Joss-reviews: [PRE REVIEW]: PyBox: An automated box-model generator for atmospheric chemistry and aerosol simulations.

[whedon]

Submitting author: @loftytopping (David Topping)
Repository: https://github.com/loftytopping/PyBox
Version: v1.0.0
Editor: @lheagy
Reviewers: @dvalters, @highendcompute

Author instructions

Thanks for submitting your paper to JOSS @loftytopping. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@loftytopping if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

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

For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[arfon]

:wave: @lheagy - the submitting author suggested you as the handling editor.

[loftytopping]

Hi guys.

Great, many thanks for progressing. Ive had a look at the existing reviewers and would suggest dvalters is ideal given he covers everything PyBox is designed for. Another reviewer who is not on the list but I would suggest is Dr Michael Bane [[email protected]] as he would offer a robust critique/testing of the automated Python-to-Fortran component.

Thanks!
Dave

[lheagy]

Hi @loftytopping, thanks for your submission! I had a quick look at the repo and have a few questions for you before we start the review.

• do you have documentation hosted somewhere? Read the Docs is a widely used platform for this. Looking at the documentation and example usage is a large part of the review (you can see the review checklist on any of the active reviews, e.g. https://github.com/openjournals/joss-reviews/issues/741)
• Though not a requirement for starting the review, do you have automated testing running? It looks like you have written tests, and there are services like TravisCI which are easy to set up so that your code is tested every time a change is pushed to the repo
• For installation, do you have instructions? It is quite common to have a requirements.txt that list all of your requirements so that a user can install the dependencies using

pip install -r requirements.txt

[loftytopping]

Hey @lheagy

Thanks for all the notes. Apologies, Ive now added documentation to readthe docs and linked this in my readme.md file. I do have unit tests, but not automated. Again, sorry for the confusion and ive now changed the section heading to remove the term 'automated'.

For the installation instructions Id actually love some feedback on this. Ive listed all the dependencies and the instructions to get each installed. However I was struggling to see how I might package these up in one automated procedure. The Assimulo package, whilst commonly used and open source, has multiple methods for installation on different platforms. As noted in the instructions, I have found it best to build from source since pip can fail depending on system configurations, as can other package managers. Installation requires the user to point to their BLAS and LAPACK libraries, and Sundials solvers. The Assimulo homepage instructions work fine. In addition, once cloned, the user will need to point PyBox to their copy of UManSysProp. Details are given in the installation section. I would value reviewer comments on this for sure.

[lheagy]

Thanks @loftytopping! I will send an email to Dr. Michael Bane and see if he is willing to review. Do you have any other reviewer suggestions? Ideally, we get 2.

[loftytopping]

Hi! Great. Ok cool, can you get in touch with 'dvalters' from the current JOSS reviewers list too? This covers Python, OpenMP and the domain of interest so its perfect for PyBox if they can review :).

[lheagy]

👋 Hi @dvalters, would you be willing to review this submission for JOSS?

[dvalters]

Hi @lheagy - sure I can review

[lheagy]

Thanks @dvalters! Michael has also agreed to review - I am just waiting to get his github handle and we can get started.

[lheagy]

@whedon assign @dvalters as reviewer

[whedon]

OK, the reviewer is @dvalters

[lheagy]

@whedon add @highendcompute as reviewer

[whedon]

OK, @highendcompute is now a reviewer

[lheagy]

@whedon start review

[whedon]

You didn't say the magic word! Try this:

@whedon start review magic-word=bananas

[lheagy]

@whedon start review magic-word=bananas

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/755. Feel free to close this issue now!