[REVIEW]: ChemPy: A package useful for chemistry written in Python

[whedon]

Submitting author: @bjodah (Björn Dahlgren)
Repository: github.com/bjodah/chempy
Version: v0.6.3
Editor: @kyleniemeyer
Reviewer: @bryanwweber
Archive: 10.5281/zenodo.1212469

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• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (v0.6.3)?
• Authorship: Has the submitting author (@bjodah) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @bryanwweber it looks like you're currently assigned as the reviewer for this paper 🎉.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #565 with the following error: 

 Can't find any papers to compile :-(

[kyleniemeyer]

here is the initial version of the compiled paper: https://github.com/openjournals/joss-papers/blob/joss.00552/joss.00552/10.21105.joss.00552.pdf

[bryanwweber]

@bjodah Since this comment is related more to the paper than to the software, I'll put it here. You should specify the target audience for the software - is it undergraduates doing homework problems, research scientists, government agencies, teachers, etc.

[kyleniemeyer]

@bryanwweber I noticed a few unchecked boxes above—are those issues related to the bjodah/chempy#80 and bjodah/chempy#81 issues you filed?

[bjodah]

Sorry, I haven't addressed those yet. @bryanwweber pointed out that I don't provide conda packages for all platforms (only Linux). So I have been working on trying to support all (optional) dependencies of ChemPy for both OS X and Windows, but since many of them needs to be compiled with quite recent C++ features that endeavor quickly turned into a real rabbit hole.

I think I will just do what @bryanwweber suggested and clearly state that Linux is currently the "officially supported" platform, and then I'll continue to work on adding support for more platforms at a later stage. (I know people have gotten many things to work on OS X and windows using pip so it is doable but I don't have any computers with those systems for testing at the moment).

[kyleniemeyer]

@bjodah ok—regarding the platform issue, that seems reasonable as long as you are clear. If you do limit the conda route to Linux, then it would be helpful to explain how the package can be installed/used on other platforms.

[kyleniemeyer]

@arfon FYI, the Repository link above seems to have some extra junk prepended on it, not sure if that has already been fixed in whedon: https://github.com/openjournals/joss-reviews/issues/www.github.com/bjodah/chempy instead of www.github.com/bjodah/chempy

[bryanwweber]

@kyleniemeyer @bjodah The two about the "Statement of Need" are related to my comment on this issue: #565 (comment) The installation instructions are covered by the two issues in the ChemPy repository (and I'm satisfied with the response to them generally, which I'll mark on those two issues). The last one is the functionality testing, which is on me, I didn't get a chance to do that yet, will do so ASAP.

[kyleniemeyer]

Hi @bryanwweber have you been able to complete your review?

[bryanwweber]

@kyleniemeyer @bjodah Sorry! This fell off my radar. I'll try finish ASAP

[bjodah]

The second entry in the references in https://github.com/openjournals/joss-papers/blob/joss.00552/joss.00552/10.21105.joss.00552.pdf does not render properly. Any idea what's going wrong there?

[kyleniemeyer]

@bjodah the reference style we use avoids repeating the same author name multiple times in a row, so the line is just to indicate the same author as the reference before it

[bryanwweber]

I'm satisfied that the package functions as specified, with the exception of an error in one of the demo scripts (linked above, issue on chempy repo). However, the paper appears to have not been updated with the target audience, as suggested in the review criteria, and as I noted in #565 (comment) Is there an updated version of the paper I missed?

[bjodah]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #565 with the following error:

Can't find any papers to compile :-(

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[bryanwweber]

This LGTM now, what do I need to do to approve?

[bjodah]

(I updated the paper with 2 new references since a PR was merged in between with fixes that added PuLP as a dependency)

[bjodah]

I've tagged a new version (v0.6.6) and updated joss-paper/codemeta.json with the new version number and the new zenodo doi.

[kyleniemeyer]

Hi @bjodah, just a few comments on the paper:

• Could you add the city and country to your affiliation?
• Could you put commas around the "e.g." in the second, third, and last paragraphs?
• Reference mitchell2011pulp does not have correct bibliographic information (Citeseer is not a journal); I'm not sure what the correct info should be though... perhaps it is a conference paper, as suggested at https://www.semanticscholar.org/paper/PuLP%3A-A-Linear-Programming-Toolkit-for-Python-Mitchell-Consulting/24c9ad0d66f6a05ad41563a7dade60bff6f59106 ?
• in the last paragraph, I think you need a semicolon in the combined citation [@mitchell2011pulp,@lougee2003common]

[bjodah]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #565 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 15 0 15 0 0 108 0 --:--:-- --:--:-- --:--:-- 109
Error reading bibliography ./paper.bib (line 70, column 3):
unexpected "y"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[bjodah]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[bjodah]

@kyleniemeyer thanks!
I (hopefully) fixed the points you raised. Let me know if you want me to change anything else.

[kyleniemeyer]

@bjodah I made a few more in bjodah/chempy#90, please merge that and then archive the repo to get a DOI

[bjodah]

@kyleniemeyer thanks again. Merged, tagged & updated codemeta.json with new tag & DOI.

[kyleniemeyer]

@whedon set 10.5281/zenodo.1212469 as archive

[whedon]

OK. 10.5281/zenodo.1212469 is the archive.

[kyleniemeyer]

@arfon this paper is now ready to accept.

[arfon]

@bryanwweber - many thanks for your review here and to @kyleniemeyer for editing this submission ✨

@bjodah - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00565 ⚡ 🚀 💥

[whedon]

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

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[bjodah]

That's great. Thank you all!