Closed whedon closed 6 years ago
Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @tshu it looks like you're currently assigned as the reviewer for this paper :tada:.
:star: Important :star:
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:
For a list of things I can do to help you, just type:
@whedon commands
Attempting PDF compilation. Reticulating splines etc...
@dhhagan this is where the review takes place. My colleague @tshu has the device and will start review shortly.
Hi @dhhagan your references field in the paper appears empty. Can you check this out? If you make changes to the paper and want to re-generate the pdf here you can also use:
@whedon generate pdf
Let me know if you have questions.
@Kevin-Mattheus-Moerman Interesting - I thought they were supposed to be somehow pulled from the bib file? I tried copying over from some accepted repositories; is there an easy way to pull them in this way?
@dhhagan - you need to cite them directly for them to be included in the compilation. (You can read how to do that here)
@dhhagan Thanks for your submission. I should be able to finish this end of week so long as there are no major roadblocks. I will keep you posted if there are any.
@whedon commands
Here are some things you can ask me to do:
# List all of Whedon's capabilities
@whedon commands
# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer
# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer
# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer
# List of editor GitHub usernames
@whedon list editors
# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers
# Change editorial assignment
@whedon assign @username as editor
# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive
# Open the review issue
@whedon start review
🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧
# Compile the paper
@whedon generate pdf
@Kevin-Mattheus-Moerman @arfon Is there a way to update the version number being reviewed? Since it's been a while since submission, the software is now at v1.6 as opposed to 1.4.1.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@arfon Is there a way to locally generate the pdf to validate the references show up? It seems like there must be an error with the BibTex syntax, but I can't seem to figure out what's going on. Is there any output from the @whedon generate pdf
command?
@dhhagan does this help? https://github.com/greatfireball/docker_whedon_translate4joss
This is the command that Whedon executes to compile the PDF.
@dhhagan I've added issues #68-70 at https://github.com/dhhagan/py-opc/issues. In addition to these, the pypi package version is 1.5.0 as listed on the repository while the review sheet is still at 1.4.1. I have updated the review sheet so that we are considering 1.5.0. Finally, the references in the paper.md
are still in the wrong location.
Once the issues are addressed, I'll be happy to finish checking off the boxes.
@tshu Thanks for the help! I have fixed most of the concerns and will merge/push later today. I am still trying to figure out what is wrong with the references - seems to be a syntax error somewhere in paper.bib
. Also, the final version with changes you suggested will be at v1.6.1
. Is that an issue?
@dhhagan in relation to the release/version number. This is no problem. We can update the version number at a later stage.
@whedon generate pdf
@dhhagan Everything looks good. Once I can check the pdf for fixed references, my review will be complete.
@Kevin-Mattheus-Moerman whedon isn't working?
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
hmm perhaps only authors and editors can call whedon like that. Anyway the PDF is now regenerated.
Thanks @tshu I'll try and figure out what's wrong with the papers.bib
file a bit later today...not sure what's going on there.
@dhagan did you try building the paper locally to trouble shoot this? perhaps remove the references and add a sigle bib file entry at a time to try to figure out what is going on.
The issue here is that you're not actually citing your references in the paper.md
file which means they aren't included by Pandoc. Can you cite them directly please? (You can read how to do that here)
\hijack-thread-on
@arfon - can we provide some guidance on this in our docs? (which maybe just means pointing to the link you provided as part of a "how to write a JOSS paper and include references" section)
\hijack-thread-off
So @dhhagan it looks like you need to cite them inline in the text e.g. like:
Bla bla @py_usbiss and bla bla @py_spidev, bladibla @alphasense_opcn2.
Please also specifically cite the Crilley et al. article that is in review, this way it also appears in the reference list.
@arfon - can we provide some guidance on this in our docs? (which maybe just means pointing to the link you provided as part of a "how to write a JOSS paper and include references" section)
@danielskatz - we already having this in the example paper.md
here: http://joss.theoj.org/about#author_guidelines but perhaps we could make this more obvious?
[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html)
format.```
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@arfon @Kevin-Mattheus-Moerman Thanks for the help - I didn't notice the individual citations throughout the abstract the first time around - I assumed it was just including the line bibliography: paper.bib
. Regardless, it should be good now. Thanks!
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@dhhagan great it looks like we are nearly there. @dhhagan
1) About the citation for doceme 2015
, the author name field is a github name. Perhaps this is okay but it would be nice if we could replace this by a human name. I cannot see the name of this author either so perhaps we are forced to do it that way. @doceme How can we best cite you here?
@arfon
1) Do you know if the citations (doceme 2015, Tolmie (2016))
render okay? Seems inconsistent to have name date
and name (date)
like that, it seems to mix two formats? Or is that normal for our reference format, like one is rendered as a url accessed on a particular data and the other is an article citation?
2) For some reason all references in this paper have the date in them twice. Is this normal? Other papers do not seem to have it like that. I did notice that there is a year
field as well as a urldate
field in 3 of the 4 references but the 4th reference does not have that...
I just added my name (Stephen Caudle) to my profile. Feel free to use that.
@dhhagan @doceme wow this open peer review thing really works well eh: :rocket: :robot:
@Kevin-Mattheus-Moerman Open FTW!
@doceme thanks for "improving" your profile. Also, as a tip, and if you care (academics tend to) you could consider following these steps to create a citable DOI for your work: https://guides.github.com/activities/citable-code/. That way there is a common and permanent citable object. If you decide to do this and do it really soon let me know and we can add the DOI in the citation of the paper here. If not no worries then we'll leave it as is.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
Nice @dhhagan. Now I'll just wait for @arfon to weigh in on my questions about those references but other than that we are in good shape.
@Kevin-Mattheus-Moerman Done.
Do you know if the citations (doceme 2015, Tolmie (2016)) render okay? Seems inconsistent to have name date and name (date) like that, it seems to mix two formats? Or is that normal for our reference format, like one is rendered as a url accessed on a particular data and the other is an article citation?
This can be fixed by citing the papers like this [@py_spidev; @py_usbiss]
For some reason all references in this paper have the date in them twice. Is this normal? Other papers do not seem to have it like that. I did notice that there is a year field as well as a urldate field in 3 of the 4 references but the 4th reference does not have that...
I think this is because these are type online
. The Crilley:2018
reference should be article
type which will remove the extra date.
@whedon generate pdf
Submitting author: @dhhagan (David Henry Hagan) Repository: https://github.com/dhhagan/py-opc Version: v1.6.0 Editor: @Kevin-Mattheus-Moerman Reviewer: @tshu Archive: 10.5281/zenodo.1299205
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@tshu, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.
Review checklist for @tshu
Conflict of interest
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Software paper
paper.md
file include a list of authors with their affiliations?