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rOpenSci Software Peer Review.
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outsider -- submission #282

Closed DomBennett closed 4 years ago

DomBennett commented 5 years ago

Submitting Author: Dom Bennett (@dombennett)
Repository: https://github.com/AntonelliLab/outsider Version submitted: 0.0.0 Editor: @annakrystalli
Reviewer 1: @nuest
Reviewer 2: @hrbrmstr Archive: TBD
Version accepted: 0.1.0 

Package: outsider
Type: Package
Title: Install and run programs, outside of R, inside of R
Version: 0.0.0
Authors@R: person("Dom", "Bennett", role = c("aut", "cre"),
    email = "dominic.john.bennett@gmail.com",
    comment = c(ORCID = "0000-0003-2722-1359"))
Maintainer: Dom Bennett <dominic.john.bennett@gmail.com>
Description: Install and run external command-line programs in R through use of
    'Docker' <https://www.docker.com/> and 'GitHub' <http://github.com/>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
SystemRequirements: docker (>=18.0.0)
URL: https://antonellilab.github.io/outsider
BugReports: https://github.com/antonellilab/outsider/issues
Language: en-GB
Depends:
    R (>= 3.3.0)
Imports:
    utils (>= 3.1),
    crayon,
    devtools (>= 1.1),
    jsonlite (>= 1.1),
    sys (>= 2.1),
    yaml (>= 2.0),
    callr (>= 3.0.0),
    withr (>= 2.0),
    stringr,
    tibble,
    cli,
    praise
Suggests:
    testthat (>= 2.0),
    knitr (>= 1.0)

Scope

The aim of the package is to enable R users to install and run, within R, software, packages and programs external to R. This allows users to more readily create workflows and pipelines that are portable, reproducible and make use of a wide range of available methods outside of R.

The target audience are data scientists, bioinformaticians and general scientists interested in running external programs within R.

There are many available packages that allow the interfacing between software external to R (e.g. packages for interacting with python or java). There does not, however, seem to be any packages that make use of docker (www.docker.com) to import external software as this package does. The closest packages to this one appear to be things like rocker. Rocker, however, uses docker to make R more portable, not external software accessible within R.

Technical checks

Confirm each of the following by checking the box. This package:

Publication options

JOSS Options - [x] The package has an **obvious research application** according to [JOSS's definition](https://joss.readthedocs.io/en/latest/submitting.html#submission-requirements). - [x] The package contains a `paper.md` matching [JOSS's requirements](https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain) with a high-level description in the package root or in `inst/`. - [x] The package is deposited in a long-term repository with the DOI: - (*Do not submit your package separately to JOSS*)
MEE Options - [ ] The package is novel and will be of interest to the broad readership of the journal. - [ ] The manuscript describing the package is no longer than 3000 words. - [ ] You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see [MEE's Policy on Publishing Code](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) - (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) for your manuscript. We make no guarantee that your manuscript will be within MEE scope.*) - (*Although not required, we strongly recommend having a full manuscript prepared when you submit here.*) - (*Please do not submit your package separately to Methods in Ecology and Evolution*)

Code of conduct

DomBennett commented 4 years ago

Thanks!

outsider-testsuite is not user facing. In the review one of the suggestions was to have a demonstrated pipeline of how multiple modules could be stringed together to test the overall outsider "universe".

Currently, there is only 1 functioning test suite for a phylogenetic pipeline. I do invite people to contribute their own suites (but now i'm now sure where I wrote that..... šŸ˜•)

(It seemed a bit much to have so many tests in one of the packages.)

annakrystalli commented 4 years ago

OK great, thanks for the clarification. I'll get right back to you.

annakrystalli commented 4 years ago

OK! I've heard back and all is good. All 4 repos are fine in rOpenSci and as part of the outsider team. Just make sure (which currently you have) that the peer-reviewed badge is only on the two packages.

I'm pretty much ready to close the issue once you confirm all the approval checklist items have been tackled. šŸ˜ƒ

DomBennett commented 4 years ago

The ROpenSci gods have spoken, And their word is good!

Yes. I've completed all the steps, with the exception of the JOSS steps. I'm waiting to hear if @annakrystalli @nuest @hrbrmstr is against being cited as a "rev" in the DESCRIPTION before I archive the package for eternity on Zenodo.

Currently, the DESCRIPTION looks like: https://github.com/ropensci/outsider/blob/master/DESCRIPTION

annakrystalli commented 4 years ago

I'm happy to go on as a reviewer :)

DomBennett commented 4 years ago

Now published: https://joss.theoj.org/papers/10.21105/joss.02038#

I've removed @nuest and @hrbrmstr as "rev" in the DESCRIPTION file for now just to get things moving along. Happy to add you at a later date, of course!

Thanks again to you all for making this happen!

annakrystalli commented 4 years ago

Great news on the JOSS publication. As for reviewer acknowledgement, that seems fair enough. Reviewers just ping in this issue if you would like to be officially acknowledged.

Going to close the issue and officially conclude the review. Great work again!