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[REVIEW]: ChemPy: A package useful for chemistry written in Python #565
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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 🎉. ⭐ Important ⭐ If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿 To fix this do the following two things:
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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 |
@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. |
@bryanwweber I noticed a few unchecked boxes above—are those issues related to the bjodah/chempy#80 and bjodah/chempy#81 issues you filed? |
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). |
@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. |
@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: |
@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. |
Hi @bryanwweber have you been able to complete your review? |
@kyleniemeyer @bjodah Sorry! This fell off my radar. I'll try finish ASAP |
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? |
@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 |
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? |
@whedon generate pdf |
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PDF failed to compile for issue #565 with the following error: Can't find any papers to compile :-( |
@whedon generate pdf |
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This LGTM now, what do I need to do to approve? |
I've tagged a new version (v0.6.6) and updated |
Hi @bjodah, just a few comments on the paper:
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To address openjournals/joss-reviews#565 (comment) - Comma after 'e.g.' - Changed PuLP citation to a 'misc' entry (with some precedence in google scholar) - Added city and country to 'affiliation' in codemeta.json
@whedon generate pdf |
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PDF failed to compile for issue #565 with the following error: % Total % Received % Xferd Average Speed Time Time Time Current 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 |
@whedon generate pdf |
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@kyleniemeyer thanks! |
@bjodah I made a few more in bjodah/chempy#90, please merge that and then archive the repo to get a DOI |
@kyleniemeyer thanks again. Merged, tagged & updated codemeta.json with new tag & DOI. |
@whedon set 10.5281/zenodo.1212469 as archive |
OK. 10.5281/zenodo.1212469 is the archive. |
@arfon this paper is now ready to accept. |
@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 ⚡ 🚀 💥 |
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That's great. Thank you all! |
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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