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[REVIEW]: ThermoFun: A C++/Python library for computing standard thermodynamic properties of substances and reactions across wide ranges of temperatures and pressures
Submitting author: @gdmiron (George Miron) Repository: https://github.com/thermohub/thermofun Branch with paper.md (empty if default branch): paper Version: v0.3.9 Editor: @lucydot Reviewers: @darinddv, @hgandhi2411 Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/6b76d3c12421312f309b515e8b259dc0"><img src="https://joss.theoj.org/papers/6b76d3c12421312f309b515e8b259dc0/status.svg"></a>
Markdown: [](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
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
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
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Review checklist for @hgandhi2411
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/thermohub/thermofun?
- [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 (@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
- [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).
- [ ] 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?
- [ ] 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?
@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).
@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.
@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.
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.
@lucydot Hello everybody. How can we proceed with the review? Do you need some support from my side?
@gdmiron I've just emailed the reviewers @darinddv @hgandhi2411 - if no response within the next week we'll make an alternative plan - Lucy
@lucydot @gdmiron Sorry about the delay. I'll finish the review soon, give me until the end of October. Thanks for your patience.
@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
@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)
@lucydot some potential reviewers I found by searching the list of reviewers usernames: vidalgp, sgrieve, bobmyhill, yes, (espottesmith) - has an active review. reviewers list.
Hi @lucydot, apologies for not having answered earlier. I could review the manuscript in a time frame of ~2 weeks - would that work?
@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
@fnattino please generate your review checklist using the command @editorialbot generate my checklist in this discussion thread. Any questions, don't hesitate to ask.
Review checklist for @fnattino
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/thermohub/thermofun?
- [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 (@gdmiron) 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?
- [ ] 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).
- [ ] 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?
- [ ] 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?
- [ ] 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?
@fnattino @hgandhi2411 - any updates on your review? or indicative timeline for when next updates will be? ---> I'm keen to keep this review moving along..
remember, if there are any uncertainties, we can use this thread as a place for discussion..
Hi @lucydot - sorry for the delay, I will definitely complete this before the end of the week. Apologies again!
Hi @lucydot, apologies for the delay. Nice work @gdmiron! I have carried out my review and submitted my comments via the following issues:
- https://github.com/thermohub/thermofun/issues/52
- https://github.com/thermohub/thermofun/issues/53
- https://github.com/thermohub/thermofun/issues/54
- https://github.com/thermohub/thermofun/issues/55
@lucydot @gdmiron i have done my review and submitted my comments through issues. Some of them were already addressed, thanks for a quick turnaround @gdmiron
@hgandhi2411 and @fnattino Thanks for the comments, suggestions and valuable time spent on this. I will have a look in the coming days.
Thank you @hgandhi2411 and @fnattino for your time spent on the review, and for the updates.
@gdmiron - yup, it looks like you have a few things to work on. If you have any questions, please do let me know here.