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[REVIEW]: ThermoCodegen: a python/C++ package for the generation of custom thermodynamic models #4874

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editorialbot opened this issue Oct 23, 2022 · 66 comments
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[REVIEW]: ThermoCodegen: a python/C++ package for the generation of custom thermodynamic models #4874

editorialbot opened this issue Oct 23, 2022 · 66 comments
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accepted C++ published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Track: 3 (PE) Physics and Engineering

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editorialbot commented Oct 23, 2022 •
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Submitting author: @mspieg (Marc Spiegelman)
Repository: https://gitlab.com/ENKI-portal/ThermoCodegen
Branch with paper.md (empty if default branch): joss_paper
Version: v1.0.0
Editor: @kyleniemeyer
Reviewers: @bocklund, @rdguha1995
Archive: 10.5281/zenodo.8102054

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/776246584f3015f7ade39f695bf832fc"><img src="https://joss.theoj.org/papers/776246584f3015f7ade39f695bf832fc/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/776246584f3015f7ade39f695bf832fc/status.svg)](https://joss.theoj.org/papers/776246584f3015f7ade39f695bf832fc)

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

@bocklund & @rdguha1995, 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 @kyleniemeyer 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 @rdguha1995

📝 Checklist for @bocklund
@editorialbot editorialbot added CMake Dockerfile review Shell Track: 3 (PE) Physics and Engineering waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Oct 23, 2022
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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

@editorialbot editorialbot mentioned this issue Oct 23, 2022
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Software report:

github.com/AlDanial/cloc v 1.88  T=5.18 s (316.1 files/s, 138049.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
HTML                            292          11712              0          96861
Python                          117          21704          26527          79399
Objective-C                      88          11791           4459          78039
Jupyter Notebook                282              0         149295          50965
C                                47           2949           1084          29397
C/C++ Header                    164           4504           2697          26051
XML                             132            463            123          24774
CSS                               8            298            168           9648
JavaScript                       10           2205           2244           8371
Cython                           12            216             95           7071
Markdown                        252           2112              0           6431
reStructuredText                 95           8034          19604           5212
LESS                             48            838            961           4524
SVG                               8              2             20           4016
C++                              14            141            452           2666
TeX                               3            244             16           1460
CMake                            11            247            332            764
YAML                             10             39             59            686
Bourne Shell                     28             78             48            641
make                              5             55             40            465
Dockerfile                        4             90            121            437
Java                              1             38             37            415
Bourne Again Shell                2              7             16             30
DOS Batch                         1              8              1             27
INI                               1              0              0              8
JSON                              1              0              0              1
--------------------------------------------------------------------------------
SUM:                           1636          67775         208399         438359
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1556

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

OK DOIs

- 10.5194/gmd-2-33-2009 is OK
- 10.1029/2001GC000217 is OK
- 10.1111/j.1525-1314.1998.00140.x is OK
- 10.1111/j.1525-1314.1998.00140.x is OK
- 10.1002/2016GC006702 is OK
- 10.1007/BF00307281 is OK
- 10.1111/j.1525-1314.2010.00923.x is OK
- 10.1093/petrology/29.2.445 is OK
- 10.1111/j.1365-246X.2005.02642.x is OK
- 10.1111/j.1365-246X.2010.04890.x is OK
- 10.1111/j.1365-246X.2012.05609.x is OK
- 10.1093/gji/ggx195 is OK
- 10.5281/ZENODO.5131909 is OK
- 10.6084/M9.FIGSHARE.4865333 is OK
- 10.7916/d8-wh72-vb08 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@kyleniemeyer
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👋 @mspieg @bocklund @rdguha1995 the actual review will take place here.

Per the instructions above, when you are ready to do your review, comment with @editorialbot generate my checklist to generate your reviewer checklists.

@kyleniemeyer kyleniemeyer added Python C++ and removed waitlisted Submissions in the JOSS backlog due to reduced service mode. Shell CMake Dockerfile labels Oct 24, 2022
@rdguha1995
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rdguha1995 commented Oct 26, 2022 •
edited

Review checklist for @rdguha1995

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

General checks

  • Repository: Is the source code for this software available at the https://gitlab.com/ENKI-portal/ThermoCodegen?
  • 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 (@mspieg) 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?

@kyleniemeyer
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Hi @bocklund and @rdguha1995, just wanted to check on the status of your review. Would it be possible to wrap these up before the end of the month / year? Thanks!

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mspieg commented Dec 12, 2022 via email

@rdguha1995
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Hey Team,

Apologies for the delay. I have gone through most of the paper, but I am left with some of the functional checks. I should be able to knock them off before the break.

@rdguha1995
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Hey @mspieg , I am having some issues with the installation and I have opened an issue at the repository. Let me know what is going wrong here and I can continue the review from there.

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mspieg commented Dec 12, 2022 via email

@rdguha1995
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Hey Team,

I think I have gone over all the checklist items in the review. As mentioned in the issue I have opened in the target repository, the only sticking point I have is the convoluted interdependencies users might face if they decide to install the package locally. The docker containers are working great, which is what the advisable usage case is (as mentioned in the documentation), but it would be great if the authors can provide streamlined instructions for local installation as well in their documentation. A couple of potential suggestions from my end are:-

  1. Instructing the users to only try installing the package in a fresh conda environment
  2. Reducing the number of interdependent home-brew and pypi packages
  3. Having a requirements.txt file which can automatically install all dependencies.

Besides the complications in the installation, everything else looks good to me. Great job @mspieg and team for the comprehensive documentation and examples.

@kyleniemeyer
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Thanks @rdguha1995 for the comments!

@mspieg have you been able to take a look at the above issues?

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Hi @bocklund, do you anticipate being able to complete your review soon?

@mspieg
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mspieg commented Jan 6, 2023

Hi @kyleniemeyer,
Cian and I are discussing appropriate additions/cautions to the installation instructions. But our primary recommendation of getting started using the containers stands (and @rdguha1995 confirms that these work out of the box) as this will still probably be the most stable solution for an arbitrary users platform. We're also waiting to hear back from @Bockland. Thanks everyone for all your help.

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@editorialbot set v1.0.0 as version

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Done! version is now v1.0.0

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

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kyleniemeyer commented Jun 30, 2023 •
edited

Hi @mspieg, there is a minor issue with the Connolly 2009 reference ("n/a-n/a" as the pages). Looking at the PDF at https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2009GC002540 it seems they would like "Q10014" listed as the page number. Could you fix that?

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mspieg commented Jun 30, 2023 via email

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mspieg commented Jun 30, 2023 via email

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mspieg commented Jun 30, 2023

@editorialbot generate pdf

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

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.5194/gmd-2-33-2009 is OK
- 10.1029/2001GC000217 is OK
- 10.1111/j.1525-1314.1998.00140.x is OK
- 10.1111/j.1525-1314.1998.00140.x is OK
- 10.1002/2016GC006702 is OK
- 10.1007/BF00307281 is OK
- 10.1111/j.1525-1314.2010.00923.x is OK
- 10.1093/petrology/29.2.445 is OK
- 10.1111/j.1365-246X.2005.02642.x is OK
- 10.1111/j.1365-246X.2010.04890.x is OK
- 10.1111/j.1365-246X.2012.05609.x is OK
- 10.1093/gji/ggx195 is OK
- 10.5281/ZENODO.5131909 is OK
- 10.6084/M9.FIGSHARE.4865333 is OK
- 10.7916/d8-wh72-vb08 is OK
- 10.1093/petrology/egy048 is OK
- 10.1093/petrology/egv020 is OK
- 10.1039/FT9928800803 is OK
- 10.2475/ajs.288.1.19 is OK
- 10.1180/minmag.1996.060.398.03 is OK
- 10.2138/am-1998-9-1022 is OK
- 10.1029/2001GC000217 is OK
- 10.1093/petrology/egr080 is OK
- 10.1007/s00410-015-1141-8 is OK
- 10.2475/ajs.290.6.666 is OK
- 10.1016/j.epsl.2005.04.033 is OK
- 10.1029/2009GC002540 is OK
- 10.1111/j.1525-1314.1998.00157.x is OK
- 10.2138/am.2010.3354 is OK
- 10.1029/2021GC010303 is OK
- 10.1029/2004GC000816 is OK
- 10.1029/2022GC010427 is OK

MISSING DOIs

- Errored finding suggestions for "pybind11 – Seamless operability between C++11 and ...", please try later

INVALID DOIs

- None

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👋 @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#4365, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 30, 2023
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@editorialbot accept

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

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff 

cff-version: "1.2.0"
authors:
- family-names: Spiegelman
  given-names: Marc
  orcid: "https://orcid.org/0000-0002-5218-7466"
- family-names: Evans
  given-names: Owen
- family-names: Ghiorso
  given-names: Mark
  orcid: "https://orcid.org/0000-0002-0489-0018"
- family-names: Tweed
  given-names: Lucy
  orcid: "https://orcid.org/0009-0009-4506-2110"
- family-names: Wilson
  given-names: Cian
  orcid: "https://orcid.org/0000-0002-4083-6529"
contact:
- family-names: Spiegelman
  given-names: Marc
  orcid: "https://orcid.org/0000-0002-5218-7466"
doi: 10.5281/zenodo.8102054
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Spiegelman
    given-names: Marc
    orcid: "https://orcid.org/0000-0002-5218-7466"
  - family-names: Evans
    given-names: Owen
  - family-names: Ghiorso
    given-names: Mark
    orcid: "https://orcid.org/0000-0002-0489-0018"
  - family-names: Tweed
    given-names: Lucy
    orcid: "https://orcid.org/0009-0009-4506-2110"
  - family-names: Wilson
    given-names: Cian
    orcid: "https://orcid.org/0000-0002-4083-6529"
  date-published: 2023-06-30
  doi: 10.21105/joss.04874
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4874
  title: "ThermoCodegen: a python/C++ package for the generation of
    custom thermodynamic models"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04874"
  volume: 8
title: "ThermoCodegen: a python/C++ package for the generation of custom
  thermodynamic models"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04874 joss-papers#4366
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04874
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Jun 30, 2023
@kyleniemeyer
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Congratulations @mspieg on your article's publication in JOSS! If you haven't already, please consider signing up as a future reviewer.

On my end, I'm seeing a website error for this paper, so I'm going to leave this issue open until that resolves.

Many thanks to @bocklund and @rdguha1995 for reviewing this submission.

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mspieg commented Jun 30, 2023 via email

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@editorialbot reaccept

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Rebuilding paper!

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🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#4368

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@mspieg all looks good now!

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04874/status.svg)](https://doi.org/10.21105/joss.04874)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04874">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04874/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04874/status.svg
   :target: https://doi.org/10.21105/joss.04874

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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mspieg commented Jul 2, 2023 via email

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