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[REVIEW]: pyscses - a python space charge site explicit solver #1209

Closed whedon closed 5 years ago

whedon commented 5 years ago

Submitting author: @georgiewellock (Georgina Wellock) Repository: https://github.com/bjmorgan/pyscses Version: v1.0.0 Editor: @labarba Reviewer: @ncclementi, @vyasr Archive: 10.5281/zenodo.2599955

Status

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Markdown: [![status](http://joss.theoj.org/papers/803ed6dd19f453819bdd3ed9ceadf3b3/status.svg)](http://joss.theoj.org/papers/803ed6dd19f453819bdd3ed9ceadf3b3)

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) 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

@ncclementi & @vyasr, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @labarba know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @ncclementi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @vyasr

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

georgiewellock commented 5 years ago

Regarding the tests:

  1. I wasn't able to run the notebooks, I got an error since the folder generated_outputs doesn't exist. You should create this directory before the numpy.savetxt() line.

A check has been added for the generated_outputs directory and creates it if it doesn't exist in commit: https://github.com/bjmorgan/pyscses/commit/74af68b52c91ba9e955ef918f8b6081bb86acec4

  1. In the notebooks I'd add a header line that tells me what is this test about and how long it'll take to run. Similar to what you did in the examples.

Descriptions and approximate run times have been added to each test notebook and the associated README in commit: https://github.com/bjmorgan/pyscses/commit/6590f8cbd0b72866a67901b0211d1565207cde0f

ncclementi commented 5 years ago

Added a comment on the paragraph regarding the tests https://github.com/bjmorgan/pyscses/commit/6590f8cbd0b72866a67901b0211d1565207cde0f#r32824525

georgiewellock commented 5 years ago

I have rephrased the paragraph in commit https://github.com/bjmorgan/pyscses/commit/9e1865db501d23eb946651fb5545c751ae6ff204

ncclementi commented 5 years ago

Test notebooks now run properly. I have nothing else to add or request on my end. Great job @bjmorgan and @georgiewellock

labarba commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

labarba commented 5 years ago

Editorial fixes:

¶2 typo: obtined >> obtained

page 2: comma after "i.e."

"a range of numerical models" ... did you mean what follows to be a bulleted list? If not, delete the hyphens and numerate in-sentence. If yes, work on the formatting. (But I think it will look better as a bulleted list.) Same for next paragraph.

bjmorgan commented 5 years ago

Editorial fixes:

¶2 typo: obtined >> obtained

page 2: comma after "i.e."

"a range of numerical models" ... did you mean what follows to be a bulleted list? If not, delete the hyphens and numerate in-sentence. If yes, work on the formatting. (But I think it will look better as a bulleted list.) Same for next paragraph.

Typos and formatting updated: https://github.com/bjmorgan/pyscses/commit/580f4ae8aa64efc65e74acd9b8c811221d796aa3.

labarba commented 5 years ago

Great. It's now time to make a tagged release (report release number here) and make an archive of the software in Zenodo (or similar service). Make sure to manually edit the Zenodo metadata so the title and author list matches the JOSS paper, then report the archive DOI here.

bjmorgan commented 5 years ago

Version number bumped to 1.0.0 and released (also updated on PyPI). The Zenodo doi for this version is 10.5281/zenodo.2599955.

labarba commented 5 years ago

@whedon set v1.0.0 as version

whedon commented 5 years ago

OK. v1.0.0 is the version.

labarba commented 5 years ago

@whedon set 10.5281/zenodo.2599955 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.2599955 is the archive.

labarba commented 5 years ago

@whedon accept

whedon commented 5 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 5 years ago 

OK DOIs

- 10.1371/journal.pcbi.1003285 is OK
- 10.1016/j.ssi.2013.04.008 is OK
- 10.1063/1.3681169 is OK
- 10.1016/j.pmatsci.2005.07.001 is OK
- 10.1016/0167-2738(81)90017-5 is OK
- 10.1016/j.pmatsci.2015.01.001 is OK
- 10.1016/j.jpowsour.2018.04.022 is OK
- 10.1002/bbpc.198400007 is OK
- 10.1016/0022-3697(85)90172-6 is OK
- 10.1016/S0167-2738(98)00502-5 is OK
- 10.1016/0167-2738(96)00316-5 is OK
- 10.1016/S0167-2738(02)00229-1 is OK
- 10.1149/1.1507597 is OK
- 10.1063/1.117366 is OK
- 10.1016/0079-6786(95)00004-E is OK
- 10.1016/j.ssi.2011.07.001 is OK
- 10.1002/fuce.201200071 is OK
- 10.1016/j.ssi.2016.10.010 is OK
- 10.1002/0470020229.ch1 is OK
- 10.1039/B300170A is OK
- 10.1023/A:1009998114205 is OK
- 10.1039/C6CP02177H is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/564

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/564, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
labarba commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 5 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/565
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01209
  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...

labarba commented 5 years ago

Congratulations, @bjmorgan and @georgiewellock — your JOSS paper is published!

With huge thanks to our reviewers: @ncclementi, @vyasr — we couldn't do this without you 🙏

whedon commented 5 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01209/status.svg)](https://doi.org/10.21105/joss.01209)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01209">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01209/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01209/status.svg
   :target: https://doi.org/10.21105/joss.01209

This is how it will look in your documentation:

DOI

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bjmorgan commented 5 years ago

Our thanks as well to @ncclementi and @vyasr. Very helpful, thoughtful reviewing.