1021/acs.jcim.1c01103 is OK
- 10.1063/1.4851455 is OK
- 10.1021/acs.iecr.2c00326 is OK
- 10.1016/B978-0-444-63428-3.50017-5 is OK
- 10.1016/j.compchemeng.2020.106769 is OK
- 10.1080/00986448708960487 is OK
- 10.1021/acs.jced.0c00723 is OK
- 10.1021/ie502203w is OK
- 10.1101/2023.08.29.555352 is OK
- 10.1021/ci990427t is OK
- 10.1002/aic.690490714 is OK
- 10.1021/ci034184n is OK
- 10.5281/zenodo.10478701 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1072.9 files/s, 208945.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              0              0           4868
Julia                           19            154            142            923
Markdown                         7             60              0            284
TeX                              1             14              0            210
YAML                             5              0              5            117
TOML                             2              7              0             32
-------------------------------------------------------------------------------
SUM:                            35            235            147           6434
-------------------------------------------------------------------------------

Commit count by author:

    46	pw0908
    29	longemen3000
     6	Andrés Riedemann

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 688

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[moyner]

Review checklist for @moyner

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/ClapeyronThermo/GCIdentifier.jl?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@pw0908) 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
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [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?

[zhubonan]

Hi @Arrondissement5etDemi, @mjohnson541, @moyner Thanks again for agreeing to review this submission 👍. @Arrondissement5etDemi, @mjohnson541 please generate your checklists and get started!

It would be great to have the review done in two weeks time as this package is relative small. Please let me know if you have any problem or require a bit time. Cheers.

[Arrondissement5etDemi]

Review checklist for @Arrondissement5etDemi

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/ClapeyronThermo/GCIdentifier.jl?
• [ ] 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 (@pw0908) 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?

[Arrondissement5etDemi]

Review checklist for @Arrondissement5etDemi

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/ClapeyronThermo/GCIdentifier.jl?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@pw0908) 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
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [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?

[Arrondissement5etDemi]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[pw0908]

No clue what happened there but it looks like the pdf compiled just fine, the bot just didn't manage to link it to this issue: https://raw.githubusercontent.com/openjournals/joss-papers/joss.06453/joss.06453/10.21105.joss.06453.pdf

[Arrondissement5etDemi]

Hi Pierre,

This works, thanks a lot!

Best regards, Haina

---

From: Pierre Walker @.> Sent: Tuesday, March 12, 2024 18:39 To: openjournals/joss-reviews @.> Cc: Haina Wang @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: GCIdentifier.jl: A Julia package for identifying molecular fragments from SMILES (Issue #6453)

No clue what happened there but it looks like the pdf compiled just fine, the bot just didn't manage to link it to this issue: https://raw.githubusercontent.com/openjournals/joss-papers/joss.06453/joss.06453/10.21105.joss.06453.pdf

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/6453#issuecomment-1993038119, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKIGQVQWDPBNCIEY6KBTXDLYX6U5VAVCNFSM6AAAAABEMSGRJGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJTGAZTQMJRHE. You are receiving this because you were mentioned.

[pw0908]

No worries Haina!

[mjohnson541]

Review checklist for @mjohnson541

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/ClapeyronThermo/GCIdentifier.jl?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@pw0908) 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
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [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?

[mjohnson541]

I was unable to install on a clean Julia 1.6.7 install from conda-forge. It looks like an issue with Cairo:

Incompatible library version: libpangocairo-1.0.0.dylib requires version 11603.0.0 or later, but libcairo.2.dylib provides version 2.0.0

[mjohnson541]

As far as the documentation, on Home it claims "GCIdentifier.jl: An extensible Julia package for the modelling of fluids using thermodynamic equations of state." Which this software does not seem to do. I suspect this was accidentally copied from Clapeyron.jl. This should have a description of the software and what it can be used to do.

[pw0908]

Hi Matt!

For the home page: that is a very silly mistake! We did copy our initital documentation template from Clapeyron, but it seems we forgot to change the opening lines. We have now fixed this.

As for the installation error, are you certain of the Julia version? I've tried installing Julia 1.6.7 from conda-forge, but there is only 1.6.6, the next version up is 1.7.0. It's also strange that the tests fail on 1.6 as our automated tests include 1.6 and they've been passing. These only currently run on ubuntu so perhaps this is an issue with the OS?

[mjohnson541]

Sorry, that was a mistake, I installed Julia v1.6.5 I am on osx though, which might be relevant.

[mjohnson541]

I can try on ubuntu later.

[pw0908]

We have now added macos and windows to our tests to see if this might be the issue. (MacOS just passed its tests)

I also made a mistake: 1.6.7 is the long-term support version of 1.6. But this was the version being tested on ubuntu either way.

Update: Windows also passed.

[pw0908]

@mjohnson541 Just tried installing GCIdentifier on a clean version of Julia 1.6.5 in Ubuntu without issue. It might just be a MacOS issue (are you using an M-series mac?).

[pw0908]

@moyner @mjohnson541 @Arrondissement5etDemi Is there anything we can help with? @longemen3000 and I would be happy to assist with any issues you might be encountering during your review!

[Arrondissement5etDemi]

Hi Pierre,

I will finish the review today. Thank you!

Best regards, Haina

---

From: Pierre Walker @.> Sent: Monday, March 25, 2024 12:44 To: openjournals/joss-reviews @.> Cc: Haina Wang @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [REVIEW]: GCIdentifier.jl: A Julia package for identifying molecular fragments from SMILES (Issue #6453)

@moynerhttps://github.com/moyner @mjohnson541https://github.com/mjohnson541 @Arrondissement5etDemihttps://github.com/Arrondissement5etDemi Is there anything we can help with? @longemen3000https://github.com/longemen3000 and I would be happy to assist with any issues you might be encountering during your review!

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/6453#issuecomment-2018778273, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKIGQVW23PZGOJV6UKME6TLY2B5A7AVCNFSM6AAAAABEMSGRJGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMJYG43TQMRXGM. You are receiving this because you were mentioned.Message ID: @.***>

[Arrondissement5etDemi]

Hi Pierre,

For the software paper, could you please cite some packages with similar functionalities in other languages since they are mentioned in the paper?

Thanks!

Best regards, Haina

[Arrondissement5etDemi]

Hi Pierre,

Other than the comment above. This is a nice package with good documentation. :) Thanks!

Best regards, Haina

[moyner]

Hi, very nice and consise package. I managed to install the package and run the examples and tests. I made some PRs over in the repo for minor fixes to the docstrings. The only other comments I have:

• One could add a point to the readme on how to get support since only contribution and issues are mentioned. This is essentially adding a third point that points people to the discussions since this is activated on the repo.
• The summary section of the paper has a well-written introduction. Some of this text could improve the documentation home page, since it currently describes more "what" than "why".
• The tests pass, but give a warning Multiple combinations of groups cover all atoms. Selecting the first one.. It is possible to catch these warnings with @test_logs in Julia if desired.

These comments relate to possible improvements rather than actual issues and not blockers for publication from my end.

[pw0908]

Thank you both @Arrondissement5etDemi and @moyner for your comments! In the latests commits to GCIdentifier, we have addressed most of these issues.

For the comment relating to the tests, I haven't thought of a fix yet. They are occurring when we perform our general tests with UNIFAC where we just want to see, for a range of molecules, if the assignment is correct. We're not really testing for this warning at this stage. Do you think this warning is helpful @moyner? It is very common for there to be multiple combinations of groups to cover all atoms, it's just some of these use fewer groups total, and this is the one we pick. For example, in the case of acetone for UNIFAC, there is an acetone group, but there are also methyl and ketone groups which could also be used to represent acetone. We pick the acetone group since it represents the entire molecule with one group, but is it useful for the users to know that there is more than one possible combination? If not, then we'll suppress the warning.

[pw0908]

@editorialbot generate pdf