[REVIEW]: ThermoFun: A C++/Python library for computing standard thermodynamic properties of substances and reactions across wide ranges of temperatures and pressures

[editorialbot]

Submitting author: @gdmiron (George Miron)
Repository: https://github.com/thermohub/thermofun
Branch with paper.md (empty if default branch): paper
Version: v0.4.2
Editor: @lucydot
Reviewers: @hgandhi2411, @fnattino
Archive: 10.5281/zenodo.7614065

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/6b76d3c12421312f309b515e8b259dc0/status.svg)](https://joss.theoj.org/papers/6b76d3c12421312f309b515e8b259dc0)

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

@darinddv & @hgandhi2411, 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 @lucydot 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 @hgandhi2411

📝 Checklist for @fnattino

[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.1007/s10596-012-9310-6 is OK
- 10.1155/2019/5750390 is OK
- 10.1016/j.gca.2020.07.020 is OK
- 10.1515/pac-2016-1107 is OK
- 10.1016/j.advwatres.2016.08.008 is OK
- 10.1016/j.gca.2016.04.026 is OK
- 10.2475/07.2017.01 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.47 s (164.9 files/s, 465886.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            27              3              0         650808
C++                             79           3921           2566          17303
C/C++ Header                    66           1766           2129           4414
Python                           9             75            134            404
CMake                           20            114            188            381
Markdown                         5            148              0            362
ProGuard                        10            171             92            313
Bourne Shell                    12             57             17            226
YAML                             6             37             44            131
TeX                              1              3              0             98
Jupyter Notebook                 2              0            407             50
DOS Batch                        5              7             34             34
INI                              1              1              0              5
-------------------------------------------------------------------------------
SUM:                           243           6303           5611         674529
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2184

[editorialbot]

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

[hgandhi2411]

Review checklist for @hgandhi2411

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/thermohub/thermofun?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@gdmiron) 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

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?

[lucydot]

A quick note to say I am holiday for one week - will be back 20th August.

[lucydot]

@darinddv, @hgandhi2411 do you have an update on the review?

@darinddv your first task is to generate a checklist - instructions at the top of the thread.

@hgandhi2411 I can see you have started ticking through the checklist. You do not need to post comments / thoughts after completing the full review - reviews tend to work best when it is an on-going discussion. So if there is something you spot now that could be fixed by the authors, please do post it now (raising an issue on the software repo if it is not something tiny like a typo or similar).

[lucydot]

@darinddv, @hgandhi2411 - let me know if I can help with anything - if you are unable to make progress on the review right now, an idea for your expected timeline would be useful.

[hgandhi2411]

@lucydot Thanks for your patience. I will be done with my review by September 15th. As suggested, I will post my comments as I make progress.

[lucydot]

Hello @hgandhi2411 , @darinddv - how are your reviews going? Please let me know if you have any questions about the process. An indication of the timeline you are working to would be useful.

@darinddv are you still able to review this submission? I can see that you have not generated the checklist yet - let me know if you have any questions.

[gdmiron]

@lucydot Hello everybody. How can we proceed with the review? Do you need some support from my side?

[lucydot]

@gdmiron I've just emailed the reviewers @darinddv @hgandhi2411 - if no response within the next week we'll make an alternative plan - Lucy

[hgandhi2411]

@lucydot @gdmiron Sorry about the delay. I'll finish the review soon, give me until the end of October. Thanks for your patience.

[lucydot]

@gdmiron I haven't heard anything from @darinddv so will start looking for alternative reviewers - if you can suggest anyone it would be appreciated.

Thanks for the update @hgandhi2411

[lucydot]

@paleolimbot @alejandrogallo @fnattino do any of you have time to review this? (apologies for re-asking - your previous replies in the pre-review are noted! - our original reviewer seems to be no longer available)

[gdmiron]

@lucydot some potential reviewers I found by searching the list of reviewers usernames: vidalgp, sgrieve, bobmyhill, yes, (espottesmith) - has an active review. reviewers list.

[fnattino]

Hi @lucydot, apologies for not having answered earlier. I could review the manuscript in a time frame of ~2 weeks - would that work?

[lucydot]

@fnattino , yes it would - that would be perfect 👍 - I'll add you as a reviewer now.

@gdmiron thanks for the suggestions.

@hgandhi2411 a friendly reminder prompt for your review

[lucydot]

@editorialbot add @fnattino as reviewer

[editorialbot]

@fnattino added to the reviewers list!

[editorialbot]

Done! Archive is now 10.5281/zenodo.7614065

[lucydot]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1021/acs.iecr.2c00237 is OK
- 10.1007/s10596-012-9310-6 is OK
- 10.1155/2019/5750390 is OK
- 10.1016/j.gca.2020.07.020 is OK
- 10.1515/pac-2016-1107 is OK
- 10.1016/j.advwatres.2016.08.008 is OK
- 10.1016/j.gca.2016.04.026 is OK
- 10.2475/07.2017.01 is OK
- 10.1016/0098-3004(92)90029-Q is OK
- 10.1016/j.cageo.2016.02.013 is OK
- 10.1016/j.chemgeo.2022.120984 is OK
- 10.3389/feart.2019.00180 is OK
- 10.48550/ARXIV.2105.14096 is OK
- 10.1021/acs.iecr.2c01427 is OK
- 10.1021/ie4033999 is OK
- 10.21105/joss.04757 is OK
- 10.1515/pac-2016-1107 is OK
- 10.5281/zenodo.6387882 is OK
- 10.5281/zenodo.6527840 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

ID ref-Leal2017 already defined

[lucydot]

This review started pre-tracks but I'll ping @openjournals/pe-eics to flag up the error above...

[xuanxu]

The error happens because there are two different bib entries with the same name (Leal2017): here and here

[gdmiron]

@lucydot I removed the duplicate bib entry.

[lucydot]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

👋 @openjournals/pe-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#3994, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[editorialbot]

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

OK DOIs

- 10.1021/acs.iecr.2c00237 is OK
- 10.1007/s10596-012-9310-6 is OK
- 10.1155/2019/5750390 is OK
- 10.1016/j.gca.2020.07.020 is OK
- 10.1515/pac-2016-1107 is OK
- 10.1016/j.advwatres.2016.08.008 is OK
- 10.1016/j.gca.2016.04.026 is OK
- 10.2475/07.2017.01 is OK
- 10.1016/0098-3004(92)90029-Q is OK
- 10.1016/j.cageo.2016.02.013 is OK
- 10.1016/j.chemgeo.2022.120984 is OK
- 10.3389/feart.2019.00180 is OK
- 10.48550/ARXIV.2105.14096 is OK
- 10.1021/acs.iecr.2c01427 is OK
- 10.1021/ie4033999 is OK
- 10.21105/joss.04757 is OK
- 10.5281/zenodo.6387882 is OK
- 10.5281/zenodo.6527840 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kyleniemeyer]

Hi @gdmiron, just doing final checks on the paper before publishing.

One quibble in the Statement of Need:

It requires the standard thermodynamic properties of all involved substances (species) or reactions at a specific temperature (T) and pressure (P) as input.

This isn't technically true in general, since the thermodynamic modeling can also use equations of state that relate intensive properties. Could you edit to be more generally correct, versus what specifically applies to your software package?

[gdmiron]

@kyleniemeyer thanks for making the final check.

This part is related to the previous statement

Thermodynamic modeling is a powerful tool that allows for the investigation of equilibrium speciation in chemical systems under conditions and time scales that cannot be reached in laboratory settings. It requires the standard thermodynamic properties of all involved substances (species) or reactions at a specific temperature (T) and pressure (P) as input.

Then the following text refers to "the investigation of equilibrium speciation in chemical systems" for which these properties are required.

To make it more clear, should I change the text to the example below, or just change "It requires" with "This requires"

Thermodynamic modeling is a powerful tool that allows for the investigation of equilibrium speciation in chemical systems under conditions and time scales that cannot be reached in laboratory settings. For this type of calculation, it requires the standard thermodynamic properties of all involved substances (species) or reactions at a specific temperature (T) and pressure (P) as input.

[kyleniemeyer]

@gdmiron ah, that makes more sense. How about just "This type of calculation requires" for the second sentence?

[gdmiron]

@kyleniemeyer made the fix in the paper branch

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

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

[kyleniemeyer]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04624 joss-papers#4009
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04624
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

Congratulations @gdmiron on your article's publication in JOSS!

Many thanks to @hgandhi2411 and @fnattino for reviewing this, and @lucydot for editing.

[editorialbot]

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

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